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Sample records for weakly binds dashed

  1. DASH | Open Energy Information

    Open Energy Info (EERE)

    Interface: Website, Mobile Device Website: dash.by Web Application Link: dash.by Cost: Free OpenEI Keyword(s): Featured, Challenge Generated DASH Screenshot References: DASH1...

  2. Valve and dash-pot assembly

    DOE Patents [OSTI]

    Chang, Shih-Chih (Richland, WA)

    1986-01-01

    A dash-pot valve comprising a cylinder submerged in the fluid of a housing and having a piston attached to a plunger projecting into the path of closing movement of a pivotal valve member. A vortex chamber in said cylinder is provided with tangentially directed inlets to generate vortex flow upon retraction of said plunger and effect increasing resistance against said piston to progressively retard the closing rate of said valve member toward its seat.

  3. Improved valve and dash-pot assembly

    DOE Patents [OSTI]

    Chang, S.C.

    1985-04-23

    A dash-pot valve comprises a cylinder submerged in the fluid of a housing and have a piston attached to a plunger projecting into the path of closing movement of a pivotal valve member. A vortex chamber in said cylinder is provided with targentially directed inlets to generate vortex flow upon retraction of said plunger and effect increasing resistance against said piston to progressively retard the closing rate of said valve member toward its seat.

  4. Development Wells At Fenton Hill HDR Geothermal Area (Dash, Et...

    Open Energy Info (EERE)

    16, 1979. References Z. V. Dash, H. D. Murphy, R. L. Aamodt, R. G. Aguilar, D. W. Brown, D. A. Counce, H. N. Fisher, C. O. Grigsby, H. Keppler, A. W. Laughlin, R. M. Potter,...

  5. Dash for Bikes, Walk for Trikes | National Nuclear Security Administration

    National Nuclear Security Administration (NNSA)

    Dash for Bikes, Walk for Trikes | National Nuclear Security Administration Facebook Twitter Youtube Flickr RSS People Mission Managing the Stockpile Preventing Proliferation Powering the Nuclear Navy Emergency Response Recapitalizing Our Infrastructure Countering Nuclear Terrorism About Our Programs Our History Who We Are Our Leadership Our Locations Budget Our Operations Library Bios Congressional Testimony Fact Sheets Newsletters Press Releases Photo Gallery Jobs Apply for Our Jobs Our Jobs

  6. Flow Test At Fenton Hill HDR Geothermal Area (Dash, Et Al., 1983...

    Open Energy Info (EERE)

    Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Flow Test At Fenton Hill HDR Geothermal Area (Dash, Et Al., 1983) Exploration Activity Details...

  7. Flow Test At Fenton Hill HDR Geothermal Area (Dash, 1989) | Open...

    Open Energy Info (EERE)

    Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Flow Test At Fenton Hill HDR Geothermal Area (Dash, 1989) Exploration Activity Details Location...

  8. Exciton and biexciton dynamics in single self-assembled InAs/InGaAlAs/InP quantum dash emitting near 1.55??m

    SciTech Connect (OSTI)

    Dusanowski, ?.; Syperek, M. Rudno-Rudzi?ski, W.; Mrowi?ski, P.; Sek, G.; Misiewicz, J.; Somers, A.; Reithmaier, J. P.; Höfling, S.; Forchel, A.

    2013-12-16

    Exciton and biexciton dynamics in a single self-assembled InAs/In{sub 0.53}Ga{sub 0.23}Al{sub 0.24}As/InP(001) quantum dash emitting near 1.55??m has been investigated by micro-photoluminescence and time-resolved micro-photoluminescence at T?=?4.2?K. The exciton and biexciton fine structure splitting of ?60??eV, the biexciton binding energy of ?3.5?meV, and the characteristic exciton and biexciton decay times of 2.0?±?0.1?ns and 1.1?±?0.1?ns, respectively, have been determined. The measurement of the biexciton and exciton cross-correlation statistics of the photon emission confirmed the cascaded relaxation process. The exciton-to-biexciton decay time ratio and a small fine structure splitting suggest carrier localization within the investigated quantum dash.

  9. Water on BN doped benzene: A hard test for exchange-correlation functionals and the impact of exact exchange on weak binding

    SciTech Connect (OSTI)

    Al-Hamdani, Yasmine S.; Alfè, Dario; von Lilienfeld, O. Anatole; Michaelides, Angelos

    2014-10-22

    Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we show that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B?N?H?) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.

  10. Water on BN doped benzene: A hard test for exchange-correlation functionals and the impact of exact exchange on weak binding

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Al-Hamdani, Yasmine S.; Alfè, Dario; von Lilienfeld, O. Anatole; Michaelides, Angelos

    2014-10-22

    Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we showmore » that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B₃N₃H₆) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.« less

  11. Water on BN doped benzene: A hard test for exchange-correlation functionals and the impact of exact exchange on weak binding

    SciTech Connect (OSTI)

    Al-Hamdani, Yasmine S.; Michaelides, Angelos; Alfè, Dario; Lilienfeld, O. Anatole von

    2014-11-14

    Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we show that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B{sub 3}N{sub 3}H{sub 6}) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.

  12. Single photon emission at 1.55??m from charged and neutral exciton confined in a single quantum dash

    SciTech Connect (OSTI)

    Dusanowski, ?. Syperek, M.; Mrowi?ski, P.; Rudno-Rudzi?ski, W.; Misiewicz, J.; S?k, G.; Somers, A.; Kamp, M.; Höfling, S.; Reithmaier, J. P.

    2014-07-14

    We investigate charged and neutral exciton complexes confined in a single self-assembled InAs/InGaAlAs/InP quantum dash emitting at 1.55??m. The emission characteristics have been probed by measuring high-spatial-resolution polarization-resolved photoluminescence and cross-correlations of photon emission statistics at T?=?5?K. The photon auto-correlation histogram of the emission from both the neutral and charged exciton indicates a clear antibunching dip with as-measured g{sup (2)}(0) values of 0.18 and 0.31, respectively. It proves that these exciton complexes confined in single quantum dashes of InP-based material system can act as true single photon emitters being compatible with standard long-distance fiber communication technology.

  13. Weak Interaction | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Weak Interaction February 22, 2011 Jefferson Lab has an accelerator designed to do incisive medium energy physics. This program is dominated by experiments aimed at developing our...

  14. History of Weak Interactions

    DOE R&D Accomplishments [OSTI]

    Lee, T. D.

    1970-07-01

    While the phenomenon of beta-decay was discovered near the end of the last century, the notion that the weak interaction forms a separate field of physical forces evolved rather gradually. This became clear only after the experimental discoveries of other weak reactions such as muon-decay, muon-capture, etc., and the theoretical observation that all these reactions can be described by approximately the same coupling constant, thus giving rise to the notion of a universal weak interaction. Only then did one slowly recognize that the weak interaction force forms an independent field, perhaps on the same footing as the gravitational force, the electromagnetic force, and the strong nuclear and sub-nuclear forces.

  15. Weakly broken galileon symmetry

    SciTech Connect (OSTI)

    Pirtskhalava, David; Santoni, Luca; Trincherini, Enrico; Vernizzi, Filippo

    2015-09-01

    Effective theories of a scalar ϕ invariant under the internal galileon symmetryϕ→ϕ+b{sub μ}x{sup μ} have been extensively studied due to their special theoretical and phenomenological properties. In this paper, we introduce the notion of weakly broken galileon invariance, which characterizes the unique class of couplings of such theories to gravity that maximally retain their defining symmetry. The curved-space remnant of the galileon’s quantum properties allows to construct (quasi) de Sitter backgrounds largely insensitive to loop corrections. We exploit this fact to build novel cosmological models with interesting phenomenology, relevant for both inflation and late-time acceleration of the universe.

  16. Quantum discord with weak measurements

    SciTech Connect (OSTI)

    Singh, Uttam Pati, Arun Kumar

    2014-04-15

    Weak measurements cause small change to quantum states, thereby opening up the possibility of new ways of manipulating and controlling quantum systems. We ask, can weak measurements reveal more quantum correlation in a composite quantum state? We prove that the weak measurement induced quantum discord, called as the “super quantum discord”, is always larger than the quantum discord captured by the strong measurement. Moreover, we prove the monotonicity of the super quantum discord as a function of the measurement strength and in the limit of strong projective measurement the super quantum discord becomes the normal quantum discord. We find that unlike the normal discord, for pure entangled states, the super quantum discord can exceed the quantum entanglement. Our results provide new insights on the nature of quantum correlation and suggest that the notion of quantum correlation is not only observer dependent but also depends on how weakly one perturbs the composite system. We illustrate the key results for pure as well as mixed entangled states. -- Highlights: •Introduced the role of weak measurements in quantifying quantum correlation. •We have introduced the notion of the super quantum discord (SQD). •For pure entangled state, we show that the SQD exceeds the entanglement entropy. •This shows that quantum correlation depends not only on observer but also on measurement strength.

  17. Tomography and weak lensing statistics

    SciTech Connect (OSTI)

    Munshi, Dipak; Coles, Peter; Kilbinger, Martin E-mail: peter.coles@astro.cf.ac.uk

    2014-04-01

    We provide generic predictions for the lower order cumulants of weak lensing maps, and their correlators for tomographic bins as well as in three dimensions (3D). Using small-angle approximation, we derive the corresponding one- and two-point probability distribution function for the tomographic maps from different bins and for 3D convergence maps. The modelling of weak lensing statistics is obtained by adopting a detailed prescription for the underlying density contrast that involves hierarchal ansatz and lognormal distribution. We study the dependence of our results on cosmological parameters and source distributions corresponding to the realistic surveys such as LSST and DES. We briefly outline how photometric redshift information can be incorporated in our results. We also show how topological properties of convergence maps can be quantified using our results.

  18. Weak interactions at the SSC

    SciTech Connect (OSTI)

    Chanowitz, M.S.

    1986-03-01

    Prospects for the study of standard model weak interactions at the SSC are reviewed, with emphasis on the unique capability of the SSC to study the mechanism of electroweak symmetry breaking whether the associated new quanta are at the TeV scale or higher. Symmetry breaking by the minimal Higgs mechanism and by related strong interaction dynamical variants is summarized. A set of measurements is outlined that would calibrate the proton structure functions and the backgrounds to new physics. The ability to measure the three weak gauge boson vertex is found to complement LEP II, with measurements extending to larger Q/sup 2/ at a comparable statistical level in detectable decays. B factory physics is briefly reviewed as one example of a possible broad program of high statistics studies of sub-TeV scale phenomena. The largest section of the talk is devoted to the possible manifestations of symmetry breaking in the WW and ZZ production cross sections. Some new results are presented bearing on the ability to detect high mass WW and ZZ pairs. The principal conclusion is that although nonstandard model scenarios are typically more forgiving, the capability to study symmetry breaking in the standard model (and in related strong interaction dynamical variants) requires achieving the SSC design goals of ..sqrt.. s,L = 40Tev, 10/sup 33/cm/sup -2/sec/sup -1/. 28 refs., 5 figs.

  19. Weak rigidity in the PPN formalism

    SciTech Connect (OSTI)

    del Olmo, V.; Olivert, J.

    1987-04-01

    The influence of the concept of weakly rigid almost-thermodynamic material schemes on the classical deformations is analyzed. The methods of the PPN approximation are considered. In this formalism, the equations that characterize the weak rigidity are expressed. As a consequence of that, an increase of two orders of magnitude in the strain rate tensor is obtained.

  20. CP Violation, Neutral Currents, and Weak Equivalence

    DOE R&D Accomplishments [OSTI]

    Fitch, V. L.

    1972-03-23

    Within the past few months two excellent summaries of the state of our knowledge of the weak interactions have been presented. Correspondingly, we will not attempt a comprehensive review but instead concentrate this discussion on the status of CP violation, the question of the neutral currents, and the weak equivalence principle.

  1. Q-weak Experiment Determines Proton's Weak Charge | U.S. DOE Office of

    Office of Science (SC) Website

    Science (SC) Q-weak Experiment Determines Proton's Weak Charge Nuclear Physics (NP) NP Home About Research Facilities Science Highlights Benefits of NP Funding Opportunities Nuclear Science Advisory Committee (NSAC) Community Resources Contact Information Nuclear Physics U.S. Department of Energy SC-26/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-3613 F: (301) 903-3833 E: Email Us More Information » 05.01.14 Q-weak Experiment Determines Proton's Weak

  2. Probing the Proton's Weak Side | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    such as those that may be produced by the Large Hadron Collider at CERN in Europe. "The weak charge for the proton is exquisitely, accurately predicted by the Standard Model. ...

  3. Corrigendum and addendum. Modeling weakly nonlinear acoustic...

    Office of Scientific and Technical Information (OSTI)

    Modeling weakly nonlinear acoustic wave propagation. The Quarterly Journal of Mechanics ... OSTI Identifier: 1215511 Report Number(s): LA-UR--14-27476 Journal ID: ISSN 0033-5614 ...

  4. Steven Weinberg, Weak Interactions, and Electromagnetic Interactions

    Office of Scientific and Technical Information (OSTI)

    Steven Weinberg and Weak and Electromagnetic Interactions Resources with Additional Information Steven Weinberg Courtesy Dr. Steven Weinberg Steven "Weinberg is a professor of physics and astronomy at UT [The University of Texas] Austin and is founding director of the Theory Group in the College of Natural Sciences. [He is] well known for his development of a field theory that unifies the electromagnetic and weak nuclear forces, and for other major contributions to physics and cosmology ...

  5. Proton's Weak Charge Determined for First Time | Jefferson Lab

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Weak Charge Determined for First Time Q-weak at Jefferson Lab has measured the proton's weak charge Q-weak at Jefferson Lab has measured the proton's weak charge. NEWPORT NEWS, VA, Sept. 17, 2013 - Researchers have made the first experimental determination of the weak charge of the proton in research carried out at the Department of Energy's Thomas Jefferson National Accelerator Facility (Jefferson Lab). The results, accepted for publication in Physical Review Letters, also include the

  6. Theory and Modeling of Weakly Bound/Physisorbed Materials for...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Theory and Modeling of Weakly BoundPhysisorbed Materials for Hydrogen Storage Theory and Modeling of Weakly BoundPhysisorbed Materials for Hydrogen Storage Presentation on the...

  7. Metal Nanostructure Formation on Graphene: Weak versus Strong...

    Office of Scientific and Technical Information (OSTI)

    Metal Nanostructure Formation on Graphene: Weak versus Strong Bonding Citation Details In-Document Search Title: Metal Nanostructure Formation on Graphene: Weak versus Strong...

  8. T-728: Apache Tomcat HTTP DIGEST Authentication Weaknesses Let...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    8: Apache Tomcat HTTP DIGEST Authentication Weaknesses Let Remote Users Conduct Bypass Attacks T-728: Apache Tomcat HTTP DIGEST Authentication Weaknesses Let Remote Users Conduct...

  9. Weak measurement and Bohmian conditional wave functions

    SciTech Connect (OSTI)

    Norsen, Travis; Struyve, Ward

    2014-11-15

    It was recently pointed out and demonstrated experimentally by Lundeen et al. that the wave function of a particle (more precisely, the wave function possessed by each member of an ensemble of identically-prepared particles) can be “directly measured” using weak measurement. Here it is shown that if this same technique is applied, with appropriate post-selection, to one particle from a perhaps entangled multi-particle system, the result is precisely the so-called “conditional wave function” of Bohmian mechanics. Thus, a plausibly operationalist method for defining the wave function of a quantum mechanical sub-system corresponds to the natural definition of a sub-system wave function which Bohmian mechanics uniquely makes possible. Similarly, a weak-measurement-based procedure for directly measuring a sub-system’s density matrix should yield, under appropriate circumstances, the Bohmian “conditional density matrix” as opposed to the standard reduced density matrix. Experimental arrangements to demonstrate this behavior–and also thereby reveal the non-local dependence of sub-system state functions on distant interventions–are suggested and discussed. - Highlights: • We study a “direct measurement” protocol for wave functions and density matrices. • Weakly measured states of entangled particles correspond to Bohmian conditional states. • Novel method of observing quantum non-locality is proposed.

  10. Lossy compression of weak lensing data

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Vanderveld, R. Ali; Bernstein, Gary M.; Stoughton, Chris; Rhodes, Jason; Massey, Richard; Dobke, Benjamin M.

    2011-07-12

    Future orbiting observatories will survey large areas of sky in order to constrain the physics of dark matter and dark energy using weak gravitational lensing and other methods. Lossy compression of the resultant data will improve the cost and feasibility of transmitting the images through the space communication network. We evaluate the consequences of the lossy compression algorithm of Bernstein et al. (2010) for the high-precision measurement of weak-lensing galaxy ellipticities. This square-root algorithm compresses each pixel independently, and the information discarded is by construction less than the Poisson error from photon shot noise. For simulated space-based images (without cosmicmore » rays) digitized to the typical 16 bits per pixel, application of the lossy compression followed by image-wise lossless compression yields images with only 2.4 bits per pixel, a factor of 6.7 compression. We demonstrate that this compression introduces no bias in the sky background. The compression introduces a small amount of additional digitization noise to the images, and we demonstrate a corresponding small increase in ellipticity measurement noise. The ellipticity measurement method is biased by the addition of noise, so the additional digitization noise is expected to induce a multiplicative bias on the galaxies measured ellipticities. After correcting for this known noise-induced bias, we find a residual multiplicative ellipticity bias of m {approx} -4 x 10-4. This bias is small when compared to the many other issues that precision weak lensing surveys must confront, and furthermore we expect it to be reduced further with better calibration of ellipticity measurement methods.« less

  11. PLASMA EMISSION BY WEAK TURBULENCE PROCESSES

    SciTech Connect (OSTI)

    Ziebell, L. F.; Gaelzer, R.; Yoon, P. H.; Pavan, J. E-mail: rudi.gaelzer@ufrgs.br E-mail: joel.pavan@ufpel.edu.br

    2014-11-10

    The plasma emission is the radiation mechanism responsible for solar type II and type III radio bursts. The first theory of plasma emission was put forth in the 1950s, but the rigorous demonstration of the process based upon first principles had been lacking. The present Letter reports the first complete numerical solution of electromagnetic weak turbulence equations. It is shown that the fundamental emission is dominant and unless the beam speed is substantially higher than the electron thermal speed, the harmonic emission is not likely to be generated. The present findings may be useful for validating reduced models and for interpreting particle-in-cell simulations.

  12. Boson Hubbard model with weakly coupled fermions

    SciTech Connect (OSTI)

    Lutchyn, Roman M.; Tewari, Sumanta; Das Sarma, S.

    2008-12-01

    Using an imaginary-time path integral approach, we develop the perturbation theory suited to the boson Hubbard model and apply it to calculate the effects of a dilute gas of spin-polarized fermions weakly interacting with the bosons. The full theory captures both the static and the dynamic effects of the fermions on the generic superfluid-insulator phase diagram. We find that, in a homogenous system described by a single-band boson Hubbard Hamiltonian, the intrinsic perturbative effect of the fermions is to generically suppress the insulating lobes and to enhance the superfluid phase.

  13. Neutron Beta Decay as a Probe of Weak Interactions (Conference...

    Office of Scientific and Technical Information (OSTI)

    Conference: Neutron Beta Decay as a Probe of Weak Interactions Citation Details In-Document Search Title: Neutron Beta Decay as a Probe of Weak Interactions You are accessing a...

  14. Atmospheric Dispersion Effects in Weak Lensing Measurements

    SciTech Connect (OSTI)

    Plazas, Andrés Alejandro; Bernstein, Gary

    2012-10-01

    The wavelength dependence of atmospheric refraction causes elongation of finite-bandwidth images along the elevation vector, which produces spurious signals in weak gravitational lensing shear measurements unless this atmospheric dispersion is calibrated and removed to high precision. Because astrometric solutions and PSF characteristics are typically calibrated from stellar images, differences between the reference stars' spectra and the galaxies' spectra will leave residual errors in both the astrometric positions (dr) and in the second moment (width) of the wavelength-averaged PSF (dv) for galaxies.We estimate the level of dv that will induce spurious weak lensing signals in PSF-corrected galaxy shapes that exceed the statistical errors of the DES and the LSST cosmic-shear experiments. We also estimate the dr signals that will produce unacceptable spurious distortions after stacking of exposures taken at different airmasses and hour angles. We also calculate the errors in the griz bands, and find that dispersion systematics, uncorrected, are up to 6 and 2 times larger in g and r bands,respectively, than the requirements for the DES error budget, but can be safely ignored in i and z bands. For the LSST requirements, the factors are about 30, 10, and 3 in g, r, and i bands,respectively. We find that a simple correction linear in galaxy color is accurate enough to reduce dispersion shear systematics to insignificant levels in the r band for DES and i band for LSST,but still as much as 5 times than the requirements for LSST r-band observations. More complex corrections will likely be able to reduce the systematic cosmic-shear errors below statistical errors for LSST r band. But g-band effects remain large enough that it seems likely that induced systematics will dominate the statistical errors of both surveys, and cosmic-shear measurements should rely on the redder bands.

  15. Atmospheric Dispersion Effects in Weak Lensing Measurements

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Plazas, Andrés Alejandro; Bernstein, Gary

    2012-10-01

    The wavelength dependence of atmospheric refraction causes elongation of finite-bandwidth images along the elevation vector, which produces spurious signals in weak gravitational lensing shear measurements unless this atmospheric dispersion is calibrated and removed to high precision. Because astrometric solutions and PSF characteristics are typically calibrated from stellar images, differences between the reference stars' spectra and the galaxies' spectra will leave residual errors in both the astrometric positions (dr) and in the second moment (width) of the wavelength-averaged PSF (dv) for galaxies.We estimate the level of dv that will induce spurious weak lensing signals in PSF-corrected galaxy shapes that exceed themore »statistical errors of the DES and the LSST cosmic-shear experiments. We also estimate the dr signals that will produce unacceptable spurious distortions after stacking of exposures taken at different airmasses and hour angles. We also calculate the errors in the griz bands, and find that dispersion systematics, uncorrected, are up to 6 and 2 times larger in g and r bands,respectively, than the requirements for the DES error budget, but can be safely ignored in i and z bands. For the LSST requirements, the factors are about 30, 10, and 3 in g, r, and i bands,respectively. We find that a simple correction linear in galaxy color is accurate enough to reduce dispersion shear systematics to insignificant levels in the r band for DES and i band for LSST,but still as much as 5 times than the requirements for LSST r-band observations. More complex corrections will likely be able to reduce the systematic cosmic-shear errors below statistical errors for LSST r band. But g-band effects remain large enough that it seems likely that induced systematics will dominate the statistical errors of both surveys, and cosmic-shear measurements should rely on the redder bands.« less

  16. Magnified Weak Lensing Cross Correlation Tomography

    SciTech Connect (OSTI)

    Ulmer, Melville P., Clowe, Douglas I.

    2010-11-30

    This project carried out a weak lensing tomography (WLT) measurement around rich clusters of galaxies. This project used ground based photometric redshift data combined with HST archived cluster images that provide the WLT and cluster mass modeling. The technique has already produced interesting results (Guennou et al, 2010,Astronomy & Astrophysics Vol 523, page 21, and Clowe et al, 2011 to be submitted). Guennou et al have validated that the necessary accuracy can be achieved with photometric redshifts for our purposes. Clowe et al titled "The DAFT/FADA survey. II. Tomographic weak lensing signal from 10 high redshift clusters," have shown that for the **first time** via this purely geometrical technique, which does not assume a standard rod or candle, that a cosmological constant is **required** for flat cosmologies. The intent of this project is not to produce the best constraint on the value of the dark energy equation of state, w. Rather, this project is to carry out a sustained effort of weak lensing tomography that will naturally feed into the near term Dark Energy Survey (DES) and to provide invaluable mass calibration for that project. These results will greatly advance a key cosmological method which will be applied to the top-rated ground-based project in the Astro2020 decadal survey, LSST. Weak lensing tomography is one of the key science drivers behind LSST. CO-I Clowe is on the weak lensing LSST committee, and senior scientist on this project, at FNAL James Annis, plays a leading role in the DES. This project has built on successful proposals to obtain ground-based imaging for the cluster sample. By 1 Jan, it is anticipated the project will have accumulated complete 5-color photometry on 30 (or about 1/3) of the targeted cluster sample (public webpage for the survey is available at http://cencos.oamp.fr/DAFT/ and has a current summary of the observational status of various clusters). In all, the project has now been awarded the equivalent of over 60 nights on 4-m class telescopes, which gives concrete evidence of strong community support for this project. The WLT technique is based on the dependence of the gravitational shear signal on the angular diameter distances between the observer, the lens, and the lensed galaxy to measure cosmological parameters. By taking the ratio of measured shears of galaxies with different redshifts around the same lens, one obtains a measurement of the ratios of the angular diameter distances involved. Making these observations over a large range of lenses and background galaxy redshifts will measure the history of the expansion rate of the universe. Because this is a purely geometric measurement, it is insensitive to any form of evolution of objects or the necessity to understand the physics in the early universe. Thus, WLT was identified by the Dark Energy Task Force as perhaps the best method to measure the evolution of DE. To date, however, the conjecture of the DETF has not been experimentally verified, but will be by the proposed project. The primary reason for the lack of tomography measurements is that one must have an exceptional data-set to attempt the measurement. One needs both extremely good seeing (or space observations) in order to minimize the point spread function smearing corrections on weak lensing shear measurements and deep, multi-color data, from B to z, to measure reliable photometric redshifts of the background galaxies being lensed (which are typically too faint to obtain spectroscopic redshifts). Because the entire process from multi-drizzling the HST images, and then creating shear maps, to gathering the necessary ground based observations, to generating photo-zs and then carrying out the tomography is a complicated task, until the creation of our team, nobody has taken the time to connect all the levels of expertise necessary to carry out this project based on HST archival data. Our data are being used in 2 Ph.D. theses. Kellen Murphy, at Ohio University, is using the tomography data along with simulations in a thesis expected to be completed in Jun

  17. Inhibition of selectin binding

    DOE Patents [OSTI]

    Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Caroline (Albany, CA)

    2001-10-09

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  18. Inhibition of selectin binding

    DOE Patents [OSTI]

    Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Carolyn (Albany, CA)

    1999-10-05

    This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

  19. Inhibition of selectin binding

    DOE Patents [OSTI]

    Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Caroline (Albany, CA)

    1999-01-01

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  20. Cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  1. Cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  2. Corrigendum and addendum. Modeling weakly nonlinear acoustic wave

    Office of Scientific and Technical Information (OSTI)

    propagation (Journal Article) | SciTech Connect Corrigendum and addendum. Modeling weakly nonlinear acoustic wave propagation Citation Details In-Document Search Title: Corrigendum and addendum. Modeling weakly nonlinear acoustic wave propagation This article presents errors, corrections, and additions to the research outlined in the following citation: Christov, I., Christov, C. I., & Jordan, P. M. (2007). Modeling weakly nonlinear acoustic wave propagation. The Quarterly Journal of

  3. Origins of weak lensing systematics, and requirements on future...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Origins of weak lensing systematics, and requirements on future instrumentation (or knowledge of instrumentation) Citation Details In-Document Search Title:...

  4. Direct Measurement of the Neutral Weak Dipole Moments of the...

    Office of Scientific and Technical Information (OSTI)

    Visit OSTI to utilize additional information resources in energy science and technology. A ... We present direct measurements of the neutral weak anomalous magnetic dipole moment, asub ...

  5. Ultra-weak sector, Higgs boson mass, and the dilaton

    SciTech Connect (OSTI)

    Allison, Kyle; Hill, Christopher T.; Ross, Graham G.

    2014-11-01

    The Higgs boson mass may arise from a portal coupling to a singlet field $\\sigma$ which has a very large VEV $f \\gg m_\\text{Higgs}$. This requires a sector of "ultra-weak" couplings $\\zeta_i$, where $\\zeta_i \\lesssim m_\\text{Higgs}^2 / f^2$. Ultra-weak couplings are technically naturally small due to a custodial shift symmetry of $\\sigma$ in the $\\zeta_i \\rightarrow 0$ limit. The singlet field $\\sigma$ has properties similar to a pseudo-dilaton. We engineer explicit breaking of scale invariance in the ultra-weak sector via a Coleman-Weinberg potential, which requires hierarchies amongst the ultra-weak couplings.

  6. Evidence for a Weak Iron Core at Earth's Center

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Evidence for a Weak Iron Core at Earth's Center Print Seismic waves that pass through the center of the Earth travel faster going from pole to pole than along the equatorial...

  7. Ultra-weak sector, Higgs boson mass, and the dilaton

    SciTech Connect (OSTI)

    Allison, Kyle; Hill, Christopher T.; Ross, Graham G.

    2014-09-26

    The Higgs boson mass may arise from a portal coupling to a singlet field $\\sigma$ which has a very large VEV $f \\gg m_\\text{Higgs}$. This requires a sector of "ultra-weak" couplings $\\zeta_i$, where $\\zeta_i \\lesssim m_\\text{Higgs}^2 / f^2$. Ultra-weak couplings are technically naturally small due to a custodial shift symmetry of $\\sigma$ in the $\\zeta_i \\rightarrow 0$ limit. The singlet field $\\sigma$ has properties similar to a pseudo-dilaton. We engineer explicit breaking of scale invariance in the ultra-weak sector via a Coleman-Weinberg potential, which requires hierarchies amongst the ultra-weak couplings.

  8. Ultra-weak sector, Higgs boson mass, and the dilaton

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Allison, Kyle; Hill, Christopher T.; Ross, Graham G.

    2014-09-26

    The Higgs boson mass may arise from a portal coupling to a singlet fieldmore » $$\\sigma$$ which has a very large VEV $$f \\gg m_\\text{Higgs}$$. This requires a sector of "ultra-weak" couplings $$\\zeta_i$$, where $$\\zeta_i \\lesssim m_\\text{Higgs}^2 / f^2$$. Ultra-weak couplings are technically naturally small due to a custodial shift symmetry of $$\\sigma$$ in the $$\\zeta_i \\rightarrow 0$$ limit. The singlet field $$\\sigma$$ has properties similar to a pseudo-dilaton. We engineer explicit breaking of scale invariance in the ultra-weak sector via a Coleman-Weinberg potential, which requires hierarchies amongst the ultra-weak couplings.« less

  9. HISTORY OF WEAK INTERACTIONS. (Technical Report) | SciTech Connect

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    HISTORY OF WEAK INTERACTIONS. Citation Details In-Document Search Title: HISTORY OF WEAK INTERACTIONS. × You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a product of DOE's Office of Scientific and Technical Information (OSTI) and is provided as a public service. Visit OSTI to utilize additional information resources in energy science and technology. A paper copy of this document is also available for sale to the public from the National Technical

  10. A comparison of weak-turbulence and particle-in-cell simulations of weak electron-beam plasma interaction

    SciTech Connect (OSTI)

    Ratcliffe, H. Brady, C. S.; Che Rozenan, M. B.; Nakariakov, V. M.

    2014-12-15

    Quasilinear theory has long been used to treat the problem of a weak electron beam interacting with plasma and generating Langmuir waves. Its extension to weak-turbulence theory treats resonant interactions of these Langmuir waves with other plasma wave modes, in particular, ion-sound waves. These are strongly damped in plasma of equal ion and electron temperatures, as sometimes seen in, for example, the solar corona and wind. Weak turbulence theory is derived in the weak damping limit, with a term describing ion-sound wave damping then added. In this paper, we use the EPOCH particle-in-cell code to numerically test weak turbulence theory for a range of electron-ion temperature ratios. We find that in the cold ion limit, the results agree well, but for increasing ion temperature the three-wave resonance becomes broadened in proportion to the ion-sound wave damping rate. Additionally, we establish lower limits on the number of simulation particles needed to accurately reproduce the electron and wave distributions in their saturated states and to reproduce their intermediate states and time evolution. These results should be taken into consideration in, for example, simulations of plasma wave generation in the solar corona of Type III solar radio bursts from the corona to the solar wind and in weak turbulence investigations of ion-acoustic lines in the ionosphere.

  11. Evidence for a Weak Iron Core at Earth's Center

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Evidence for a Weak Iron Core at Earth's Center Evidence for a Weak Iron Core at Earth's Center Print Wednesday, 30 April 2014 00:00 Seismic waves that pass through the center of the Earth travel faster going from pole to pole than along the equatorial plane-why? One theory is that the grains of iron that make up most of the solid inner core could be aligned in a way that transmits waves more efficiently in one direction than the other. Recent evidence for this "texturing" of iron

  12. Malaria Researchers Find Weakness in Global Killer | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Malaria Researchers Find Weakness in Global Killer Malaria Researchers Find Weakness in Global Killer February 1, 2012 - 9:16am Addthis The protozoan <i>Plasmodium falciparum</i> gliding through a cell in the gut of a mosquito, its primary host. Although five different species of <i>Plasmodium</i> can cause malaria, <i>Plasmodium falciparum</i> causes the most severe disease. | Photo courtesy of Wikipedia Commons. The protozoan Plasmodium falciparum gliding

  13. Corrigendum and addendum. Modeling weakly nonlinear acoustic wave propagation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Christov, Ivan; Christov, C. I.; Jordan, P. M.

    2014-12-18

    This article presents errors, corrections, and additions to the research outlined in the following citation: Christov, I., Christov, C. I., & Jordan, P. M. (2007). Modeling weakly nonlinear acoustic wave propagation. The Quarterly Journal of Mechanics and Applied Mathematics, 60(4), 473-495.

  14. Lossy compression of weak lensing data (Journal Article) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Lossy compression of weak lensing data Citation Details In-Document Search Title: Lossy compression of weak lensing data You are accessing a document from the Department of...

  15. Lossy compression of weak lensing data (Journal Article) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Lossy compression of weak lensing data Citation Details In-Document Search Title: Lossy compression of weak lensing data Future orbiting observatories will survey...

  16. How Dynein Binds to Microtubules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    how it binds to microtubules and gives some hints into the fascinating question of how communication passes along the stalk from the MTBD to the rest of the motor. Lucky Break...

  17. How Dynein Binds to Microtubules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    How Dynein Binds to Microtubules How Dynein Binds to Microtubules Print Wednesday, 29 April 2009 00:00 Cytoplasmic dynein is a protein complex responsible for the transport of a large variety of cargoes, from specific RNAs and proteins to whole organelles, in a directional fashion along microtubules that serve as cellular conveyor belts. Consistent with this central role, cytoplasmic dynein is associated with a number of disease-related processes, including the transport of viruses,

  18. Capture and release of acid-gasses with acid-gas binding organic compounds

    DOE Patents [OSTI]

    Heldebrant, David J; Yonker, Clement R; Koech, Phillip K

    2015-03-17

    A system and method for acid-gas capture wherein organic acid-gas capture materials form hetero-atom analogs of alkyl-carbonate when contacted with an acid gas. These organic-acid gas capture materials include combinations of a weak acid and a base, or zwitterionic liquids. This invention allows for reversible acid-gas binding to these organic binding materials thus allowing for the capture and release of one or more acid gases. These acid-gas binding organic compounds can be regenerated to release the captured acid gasses and enable these organic acid-gas binding materials to be reused. This enables transport of the liquid capture compounds and the release of the acid gases from the organic liquid with significant energy savings compared to current aqueous systems.

  19. The DES Science Verification Weak Lensing Shear Catalogs

    SciTech Connect (OSTI)

    Jarvis, M.

    2015-07-20

    We present weak lensing shear catalogs for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogs of 2.12 million and 3.44 million galaxies respectively. We also detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. Furthermore, we discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogs for the full 5-year DES, which is expected to cover 5000 square degrees.

  20. Constraints on axion inflation from the weak gravity conjecture

    SciTech Connect (OSTI)

    Rudelius, Tom

    2015-09-08

    We derive constraints facing models of axion inflation based on decay constant alignment from a string-theoretic and quantum gravitational perspective. In particular, we investigate the prospects for alignment and ‘anti-alignment’ of C{sub 4} axion decay constants in type IIB string theory, deriving a strict no-go result in the latter case. We discuss the relationship of axion decay constants to the weak gravity conjecture and demonstrate agreement between our string-theoretic constraints and those coming from the ‘generalized’ weak gravity conjecture. Finally, we consider a particular model of decay constant alignment in which the potential of C{sub 4} axions in type IIB compactifications on a Calabi-Yau three-fold is dominated by contributions from D7-branes, pointing out that this model evades some of the challenges derived earlier in our paper but is highly constrained by other geometric considerations.

  1. Weakly Turbulent Magnetohydrodynamic Waves in Compressible Low-{beta} Plasmas

    SciTech Connect (OSTI)

    Chandran, Benjamin D. G.

    2008-12-05

    In this Letter, weak-turbulence theory is used to investigate interactions among Alfven waves and fast and slow magnetosonic waves in collisionless low-{beta} plasmas. The wave kinetic equations are derived from the equations of magnetohydrodynamics, and extra terms are then added to model collisionless damping. These equations are used to provide a quantitative description of a variety of nonlinear processes, including parallel and perpendicular energy cascade, energy transfer between wave types, 'phase mixing', and the generation of backscattered Alfven waves.

  2. Tsung-Dao Lee, Weak Interactions, and Nonconservation of Parity

    Office of Scientific and Technical Information (OSTI)

    Tsung-Dao Lee, Weak Interactions, and Nonconservation of Parity Resources with Additional Information Tsung-Dao Lee Courtesy of Brookhaven National Laboratory T. D. Lee "has devoted his long career to the study of the theoretical aspects of particle and nuclear physics. In 1957, Lee and Chen Ning Yang won the Nobel Prize in physics for disproving a tenet of physics known as the conservation of parity. Their finding was based on research carried out at Brookhaven's particle accelerator, the

  3. Chen Ning Yang, Weak Interactions, and Parity Violation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Chen Ning Yang, Weak Interactions, and Parity Violation Resources with Additional Information * Yang Honored C.N. Yang Courtesy of Brookhaven National Laboratory Chen Ning Yang shared the 1957 Nobel Prize for Physics with Tsung Dao Lee "for their penetrating investigation of the so-called parity laws which has led to important discoveries regarding the elementary particles". "Yang and Lee made a fundamental theoretical breakthrough of non-conservation of parity. Because of the

  4. Optimizing weak lensing mass estimates for cluster profile uncertainty

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gruen, D.; Bernstein, G. M.; Lam, T. Y.; Seitz, S.

    2011-09-11

    Weak lensing measurements of cluster masses are necessary for calibrating mass-observable relations (MORs) to investigate the growth of structure and the properties of dark energy. However, the measured cluster shear signal varies at fixed mass M200m due to inherent ellipticity of background galaxies, intervening structures along the line of sight, and variations in the cluster structure due to scatter in concentrations, asphericity and substructure. We use N-body simulated halos to derive and evaluate a weak lensing circular aperture mass measurement Map that minimizes the mass estimate variance <(Map - M200m)2> in the presence of all these forms of variability. Dependingmore » on halo mass and observational conditions, the resulting mass estimator improves on Map filters optimized for circular NFW-profile clusters in the presence of uncorrelated large scale structure (LSS) about as much as the latter improve on an estimator that only minimizes the influence of shape noise. Optimizing for uncorrelated LSS while ignoring the variation of internal cluster structure puts too much weight on the profile near the cores of halos, and under some circumstances can even be worse than not accounting for LSS at all. As a result, we discuss the impact of variability in cluster structure and correlated structures on the design and performance of weak lensing surveys intended to calibrate cluster MORs.« less

  5. Approximations of very weak solutions to boundary-value problems.

    SciTech Connect (OSTI)

    Berggren, Martin Olof

    2003-03-01

    Standard weak solutions to the Poisson problem on a bounded domain have square-integrable derivatives, which limits the admissible regularity of inhomogeneous data. The concept of solution may be further weakened in order to define solutions when data is rough, such as for inhomogeneous Dirichlet data that is only square-integrable over the boundary. Such very weak solutions satisfy a nonstandard variational form (u, v) = G(v). A Galerkin approximation combined with an approximation of the right-hand side G defines a finite-element approximation of the very weak solution. Applying conforming linear elements leads to a discrete solution equivalent to the text-book finite-element solution to the Poisson problem in which the boundary data is approximated by L{sub 2}-projections. The L{sub 2} convergence rate of the discrete solution is O(h{sub s}) for some s {element_of} (0,1/2) that depends on the shape of the domain, asserting a polygonal (two-dimensional) or polyhedral (three-dimensional) domain without slits and (only) square-integrable boundary data.

  6. Catastrophic photometric redshift errors: Weak-lensing survey requirements

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bernstein, Gary; Huterer, Dragan

    2010-01-11

    We study the sensitivity of weak lensing surveys to the effects of catastrophic redshift errors - cases where the true redshift is misestimated by a significant amount. To compute the biases in cosmological parameters, we adopt an efficient linearized analysis where the redshift errors are directly related to shifts in the weak lensing convergence power spectra. We estimate the number Nspec of unbiased spectroscopic redshifts needed to determine the catastrophic error rate well enough that biases in cosmological parameters are below statistical errors of weak lensing tomography. While the straightforward estimate of Nspec is ~106 we find that using onlymore » the photometric redshifts with z ≤ 2.5 leads to a drastic reduction in Nspec to ~ 30,000 while negligibly increasing statistical errors in dark energy parameters. Therefore, the size of spectroscopic survey needed to control catastrophic errors is similar to that previously deemed necessary to constrain the core of the zs – zp distribution. We also study the efficacy of the recent proposal to measure redshift errors by cross-correlation between the photo-z and spectroscopic samples. We find that this method requires ~ 10% a priori knowledge of the bias and stochasticity of the outlier population, and is also easily confounded by lensing magnification bias. In conclusion, the cross-correlation method is therefore unlikely to supplant the need for a complete spectroscopic redshift survey of the source population.« less

  7. Synthetic heparin-binding growth factor analogs

    DOE Patents [OSTI]

    Pena, Louis A.; Zamora, Paul; Lin, Xinhua; Glass, John D.

    2007-01-23

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain that binds a heparin-binding growth factor receptor, covalently bound to a hydrophobic linker, which is in turn covalently bound to a non-signaling peptide that includes a heparin-binding domain. The synthetic heparin-binding growth factor analogs are useful as soluble biologics or as surface coatings for medical devices.

  8. Dark-Matter-Induced Violation of the Weak Equivalence Principle

    SciTech Connect (OSTI)

    Carroll, Sean M.; Mantry, Sonny [California Institute of Technology, Pasadena, California 91125 (United States); Ramsey-Musolf, Michael J. [University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); California Institute of Technology, Pasadena, California 91125 (United States); Stubbs, Christoper W. [Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138 (United States)

    2009-07-03

    A long-range fifth force coupled to dark matter can induce a coupling to ordinary matter if the dark matter interacts with standard model fields. We consider constraints on such a scenario from both astrophysical observations and laboratory experiments. We also examine the case where the dark matter is a weakly interacting massive particle, and derive relations between the coupling to dark matter and the coupling to ordinary matter for different models. Currently, this scenario is most tightly constrained by galactic dynamics, but improvements in Eoetvoes experiments can probe unconstrained regions of parameter space.

  9. Merging weak and QCD showers with matrix elements

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Christiansen, Jesper Roy; Prestel, Stefan

    2016-01-22

    In this study, we present a consistent way of combining associated weak boson radiation in hard dijet events with hard QCD radiation in Drell–Yan-like scatterings. This integrates multiple tree-level calculations with vastly different cross sections, QCD- and electroweak parton-shower resummation into a single framework. The new merging strategy is implemented in the P ythia event generator and predictions are confronted with LHC data. Improvements over the previous strategy are observed. Results of the new electroweak-improved merging at a future 100 TeV proton collider are also investigated.

  10. Evidence for a Weak Iron Core at Earth's Center

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Evidence for a Weak Iron Core at Earth's Center Print Seismic waves that pass through the center of the Earth travel faster going from pole to pole than along the equatorial plane-why? One theory is that the grains of iron that make up most of the solid inner core could be aligned in a way that transmits waves more efficiently in one direction than the other. Recent evidence for this "texturing" of iron grains in the Earth's inner core comes from x-ray spectroscopy and diffraction

  11. Evidence for a Weak Iron Core at Earth's Center

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Evidence for a Weak Iron Core at Earth's Center Print Seismic waves that pass through the center of the Earth travel faster going from pole to pole than along the equatorial plane-why? One theory is that the grains of iron that make up most of the solid inner core could be aligned in a way that transmits waves more efficiently in one direction than the other. Recent evidence for this "texturing" of iron grains in the Earth's inner core comes from x-ray spectroscopy and diffraction

  12. Evidence for a Weak Iron Core at Earth's Center

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Evidence for a Weak Iron Core at Earth's Center Print Seismic waves that pass through the center of the Earth travel faster going from pole to pole than along the equatorial plane-why? One theory is that the grains of iron that make up most of the solid inner core could be aligned in a way that transmits waves more efficiently in one direction than the other. Recent evidence for this "texturing" of iron grains in the Earth's inner core comes from x-ray spectroscopy and diffraction

  13. Evidence for a Weak Iron Core at Earth's Center

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Evidence for a Weak Iron Core at Earth's Center Print Seismic waves that pass through the center of the Earth travel faster going from pole to pole than along the equatorial plane-why? One theory is that the grains of iron that make up most of the solid inner core could be aligned in a way that transmits waves more efficiently in one direction than the other. Recent evidence for this "texturing" of iron grains in the Earth's inner core comes from x-ray spectroscopy and diffraction

  14. Evidence for a Weak Iron Core at Earth's Center

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Evidence for a Weak Iron Core at Earth's Center Print Seismic waves that pass through the center of the Earth travel faster going from pole to pole than along the equatorial plane-why? One theory is that the grains of iron that make up most of the solid inner core could be aligned in a way that transmits waves more efficiently in one direction than the other. Recent evidence for this "texturing" of iron grains in the Earth's inner core comes from x-ray spectroscopy and diffraction

  15. Evidence for a Weak Iron Core at Earth's Center

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Evidence for a Weak Iron Core at Earth's Center Print Seismic waves that pass through the center of the Earth travel faster going from pole to pole than along the equatorial plane-why? One theory is that the grains of iron that make up most of the solid inner core could be aligned in a way that transmits waves more efficiently in one direction than the other. Recent evidence for this "texturing" of iron grains in the Earth's inner core comes from x-ray spectroscopy and diffraction

  16. Adsorption of small weak organic acids on goethite: Modeling of mechanisms

    SciTech Connect (OSTI)

    Filius, J.D.; Hiemstra, T.; Riemsdijk, W.H. Van

    1997-11-15

    The adsorption of lactate, oxalate, malonate, phthalate, and citrate has been determined experimentally as a function of concentration, pH, and ionic strength. The data have been described with the CD-MUSIC model of Hiemstra and Van Riemsdijk which allows a distribution of charge of the organic molecule over the surface and the Stern layer. Simultaneously, the concentration, pH, and salt dependency as well as the basic charging behavior of goethite could be described well. On the basis of model calculations, a distinction is made between inner and outer sphere complexation of weak organic acids by goethite. The results indicate that the affinity of the organic acids is dominated by the electrostatic attraction. The intrinsic affinity constants for the exchange reaction of surface water groups and organic acids, expressed per bond, increases with increasing number of reactive groups on the organic molecule. Ion pair formation between noncoordinated carboxylic groups of adsorbed organic acids and cations of the background electrolyte proved to be important for the salt dependency. The knowledge obtained may contribute to the interpretation of the binding of larger organic acids like fulvic and humic acids.

  17. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1998-02-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  18. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  19. The emergence of weakly twisted magnetic fields in the sun

    SciTech Connect (OSTI)

    Archontis, V.; Hood, A. W.; Tsinganos, K.

    2013-11-20

    We have studied the emergence of a weakly twisted magnetic flux tube from the upper convection zone into the solar atmosphere. It is found that the rising magnetized plasma does not undergo the classical, single ?-shaped loop emergence, but it becomes unstable in two places, forming two magnetic lobes that are anchored in small-scale bipolar structures at the photosphere, between the two main flux concentrations. The two magnetic lobes rise and expand into the corona, forming an overall undulating magnetic flux system. The dynamical interaction of the lobes results in the triggering of high-speed and hot jets and the formation of successive cool and hot loops that coexist in the emerging flux region. Although the initial emerging field is weakly twisted, a highly twisted magnetic flux rope is formed at the low atmosphere, due to shearing and reconnection. The new flux rope (hereafter post-emergence flux rope) does not erupt. It remains confined by the overlying field. Although there is no ejective eruption of the post-emergence rope, it is found that a considerable amount of axial and azimuthal flux is transferred into the solar atmosphere during the emergence of the magnetic field.

  20. PROTOSTELLAR DISK FORMATION ENABLED BY WEAK, MISALIGNED MAGNETIC FIELDS

    SciTech Connect (OSTI)

    Krumholz, Mark R.; Crutcher, Richard M.; Hull, Charles L. H.

    2013-04-10

    The gas from which stars form is magnetized, and strong magnetic fields can efficiently transport angular momentum. Most theoretical models of this phenomenon find that it should prevent formation of large (>100 AU), rotationally supported disks around most protostars, even when non-ideal magnetohydrodynamic (MHD) effects that allow the field and gas to decouple are taken into account. Using recent observations of magnetic field strengths and orientations in protostellar cores, we show that this conclusion is incorrect. The distribution of magnetic field strengths is very broad, and alignments between fields and angular momentum vectors within protostellar cores are essentially random. By combining the field strength and misalignment data with MHD simulations showing that disk formation is expected for both weak and misaligned fields, we show that these observations imply that we should expect disk fractions of {approx}10%-50% even when protostars are still deeply embedded in their parent cores, and even if the gas is governed by ideal MHD.

  1. How Dynein Binds to Microtubules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    How Dynein Binds to Microtubules Print Cytoplasmic dynein is a protein complex responsible for the transport of a large variety of cargoes, from specific RNAs and proteins to whole organelles, in a directional fashion along microtubules that serve as cellular conveyor belts. Consistent with this central role, cytoplasmic dynein is associated with a number of disease-related processes, including the transport of viruses, neurodegeneration, and the mitotic checkpoint malfunctions that lead to

  2. How Dynein Binds to Microtubules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    How Dynein Binds to Microtubules Print Cytoplasmic dynein is a protein complex responsible for the transport of a large variety of cargoes, from specific RNAs and proteins to whole organelles, in a directional fashion along microtubules that serve as cellular conveyor belts. Consistent with this central role, cytoplasmic dynein is associated with a number of disease-related processes, including the transport of viruses, neurodegeneration, and the mitotic checkpoint malfunctions that lead to

  3. How Dynein Binds to Microtubules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    How Dynein Binds to Microtubules Print Cytoplasmic dynein is a protein complex responsible for the transport of a large variety of cargoes, from specific RNAs and proteins to whole organelles, in a directional fashion along microtubules that serve as cellular conveyor belts. Consistent with this central role, cytoplasmic dynein is associated with a number of disease-related processes, including the transport of viruses, neurodegeneration, and the mitotic checkpoint malfunctions that lead to

  4. Predicting weak lensing statistics from halo mass reconstructions - Final Paper

    SciTech Connect (OSTI)

    Everett, Spencer

    2015-08-20

    As dark matter does not absorb or emit light, its distribution in the universe must be inferred through indirect effects such as the gravitational lensing of distant galaxies. While most sources are only weakly lensed, the systematic alignment of background galaxies around a foreground lens can constrain the mass of the lens which is largely in the form of dark matter. In this paper, I have implemented a framework to reconstruct all of the mass along lines of sight using a best-case dark matter halo model in which the halo mass is known. This framework is then used to make predictions of the weak lensing of 3,240 generated source galaxies through a 324 arcmin² field of the Millennium Simulation. The lensed source ellipticities are characterized by the ellipticity-ellipticity and galaxy-mass correlation functions and compared to the same statistic for the intrinsic and ray-traced ellipticities. In the ellipticity-ellipticity correlation function, I and that the framework systematically under predicts the shear power by an average factor of 2.2 and fails to capture correlation from dark matter structure at scales larger than 1 arcminute. The model predicted galaxy-mass correlation function is in agreement with the ray-traced statistic from scales 0.2 to 0.7 arcminutes, but systematically underpredicts shear power at scales larger than 0.7 arcminutes by an average factor of 1.2. Optimization of the framework code has reduced the mean CPU time per lensing prediction by 70% to 24 ± 5 ms. Physical and computational shortcomings of the framework are discussed, as well as potential improvements for upcoming work.

  5. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, Gisela K.

    1997-01-01

    Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described.

  6. Erythropoietin binding protein from mammalian serum

    DOE Patents [OSTI]

    Clemons, G.K.

    1997-04-29

    Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described. 11 figs.

  7. Synthetic heparin-binding factor analogs

    DOE Patents [OSTI]

    Pena, Louis A.; Zamora, Paul O.; Lin, Xinhua; Glass, John D.

    2010-04-20

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  8. Weak Lensing by Galaxy Troughs in DES Science Verification Data

    SciTech Connect (OSTI)

    Gruen, D.

    2015-09-29

    We measure the weak lensing shear around galaxy troughs, i.e. the radial alignment of background galaxies relative to underdensities in projections of the foreground galaxy field over a wide range of redshift in Science Verification data from the Dark Energy Survey. Our detection of the shear signal is highly significant (10?–15? for the smallest angular scales) for troughs with the redshift range z ? [0.2, 0.5] of the projected galaxy field and angular diameters of 10 arcmin…1°. These measurements probe the connection between the galaxy, matter density, and convergence fields. By assuming galaxies are biased tracers of the matter density with Poissonian noise, we find agreement of our measurements with predictions in a fiducial ? cold dark matter model. Furthermore, the prediction for the lensing signal on large trough scales is virtually independent of the details of the underlying model for the connection of galaxies and matter. Our comparison of the shear around troughs with that around cylinders with large galaxy counts is consistent with a symmetry between galaxy and matter over- and underdensities. In addition, we measure the two-point angular correlation of troughs with galaxies which, in contrast to the lensing signal, is sensitive to galaxy bias on all scales. Finally, the lensing signal of troughs and their clustering with galaxies is therefore a promising probe of the statistical properties of matter underdensities and their connection to the galaxy field.

  9. Photoexcited energy transfer in a weakly coupled dimer

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Hernandez, Laura Alfonso; Nelson, Tammie; Tretiak, Sergei; Fernandez-Alberti, Sebastian

    2015-01-08

    Nonadiabatic excited-state molecular dynamics (NA-ESMD) simulations have been performed in order to study the time-dependent exciton localization during energy transfer between two chromophore units of the weakly coupled anthracene dimer dithia-anthracenophane (DTA). Simulations are done at both low temperature (10 K) and room temperature (300 K). The initial photoexcitation creates an exciton which is primarily localized on a single monomer unit. Subsequently, the exciton experiences an ultrafast energy transfer becoming localized on either one monomer unit or the other, whereas delocalization between both monomers never occurs. In half of the trajectories, the electronic transition density becomes completely localized on themore » same monomer as the initial excitation, while in the other half, it becomes completely localized on the opposite monomer. In this article, we present an analysis of the energy transfer dynamics and the effect of thermally induced geometry distortions on the exciton localization. Finally, simulated fluorescence anisotropy decay curves for both DTA and the monomer unit dimethyl anthracene (DMA) are compared. As a result, our analysis reveals that changes in the transition density localization caused by energy transfer between two monomers in DTA is not the only source of depolarization and exciton relaxation within a single DTA monomer unit can also cause reorientation of the transition dipole.« less

  10. Weak lensing by galaxy troughs in DES Science Verification data

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gruen, D.; Friedrich, O.; Amara, A.; Bacon, D.; Bonnett, C.; Hartley, W.; Jain, B.; M. Jarvis; Kavprzak, T.; Krause, E.; et al

    2015-11-29

    In this study, we measure the weak lensing shear around galaxy troughs, i.e. the radial alignment of background galaxies relative to underdensities in projections of the foreground galaxy field over a wide range of redshift in Science Verification data from the Dark Energy Survey. Our detection of the shear signal is highly significant (10σ–15σ for the smallest angular scales) for troughs with the redshift range z ϵ [0.2, 0.5] of the projected galaxy field and angular diameters of 10 arcmin…1°. These measurements probe the connection between the galaxy, matter density, and convergence fields. By assuming galaxies are biased tracers ofmore » the matter density with Poissonian noise, we find agreement of our measurements with predictions in a fiducial Λ cold dark matter model. The prediction for the lensing signal on large trough scales is virtually independent of the details of the underlying model for the connection of galaxies and matter. Our comparison of the shear around troughs with that around cylinders with large galaxy counts is consistent with a symmetry between galaxy and matter over- and underdensities. In addition, we measure the two-point angular correlation of troughs with galaxies which, in contrast to the lensing signal, is sensitive to galaxy bias on all scales. The lensing signal of troughs and their clustering with galaxies is therefore a promising probe of the statistical properties of matter underdensities and their connection to the galaxy field.« less

  11. Photoexcited energy transfer in a weakly coupled dimer

    SciTech Connect (OSTI)

    Hernandez, Laura Alfonso; Nelson, Tammie; Tretiak, Sergei; Fernandez-Alberti, Sebastian

    2015-01-08

    Nonadiabatic excited-state molecular dynamics (NA-ESMD) simulations have been performed in order to study the time-dependent exciton localization during energy transfer between two chromophore units of the weakly coupled anthracene dimer dithia-anthracenophane (DTA). Simulations are done at both low temperature (10 K) and room temperature (300 K). The initial photoexcitation creates an exciton which is primarily localized on a single monomer unit. Subsequently, the exciton experiences an ultrafast energy transfer becoming localized on either one monomer unit or the other, whereas delocalization between both monomers never occurs. In half of the trajectories, the electronic transition density becomes completely localized on the same monomer as the initial excitation, while in the other half, it becomes completely localized on the opposite monomer. In this article, we present an analysis of the energy transfer dynamics and the effect of thermally induced geometry distortions on the exciton localization. Finally, simulated fluorescence anisotropy decay curves for both DTA and the monomer unit dimethyl anthracene (DMA) are compared. As a result, our analysis reveals that changes in the transition density localization caused by energy transfer between two monomers in DTA is not the only source of depolarization and exciton relaxation within a single DTA monomer unit can also cause reorientation of the transition dipole.

  12. Natural Scherk-Schwarz theories of the weak scale

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    García, Isabel Garcia; Howe, Kiel; March-Russell, John

    2015-12-01

    Natural supersymmetric theories of the weak scale are under growing pressure given present LHC constraints, raising the question of whether untuned supersymmetric (SUSY) solutions to the hierarchy problem are possible. In this paper, we explore a class of 5-dimensional natural SUSY theories in which SUSY is broken by the Scherk-Schwarz mechanism. We pedagogically explain how Scherk-Schwarz elegantly solves the traditional problems of 4-dimensional SUSY theories (based on the MSSM and its many variants) that usually result in an unsettling level of fine-tuning. The minimal Scherk-Schwarz set up possesses novel phenomenology, which we briefly outline. In this study, we show thatmore » achieving the observed physical Higgs mass motivates extra structure that does not significantly affect the level of tuning (always better than ~10%) and we explore three qualitatively different extensions: the addition of extra matter that couples to the Higgs, an extra U(1)' gauge group under which the Higgs is charged and an NMSSM-like solution to the Higgs mass problem.« less

  13. Natural Scherk-Schwarz theories of the weak scale

    SciTech Connect (OSTI)

    García, Isabel Garcia; Howe, Kiel; March-Russell, John

    2015-12-01

    Natural supersymmetric theories of the weak scale are under growing pressure given present LHC constraints, raising the question of whether untuned supersymmetric (SUSY) solutions to the hierarchy problem are possible. In this paper, we explore a class of 5-dimensional natural SUSY theories in which SUSY is broken by the Scherk-Schwarz mechanism. We pedagogically explain how Scherk-Schwarz elegantly solves the traditional problems of 4-dimensional SUSY theories (based on the MSSM and its many variants) that usually result in an unsettling level of fine-tuning. The minimal Scherk-Schwarz set up possesses novel phenomenology, which we briefly outline. In this study, we show that achieving the observed physical Higgs mass motivates extra structure that does not significantly affect the level of tuning (always better than ~10%) and we explore three qualitatively different extensions: the addition of extra matter that couples to the Higgs, an extra U(1)' gauge group under which the Higgs is charged and an NMSSM-like solution to the Higgs mass problem.

  14. Weakly Ionized Plasmas in Hypersonics: Fundamental Kinetics and Flight Applications

    SciTech Connect (OSTI)

    Macheret, Sergey

    2005-05-16

    The paper reviews some of the recent studies of applications of weakly ionized plasmas to supersonic/hypersonic flight. Plasmas can be used simply as means of delivering energy (heating) to the flow, and also for electromagnetic flow control and magnetohydrodynamic (MHD) power generation. Plasma and MHD control can be especially effective in transient off-design flight regimes. In cold air flow, nonequilibrium plasmas must be created, and the ionization power budget determines design, performance envelope, and the very practicality of plasma/MHD devices. The minimum power budget is provided by electron beams and repetitive high-voltage nanosecond pulses, and the paper describes theoretical and computational modeling of plasmas created by the beams and repetitive pulses. The models include coupled equations for non-local and unsteady electron energy distribution function (modeled in forward-back approximation), plasma kinetics, and electric field. Recent experimental studies at Princeton University have successfully demonstrated stable diffuse plasmas sustained by repetitive nanosecond pulses in supersonic air flow, and for the first time have demonstrated the existence of MHD effects in such plasmas. Cold-air hypersonic MHD devices are shown to permit optimization of scramjet inlets at Mach numbers higher than the design value, while operating in self-powered regime. Plasma energy addition upstream of the inlet throat can increase the thrust by capturing more air (Virtual Cowl), or it can reduce the flow Mach number and thus eliminate the need for an isolator duct. In the latter two cases, the power that needs to be supplied to the plasma would be generated by an MHD generator downstream of the combustor, thus forming the 'reverse energy bypass' scheme. MHD power generation on board reentry vehicles is also discussed.

  15. Chirality of weakly bound complexes: The potential energy surfaces for the

    Office of Scientific and Technical Information (OSTI)

    hydrogen-peroxide-noble-gas interactions (Journal Article) | SciTech Connect Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide-noble-gas interactions Citation Details In-Document Search Title: Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide-noble-gas interactions We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound

  16. Theory and Modeling of Weakly Bound/Physisorbed Materials for Hydrogen

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Storage | Department of Energy Theory and Modeling of Weakly Bound/Physisorbed Materials for Hydrogen Storage Theory and Modeling of Weakly Bound/Physisorbed Materials for Hydrogen Storage Presentation on the Theory and Modeling of Weakly Bound/Physisorbed Materials for Hydrogen Storage given at the DOE Theory Focus Session on Hydrogen Storage Materials on May 18, 2006. PDF icon storage_theory_session_williamson.pdf More Documents & Publications Summary Report from Theory Focus Session

  17. V-234: EMC RSA Archer GRC Open Redirection Weakness and Security Bypass

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Security Issue | Department of Energy 4: EMC RSA Archer GRC Open Redirection Weakness and Security Bypass Security Issue V-234: EMC RSA Archer GRC Open Redirection Weakness and Security Bypass Security Issue September 4, 2013 - 6:00am Addthis PROBLEM: A weakness and a security issue have been reported in EMC RSA Archer GRC PLATFORM: EMC RSA Archer GRC 5.x ABSTRACT: This fixes multiple vulnerabilities, which can be exploited to bypass certain security restrictions and to conduct spoofing

  18. Binding Organic Liquids - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    More Like This Return to Search Binding Organic Liquids Pacific Northwest National Laboratory Contact PNNL About This Technology Technology Marketing Summary Researchers at...

  19. Combining weak-lensing tomography and spectroscopic redshift surveys

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cai, Yan -Chuan; Bernstein, Gary

    2012-05-11

    Redshift space distortion (RSD) is a powerful way of measuring the growth of structure and testing General Relativity, but it is limited by cosmic variance and the degeneracy between galaxy bias b and the growth rate factor f. The cross-correlation of lensing shear with the galaxy density field can in principle measure b in a manner free from cosmic variance limits, breaking the f-b degeneracy and allowing inference of the matter power spectrum from the galaxy survey. We analyze the growth constraints from a realistic tomographic weak lensing photo-z survey combined with a spectroscopic galaxy redshift survey over the samemore » sky area. For sky coverage fsky = 0.5, analysis of the transverse modes measures b to 2-3% accuracy per Δz = 0.1 bin at z < 1 when ~10 galaxies arcmin–2 are measured in the lensing survey and all halos with M > Mmin = 1013h–1M⊙ have spectra. For the gravitational growth parameter parameter γ (f = Ωγm), combining the lensing information with RSD analysis of non-transverse modes yields accuracy σ(γ) ≈ 0.01. Adding lensing information to the RSD survey improves \\sigma(\\gamma) by an amount equivalent to a 3x (10x) increase in RSD survey area when the spectroscopic survey extends down to halo mass 1013.5 (1014) h–1 M⊙. We also find that the σ(γ) of overlapping surveys is equivalent to that of surveys 1.5-2 times larger if they are separated on the sky. This gain is greatest when the spectroscopic mass threshold is 1013 -1014 h–1 M⊙, similar to LRG surveys. The gain of overlapping surveys is reduced for very deep or very shallow spectroscopic surveys, but any practical surveys are more powerful when overlapped than when separated. As a result, the gain of overlapped surveys is larger in the case when the primordial power spectrum normalization is uncertain by > 0.5%.« less

  20. Nicotinamide mononucleotide adenylyltransferase displays alternate binding

    Office of Scientific and Technical Information (OSTI)

    modes for nicotinamide nucleotides (Journal Article) | SciTech Connect Nicotinamide mononucleotide adenylyltransferase displays alternate binding modes for nicotinamide nucleotides Citation Details In-Document Search Title: Nicotinamide mononucleotide adenylyltransferase displays alternate binding modes for nicotinamide nucleotides Authors: Pfoh, Roland ; Pai, Emil F. ; Saridakis, Vivian [1] ; Toronto) [2] + Show Author Affiliations (York) ( Publication Date: 2015-11-23 OSTI Identifier:

  1. Capture and release of mixed acid gasses with binding organic liquids

    DOE Patents [OSTI]

    Heldebrant, David J. (Richland, WA); Yonker, Clement R. (Kennewick, WA)

    2010-09-21

    Reversible acid-gas binding organic liquid systems that permit separation and capture of one or more of several acid gases from a mixed gas stream, transport of the liquid, release of the acid gases from the ionic liquid and reuse of the liquid to bind more acid gas with significant energy savings compared to current aqueous systems. These systems utilize acid gas capture compounds made up of strong bases and weak acids that form salts when reacted with a selected acid gas, and which release these gases when a preselected triggering event occurs. The various new materials that make up this system can also be included in various other applications such as chemical sensors, chemical reactants, scrubbers, and separators that allow for the specific and separate removal of desired materials from a gas stream such as flue gas.

  2. Existence of global weak solution for a reduced gravity two and a half layer model

    SciTech Connect (OSTI)

    Guo, Zhenhua Li, Zilai Yao, Lei

    2013-12-15

    We investigate the existence of global weak solution to a reduced gravity two and a half layer model in one-dimensional bounded spatial domain or periodic domain. Also, we show that any possible vacuum state has to vanish within finite time, then the weak solution becomes a unique strong one.

  3. Applications of Laminar Weak-Link Mechanisms for Ultraprecision Synchrotron Radiation Instruments

    SciTech Connect (OSTI)

    Shu, D.; Toellner, T. S.; Alp, E. E.; Maser, J.; Ilavsky, J.; Shastri, S. D.; Lee, P. L.; Narayanan, S.; Long, G. G. [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2007-01-19

    Unlike traditional kinematic flexure mechanisms, laminar overconstrained weak-link mechanisms provide much higher structure stiffness and stability. Using a laminar structure configured and manufactured by chemical etching and lithography techniques, we are able to design and build linear and rotary weak-link mechanisms with ultrahigh positioning sensitivity and stability for synchrotron radiation applications. Applications of laminar rotary weak-link mechanism include: high-energy-resolution monochromators for inelastic x-ray scattering and x-ray analyzers for ultra-small-angle scattering and powder-diffraction experiments. Applications of laminar linear weak-link mechanism include high-stiffness piezo-driven stages with subnanometer resolution for an x-ray microscope. In this paper, we summarize the recent designs and applications of the laminar weak-link mechanisms at the Advanced Photon Source.

  4. Improved flow cytometer measurement of binding assays

    DOE Patents [OSTI]

    Saunders, G.C.

    1984-05-30

    The invention relates to a method of measuring binding assays carried out with different size particles wherein the binding assay sample is run through a flow cytometer without separating the sample from the marking agent. The amount of a binding reactant present in a sample is determined by providing particles with a coating of binder and also a known quantity of smaller particles with a coating of binder reactant. The binding reactant is the same as the binding reactant present in the sample. The smaller particles also contain a fluorescent chemical. The particles are combined with the sample and the binding reaction is allowed to occur for a set length of time followed by combining the smaller particles with the mixture of the particles and the sample produced and allowing the binding reactions to proceed to equilibrium. The fluorescence and light scatter of the combined mixture is then measured as the combined mixture passes through a flow cytometer equipped with a laser to bring about fluorescence, and the number and strength of fluorescent events are compared. A similar method is also provided for determining the amount of antigen present in the sample by providing spheres with an antibody coating and some smaller spheres with an antigen coating. (LEW)

  5. Observation Wells At Fenton Hill HDR Geothermal Area (Dash, Et...

    Open Energy Info (EERE)

    Dennis, Donald S. Dreesen, Leigh S. House, Hugh D. Murphy, Bruce A. Robinson, Morton C. Smith (1987) The US Hot Dry Rock Project Additional References Retrieved from "http:...

  6. Method and apparatus for evaluating structural weakness in polymer matrix composites

    DOE Patents [OSTI]

    Wachter, Eric A. (Oak Ridge, TN); Fisher, Walter G. (Knoxville, TN)

    1996-01-01

    A method and apparatus for evaluating structural weaknesses in polymer matrix composites is described. An object to be studied is illuminated with laser radiation and fluorescence emanating therefrom is collected and filtered. The fluorescence is then imaged and the image is studied to determine fluorescence intensity over the surface of the object being studied and the wavelength of maximum fluorescent intensity. Such images provide a map of the structural integrity of the part being studied and weaknesses, particularly weaknesses created by exposure of the object to heat, are readily visible in the image.

  7. Method and apparatus for evaluating structural weakness in polymer matrix composites

    DOE Patents [OSTI]

    Wachter, E.A.; Fisher, W.G.

    1996-01-09

    A method and apparatus for evaluating structural weaknesses in polymer matrix composites is described. An object to be studied is illuminated with laser radiation and fluorescence emanating therefrom is collected and filtered. The fluorescence is then imaged and the image is studied to determine fluorescence intensity over the surface of the object being studied and the wavelength of maximum fluorescent intensity. Such images provide a map of the structural integrity of the part being studied and weaknesses, particularly weaknesses created by exposure of the object to heat, are readily visible in the image. 6 figs.

  8. Hardware device binding and mutual authentication

    DOE Patents [OSTI]

    Hamlet, Jason R; Pierson, Lyndon G

    2014-03-04

    Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

  9. Sequestering Uranium from Seawater: Binding Strength and Modes...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl...

  10. Fragment-Based Exploration of Binding Site Flexibility in Mycobacteriu...

    Office of Scientific and Technical Information (OSTI)

    Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium tuberculosis BioA Citation Details In-Document Search Title: Fragment-Based Exploration of Binding Site ...

  11. V-234: EMC RSA Archer GRC Open Redirection Weakness and Security...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    V-234: EMC RSA Archer GRC Open Redirection Weakness and Security Bypass Security Issue ... Vendor recommends updating to version 5.4 Addthis Related Articles V-084: RSA Archer eGRC ...

  12. Method of Control o Multiple Contraction in the volume of Weakly...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Method of Control o Multiple Contraction in the volume of Weakly Ionized Plasma by Standing Acoustic Wave Excitation. This invention is a process that uses a standing acoustic wave...

  13. RNA binding protein and binding site useful for expression of recombinant molecules

    DOE Patents [OSTI]

    Mayfield, Stephen

    2000-01-01

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  14. RNA binding protein and binding site useful for expression of recombinant molecules

    DOE Patents [OSTI]

    Mayfield, Stephen P.

    2006-10-17

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  15. Weak charge form factor and radius of 208Pb through parity violation in electron scattering

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Horowitz, C. J.; Ahmed, Z.; Jen, C. -M.; Rakhman, A.; Souder, P. A.; Dalton, M. M.; Liyanage, N.; Paschke, K. D.; Saenboonruang, K.; Silwal, R.; et al

    2012-03-26

    We use distorted wave electron scattering calculations to extract the weak charge form factor FW(more » $$\\bar{q}$$), the weak charge radius RW, and the point neutron radius Rn, of 208Pb from the PREX parity violating asymmetry measurement. The form factor is the Fourier transform of the weak charge density at the average momentum transfer $$\\bar{q}$$ = 0.475 fm-1. We find FW($$\\bar{q}$$) = 0.204 ± 0.028(exp) ± 0.001(model). We use the Helm model to infer the weak radius from FW($$\\bar{q}$$). We find RW = 5.826 ± 0.181(exp) ± 0.027(model) fm. Here the exp error includes PREX statistical and systematic errors, while the model error describes the uncertainty in RW from uncertainties in the surface thickness σ of the weak charge density. The weak radius is larger than the charge radius, implying a 'weak charge skin' where the surface region is relatively enriched in weak charges compared to (electromagnetic) charges. We extract the point neutron radius Rn = 5.751 ± 0.175 (exp) ± 0.026(model) ± 0.005(strange) fm, from RW. Here there is only a very small error (strange) from possible strange quark contributions. We find Rn to be slightly smaller than RW because of the nucleon's size. As a result, we find a neutron skin thickness of Rn-Rp = 0.302 ± 0.175 (exp) ± 0.026 (model) ± 0.005 (strange) fm, where Rp is the point proton radius.« less

  16. Neutron Beta Decay as a Probe of Weak Interactions (Conference) | SciTech

    Office of Scientific and Technical Information (OSTI)

    Connect Conference: Neutron Beta Decay as a Probe of Weak Interactions Citation Details In-Document Search Title: Neutron Beta Decay as a Probe of Weak Interactions Authors: Saunders, Alexander [1] + Show Author Affiliations Los Alamos National Laboratory Publication Date: 2013-06-13 OSTI Identifier: 1083839 Report Number(s): LA-UR-13-24323 DOE Contract Number: AC52-06NA25396 Resource Type: Conference Resource Relation: Conference: International Nuclear Physics Conference ; 2013-06-01 -

  17. The Impact of Camera Optical Alignments on Weak Lensing Measures for the

    Office of Scientific and Technical Information (OSTI)

    Dark Energy Survey (Journal Article) | SciTech Connect The Impact of Camera Optical Alignments on Weak Lensing Measures for the Dark Energy Survey Citation Details In-Document Search Title: The Impact of Camera Optical Alignments on Weak Lensing Measures for the Dark Energy Survey Authors: Antonik, Michelle L. ; /University Coll. London ; Bacon, David J. ; /Portsmouth U. ; Bridle, Sarah ; /University Coll. London ; Doel, Peter ; /University Coll. London ; Brooks, David ; /University Coll.

  18. Upper bounds on sparticle masses from naturalness or how to disprove weak

    Office of Scientific and Technical Information (OSTI)

    scale supersymmetry (Journal Article) | SciTech Connect Upper bounds on sparticle masses from naturalness or how to disprove weak scale supersymmetry Citation Details In-Document Search This content will become publicly available on February 15, 2017 Title: Upper bounds on sparticle masses from naturalness or how to disprove weak scale supersymmetry Authors: Baer, Howard ; Barger, Vernon ; Savoy, Michael Publication Date: 2016-02-16 OSTI Identifier: 1238092 Type: Publisher's Accepted

  19. COMPARING DENSE GALAXY CLUSTER REDSHIFT SURVEYS WITH WEAK-LENSING MAPS

    SciTech Connect (OSTI)

    Hwang, Ho Seong; Geller, Margaret J.; Zahid, H. Jabran; Diaferio, Antonaldo; Rines, Kenneth J. E-mail: mgeller@cfa.harvard.edu E-mail: diaferio@ph.unito.it

    2014-12-20

    We use dense redshift surveys of nine galaxy clusters at z ∼ 0.2 to compare the galaxy distribution in each system with the projected matter distribution from weak lensing. By combining 2087 new MMT/Hectospec redshifts and the data in the literature, we construct spectroscopic samples within the region of weak-lensing maps of high (70%-89%) and uniform completeness. With these dense redshift surveys, we construct galaxy number density maps using several galaxy subsamples. The shape of the main cluster concentration in the weak-lensing maps is similar to the global morphology of the number density maps based on cluster members alone, mainly dominated by red members. We cross-correlate the galaxy number density maps with the weak-lensing maps. The cross-correlation signal when we include foreground and background galaxies at 0.5z {sub cl} < z < 2z {sub cl} is 10%-23% larger than for cluster members alone at the cluster virial radius. The excess can be as high as 30% depending on the cluster. Cross-correlating the galaxy number density and weak-lensing maps suggests that superimposed structures close to the cluster in redshift space contribute more significantly to the excess cross-correlation signal than unrelated large-scale structure along the line of sight. Interestingly, the weak-lensing mass profiles are not well constrained for the clusters with the largest cross-correlation signal excesses (>20% for A383, A689, and A750). The fractional excess in the cross-correlation signal including foreground and background structures could be a useful proxy for assessing the reliability of weak-lensing cluster mass estimates.

  20. Design of Bcl-2 and Bcl-xL Inhibitors with Subnanomolar Binding Affinities Based upon a New Scaffold

    SciTech Connect (OSTI)

    Zhou, Haibin; Chen, Jianfang; Meagher, Jennifer L.; Yang, Chao-Yie; Aguilar, Angelo; Liu, Liu; Bai, Longchuan; Cong, Xin; Cai, Qian; Fang, Xueliang; Stuckey, Jeanne A.; Wang, Shaomeng

    2014-10-02

    Employing a structure-based strategy, we have designed a new class of potent small-molecule inhibitors of the anti-apoptotic proteins Bcl-2 and Bcl-xL. An initial lead compound with a new scaffold was designed based upon the crystal structure of Bcl-xL and U.S. Food and Drug Administration (FDA) approved drugs and was found to have an affinity of 100 {micro}M for both Bcl-2 and Bcl-xL. Linking this weak lead to another weak-affinity fragment derived from Abbott's ABT-737 led to an improvement of the binding affinity by a factor of >10,000. Further optimization ultimately yielded compounds with subnanomolar binding affinities for both Bcl-2 and Bcl-xL and potent cellular activity. The best compound (21) binds to Bcl-xL and Bcl-2 with K{sub i} < 1 nM, inhibits cell growth in the H146 and H1417 small-cell lung cancer cell lines with IC{sub 50} values of 60-90 nM, and induces robust cell death in the H146 cancer cell line at 30-100 nM.

  1. Exciton binding energy in semiconductor quantum dots

    SciTech Connect (OSTI)

    Pokutnii, S. I.

    2010-04-15

    In the adiabatic approximation in the context of the modified effective mass approach, in which the reduced exciton effective mass {mu} = {mu}(a) is a function of the radius a of the semiconductor quantum dot, an expression for the exciton binding energy E{sub ex}(a) in the quantum dot is derived. It is found that, in the CdSe and CdS quantum dots with the radii a comparable to the Bohr exciton radii a{sub ex}, the exciton binding energy E{sub ex}(a) is substantially (respectively, 7.4 and 4.5 times) higher than the exciton binding energy in the CdSe and CdS single crystals.

  2. Parameter-induced stochastic resonance based on spectral entropy and its application to weak signal detection

    SciTech Connect (OSTI)

    Zhang, Jinjing; Zhang, Tao

    2015-02-15

    The parameter-induced stochastic resonance based on spectral entropy (PSRSE) method is introduced for the detection of a very weak signal in the presence of strong noise. The effect of stochastic resonance on the detection is optimized using parameters obtained in spectral entropy analysis. Upon processing employing the PSRSE method, the amplitude of the weak signal is enhanced and the noise power is reduced, so that the frequency of the signal can be estimated with greater precision through spectral analysis. While the improvement in the signal-to-noise ratio is similar to that obtained using the Duffing oscillator algorithm, the computational cost reduces from O(N{sup 2}) to O(N). The PSRSE approach is applied to the frequency measurement of a weak signal made by a vortex flow meter. The results are compared with those obtained applying the Duffing oscillator algorithm.

  3. Review Article: The weak interactive characteristic of resonance cells and broadband effect of metamaterials

    SciTech Connect (OSTI)

    Zhao, Xiaopeng Song, Kun

    2014-10-15

    Metamaterials are artificial media designed to control electromagnetic wave propagation. Due to resonance, most present-day metamaterials inevitably suffer from narrow bandwidth, extremely limiting their practical applications. On the basis of tailored properties, a metamaterial within which each distinct unit cell resonates at its inherent frequency and has almost no coupling effect with the other ones, termed as weak interaction system, can be formulated. The total response of a weak interaction system can be treated as an overlap of the single resonance spectrum of each type of different unit cells. This intriguing feature therefore makes it possible to accomplish multiband or broadband metamaterials in a simple way. By introducing defects into metamaterials to form a weak interaction system, multiband and broadband electromagnetic metamaterials have first been experimentally demonstrated by our group. The similar concept can also be readily extended to acoustic and seismic metamaterials.

  4. Stabilized sulfur binding using activated fillers

    DOE Patents [OSTI]

    Kalb, Paul D.; Vagin, Vyacheslav P.; Vagin, Sergey P.

    2015-07-21

    A method of making a stable, sulfur binding composite comprising impregnating a solid aggregate with an organic modifier comprising unsaturated hydrocarbons with at least one double or triple covalent bond between adjacent carbon atoms to create a modifier-impregnated aggregate; heating and drying the modifier-impregnated aggregate to activate the surface of the modifier-impregnated aggregate for reaction with sulfur.

  5. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1996-03-05

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 15 figs.

  6. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1996-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  7. Note: On-line weak signal detection via adaptive stochastic resonance

    SciTech Connect (OSTI)

    Lu, Siliang; He, Qingbo Kong, Fanrang

    2014-06-15

    We design an instrument with a novel embedded adaptive stochastic resonance (SR) algorithm that consists of a SR module and a digital zero crossing detection module for on-line weak signal detection in digital signal processing applications. The two modules are responsible for noise filtering and adaptive parameter configuration, respectively. The on-line weak signal detection can be stably achieved in seconds. The prototype instrument exhibits an advance of 20 dB averaged signal-to-noise ratio and 5 times averaged adjust R-square as compared to the input noisy signal, in considering different driving frequencies and noise levels.

  8. Impact of magnification and size bias on the weak lensing power spectrum

    Office of Scientific and Technical Information (OSTI)

    and peak statistics (Journal Article) | SciTech Connect Impact of magnification and size bias on the weak lensing power spectrum and peak statistics Citation Details In-Document Search Title: Impact of magnification and size bias on the weak lensing power spectrum and peak statistics Authors: Liu J. ; May M. ; Haiman, Z. ; Hui, L. ; Kratochvil, J.M. Publication Date: 2014-01-21 OSTI Identifier: 1132481 Report Number(s): BNL--104426-2014-JA KA3201020 DOE Contract Number: DE-AC02-98CH10886

  9. High-energy jet quenching in weakly coupled quark-gluon plasmas

    SciTech Connect (OSTI)

    Arnold, Peter; Xiao Wei

    2008-12-15

    q is the average squared transverse momentum transfer per unit length to a high-energy particle traversing a QCD medium such as a quark-gluon plasma. We find the (UV-regulated) value of q to leading order in the weak coupling limit, {alpha}{sub s}(T)<<1. We then use this value to generalize previous analytic results on the gluon bremsstrahlung and pair production rates for massless high-energy particles in a weakly coupled quark-gluon plasma, at next-to-leading logarithmic order.

  10. Carbon Lock-in Through Capital Stock Inertia Associated with Weak Near-term Climate Policies

    SciTech Connect (OSTI)

    Bertram, Christoph; Johnson, Nils; Luderer, Gunnar; Riahi, Keywan; Isaac, Morna; Eom, Jiyong

    2015-01-01

    Stringent long-term climate targets necessitate a strict limit on cumulative emissions in this century for which sufficient policy signals are so far lacking. Based on an ensemble of ten energy-economy models, we explore how long-term transformation pathways depend on policies pursued during the next two decades. We find that weak GHG emission targets for 2030 lead, in that year alone, to excess carbon dioxide emissions of nearly half of the annual emissions in 2010, mainly through coal electricity generation. Furthermore, by consuming more of the long-term cumulative emissions budget in the first two decades, weak policy increases the likelihood of overshooting the budget and the urgency of reducing GHG emissions. Therefore, to be successful under weak policies, models must prematurely retire much of the additional coal capacity post-2030 and remove large quantities of carbon dioxide from the atmosphere in the latter half of the century. While increased energy efficiency lowers mitigation costs considerably, even with weak near-term policies, it does not substantially reduce the short term reliance on coal electricity. However, increased energy efficiency does allow the energy system more flexibility in mitigating emissions and, thus, makes the post-2030 transition easier.

  11. Measuring the Weak Charge of the Proton via Elastic Electron-Proton Scattering

    SciTech Connect (OSTI)

    Jones, Donald C.

    2015-10-01

    The Qweak experiment which ran in Hall C at Jefferson Lab in Newport News, VA, and completed data taking in May 2012, measured the weak charge of the proton QpW via elastic electron-proton scattering. Longitudinally polarized electrons were scattered from an unpolarized liquid hydrogen target. The helicity of the electron beam was flipped at approximately 1 kHz between left and right spin states. The Standard Model predicts a small parity-violating asymmetry of scattering rates between right and left helicity states due to the weak interaction. An initial result using 4% of the data was published in October 2013 [1] with a measured parity-violating asymmetry of -279 ± 35(stat) ± 31 (syst) ppb. This asymmetry, along with other data from parity-violating electron scattering experiments, provided the world's first determination of the weak charge of the proton. The weak charge of the proton was found to be pW = 0.064 ± 0.012, in good agreement with the Standard Model prediction of pW(SM) = 0.0708 ± 0.0003[2].

  12. Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers

    SciTech Connect (OSTI)

    Nap, R. J.; Tagliazucchi, M.; Szleifer, I.

    2014-01-14

    This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads to systematic, but in general small, corrections to earlier theoretical predictions describing the behavior of weak polyelectrolyte layers. However, polyelectrolyte uncharging results in a decrease in the concentration of counterions and inclusion of the Born Energy can result in a substantial decrease of the counterion concentration. The effect of considering the Born energy contribution is explored for end-grafted weak polyelectrolyte layers by calculating experimental observables which are known to depend on the presence of charges within the polyelectrolyte layer: inclusion of the Born energy contribution leads to a decrease in the capacitance of polyelectrolyte-modified electrodes, a decrease of conductivity of polyelectrolyte-modified nanopores and an increase in the repulsion exerted by a planar polyelectrolyte layer confined by an opposing wall.

  13. Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhu, Xueyong; Viswanathan, Karthik; Raman, Rahul; Yu, Wenli; Sasisekharan, Ram; Wilson, Ian A.

    2015-11-01

    Avian H5N1 influenza viruses continue to spread in wild birds and domestic poultry with sporadic infection in humans. Receptor binding specificity changes are a prerequisite for H5N1 viruses and other zoonotic viruses to be transmitted among humans. Previous reported hemagglutinin (HA) mutants from ferret-transmissible H5N1 viruses of A/Viet Nam/1203/04 and A/Indonesia/5/05 showed slightly increased, but still very weak, binding to human receptors. From mutagenesis and glycan array studies, we previously identified two H5N1 HA mutants that could more effectively switch receptor specificity to human-like α2-6 linked sialosides with avidity comparable to wild-type H5 HA binding to avian-like α2-3 linked sialosides.more »Here, crystal structures of these two H5 HA mutants free and in complex with human and avian glycan receptor analogues reveal the structural basis for their preferential binding to human receptors. These findings suggest continuous surveillance should be maintained to monitor and assess human-to-human transmission potential of H5N1 viruses.« less

  14. X-ray crystallographic analysis of adipocyte fatty acid binding...

    Office of Scientific and Technical Information (OSTI)

    binding protein (aP2) modified with 4-hydroxy-2-nonenal Citation Details In-Document Search Title: X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) ...

  15. Multidomain Carbohydrate-binding Proteins Involved in Bacteroides...

    Office of Scientific and Technical Information (OSTI)

    Title: Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism Authors: Cameron, Elizabeth A. ; Maynard, Mallory A. ; Smith, ...

  16. Discrete kinetic eigenmode spectra of electron plasma oscillations in weakly collisional plasma: A numerical study

    SciTech Connect (OSTI)

    Black, Carrie; Ng, C. S.

    2013-01-15

    It has been demonstrated that in the presence of weak collisions, described by the Lenard-Bernstein (LB) collision operator, the Landau-damped solutions become true eigenmodes of the system and constitute a complete set [C.-S. Ng et al., Phys. Rev. Lett. 83, 1974 (1999) and C. S. Ng et al., Phys. Rev. Lett. 96, 065002 (2004)]. We present numerical results from an Eulerian Vlasov code that incorporates the Lenard-Bernstein collision operator [A. Lenard and I. B. Bernstein, Phys. Rev. 112, 1456 (1958)]. The effect of collisions on the numerical recursion phenomenon seen in Vlasov codes is discussed. The code is benchmarked against exact linear eigenmode solutions in the presence of weak collisions, and a spectrum of Landau-damped solutions is determined within the limits of numerical resolution. Tests of the orthogonality and the completeness relation are presented.

  17. Forward Compton scattering with weak neutral current: Constraints from sum rules

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gorchtein, Mikhail; Zhang, Xilin

    2015-06-09

    We generalize forward real Compton amplitude to the case of the interference of the electromagnetic and weak neutral current, formulate a low-energy theorem, relate the new amplitudes to the interference structure functions and obtain a new set of sum rules. Furthermore, we address a possible new sum rule that relates the product of the axial charge and magnetic moment of the nucleon to the 0th moment of the structure function g5(ν, 0). For the dispersive γ Z-box correction to the proton’s weak charge, the application of the GDH sum rule allows us to reduce the uncertainty due to resonance contributionsmore » by a factor of two. Finally, the finite energy sum rule helps addressing the uncertainty in that calculation due to possible duality violations.« less

  18. Electronic structure and weak itinerant magnetism in metallic Y2Ni7

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Singh, David J.

    2015-11-03

    We describe a density functional study of the electronic structure and magnetism of Y₂Ni₇. The results show itinerant magnetism very similar to that in the weak itinerant ferromagnet Ni₃Al. The electropositive Y atoms in Y₂Ni₇ donate charge to the Ni host mostly in the form of s electrons. The non-spin-polarized state shows a high density of states at the Fermi level, N (EF), due to flat bands. This leads to a ferromagnetic instability. However, there are also several much more dispersive bands crossing E(F), which should promote the conductivity. Spin fluctuation effects appear to be comparable to or weaker thanmore » Ni₃Al, based on comparison with experimental data. Y₂Ni₇ provides a uniaxial analog to cubic Ni₃Al, for studying weak itinerant ferromagnetism, suggesting detailed measurements of its low temperature physical properties and spin fluctuations, as well as experiments under pressure.« less

  19. Symmetries of the triple degenerate DNLS equations for weakly nonlinear dispersive MHD waves

    SciTech Connect (OSTI)

    Webb, G. M.; Brio, M.; Zank, G. P.

    1996-07-20

    A formulation of Hamiltonian and Lagrangian variational principles, Lie point symmetries and conservation laws for the triple degenerate DNLS equations describing the propagation of weakly nonlinear dispersive MHD waves along the ambient magnetic field, in {beta}{approx}1 plasmas is given. The equations describe the interaction of the Alfven and magnetoacoustic modes near the triple umbilic point, where the fast magnetosonic, slow magnetosonic and Alfven speeds coincide and a{sub g}{sup 2}=V{sub A}{sup 2} where a{sub g} is the gas sound speed and V{sub A} is the Alfven speed. A discussion is given of the travelling wave similarity solutions of the equations, which include solitary wave and periodic traveling waves. Strongly compressible solutions indicate the necessity for the insertion of shocks in the flow, whereas weakly compressible, near Alfvenic solutions resemble similar, shock free travelling wave solutions of the DNLS equation.

  20. Forward Compton scattering with weak neutral current: Constraints from sum rules

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Gorchtein, Mikhail; Zhang, Xilin

    2015-07-01

    We generalize forward real Compton amplitude to the case of the interference of the electromagnetic and weak neutral current, formulate a low-energy theorem, relate the new amplitudes to the interference structure functions and obtain a new set of sum rules. We address a possible new sum rule that relates the product of the axial charge and magnetic moment of the nucleon to the 0th moment of the structure function g?(?0). For the dispersive ? ?-box correction to the proton's weak charge, the application of the GDH sum rule allows us to reduce the uncertainty due to resonance contributions by amore »factor of two. The finite energy sum rule helps addressing the uncertainty in that calculation due to possible duality violations.« less

  1. Test of weak and strong factorization in nucleus-nucleuscollisions atseveral hundred MeV/nucleon

    SciTech Connect (OSTI)

    La Tessa, Chiara; Sihver, Lembit; Zeitlin, Cary; Miller, Jack; Guetersloh, Stephen; Heilbronn, Lawrence; Mancusi, Davide; Iwata,Yoshiuki; Murakami, Takeshi

    2006-06-21

    Total and partial charge-changing cross sections have been measured for argon projectiles at 400 MeV/nucleon in carbon, aluminum, copper, tin and lead targets; cross sections for hydrogen were also obtained, using a polyethylene target. The validity of weak and strong factorization properties has been investigated for partial charge-changing cross sections; preliminary cross section values obtained for carbon, neon and silicon at 290 and 400 MeV/nucleon and iron at 400 MeV/nucleon, in carbon, aluminum, copper, tin and lead targets have been also used for testing these properties. Two different analysis methods were applied and both indicated that these properties are valid, without any significant difference between weak and strong factorization. The factorization parameters have then been calculated and analyzed in order to find some systematic behavior useful for modeling purposes.

  2. Magnetic fields and fluctuations in weakly Mn doped ZnGeP{sub 2}

    SciTech Connect (OSTI)

    Mengyan, P. W.; Lichti, R. L.; Baker, B. B.; Celebi, Y. G.; Catak, E.; Carroll, B. R.; Zawilski, K. T.; Schunemann, P. G.

    2014-02-21

    We report on our measurements of local and bulk magnetic features in weakly Mn doped ZnGeP{sub 2}. Utilizing muon spin rotation and relaxation measurements, we identify local ferromagnetic order and fluctuations in the local fields as sampled by an implanted muon (?{sup +}). We also report on field induced ferromagnetism occurring above the claimed paramagnetic to ferromagnetic transition temperature (T{sub c} = 312 K)

  3. Dual chain synthetic heparin-binding growth factor analogs

    DOE Patents [OSTI]

    Zamora, Paul O.; Pena, Louis A.; Lin, Xinhua

    2009-10-06

    The invention provides synthetic heparin-binding growth factor analogs having two peptide chains each branched from a branch moiety, such as trifunctional amino acid residues, the branch moieties separated by a first linker of from 3 to about 20 backbone atoms, which peptide chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a second linker, which may be a hydrophobic second linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  4. Dual chain synthetic heparin-binding growth factor analogs

    DOE Patents [OSTI]

    Zamora, Paul O.; Pena, Louis A.; Lin, Xinhua

    2012-04-24

    The invention provides synthetic heparin-binding growth factor analogs having two peptide chains each branched from a branch moiety, such as trifunctional amino acid residues, the branch moieties separated by a first linker of from 3 to about 20 backbone atoms, which peptide chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a second linker, which may be a hydrophobic second linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  5. CONDUCTION IN LOW MACH NUMBER FLOWS. I. LINEAR AND WEAKLY NONLINEAR REGIMES

    SciTech Connect (OSTI)

    Lecoanet, Daniel; Brown, Benjamin P.; Zweibel, Ellen G.; Burns, Keaton J.; Oishi, Jeffrey S.; Vasil, Geoffrey M.

    2014-12-20

    Thermal conduction is an important energy transfer and damping mechanism in astrophysical flows. Fourier's law, in which the heat flux is proportional to the negative temperature gradient, leading to temperature diffusion, is a well-known empirical model of thermal conduction. However, entropy diffusion has emerged as an alternative thermal conduction model, despite not ensuring the monotonicity of entropy. This paper investigates the differences between temperature and entropy diffusion for both linear internal gravity waves and weakly nonlinear convection. In addition to simulating the two thermal conduction models with the fully compressible Navier-Stokes equations, we also study their effects in the reduced ''soundproof'' anelastic and pseudoincompressible (PI) equations. We find that in the linear and weakly nonlinear regime, temperature and entropy diffusion give quantitatively similar results, although there are some larger errors in the PI equations with temperature diffusion due to inaccuracies in the equation of state. Extrapolating our weakly nonlinear results, we speculate that differences between temperature and entropy diffusion might become more important for strongly turbulent convection.

  6. Higgs gravitational interaction, weak boson scattering, and Higgs inflation in Jordan and Einstein frames

    SciTech Connect (OSTI)

    Ren, Jing; Xianyu, Zhong-Zhi; He, Hong-Jian E-mail: xianyuzhongzhi@gmail.com

    2014-06-01

    We study gravitational interaction of Higgs boson through the unique dimension-4 operator ?H{sup †}HR, with H  the Higgs doublet and R  the Ricci scalar curvature. We analyze the effect of this dimensionless nonminimal coupling ?  on weak gauge boson scattering in both Jordan and Einstein frames. We explicitly establish the longitudinal-Goldstone equivalence theorem with nonzero ? coupling in both frames, and analyze the unitarity constraints. We study the ?-induced weak boson scattering cross sections at O(1?30) TeV scales, and propose to probe the Higgs-gravity coupling via weak boson scattering experiments at the LHC (14 TeV) and the next generation pp colliders (50-100 TeV). We further extend our study to Higgs inflation, and quantitatively derive the perturbative unitarity bounds via coupled channel analysis, under large field background at the inflation scale. We analyze the unitarity constraints on the parameter space in both the conventional Higgs inflation and the improved models in light of the recent BICEP2 data.

  7. WEAK GRAVITATIONAL LENSING AS A PROBE OF PHYSICAL PROPERTIES OF SUBSTRUCTURES IN DARK MATTER HALOS

    SciTech Connect (OSTI)

    Shirasaki, Masato

    2015-02-01

    We propose a novel method to select satellite galaxies in outer regions of galaxy groups or clusters using weak gravitational lensing. The method is based on the theoretical expectation that the tangential shear pattern around satellite galaxies would appear with negative values at an offset distance from the center of the main halo. We can thus locate the satellite galaxies statistically with an offset distance of several lensing smoothing scales by using the standard reconstruction of surface mass density maps from weak lensing observation. We test the idea using high-resolution cosmological simulations. We show that subhalos separated from the center of the host halo are successfully located even without assuming the position of the center. For a number of such subhalos, the characteristic mass and offset length can be also estimated on a statistical basis. We perform a Fisher analysis to show how well upcoming weak lensing surveys can constrain the mass density profile of satellite galaxies. In the case of the Large Synoptic Survey Telescope with a sky coverage of 20,000 deg{sup 2}, the mass of the member galaxies in the outer region of galaxy clusters can be constrained with an accuracy of ?0.1 dex for galaxy clusters with mass 10{sup 14} h {sup –1} M {sub ?} at z = 0.15. Finally we explore the detectability of tidal stripping features for subhalos having a wide range of masses of 10{sup 11}-10{sup 13} h {sup –1} M {sub ?}.

  8. Qweak: First Direct Measurement of the Weak Charge of the Proton

    SciTech Connect (OSTI)

    Nuruzzaman, NFN

    2014-04-01

    The Qweak experiment at Hall C of Thomas Jefferson National Accelerator Facility has made the first direct measurement of the weak charge of the proton, QWp, through a precision measurement of the parity-violating asymmetry in elastic e-p scattering at low momentum transfer Q2= 0.025 (GeV/c)2 with incident electron beam energy of 1.155 GeV. The Qweak experiment, along with earlier results of parity violating elastic scattering experiments, is expected to determine the most precise value of QWp which is suppressed in the Standard Model. If this result is further combined with the 133Cs atomic parity violation (APV) measurement, significant constraints on the weak charge of the up quark, down quark, and neutron can be extracted. This data will also be used to determine the weak-mixing angle, sin2 ?W, with a relative uncertainty of < 0.5% that will provide a competitive measurement of the running of sin2 ?W to low Q2. An overview of the experiment and its results using the commissioning dataset, constituting approximately 4% of the data collected in the experiment, are reported here.

  9. Gene encoding herbicide safener binding protein

    DOE Patents [OSTI]

    Walton, Jonathan D.; Scott-Craig, John S.

    1999-01-01

    The cDNA encoding safener binding protein (SafBP), also referred to as SBP1, is set forth in FIG. 5 and SEQ ID No. 1. The deduced amino acid sequence is provided in FIG. 5 and SEQ ID No. 2. Methods of making and using SBP1 and SafBP to alter a plant's sensitivity to certain herbicides or a plant's responsiveness to certain safeners are also provided, as well as expression vectors, transgenic plants or other organisms transfected with said vectors and seeds from said plants.

  10. Polynucleotides encoding TRF1 binding proteins

    DOE Patents [OSTI]

    Campisi, Judith (Berkeley, CA); Kim, Sahn-Ho (Albany, CA)

    2002-01-01

    The present invention provides a novel telomere associated protein (Trf1-interacting nuclear protein 2 "Tin2") that hinders the binding of Trf1 to its specific telomere repeat sequence and mediates the formation of a Tin2-Trf1-telomeric DNA complex that limits telomerase access to the telomere. Also included are the corresponding nucleic acids that encode the Tin2 of the present invention, as well as mutants of Tin2. Methods of making, purifying and using Tin2 of the present invention are described. In addition, drug screening assays to identify drugs that mimic and/or complement the effect of Tin2 are presented.

  11. Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics

    SciTech Connect (OSTI)

    Borbulevych, Oleg Y.; Piepenbrink, Kurt H.; Baker, Brian M.

    2012-03-16

    Molecular mimicry between foreign and self Ags is a mechanism of TCR cross-reactivity and is thought to contribute to the development of autoimmunity. The {alpha}{beta} TCR A6 recognizes the foreign Ag Tax from the human T cell leukemia virus-1 when presented by the class I MHC HLA-A2. In a possible link with the autoimmune disease human T cell leukemia virus-1-associated myelopathy/tropical spastic paraparesis, A6 also recognizes a self peptide from the neuronal protein HuD in the context of HLA-A2. We found in our study that the complexes of the HuD and Tax epitopes with HLA-A2 are close but imperfect structural mimics and that in contrast with other recent structures of TCRs with self Ags, A6 engages the HuD Ag with the same traditional binding mode used to engage Tax. Although peptide and MHC conformational changes are needed for recognition of HuD but not Tax and the difference of a single hydroxyl triggers an altered TCR loop conformation, TCR affinity toward HuD is still within the range believed to result in negative selection. Probing further, we found that the HuD-HLA-A2 complex is only weakly stable. Overall, these findings help clarify how molecular mimicry can drive self/nonself cross-reactivity and illustrate how low peptide-MHC stability can permit the survival of T cells expressing self-reactive TCRs that nonetheless bind with a traditional binding mode.

  12. ELLIPTICAL WEIGHTED HOLICs FOR WEAK LENSING SHEAR MEASUREMENT. III. THE EFFECT OF RANDOM COUNT NOISE ON IMAGE MOMENTS IN WEAK LENSING ANALYSIS

    SciTech Connect (OSTI)

    Okura, Yuki; Futamase, Toshifumi E-mail: tof@astr.tohoku.ac.jp

    2013-07-01

    This is the third paper on the improvement of systematic errors in weak lensing analysis using an elliptical weight function, referred to as E-HOLICs. In previous papers, we succeeded in avoiding errors that depend on the ellipticity of the background image. In this paper, we investigate the systematic error that depends on the signal-to-noise ratio of the background image. We find that the origin of this error is the random count noise that comes from the Poisson noise of sky counts. The random count noise makes additional moments and centroid shift error, and those first-order effects are canceled in averaging, but the second-order effects are not canceled. We derive the formulae that correct this systematic error due to the random count noise in measuring the moments and ellipticity of the background image. The correction formulae obtained are expressed as combinations of complex moments of the image, and thus can correct the systematic errors caused by each object. We test their validity using a simulated image and find that the systematic error becomes less than 1% in the measured ellipticity for objects with an IMCAT significance threshold of {nu} {approx} 11.7.

  13. NOISY WEAK-LENSING CONVERGENCE PEAK STATISTICS NEAR CLUSTERS OF GALAXIES AND BEYOND

    SciTech Connect (OSTI)

    Fan Zuhui; Shan Huanyuan; Liu Jiayi

    2010-08-20

    Taking into account noise from intrinsic ellipticities of source galaxies, in this paper, we study the peak statistics in weak-lensing convergence maps around clusters of galaxies and beyond. We emphasize how the noise peak statistics is affected by the density distribution of nearby clusters, and also how cluster-peak signals are changed by the existence of noise. These are the important aspects to be thoroughly understood in weak-lensing analyses for individual clusters as well as in cosmological applications of weak-lensing cluster statistics. We adopt Gaussian smoothing with the smoothing scale {theta} {sub G} = 0.5arcmin in our analyses. It is found that the noise peak distribution near a cluster of galaxies sensitively depends on the density profile of the cluster. For a cored isothermal cluster with the core radius R{sub c} , the inner region with R {<=} R{sub c} appears noisy containing on average {approx}2.4 peaks with {nu} {>=} 5 for R{sub c} = 1.7arcmin and the true peak height of the cluster {nu} = 5.6, where {nu} denotes the convergence signal-to-noise ratio. For a Navarro-Frenk-White (NFW) cluster of the same mass and the same central {nu}, the average number of peaks with {nu} {>=} 5 within R {<=} R{sub c} is {approx}1.6. Thus a high peak corresponding to the main cluster can be identified more cleanly in the NFW case. In the outer region with R{sub c} < R {<=} 5R{sub c} , the number of high noise peaks is considerably enhanced in comparison with that of the pure noise case without the nearby cluster. For {nu} {>=} 4, depending on the treatment of the mass-sheet degeneracy in weak-lensing analyses, the enhancement factor f is in the range of {approx}5 to {approx}55 for both clusters as their outer density profiles are similar. The properties of the main-cluster-peak identified in convergence maps are also significantly affected by the presence of noise. Scatters as well as a systematic shift for the peak height are present. The height distribution is peaked at {nu} {approx} 6.6, rather than at {nu} = 5.6, corresponding to a shift of {Delta}{nu} {approx} 1, for the isothermal cluster. For the NFW cluster, {Delta}{nu} {approx} 0.8. The existence of noise also causes a location offset for the weak-lensing identified main-cluster-peak with respect to the true center of the cluster. The offset distribution is very broad and extends to R {approx} R{sub c} for the isothermal case. For the NFW cluster, it is relatively narrow and peaked at R {approx} 0.2R{sub c} . We also analyze NFW clusters of different concentrations. It is found that the more centrally concentrated the mass distribution of a cluster is, the less its weak-lensing signal is affected by noise. Incorporating these important effects and the mass function of NFW dark matter halos, we further present a model calculating the statistical abundances of total convergence peaks, true and false ones, over a large field beyond individual clusters. The results are in good agreement with those from numerical simulations. The model then allows us to probe cosmologies with the convergence peaks directly without the need of expensive follow-up observations to differentiate true and false peaks.

  14. Effects of a weakly 3-D equilibrium on ideal magnetohydrodynamic instabilities

    SciTech Connect (OSTI)

    Hegna, C. C.

    2014-07-15

    The effect of a small three-dimensional equilibrium distortion on an otherwise axisymmetric configuration is shown to be destabilizing to ideal magnetohydrodynamic modes. The calculations assume that the 3-D fields are weak and that shielding physics is present so that no islands appear in the resulting equilibrium. An eigenfunction that has coupled harmonics of different toroidal mode number is constructed using a perturbation approach. The theory is applied to the case of tokamak H-modes with shielded resonant magnetic perturbations (RMPs) present indicating RMPs can be destabilizing to intermediate-n peeling-ballooning modes.

  15. Neutral weak-current two-body contributions in inclusive scattering from {sup 12}C

    SciTech Connect (OSTI)

    Lovato, Alessandro; Gandolfi, Stefano; Carlson, Joseph; Pieper, S. C.; Schiavilla, Rocco

    2014-05-01

    An {\\it ab initio} calculation of the sum rules of the neutral weak response functions in $^{12}$C is reported, based on a realistic Hamiltonian, including two- and three-nucleon potentials, and on realistic currents, consisting of one- and two-body terms. We find that the sum rules of the response functions associated with the longitudinal and transverse components of the (space-like) neutral current are largest and that a significant portion ($\\simeq 30$\\%) of the calculated strength is due to two-body terms. This fact may have implications for the MiniBooNE and other neutrino quasi-elastic scattering data on nuclei.

  16. SORPTION BEHAVIOR OF MONOSODIUM TITANATE AND AMORPHOUS PEROXOTITANATE MATERIALS UNDER WEAKLY ACIDIC CONDITIONS

    SciTech Connect (OSTI)

    Hobbs, D.; Elvington, M.; Click, D.

    2009-11-11

    Inorganic, titanate-based sorbents are tested with respect to adsorption of a variety of sorbates under weakly acidic conditions (pH 3). Specifically, monosodium titanate (MST) and amorphous peroxotitanate (APT) sorption characteristics are initially probed through a screening process consisting of a pair of mixed metal solutions containing a total of 29 sorbates including alkali metals, alkaline earth metals, transition metals, metalloids and nonmetals. MST and APT sorption characteristics are further analyzed individually with chromium(III) and cadmium(II) using a batch method at ambient laboratory temperature, varying concentrations of the sorbents and sorbates and contact times. Maximum sorbate loadings are obtained from the respective adsorption isotherms.

  17. Perturbative analysis of sheared flow Kelvin-Helmholtz instability in a weakly relativistic magnetized electron fluid

    SciTech Connect (OSTI)

    Sundar, Sita; Das, Amita; Kaw, Predhiman [Institute for Plasma Research, Bhat, Gandhinagar-382428 (India)

    2012-05-15

    In the interaction of intense lasers with matter/plasma, energetic electrons having relativistic energies get created. These energetic electrons can often have sheared flow profiles as they propagate through the plasma medium. In an earlier study [Phys. Plasmas 17, 022101 (2010)], it was shown that a relativistic sheared electron flow modifies the growth rate and threshold condition of the conventional Kelvin-Helmholtz instability. A perturbative analytic treatment for the case of weakly relativistic regime has been provided here. It provides good agreement with the numerical results obtained earlier.

  18. Stopping distance for high energy jets in weakly coupled quark-gluon plasmas

    SciTech Connect (OSTI)

    Arnold, Peter; Cantrell, Sean; Xiao Wei

    2010-02-15

    We derive a simple formula for the stopping distance for a high-energy quark traveling through a weakly coupled quark-gluon plasma. The result is given to next-to-leading order in an expansion in inverse logarithms ln(E/T), where T is the temperature of the plasma. We also define a stopping distance for gluons and give a leading-log result. Discussion of stopping distance has a theoretical advantage over discussion of energy loss rates in that stopping distances can be generalized to the case of strong coupling, where one may not speak of individual partons.

  19. Origins of weak lensing systematics, and requirements on future instrumentation (or knowledge of instrumentation)

    SciTech Connect (OSTI)

    Massey, Richard; Hoekstra, Henk; Kitching, Thomas; Rhodes, Jason; Cropper, Mark; Amiaux, Jerome; Harvey, David; Mellier, Yannick; Meneghetti, Massimo; Miller, Lance; Paulin-Henriksson, Stephane; Pires, Sandrine; Scaramella, Roberto; Schrabback, Tim

    2012-12-13

    The first half of this paper explores the origin of systematic biases in the measurement of weak gravitational lensing. Compared to previous work, we expand the investigation of point spread function instability and fold in for the first time the effects of non-idealities in electronic imaging detectors and imperfect galaxy shape measurement algorithms. In addition, these now explain the additive A(?) and multiplicative M(?) systematics typically reported in current lensing measurements. We find that overall performance is driven by a product of a telescope/camera's absolute performance, and our knowledge about its performance.

  20. Apparatus and method for measurement of weak optical absorptions by thermally induced laser pulsing

    DOE Patents [OSTI]

    Cremers, D.A.; Keller, R.A.

    1985-10-01

    The thermal lensing phenomenon is used as the basis for measurement of weak optical absorptions when a cell containing the sample to be investigated is inserted into a normally continuous-wave operation laser-pumped dye laser cavity for which the output coupler is deliberately tilted relative to intracavity circulating laser light, and pulsed laser output ensues, the pulsewidth of which can be related to the sample absorptivity by a simple algorithm or calibration curve. A minimum detection limit of less than 10[sup [minus]5] cm[sup [minus]1] has been demonstrated using this technique. 6 figs.

  1. Apparatus and method for measurement of weak optical absorptions by thermally induced laser pulsing

    DOE Patents [OSTI]

    Cremers, D.A.; Keller, R.A.

    1982-06-08

    The thermal lensing phenomenon is used as the basis for measurement of weak optical absorptions when a cell containing the sample to be investigated is inserted into a normally continuous-wave operation laser-pumped dye laser cavity for which the output coupler is deliberately tilted relative to intracavity circulating laser light, and pulsed laser output ensues, the pulsewidth of which can be rlated to the sample absorptivity by a simple algorithm or calibration curve. A minimum detection limit of less than 10/sup -5/ cm/sup -1/ has been demonstrated using this technique.

  2. Weak Interaction Models with New Quarks and Right-handed Currents

    DOE R&D Accomplishments [OSTI]

    Wilczek, F. A.; Zee, A.; Kingsley, R. L.; Treiman, S. B.

    1975-06-01

    We discuss various weak interaction issues for a general class of models within the SU(2) x U(1) gauge theory framework, with special emphasis on the effects of right-handed, charged currents and of quarks bearing new quantum numbers. In particular we consider the restrictions on model building which are imposed by the small KL - KS mass difference and by the .I = = rule; and we classify various possibilities for neutral current interactions and, in the case of heavy mesons with new quantum numbers, various possibilities for mixing effects analogous to KL - KS mixing.

  3. Field theory and weak Euler-Lagrange equation for classical particle-field systems

    SciTech Connect (OSTI)

    Qin, Hong; Burby, Joshua W; Davidson, Ronald C

    2014-10-01

    It is commonly believed that energy-momentum conservation is the result of space-time symmetry. However, for classical particle-field systems, e.g., Klimontovich-Maxwell and Klimontovich- Poisson systems, such a connection hasn't been formally established. The difficulty is due to the fact that particles and the electromagnetic fields reside on different manifolds. To establish the connection, the standard Euler-Lagrange equation needs to be generalized to a weak form. Using this technique, energy-momentum conservation laws that are difficult to find otherwise can be systematically derived.

  4. Method and apparatus for detecting chemical binding

    DOE Patents [OSTI]

    Warner, Benjamin P.; Havrilla, George J.; Miller, Thomasin C.; Wells, Cyndi A.

    2007-07-10

    The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

  5. Method And Apparatus For Detecting Chemical Binding

    DOE Patents [OSTI]

    Warner, Benjamin P.; Havrilla, George J.; Miller, Thomasin C.; Wells, Cyndi A.

    2005-02-22

    The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

  6. Neptunium Binding Kinetics with Arsenazo(III)

    SciTech Connect (OSTI)

    Leigh R. Martin; Aaron T. Johnson; Stephen P. Mezyk

    2014-08-01

    This document has been prepared to meet FCR&D level 2 milestone M2FT-14IN0304021, “Report on the results of actinide binding kinetics with aqueous phase complexants” This work was carried out under the auspices of the Thermodynamics and Kinetics of Advanced Separations Systems FCR&D work package. The report details kinetics experiments that were performed to measure rates of aqueous phase complexation for pentavalent neptunium with the chromotropic dye Arsenazo III (AAIII). The studies performed were designed to determine how pH, ionic strength and AAIII concentration may affect the rate of the reaction. A brief comparison with hexavalent neptunium is also made. It was identified that as pH was increased the rate of reaction also increased, however increasing the ionic strength and concentration of AAIII had the opposite effect. Interestingly, the rate of reaction of Np(VI) with AAIII was found to be slower than that of the Np(V) reaction.

  7. Hardware device to physical structure binding and authentication

    DOE Patents [OSTI]

    Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

    2013-08-20

    Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

  8. The Effects of Somatic Hypermutation on Neutralization and Binding...

    Office of Scientific and Technical Information (OSTI)

    Hypermutation on Neutralization and Binding in the PGT121 Family of Broadly Neutralizing HIV Antibodies Citation Details In-Document Search Title: The Effects of Somatic...

  9. U-183: ISC BIND DNS Resource Records Handling Vulnerability

    Broader source: Energy.gov [DOE]

    This problem was uncovered while testing with experimental DNS record types. It is possible to add records to BIND with null (zero length) rdata fields.

  10. Developing Adnectins That Target SRC Co-Activator Binding to...

    Office of Scientific and Technical Information (OSTI)

    Developing Adnectins That Target SRC Co-Activator Binding to PXR: A Structural Approach toward Understanding Promiscuity of PXR Citation Details In-Document Search Title: ...

  11. Structural and functional analysis of FIP2 binding to theendosome...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Structural and functional analysis of FIP2 binding to the endosome-localised Rab25 GTPase Citation Details In-Document Search Title: Structural and functional ...

  12. Resonance reactions and enhancement of weak interactions in collisions of cold molecules

    SciTech Connect (OSTI)

    Flambaum, V. V.; Ginges, J. S. M. [School of Physics, University of New South Wales, Sydney 2052 (Australia)

    2006-08-15

    With the creation of ultracold atoms and molecules, a new type of chemistry - 'resonance' chemistry - emerges: chemical reactions can occur when the energy of colliding atoms and molecules matches a bound state of the combined molecule (Feshbach resonance). This chemistry is rather similar to reactions that take place in nuclei at low energies. In this paper we suggest some problems for future experimental and theoretical work related to the resonance chemistry of ultracold molecules. Molecular Bose-Einstein condensates are particularly interesting because in this system collisions and chemical reactions are extremely sensitive to weak fields; also, a preferred reaction channel may be enhanced due to a finite number of final states. The sensitivity to weak fields arises due to the high density of narrow compound resonances and the macroscopic number of molecules with kinetic energy E=0 (in the ground state of a mean-field potential). The high sensitivity to the magnetic field may be used to measure the distribution of energy intervals, widths, and magnetic moments of compound resonances and study the onset of quantum chaos. A difference in the production rate of right-handed and left-handed chiral molecules may be produced by external electric E and magnetic B fields and the finite width {gamma} of the resonance (correlation {gamma}E{center_dot}B). The same effect may be produced by the parity-violating energy difference in chiral molecules.

  13. Positron impact excitations of hydrogen atom embedded in weakly coupled plasmas: Formation of Rydberg atoms

    SciTech Connect (OSTI)

    Rej, Pramit; Ghoshal, Arijit

    2014-09-15

    Formation of Rydberg atoms due to 1s?nlm excitations of hydrogen, for arbitrary n, l, m, by positron impact in weakly coupled plasma has been investigated using a distorted-wave theory in the momentum space. The interactions among the charged particles in the plasma have been represented by Debye-Huckel potentials. Making use of a simple variationally determined wave function for the hydrogen atom, it has been possible to obtain the distorted-wave scattering amplitude in a closed analytical form. A detailed study has been made on the effects of plasma screening on the differential and total cross sections in the energy range 20–300?eV of incident positron. For the unscreened case, our results agree nicely with some of the most accurate results available in the literature. To the best of our knowledge, such a study on the differential and total cross sections for 1s?nlm inelastic positron-hydrogen collisions for arbitrary n, l, m in weakly coupled plasmas is the first reported in the literature.

  14. The Weak Charge of the Proton: A Search For Physics Beyond the Standard Model

    SciTech Connect (OSTI)

    MacEwan, Scott

    2015-05-01

    The Qweak experiment, which completed running in May of 2012 at Jefferson Laboratory, has measured the parity-violating asymmetry in elastic electron-proton scattering at four-momentum transfer Q^2=0.025 (GeV/c)^2 in order to provide the first direct measurement of the proton?s weak charge, Qpw. The Standard Model makes firm predictions for the weak charge; deviations from the predicted value would provide strong evidence of new physics beyond the Standard Model. Using an 89% polarized electron beam at 145 microA scattering from a 34.4 cm long liquid hydrogen target, scattered electrons were detected using an array of eight fused-silica detectors placed symmetric about the beam axis. The parity-violating asymmetry was then measured by reversing the helicity of the incoming electrons and measuring the normalized difference in rate seen in the detectors. The low Q^2 enables a theoretically clean measurement; the higher order hadronic corrections are constrained using previous parity-violating electron scattering world data. The experimental method will be discussed, with recent results constituting 4% of our total data and projections of our proposed uncertainties on the full data set.

  15. Corrections to Morse and Ingard's variational-based treatment of weakly-nonlinear acoustics in lossless gases

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Christov, Ivan C.; Jordan, Pedro M.

    2015-07-17

    Errors in Morse and Ingard’s treatment of the topic of weakly-nonlinear acoustics in §6.2 of their book [Theoretical Acoustics (McGraw-Hill, New York, 1968)] are noted and corrected.

  16. Kinetic and equilibrium studies of acrylonitrile binding to cytochrome c peroxidase and oxidation of acrylonitrile by cytochrome c peroxidase compound I

    SciTech Connect (OSTI)

    Chinchilla, Diana, E-mail: Diana_Chinchilla@yahoo.com; Kilheeney, Heather, E-mail: raindropszoo@yahoo.com; Vitello, Lidia B., E-mail: lvitello@niu.edu; Erman, James E., E-mail: jerman@niu.edu

    2014-01-03

    Highlights: •Cytochrome c peroxidase (CcP) binds acrylonitrile in a pH-independent fashion. •The spectrum of the CcP/acrylonitrile complex is that of a 6c–ls ferric heme. •The acrylonitrile/CcP complex has a K{sub D} value of 1.1 ± 0.2 M. •CcP compound I oxidizes acrylonitrile with a maximum turnover rate of 0.61 min{sup ?1}. -- Abstract: Ferric heme proteins bind weakly basic ligands and the binding affinity is often pH dependent due to protonation of the ligand as well as the protein. In an effort to find a small, neutral ligand without significant acid/base properties to probe ligand binding reactions in ferric heme proteins we were led to consider the organonitriles. Although organonitriles are known to bind to transition metals, we have been unable to find any prior studies of nitrile binding to heme proteins. In this communication we report on the equilibrium and kinetic properties of acrylonitrile binding to cytochrome c peroxidase (CcP) as well as the oxidation of acrylonitrile by CcP compound I. Acrylonitrile binding to CcP is independent of pH between pH 4 and 8. The association and dissociation rate constants are 0.32 ± 0.16 M{sup ?1} s{sup ?1} and 0.34 ± 0.15 s{sup ?1}, respectively, and the independently measured equilibrium dissociation constant for the complex is 1.1 ± 0.2 M. We have demonstrated for the first time that acrylonitrile can bind to a ferric heme protein. The binding mechanism appears to be a simple, one-step association of the ligand with the heme iron. We have also demonstrated that CcP can catalyze the oxidation of acrylonitrile, most likely to 2-cyanoethylene oxide in a “peroxygenase”-type reaction, with rates that are similar to rat liver microsomal cytochrome P450-catalyzed oxidation of acrylonitrile in the monooxygenase reaction. CcP compound I oxidizes acrylonitrile with a maximum turnover number of 0.61 min{sup ?1} at pH 6.0.

  17. Mask effects on cosmological studies with weak-lensing peak statistics

    SciTech Connect (OSTI)

    Liu, Xiangkun; Pan, Chuzhong; Fan, Zuhui; Wang, Qiao

    2014-03-20

    With numerical simulations, we analyze in detail how the bad data removal, i.e., the mask effect, can influence the peak statistics of the weak-lensing convergence field reconstructed from the shear measurement of background galaxies. It is found that high peak fractions are systematically enhanced because of the presence of masks; the larger the masked area is, the higher the enhancement is. In the case where the total masked area is about 13% of the survey area, the fraction of peaks with signal-to-noise ratio ? ? 3 is ?11% of the total number of peaks, compared with ?7% of the mask-free case in our considered cosmological model. This can have significant effects on cosmological studies with weak-lensing convergence peak statistics, inducing a large bias in the parameter constraints if the effects are not taken into account properly. Even for a survey area of 9 deg{sup 2}, the bias in (? {sub m}, ?{sub 8}) is already intolerably large and close to 3?. It is noted that most of the affected peaks are close to the masked regions. Therefore, excluding peaks in those regions in the peak statistics can reduce the bias effect but at the expense of losing usable survey areas. Further investigations find that the enhancement of the number of high peaks around the masked regions can be largely attributed to the smaller number of galaxies usable in the weak-lensing convergence reconstruction, leading to higher noise than that of the areas away from the masks. We thus develop a model in which we exclude only those very large masks with radius larger than 3' but keep all the other masked regions in peak counting statistics. For the remaining part, we treat the areas close to and away from the masked regions separately with different noise levels. It is shown that this two-noise-level model can account for the mask effect on peak statistics very well, and the bias in cosmological parameters is significantly reduced if this model is applied in the parameter fitting.

  18. Multidomain Carbohydrate-binding Proteins Involved in Bacteroides

    Office of Scientific and Technical Information (OSTI)

    thetaiotaomicron Starch Metabolism (Journal Article) | SciTech Connect Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism Citation Details In-Document Search Title: Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism Authors: Cameron, Elizabeth A. ; Maynard, Mallory A. ; Smith, Christopher J. ; Smith, Thomas J. ; Koropatkin, Nicole M. ; Martens, Eric C. [1] ; Danforth) [2] + Show Author

  19. Neutron and weak-charge distributions of the 48Ca nucleus

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Hagen, Gaute; Forssen, Christian; Nazarewicz, Witold; Papenbrock, Thomas F.; Bacca, S.; Barnea, Nir; Carlsson, Boris; Drischler, Christian; Hebeler, Kai; Hjorth-Jensen, M.; et al

    2015-11-02

    What is the size of the atomic nucleus? This deceivably simple question is difficult to answer. Although the electric charge distributions in atomic nuclei were measured accurately already half a century ago, our knowledge of the distribution of neutrons is still deficient. In addition to constraining the size of atomic nuclei, the neutron distribution also impacts the number of nuclei that can exist and the size of neutron stars. We present an ab initio calculation of the neutron distribution of the neutron-rich nucleus 48Ca. We show that the neutron skin (difference between the radii of the neutron and proton distributions)more » is significantly smaller than previously thought. We also make predictions for the electric dipole polarizability and the weak form factor; both quantities that are at present targeted by precision measurements. Here, based on ab initio results for 48Ca, we provide a constraint on the size of a neutron star.« less

  20. Analytical study of the propagation of acoustic waves in a 1D weakly disordered lattice

    SciTech Connect (OSTI)

    Richoux, O. Morand, E.; Simon, L.

    2009-09-15

    This paper presents an analytical approach of the propagation of an acoustic wave through a normally distributed disordered lattice made up of Helmholtz resonators connected to a cylindrical duct. This approach allows to determine analytically the exact transmission coefficient of a weakly disordered lattice. Analytical results are compared to a well-known numerical method based on a matrix product. Furthermore, this approach gives an analytical expression of the localization length apart from the Bragg stopband which depends only on the standard deviation of the normal distribution disorder. This expression permits to study on one hand the localization length as a function of both disorder strength and frequency, and on the other hand, the propagation characteristics on the edges of two sorts of stopbands (Bragg and Helmholtz stopbands). Lastly, the value of the localization length inside the Helmholtz stopband is compared to the localization length in the Bragg stopband.

  1. Electron density and temperature measurement by continuum radiation emitted from weakly ionized atmospheric pressure plasmas

    SciTech Connect (OSTI)

    Park, Sanghoo; Choe, Wonho, E-mail: wchoe@kaist.ac.kr [Department of Physics, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Youn Moon, Se [High-enthalpy Plasma Research Center, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 561-756 (Korea, Republic of); Park, Jaeyoung [5771 La Jolla Corona Drive, La Jolla, CA 92037 (United States)

    2014-02-24

    The electron-atom neutral bremsstrahlung continuum radiation emitted from weakly ionized plasmas is investigated for electron density and temperature diagnostics. The continuum spectrum in 450–1000?nm emitted from the argon atmospheric pressure plasma is found to be in excellent agreement with the neutral bremsstrahlung formula with the electron-atom momentum transfer cross-section given by Popovi?. In 280–450?nm, however, a large discrepancy between the measured and the neutral bremsstrahlung emissivities is observed. We find that without accounting for the radiative H{sub 2} dissociation continuum, the temperature, and density measurements would be largely wrong, so that it should be taken into account for accurate measurement.

  2. Photo-induced strengthening of weak bonding in noble gas dimers

    SciTech Connect (OSTI)

    Miyamoto, Yoshiyuki; Miyazaki, Takehide; Rubio, Angel

    2014-05-19

    We demonstrate through extensive first-principles time-dependent density functional calculations that attractive van der Waals interaction between closed-shell atoms can be enhanced by light with constant spatial intensity. We illustrate this general phenomenon for a He dimer as a prototypical case of complex van der Waals interactions and show that when excited by light with a frequency close to the 1s ? 2p He-atomic transition, an attractive force larger than 7 pN is produced. This force gain is manifested as a larger acceleration of He-He contraction under an optical field. The concerted dynamical motions of the He atoms together with polarity switching of the charge-induced dipole cause the contraction of the dimer. These findings are relevant for the photo-induced control of weakly bonded molecular species, either in gas phase or in solution.

  3. Redshift Distributions of Galaxies in the DES Science Verification Shear Catalogue and Implications for Weak Lensing

    SciTech Connect (OSTI)

    Bonnett, C.

    2015-07-21

    We present photometric redshift estimates for galaxies used in the weak lensing analysis of the Dark Energy Survey Science Verification (DES SV) data. Four model- or machine learning-based photometric redshift methods { annz2, bpz calibrated against BCC-U fig simulations, skynet, and tpz { are analysed. For training, calibration, and testing of these methods, we also construct a catalogue of spectroscopically confirmed galaxies matched against DES SV data. The performance of the methods is evalu-ated against the matched spectroscopic catalogue, focusing on metrics relevant for weak lensing analyses, with additional validation against COSMOS photo-zs. From the galaxies in the DES SV shear catalogue, which have mean redshift 0.72 ±0.01 over the range 0:3 < z < 1:3, we construct three tomographic bins with means of z = {0.45; 0.67,1.00g}. These bins each have systematic uncertainties ?z ? 0.05 in the mean of the fiducial skynet photo-z n(z). We propagate the errors in the redshift distributions through to their impact on cosmological parameters estimated with cosmic shear, and find that they cause shifts in the value of ?8 of approx. 3%. This shift is within the one sigma statistical errors on ?8 for the DES SV shear catalog. We also found that further study of the potential impact of systematic differences on the critical surface density, ?crit, contained levels of bias safely less than the statistical power of DES SV data. We recommend a final Gaussian prior for the photo-z bias in the mean of n(z) of width 0:05 for each of the three tomographic bins, and show that this is a sufficient bias model for the corresponding cosmology analysis.

  4. Determination of the weak charge of the proton through parity violating asymmetry measurements in the elastic e+p scattering

    SciTech Connect (OSTI)

    Subedi, Adesh

    2014-12-01

    The Qweak experiment has taken data to make a 2.5% measurement of parity violating elastic e+p asymmetry in the four momentum transfer region of 0.0250 (GeV/c)^2. This asymmetry is proportional to the weak charge of the proton, which is related to the weak mixing angle, sin^2(theta_W). The final Qweak measurement will provide the most precise measurement of the weak mixing angle below the Z^0 pole to test the Standard Model prediction. A description of the experimental apparatus is provided in this dissertation. The experiment was carried out using a longitudinally polarized electron beam of up to 180 microampere on a 34.5 cm long unpolarized liquid hydrogen target. The Qweak target is not only the world's highest cryogenic target ever built for a parity experiment but also is the least noisy target. This dissertation provides a detailed description of this target and presents a thorough analysis of the target performance. Statistical analysis of Run 1 data, collected between Feb - May 2011, is done to extract a blinded parity violating asymmetry of size -299.7 ± 13.4 (stat.) ± 17.2 (syst.) ± 68 (blinding) parts-per-billion. This resulted in a preliminary proton's weak charge of value 0.0865 ± 0.0085, a 9% measurement. Based on this blinded asymmetry, the weak mixing angle was determined to be sin^2(theta_W) = 0.23429 ± 0.00211.

  5. Weak phase stiffness and nature of the quantum critical point in underdoped cuprates

    SciTech Connect (OSTI)

    Yildirim, Yucel; Ku, Wei

    2015-11-02

    We demonstrate that the zero-temperature superconducting phase diagram of underdoped cuprates can be quantitatively understood in the strong binding limit, using only the experimental spectral function of the “normal” pseudogap phase without any free parameter. In the prototypical (La1–xSrx)2CuO4, a kinetics-driven d-wave superconductivity is obtained above the critical doping δc ~ 5.2%, below which complete loss of superfluidity results from local quantum fluctuation involving local p-wave pairs. Near the critical doping, an enormous mass enhancement of the local pairs is found responsible for the observed rapid decrease of phase stiffness. Lastly, a striking mass divergence is predicted at δc that dictates the occurrence of the observed quantum critical point and the abrupt suppression of the Nernst effects in the nearby region.

  6. Weak phase stiffness and nature of the quantum critical point in underdoped cuprates

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Yildirim, Yucel; Ku, Wei

    2015-11-02

    We demonstrate that the zero-temperature superconducting phase diagram of underdoped cuprates can be quantitatively understood in the strong binding limit, using only the experimental spectral function of the “normal” pseudogap phase without any free parameter. In the prototypical (La1–xSrx)2CuO4, a kinetics-driven d-wave superconductivity is obtained above the critical doping δc ~ 5.2%, below which complete loss of superfluidity results from local quantum fluctuation involving local p-wave pairs. Near the critical doping, an enormous mass enhancement of the local pairs is found responsible for the observed rapid decrease of phase stiffness. Lastly, a striking mass divergence is predicted at δc thatmore » dictates the occurrence of the observed quantum critical point and the abrupt suppression of the Nernst effects in the nearby region.« less

  7. Measurement of the Effective Weak Mixing Angle inpp¯→Z/γ*→e+e-Events

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Abazov, V.  M.; Abbott, B.; Acharya, B.  S.; Adams, M.; Adams, T.; Agnew, J.  P.; Alexeev, G.  D.; Alkhazov, G.; Alton, A.; Askew, A.; et al

    2015-07-22

    We present a measurement of the fundamental parameter of the standard model, the weak mixing angle sin2θℓeff which determines the relative strength of weak and electromagnetic interactions, in pp¯→Z/γ*→e+e- events at a center of mass energy of 1.96 TeV, using data corresponding to 9.7 fb-1 of integrated luminosity collected by the D0 detector at the Fermilab Tevatron. The effective weak mixing angle is extracted from the forward-backward charge asymmetry as a function of the invariant mass around the Z boson pole. The measured value of sin2θℓeff=0.23147±0.00047 is the most precise measurement from light quark interactions to date, with a precisionmore » close to the best LEP and SLD results.« less

  8. Measurement of the Effective Weak Mixing Angle inpp¯→Z/γ*→e+e-Events

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Abazov, V.  M.; Abbott, B.; Acharya, B.  S.; Adams, M.; Adams, T.; Agnew, J.  P.; Alexeev, G.  D.; Alkhazov, G.; Alton, A.; Askew, A.; et al

    2015-07-22

    We present a measurement of the fundamental parameter of the standard model, the weak mixing angle sin2θℓeff which determines the relative strength of weak and electromagnetic interactions, in pp¯→Z/γ*→e+e- events at a center of mass energy of 1.96 TeV, using data corresponding to 9.7 fb-1 of integrated luminosity collected by the D0 detector at the Fermilab Tevatron. The effective weak mixing angle is extracted from the forward-backward charge asymmetry as a function of the invariant mass around the Z boson pole. The measured value of sin2θℓeff=0.23147±0.00047 is the most precise measurement from light quark interactions to date, with a precisionmore »close to the best LEP and SLD results.« less

  9. Metal binding proteins, recombinant host cells and methods

    DOE Patents [OSTI]

    Summers, Anne O.; Caguiat, Jonathan J.

    2004-06-15

    The present disclosure provides artificial heavy metal binding proteins termed chelons by the inventors. These chelons bind cadmium and/or mercuric ions with relatively high affinity. Also disclosed are coding sequences, recombinant DNA molecules and recombinant host cells comprising those recombinant DNA molecules for expression of the chelon proteins. In the recombinant host cells or transgenic plants, the chelons can be used to bind heavy metals taken up from contaminated soil, groundwater or irrigation water and to concentrate and sequester those ions. Recombinant enteric bacteria can be used within the gastrointestinal tracts of animals or humans exposed to toxic metal ions such as mercury and/or cadmium, where the chelon recombinantly expressed in chosen in accordance with the ion to be rededicated. Alternatively, the chelons can be immobilized to solid supports to bind and concentrate heavy metals from a contaminated aqueous medium including biological fluids.

  10. Linear Scaling of the Exciton Binding Energy versus the Band...

    Office of Scientific and Technical Information (OSTI)

    Linear Scaling of the Exciton Binding Energy versus the Band Gap of Two-Dimensional Materials This content will become publicly available on August 6, 2016 Prev Next Title:...

  11. Weakly nonlinear Rayleigh-Taylor instability of a finite-thickness fluid layer

    SciTech Connect (OSTI)

    Wang, L. F. Ye, W. H. Liu, Jie; He, X. T.; Guo, H. Y.; Wu, J. F. Zhang, W. Y.

    2014-12-15

    A weakly nonlinear (WN) model has been developed for the Rayleigh-Taylor instability of a finite-thickness incompressible fluid layer (slab). We derive the coupling evolution equations for perturbations on the (upper) “linearly stable” and (lower) “linearly unstable” interfaces of the slab. Expressions of temporal evolutions of the amplitudes of the perturbation first three harmonics on the upper and lower interfaces are obtained. The classical feedthrough (interface coupling) solution obtained by Taylor [Proc. R. Soc. London A 201, 192 (1950)] is readily recovered by the first-order results. Our third-order model can depict the WN perturbation growth and the saturation of linear (exponential) growth of the perturbation fundamental mode on both interfaces. The dependence of the WN perturbation growth and the slab distortion on the normalized layer thickness (kd) is analytically investigated via the third-order solutions. Comparison is made with Jacobs-Catton's formula [J. W. Jacobs and I. Catton, J. Fluid Mech. 187, 329 (1988)] of the position of the “linearly unstable” interface. Using a reduced formula, the saturation amplitude of linear growth of the perturbation fundamental mode is studied. It is found that the finite-thickness effects play a dominant role in the WN evolution of the slab, especially when kd < 1. Thus, it should be included in applications where the interface coupling effects are important, such as inertial confinement fusion implosions and supernova explosions.

  12. Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons

    SciTech Connect (OSTI)

    Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M.; Boffelli, Dario

    2006-06-01

    Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.

  13. Statistics for the Relative Detectability of Chemicals in Weak Gaseous Plumes in LWIR Hyperspectral Imagery

    SciTech Connect (OSTI)

    Metoyer, Candace N.; Walsh, Stephen J.; Tardiff, Mark F.; Chilton, Lawrence

    2008-10-30

    The detection and identification of weak gaseous plumes using thermal imaging data is complicated by many factors. These include variability due to atmosphere, ground and plume temperature, and background clutter. This paper presents an analysis of one formulation of the physics-based model that describes the at-sensor observed radiance. The motivating question for the analyses performed in this paper is as follows. Given a set of backgrounds, is there a way to predict the background over which the probability of detecting a given chemical will be the highest? Two statistics were developed to address this question. These statistics incorporate data from the long-wave infrared band to predict the background over which chemical detectability will be the highest. These statistics can be computed prior to data collection. As a preliminary exploration into the predictive ability of these statistics, analyses were performed on synthetic hyperspectral images. Each image contained one chemical (either carbon tetrachloride or ammonia) spread across six distinct background types. The statistics were used to generate predictions for the background ranks. Then, the predicted ranks were compared to the empirical ranks obtained from the analyses of the synthetic images. For the simplified images under consideration, the predicted and empirical ranks showed a promising amount of agreement. One statistic accurately predicted the best and worst background for detection in all of the images. Future work may include explorations of more complicated plume ingredients, background types, and noise structures.

  14. Hyperaccretion during tidal disruption events: Weakly bound debris envelopes and jets

    SciTech Connect (OSTI)

    Coughlin, Eric R.; Begelman, Mitchell C. E-mail: mitch@jila.colorado.edu

    2014-02-01

    After the destruction of the star during a tidal disruption event (TDE), the cataclysmic encounter between a star and the supermassive black hole (SMBH) of a galaxy, approximately half of the original stellar debris falls back onto the hole at a rate that can initially exceed the Eddington limit by orders of magnitude. We argue that the angular momentum of this matter is too low to allow it to attain a disk-like configuration with accretion proceeding at a mildly super-Eddington rate, the excess energy being carried away by a combination of radiative losses and radially distributed winds. Instead, we propose that the infalling gas traps accretion energy until it inflates into a weakly bound, quasi-spherical structure with gas extending nearly to the poles. We study the structure and evolution of such 'zero-Bernoulli accretion' flows as a model for the super-Eddington phase of TDEs. We argue that such flows cannot stop extremely super-Eddington accretion from occurring, and that once the envelope is maximally inflated, any excess accretion energy escapes through the poles in the form of powerful jets. We compare the predictions of our model to Swift J1644+57, the putative super-Eddington TDE, and show that it can qualitatively reproduce some of its observed features. Similar models, including self-gravity, could be applicable to gamma-ray bursts from collapsars and the growth of SMBH seeds inside quasi-stars.

  15. Dynamical theory of strongly coupled two-dimensional Coulomb fluids in the weakly degenerate quantum domain

    SciTech Connect (OSTI)

    Das, Mukunda P.; Golden, Kenneth I.; Green, Frederick

    2001-10-01

    We study the problem of dynamical response and plasma mode dispersion in strongly coupled two-dimensional Coulomb fluids (2DCFs) in the weakly degenerate quantum domain. Adapting the nonlinear response function approach of Golden and Kalman [Phys. Rev. A 19, 2112 (1979)] to the 2DCF, we construct a self-consistent approximation scheme for the calculation of the density response functions and plasma mode dispersion at long wavelengths. The basic ingredients in the construction are (i) the first kinetic equation in the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy, (ii) the velocity-average-approximation (VAA) hypothesis, (iii) the quadratic fluctuation-dissipation theorem, and (iv) the dynamical superposition approximation (DSA) closure hypothesis. The reliability of the VAA-DSA theory can be assessed by observing that the principal coupling correction to the 2D temperature-dependent Lindhard function is identified as being precisely the part of the third-frequency-moment sum-rule coefficient proportional to the potential energy.

  16. Weak interactions between water and clathrate-forming gases at low pressures

    SciTech Connect (OSTI)

    Thuermer, Konrad; Yuan, Chunqing; Kimmel, Greg A.; Kay, Bruce D.; Smith, R. Scott

    2015-07-17

    Using scanning probe microscopy and temperature programed desorption we examined the interaction between water and two common clathrate-forming gases, methane and isobutane, at low temperature and low pressure. Water co-deposited with up to 10–1 mbar methane or 10–5 mbar isobutane at 140 K onto a Pt(111) substrate yielded pure crystalline ice, i.e., the exposure to up to ~ 107 gas molecules for each deposited water molecule did not have any detectable effect on the growing films. Exposing metastable, less than 2 molecular layers thick, water films to 10–5 mbar methane does not alter their morphology, suggesting that the presence of the Pt(111) surface is not a strong driver for hydrate formation. This weak water–gas interaction at low pressures is supported by our thermal desorption measurements from amorphous solid water and crystalline ice where 1 ML of methane desorbs near ~ 43 K and isobutane desorbs near ~ 100 K. As a result, similar desorption temperatures were observed for desorption from amorphous solid water.

  17. Validity of the Taylor hypothesis for linear kinetic waves in the weakly collisional solar wind

    SciTech Connect (OSTI)

    Howes, G. G.; Klein, K. G.; TenBarge, J. M.

    2014-07-10

    The interpretation of single-point spacecraft measurements of solar wind turbulence is complicated by the fact that the measurements are made in a frame of reference in relative motion with respect to the turbulent plasma. The Taylor hypothesis—that temporal fluctuations measured by a stationary probe in a rapidly flowing fluid are dominated by the advection of spatial structures in the fluid rest frame—is often assumed to simplify the analysis. But measurements of turbulence in upcoming missions, such as Solar Probe Plus, threaten to violate the Taylor hypothesis, either due to slow flow of the plasma with respect to the spacecraft or to the dispersive nature of the plasma fluctuations at small scales. Assuming that the frequency of the turbulent fluctuations is characterized by the frequency of the linear waves supported by the plasma, we evaluate the validity of the Taylor hypothesis for the linear kinetic wave modes in the weakly collisional solar wind. The analysis predicts that a dissipation range of solar wind turbulence supported by whistler waves is likely to violate the Taylor hypothesis, while one supported by kinetic Alfvén waves is not.

  18. Weak-triplet, color-octet scalars and the CDF dijet excess

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Dobrescu, Bogdan A.; Krnjaic, Gordan Z.

    2012-04-24

    We extend the standard model to include a weak-triplet and color-octet scalar. This 'octo-triplet' field consists of three particles, two charged and one neutral, whose masses and renormalizable interactions depend only on two new parameters. The charged octo-triplet decay into a W boson and a gluon is suppressed by a loop factor and an accidental cancellation. Thus, the main decays of the charged octo-triplet may occur through higher-dimensional operators, mediated by a heavy vectorlike fermion, into quark pairs. For an octo-triplet mass below the tb¯ threshold, the decay into Wb b¯ through an off-shell top quark has a width comparablemore »to that into cs¯ or cb¯. Pair production with one octo-triplet decaying to two jets and the other decaying to a W and two soft b jets may explain the dijet-plus-W excess reported by the CDF Collaboration. The same higher-dimensional operators lead to CP violation in Bs-B¯s mixing.« less

  19. Shape profiles and orientation bias for weak and strong lensing cluster halos

    SciTech Connect (OSTI)

    Groener, A. M.; Goldberg, D. M.

    2014-11-10

    We study the intrinsic shape and alignment of isodensities of galaxy cluster halos extracted from the MultiDark MDR1 cosmological simulation. We find that the simulated halos are extremely prolate on small scales and increasingly spherical on larger ones. Due to this trend, analytical projection along the line of sight produces an overestimation of the concentration index as a decreasing function of radius, which we quantify by using both the intrinsic distribution of three-dimensional concentrations (c {sub 200}) and isodensity shape on weak and strong lensing scales. We find this difference to be ?18% (?9%) for low- (medium-)mass cluster halos with intrinsically low concentrations (c {sub 200} = 1-3), while we find virtually no difference for halos with intrinsically high concentrations. Isodensities are found to be fairly well aligned throughout the entirety of the radial scale of each halo population. However, major axes of individual halos have been found to deviate by as much as ?30°. We also present a value-added catalog of our analysis results, which we have made publicly available to download.

  20. Weak interactions between water and clathrate-forming gases at low pressures

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Thuermer, Konrad; Yuan, Chunqing; Kimmel, Greg A.; Kay, Bruce D.; Smith, R. Scott

    2015-07-17

    Using scanning probe microscopy and temperature programed desorption we examined the interaction between water and two common clathrate-forming gases, methane and isobutane, at low temperature and low pressure. Water co-deposited with up to 10–1 mbar methane or 10–5 mbar isobutane at 140 K onto a Pt(111) substrate yielded pure crystalline ice, i.e., the exposure to up to ~ 107 gas molecules for each deposited water molecule did not have any detectable effect on the growing films. Exposing metastable, less than 2 molecular layers thick, water films to 10–5 mbar methane does not alter their morphology, suggesting that the presence ofmore » the Pt(111) surface is not a strong driver for hydrate formation. This weak water–gas interaction at low pressures is supported by our thermal desorption measurements from amorphous solid water and crystalline ice where 1 ML of methane desorbs near ~ 43 K and isobutane desorbs near ~ 100 K. As a result, similar desorption temperatures were observed for desorption from amorphous solid water.« less

  1. The effect of 12C + 12C rate uncertainties on the weak s-process component

    SciTech Connect (OSTI)

    Fryer, Christopher Lee; Hungerford, Aimee L; Hirschi, Raphael; Pignatari, Marco; Bennett, Michael E; Diehl, Steven; Herwig, Falk; Hillary, William; Richman, Debra; Rockefeller, Gabriel; Timmes, Frank X; Wiescher, Michael

    2010-09-10

    The contribution by massive stars (M > 15M{sub {circle_dot}}) to the weak s-process component of the solar system abundances is primarily due to the {sup 22}Ne neutron source, which is activated near the end of helium-core burning. The residual {sup 22}Ne left over from helium-core burning is then reignited during carbon burning, initiating further s-processing that modifies the isotopic distribution. This modification is sensitive to the stellar structure and the carbon burning reaction rate. Recent work on the {sup 12}C + {sup 12}C reaction suggests that resonances located within the Gamow peak may exist, causing a strong increase in the astrophysical S-factor and consequently the reaction rate. To investigate the effect of such a rate, 25M{sub {circle_dot}} stellar models with different carbon burning rates, at solar metallicity, were generated using the Geneva Stellar Evolution Code (GENEC) with nucleosynthesis post-processing calculated using the NuGrid Multi-zone Post-Processing Network code (MPPNP). A strongly enhanced rate can cause carbon burning to occur in a convective core rather than a radiative one and the convective core mixes the matter synthesized there up into the carbon shell, significantly altering the initial composition of the carbon-shell. In addition, an enhanced rate causes carbon-shell burning episodes to ignite earlier in the evolution of the star, igniting the {sup 22}Ne source at lower temperatures and reducing the neutron density.

  2. Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Complexes with Glutarimidedioxime Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime Print Sunday, 14 October 2012 00:00 The ocean is an important source of uranium if it can be extracted economically. Extraction of uranium from seawater is very challenging, not only because it is in an extremely low concentration, but also because

  3. Briefly Bound to Activate: Transient Binding of a Second Catalytic

    Office of Scientific and Technical Information (OSTI)

    Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis Citation Details In-Document Search Title: Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis We have

  4. Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium

    Office of Scientific and Technical Information (OSTI)

    tuberculosis BioA (Journal Article) | SciTech Connect Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium tuberculosis BioA Citation Details In-Document Search Title: Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium tuberculosis BioA Authors: Dai, Ran ; Geders, Todd W. ; Liu, Feng ; Park, Sae Woong ; Schnappinger, Dirk ; Aldrich, Courtney C. ; Finzel, Barry C. [1] ; Weill-Med) [2] + Show Author Affiliations (UMM) ( Publication Date: 2015-09-29 OSTI

  5. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of

  6. Characterization of Selective Binding of Alkali Cations with Carboxylate

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Characterization of Selective Binding of Alkali Cations with Carboxylate Characterization of Selective Binding of Alkali Cations with Carboxylate Print Wednesday, 24 September 2008 00:00 During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of

  7. Binding Behavior of Dopamine Transporter Key to Understanding Chemical

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Reactions in the Brain Binding Behavior of Dopamine Transporter Key to Understanding Chemical Reactions in the Brain Binding Behavior of Dopamine Transporter Key to Understanding Chemical Reactions in the Brain Print Wednesday, 09 December 2015 00:00 Most people have heard of adrenaline, the chemical that causes the "fight or flight" reaction in humans. Most people have also heard of the chemical substances cocaine and methamphetamine, which also elicit a particular (perhaps

  8. Computational Biology: A Recipe for Ligand-Binding Proteins

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Computational Biology: A Recipe for Ligand-Binding Proteins Authors: Ghirlanda, G. Title: Computational Biology: A Recipe for Ligand-Binding Proteins Source: Nature Year: 2013 Volume: 501 Pages: 177-178 ABSTRACT: Cellular cross-talk, enzymatic catalysis and regulation of gene expression all depend on molecular recognition. A method that allows the design of proteins with desired recognition sites could thus be revolutionary Date of online publication: Thu, 2013-09-12 Link online:

  9. Structural and functional analysis of FIP2 binding to the

    Office of Scientific and Technical Information (OSTI)

    endosome-localised Rab25 GTPase (Journal Article) | SciTech Connect Journal Article: Structural and functional analysis of FIP2 binding to the endosome-localised Rab25 GTPase Citation Details In-Document Search Title: Structural and functional analysis of FIP2 binding to the endosome-localised Rab25 GTPase Authors: Lall, Patrick ; Horgan, Conor P. ; Oda, Shunichiro ; Franklin, Edward ; Sultana, Azmiri ; Hanscom, Sara R. ; McCaffrey, Mary W. ; Khan, Amir R. [1] ; Cork) [2] + Show Author

  10. Structural basis for biomolecular recognition in overlapping binding sites

    Office of Scientific and Technical Information (OSTI)

    in a diiron enzyme system (Journal Article) | SciTech Connect Structural basis for biomolecular recognition in overlapping binding sites in a diiron enzyme system Citation Details In-Document Search Title: Structural basis for biomolecular recognition in overlapping binding sites in a diiron enzyme system Authors: Acheson, Justin F. ; Bailey, Lucas J. ; Elsen, Nathaniel L. ; Fox, Brian G. [1] + Show Author Affiliations UW Publication Date: 2016-01-22 OSTI Identifier: 1229904 Resource Type:

  11. MCM ring hexamerization is a prerequisite for DNA-binding

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Froelich, Clifford A.; Nourse, Amanda; Enemark, Eric J.

    2015-09-13

    The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings to show that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in themore » hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.« less

  12. V-172: ISC BIND RUNTIME_CHECK Error Lets Remote Users Deny Service...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    ISC BIND RUNTIMECHECK Error Lets Remote Users Deny Service Against Recursive Resolvers V-172: ISC BIND RUNTIMECHECK Error Lets Remote Users Deny Service Against Recursive...

  13. Structure and Ca[superscript 2+]-Binding Properties of the Tandem...

    Office of Scientific and Technical Information (OSTI)

    and Casuperscript 2+-Binding Properties of the Tandem Csubscript 2 Domains of E-Syt2 Citation Details In-Document Search Title: Structure and Casuperscript 2+-Binding ...

  14. Cosmology Constraints from the Weak Lensing Peak Counts and the Power Spectrum in CFHTLenS

    SciTech Connect (OSTI)

    Liu, Jia; May, Morgan; Petri, Andrea; Haiman, Zoltan; Hui, Lam; Kratochvil, Jan M.

    2015-03-04

    Lensing peaks have been proposed as a useful statistic, containing cosmological information from non-Gaussianities that is inaccessible from traditional two-point statistics such as the power spectrum or two-point correlation functions. Here we examine constraints on cosmological parameters from weak lensing peak counts, using the publicly available data from the 154 deg2 CFHTLenS survey. We utilize a new suite of ray-tracing N-body simulations on a grid of 91 cosmological models, covering broad ranges of the three parameters Ωm, σ8, and w, and replicating the galaxy sky positions, redshifts, and shape noise in the CFHTLenS observations. We then build an emulator that interpolates the power spectrum and the peak counts to an accuracy of ≤ 5%, and compute the likelihood in the three-dimensional parameter space (Ωm, σ8, w) from both observables. We find that constraints from peak counts are comparable to those from the power spectrum, and somewhat tighter when different smoothing scales are combined. Neither observable can constrain w without external data. When the power spectrum and peak counts are combined, the area of the error “banana” in the (Ωm, σ8) plane reduces by a factor of ≈ two, compared to using the power spectrum alone. For a flat Λ cold dark matter model, combining both statistics, we obtain the constraint σ8(Ωm/0.27)0.63 = 0.85+0.03-0.03.

  15. Atmospheric PSF Interpolation for Weak Lensing in Short Exposure Imaging Data

    SciTech Connect (OSTI)

    Chang, C.; Marshall, P.J.; Jernigan, J.G.; Peterson, J.R.; Kahn, S.M.; Gull, S.F.; AlSayyad, Y.; Ahmad, Z.; Bankert, J.; Bard, D.; Connolly, A.; Gibson, R.R.; Gilmore, K.; Grace, E.; Hannel, M.; Hodge, M.A.; Jones, L.; Krughoff, S.; Lorenz, S.; Marshall, S.; Meert, A.

    2012-09-19

    A main science goal for the Large Synoptic Survey Telescope (LSST) is to measure the cosmic shear signal from weak lensing to extreme accuracy. One difficulty, however, is that with the short exposure time ({approx_equal}15 seconds) proposed, the spatial variation of the Point Spread Function (PSF) shapes may be dominated by the atmosphere, in addition to optics errors. While optics errors mainly cause the PSF to vary on angular scales similar or larger than a single CCD sensor, the atmosphere generates stochastic structures on a wide range of angular scales. It thus becomes a challenge to infer the multi-scale, complex atmospheric PSF patterns by interpolating the sparsely sampled stars in the field. In this paper we present a new method, psfent, for interpolating the PSF shape parameters, based on reconstructing underlying shape parameter maps with a multi-scale maximum entropy algorithm. We demonstrate, using images from the LSST Photon Simulator, the performance of our approach relative to a 5th-order polynomial fit (representing the current standard) and a simple boxcar smoothing technique. Quantitatively, psfent predicts more accurate PSF models in all scenarios and the residual PSF errors are spatially less correlated. This improvement in PSF interpolation leads to a factor of 3.5 lower systematic errors in the shear power spectrum on scales smaller than {approx} 13, compared to polynomial fitting. We estimate that with psfent and for stellar densities greater than {approx_equal}1/arcmin{sup 2}, the spurious shear correlation from PSF interpolation, after combining a complete 10-year dataset from LSST, is lower than the corresponding statistical uncertainties on the cosmic shear power spectrum, even under a conservative scenario.

  16. Self-calibration of photometric redshift scatter in weak-lensing surveys

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhang, Pengjie; Pen, Ue -Li; Bernstein, Gary

    2010-06-11

    Photo-z errors, especially catastrophic errors, are a major uncertainty for precision weak lensing cosmology. We find that the shear-(galaxy number) density and density-density cross correlation measurements between photo-z bins, available from the same lensing surveys, contain valuable information for self-calibration of the scattering probabilities between the true-z and photo-z bins. The self-calibration technique we propose does not rely on cosmological priors nor parameterization of the photo-z probability distribution function, and preserves all of the cosmological information available from shear-shear measurement. We estimate the calibration accuracy through the Fisher matrix formalism. We find that, for advanced lensing surveys such as themore » planned stage IV surveys, the rate of photo-z outliers can be determined with statistical uncertainties of 0.01-1% for z < 2 galaxies. Among the several sources of calibration error that we identify and investigate, the galaxy distribution bias is likely the most dominant systematic error, whereby photo-z outliers have different redshift distributions and/or bias than non-outliers from the same bin. This bias affects all photo-z calibration techniques based on correlation measurements. As a result, galaxy bias variations of O(0.1) produce biases in photo-z outlier rates similar to the statistical errors of our method, so this galaxy distribution bias may bias the reconstructed scatters at several-σ level, but is unlikely to completely invalidate the self-calibration technique.« less

  17. Impact of spurious shear on cosmological parameter estimates from weak lensing observables

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Petri, Andrea; May, Morgan; Haiman, Zoltán; Kratochvil, Jan M.

    2014-12-30

    We research, residual errors in shear measurements, after corrections for instrument systematics and atmospheric effects, can impact cosmological parameters derived from weak lensing observations. Here we combine convergence maps from our suite of ray-tracing simulations with random realizations of spurious shear. This allows us to quantify the errors and biases of the triplet (Ωm,w,σ8) derived from the power spectrum (PS), as well as from three different sets of non-Gaussian statistics of the lensing convergence field: Minkowski functionals (MFs), low-order moments (LMs), and peak counts (PKs). Our main results are as follows: (i) We find an order of magnitude smaller biasesmore » from the PS than in previous work. (ii) The PS and LM yield biases much smaller than the morphological statistics (MF, PK). (iii) For strictly Gaussian spurious shear with integrated amplitude as low as its current estimate of σsys2 ≈ 10-7, biases from the PS and LM would be unimportant even for a survey with the statistical power of Large Synoptic Survey Telescope. However, we find that for surveys larger than ≈ 100 deg2, non-Gaussianity in the noise (not included in our analysis) will likely be important and must be quantified to assess the biases. (iv) The morphological statistics (MF, PK) introduce important biases even for Gaussian noise, which must be corrected in large surveys. The biases are in different directions in (Ωm,w,σ8) parameter space, allowing self-calibration by combining multiple statistics. Our results warrant follow-up studies with more extensive lensing simulations and more accurate spurious shear estimates.« less

  18. Impact of spurious shear on cosmological parameter estimates from weak lensing observables

    SciTech Connect (OSTI)

    Petri, Andrea; May, Morgan; Haiman, Zoltán; Kratochvil, Jan M.

    2014-12-30

    We research, residual errors in shear measurements, after corrections for instrument systematics and atmospheric effects, can impact cosmological parameters derived from weak lensing observations. Here we combine convergence maps from our suite of ray-tracing simulations with random realizations of spurious shear. This allows us to quantify the errors and biases of the triplet (Ωm,w,σ8) derived from the power spectrum (PS), as well as from three different sets of non-Gaussian statistics of the lensing convergence field: Minkowski functionals (MFs), low-order moments (LMs), and peak counts (PKs). Our main results are as follows: (i) We find an order of magnitude smaller biases from the PS than in previous work. (ii) The PS and LM yield biases much smaller than the morphological statistics (MF, PK). (iii) For strictly Gaussian spurious shear with integrated amplitude as low as its current estimate of σsys2 ≈ 10-7, biases from the PS and LM would be unimportant even for a survey with the statistical power of Large Synoptic Survey Telescope. However, we find that for surveys larger than ≈ 100 deg2, non-Gaussianity in the noise (not included in our analysis) will likely be important and must be quantified to assess the biases. (iv) The morphological statistics (MF, PK) introduce important biases even for Gaussian noise, which must be corrected in large surveys. The biases are in different directions in (Ωm,w,σ8) parameter space, allowing self-calibration by combining multiple statistics. Our results warrant follow-up studies with more extensive lensing simulations and more accurate spurious shear estimates.

  19. Self-calibration of photometric redshift scatter in weak-lensing surveys

    SciTech Connect (OSTI)

    Zhang, Pengjie; Pen, Ue -Li; Bernstein, Gary

    2010-06-11

    Photo-z errors, especially catastrophic errors, are a major uncertainty for precision weak lensing cosmology. We find that the shear-(galaxy number) density and density-density cross correlation measurements between photo-z bins, available from the same lensing surveys, contain valuable information for self-calibration of the scattering probabilities between the true-z and photo-z bins. The self-calibration technique we propose does not rely on cosmological priors nor parameterization of the photo-z probability distribution function, and preserves all of the cosmological information available from shear-shear measurement. We estimate the calibration accuracy through the Fisher matrix formalism. We find that, for advanced lensing surveys such as the planned stage IV surveys, the rate of photo-z outliers can be determined with statistical uncertainties of 0.01-1% for z < 2 galaxies. Among the several sources of calibration error that we identify and investigate, the galaxy distribution bias is likely the most dominant systematic error, whereby photo-z outliers have different redshift distributions and/or bias than non-outliers from the same bin. This bias affects all photo-z calibration techniques based on correlation measurements. As a result, galaxy bias variations of O(0.1) produce biases in photo-z outlier rates similar to the statistical errors of our method, so this galaxy distribution bias may bias the reconstructed scatters at several-? level, but is unlikely to completely invalidate the self-calibration technique.

  20. Impact of spurious shear on cosmological parameter estimates from weak lensing observables

    SciTech Connect (OSTI)

    Petri, Andrea; May, Morgan; Haiman, Zoltán; Kratochvil, Jan M.

    2014-12-30

    We research, residual errors in shear measurements, after corrections for instrument systematics and atmospheric effects, can impact cosmological parameters derived from weak lensing observations. Here we combine convergence maps from our suite of ray-tracing simulations with random realizations of spurious shear. This allows us to quantify the errors and biases of the triplet (?m,w,?8) derived from the power spectrum (PS), as well as from three different sets of non-Gaussian statistics of the lensing convergence field: Minkowski functionals (MFs), low-order moments (LMs), and peak counts (PKs). Our main results are as follows: (i) We find an order of magnitude smaller biases from the PS than in previous work. (ii) The PS and LM yield biases much smaller than the morphological statistics (MF, PK). (iii) For strictly Gaussian spurious shear with integrated amplitude as low as its current estimate of ?sys2 ? 10-7, biases from the PS and LM would be unimportant even for a survey with the statistical power of Large Synoptic Survey Telescope. However, we find that for surveys larger than ? 100 deg2, non-Gaussianity in the noise (not included in our analysis) will likely be important and must be quantified to assess the biases. (iv) The morphological statistics (MF, PK) introduce important biases even for Gaussian noise, which must be corrected in large surveys. The biases are in different directions in (?m,w,?8) parameter space, allowing self-calibration by combining multiple statistics. Our results warrant follow-up studies with more extensive lensing simulations and more accurate spurious shear estimates.

  1. Molecular Electronic Level Alignment at Weakly Coupled Organic Film/Metal Interfaces

    SciTech Connect (OSTI)

    Zhao, Jin; Feng, Min; Dougherty, Daniel B.; Sun, Hao; Petek, Hrvoje

    2014-10-28

    Electronic level alignment at interfaces of molecular materials with inorganic semiconductors and metals controls many interfacial phenomena. How the intrinsic properties of the interacting systems define the electronic structure of their interface remains one of the most important problems in molecular electronics and nanotechnology that can be solved through a combination of surface science experimental techniques and theoretical modeling. In this article, we address this fundamental problem through experimental and computational studies of molecular electronic level alignment of thin films of C6F6 on noble metal surfaces. The unoccupied electronic structure of C6F6 is characterized with single molecule resolution using low-temperature scanning tunneling microscopy-based constant-current distance-voltage spectroscopy. The experiments are performed on several noble metal surfaces with different work functions and distinct surface-normal projected band structures. In parallel, the electronic structures of the quantum wells (QWs) formed by the lowest unoccupied molecular orbital state of the C6F6 monolayer and multilayer films and their alignment with respect to the vacuum level of the metallic substrates are calculated by solving the Schrödinger equation for a semiempirical one-dimensional (1D) potential of the combined system using input from density functional theory. Our analysis shows that the level alignment for C6F6 molecules bound through weak van der Waals interactions to noble metal surfaces is primarily defined by the image potential of metal, the electron affinity of the molecule, and the molecule surface distance. We expect the same factors to determine the interfacial electronic structure for a broad range of molecule/metal interfaces.

  2. Van Allen Probes observation and modeling of chorus excitation and propagation during weak geomagnetic activities

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    He, Yihua; Xiao, Fuliang; Zhou, Qinghua; Yang, Chang; Liu, Si; Baker, D. N.; Kletzing, C. A.; Kurth, W. S.; Hospodarsky, G. B.; Spence, H. E.; et al

    2015-08-20

    We report correlated data on nightside chorus waves and energetic electrons during two small storm periods: 1 November 2012 (Dst ≈ –45) and 14 January 2013 (Dst ≈ –18). The Van Allen Probes simultaneously observed strong chorus waves at locations L = 5.8 – 6.3, with a lower frequency band 0.1–0.5fce and a peak spectral density ~10–4 nT2/Hz. In the same period, the fluxes and anisotropy of energetic (~10–300 keV) electrons were greatly enhanced in the interval of large negative interplanetary magnetic field Bz. Using a bi-Maxwellian distribution to model the observed electron distribution, we perform ray tracing simulations tomore » show that nightside chorus waves are indeed produced by the observed electron distribution with a peak growth for a field-aligned propagation approximately between 0.3fce and 0.4fce, at latitude <7°. Moreover, chorus waves launched with initial normal angles either θ < 90° or > 90° propagate along the field either northward or southward and then bounce back either away from Earth for a lower frequency or toward Earth for higher frequencies. The current results indicate that nightside chorus waves can be excited even during weak geomagnetic activities in cases of continuous injection associated with negative Bz. Furthermore, we examine a dayside event during a small storm C on 8 May 2014 (Dst ≈ –45) and find that the observed anisotropic energetic electron distributions potentially contribute to the generation of dayside chorus waves, but this requires more thorough studies in the future.« less

  3. Cosmology Constraints from the Weak Lensing Peak Counts and the Power Spectrum in CFHTLenS

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Liu, Jia; May, Morgan; Petri, Andrea; Haiman, Zoltan; Hui, Lam; Kratochvil, Jan M.

    2015-03-04

    Lensing peaks have been proposed as a useful statistic, containing cosmological information from non-Gaussianities that is inaccessible from traditional two-point statistics such as the power spectrum or two-point correlation functions. Here we examine constraints on cosmological parameters from weak lensing peak counts, using the publicly available data from the 154 deg2 CFHTLenS survey. We utilize a new suite of ray-tracing N-body simulations on a grid of 91 cosmological models, covering broad ranges of the three parameters Ωm, σ8, and w, and replicating the galaxy sky positions, redshifts, and shape noise in the CFHTLenS observations. We then build an emulator thatmore » interpolates the power spectrum and the peak counts to an accuracy of ≤ 5%, and compute the likelihood in the three-dimensional parameter space (Ωm, σ8, w) from both observables. We find that constraints from peak counts are comparable to those from the power spectrum, and somewhat tighter when different smoothing scales are combined. Neither observable can constrain w without external data. When the power spectrum and peak counts are combined, the area of the error “banana” in the (Ωm, σ8) plane reduces by a factor of ≈ two, compared to using the power spectrum alone. For a flat Λ cold dark matter model, combining both statistics, we obtain the constraint σ8(Ωm/0.27)0.63 = 0.85+0.03-0.03.« less

  4. Stabilization of weak ferromagnetism by strong magnetic response to epitaxial strain in multiferroic BiFeO3

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cooper, Valentino R.; Lee, Jun Hee; Krogel, Jaron T.; Okamoto, Satoshi; Dixit, Hemant M.

    2015-08-06

    Multiferroic BiFeO3 exhibits excellent magnetoelectric coupling critical for magnetic information processing with minimal power consumption. Thus, the degenerate nature of the easy spin axis in the (111) plane presents roadblocks for real world applications. Here, we explore the stabilization and switchability of the weak ferromagnetic moments under applied epitaxial strain using a combination of first-principles calculations and group-theoretic analyses. We demonstrate that the antiferromagnetic moment vector can be stabilized along unique crystallographic directions ([110] and [-110]) under compressive and tensile strains. A direct coupling between the anisotropic antiferrodistortive rotations and Dzyaloshinskii-Moria interactions drives the stabilization of weak ferromagnetism. Furthermore, energeticallymore » competing C- and G-type magnetic orderings are observed at high compressive strains, suggesting that it may be possible to switch the weak ferromagnetism on and off under application of strain. These findings emphasize the importance of strain and antiferrodistortive rotations as routes to enhancing induced weak ferromagnetism in multiferroic oxides.« less

  5. CLASH: Weak-lensing shear-and-magnification analysis of 20 galaxy clusters

    SciTech Connect (OSTI)

    Umetsu, Keiichi; Czakon, Nicole [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan (China); Medezinski, Elinor; Lemze, Doron; Ford, Holland [Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Nonino, Mario; Balestra, Italo; Biviano, Andrea [INAF-Osservatorio Astronomico di Trieste, via G.B. Tiepolo 11, I-34143 Trieste (Italy); Merten, Julian [Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109 (United States); Postman, Marc; Koekemoer, Anton [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21208 (United States); Meneghetti, Massimo [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Donahue, Megan [Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824 (United States); Molino, Alberto; Benítez, Narciso [Instituto de Astrofísica de Andalucía (CSIC), E-18008 Granada (Spain); Seitz, Stella; Gruen, Daniel [Universitäts-Sternwarte, München, Scheinerstrasse 1, D-81679 Munich Germany (Germany); Broadhurst, Tom [Ikerbasque, Basque Foundation for Science, Alameda Urquijo, 36-5 Plaza Bizkaia, E-48011 Bilbao (Spain); Grillo, Claudio [Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen (Denmark); Melchior, Peter, E-mail: keiichi@asiaa.sinica.edu.tw [Center for Cosmology and Astro-Particle Physics and Department of Physics, The Ohio State University, Columbus, OH 43210 (United States); and others

    2014-11-10

    We present a joint shear-and-magnification weak-lensing analysis of a sample of 16 X-ray-regular and 4 high-magnification galaxy clusters at 0.19 ? z ? 0.69 selected from the Cluster Lensing And Supernova survey with Hubble (CLASH). Our analysis uses wide-field multi-color imaging, taken primarily with Suprime-Cam on the Subaru Telescope. From a stacked-shear-only analysis of the X-ray-selected subsample, we detect the ensemble-averaged lensing signal with a total signal-to-noise ratio of ? 25 in the radial range of 200-3500 kpc h {sup –1}, providing integrated constraints on the halo profile shape and concentration-mass relation. The stacked tangential-shear signal is well described by a family of standard density profiles predicted for dark-matter-dominated halos in gravitational equilibrium, namely, the Navarro-Frenk-White (NFW), truncated variants of NFW, and Einasto models. For the NFW model, we measure a mean concentration of c{sub 200c}=4.01{sub ?0.32}{sup +0.35} at an effective halo mass of M{sub 200c}=1.34{sub ?0.09}{sup +0.10}×10{sup 15} M{sub ?}. We show that this is in excellent agreement with ? cold dark matter (?CDM) predictions when the CLASH X-ray selection function and projection effects are taken into account. The best-fit Einasto shape parameter is ?{sub E}=0.191{sub ?0.068}{sup +0.071}, which is consistent with the NFW-equivalent Einasto parameter of ?0.18. We reconstruct projected mass density profiles of all CLASH clusters from a joint likelihood analysis of shear-and-magnification data and measure cluster masses at several characteristic radii assuming an NFW density profile. We also derive an ensemble-averaged total projected mass profile of the X-ray-selected subsample by stacking their individual mass profiles. The stacked total mass profile, constrained by the shear+magnification data, is shown to be consistent with our shear-based halo-model predictions, including the effects of surrounding large-scale structure as a two-halo term, establishing further consistency in the context of the ?CDM model.

  6. Astrophysical Gyrokinetics: Kinetic and Fluid Turbulent Cascades In Magentized Weakly Collisional Plasmas

    SciTech Connect (OSTI)

    Schekochihin, A. A.; Cowley, S. C.; Dorland, W.; Hammett, G. W.; Howes, G. G.; Quataert, E.; Tatsuno, T.

    2009-04-23

    This paper presents a theoretical framework for understanding plasma turbulence in astrophysical plasmas. It is motivated by observations of electromagnetic and density fluctuations in the solar wind, interstellar medium and galaxy clusters, as well as by models of particle heating in accretion disks. All of these plasmas and many others have turbulentmotions at weakly collisional and collisionless scales. The paper focuses on turbulence in a strong mean magnetic field. The key assumptions are that the turbulent fluctuations are small compared to the mean field, spatially anisotropic with respect to it and that their frequency is low compared to the ion cyclotron frequency. The turbulence is assumed to be forced at some system-specific outer scale. The energy injected at this scale has to be dissipated into heat, which ultimately cannot be accomplished without collisions. A kinetic cascade develops that brings the energy to collisional scales both in space and velocity. The nature of the kinetic cascade in various scale ranges depends on the physics of plasma fluctuations that exist there. There are four special scales that separate physically distinct regimes: the electron and ion gyroscales, the mean free path and the electron diffusion scale. In each of the scale ranges separated by these scales, the fully kinetic problem is systematically reduced to a more physically transparent and computationally tractable system of equations, which are derived in a rigorous way. In the "inertial range" above the ion gyroscale, the kinetic cascade separates into two parts: a cascade of Alfvenic fluctuations and a passive cascade of density and magnetic-fieldstrength fluctuations. The former are governed by the Reduced Magnetohydrodynamic (RMHD) equations at both the collisional and collisionless scales; the latter obey a linear kinetic equation along the (moving) field lines associated with the Alfvenic component (in the collisional limit, these compressive fluctuations become the slow and entropy modes of the conventional MHD). In the "dissipation range" below ion gyroscale, there are again two cascades: the kinetic-Alfven-wave (KAW) cascade governed by two fluid-like Electron Reduced Magnetohydrodynamic (ERMHD) equations and a passive cascade of ion entropy fluctuations both in space and velocity. The latter cascade brings the energy of the inertial-range fluctuations that was Landau-damped at the ion gyroscale to collisional scales in the phase space and leads to ion heating. The KAWenergy is similarly damped at the electron gyroscale and converted into electron heat. Kolmogorov-style scaling relations are derived for all of these cascades. The relationship between the theoretical models proposed in this paper and astrophysical applications and observations is discussed in detail.

  7. Molecular dynamics investigation of the substrate binding mechanism in carboxylesterase

    SciTech Connect (OSTI)

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-he

    2015-01-01

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of the substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, we further predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase rPPEs, which will help guide future development of more efficient rPPE variants.

  8. Orientation-dependent binding energy of graphene on palladium

    SciTech Connect (OSTI)

    Kappes, Branden B.; Ebnonnasir, Abbas; Ciobanu, Cristian V. [Department of Mechanical Engineering and Materials Science Program, Colorado School of Mines, Golden, Colorado 80401 (United States)] [Department of Mechanical Engineering and Materials Science Program, Colorado School of Mines, Golden, Colorado 80401 (United States); Kodambaka, Suneel [Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095 (United States)] [Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095 (United States)

    2013-02-04

    Using density functional theory calculations, we show that the binding strength of a graphene monolayer on Pd(111) can vary between physisorption and chemisorption depending on its orientation. By studying the interfacial charge transfer, we have identified a specific four-atom carbon cluster that is responsible for the local bonding of graphene to Pd(111). The areal density of such clusters varies with the in-plane orientation of graphene, causing the binding energy to change accordingly. Similar investigations can also apply to other metal substrates and suggests that physical, chemical, and mechanical properties of graphene may be controlled by changing its orientation.

  9. Energy dependence of the optical potential of weakly and tightly bound nuclei as projectiles on a medium-mass target

    SciTech Connect (OSTI)

    Figueira, J. M.; Arazi, A.; Carnelli, P.; Heimann, D. Martinez; Negri, A. E.; Pacheco, A. J.; Niello, J. O. Fernandez; Capurro, O. A.; Fimiani, L.; Marti, G. V.; Lubian, J.; Monteiro, D. S.; Gomes, P. R. S.

    2010-02-15

    Angular distributions for the elastic scattering of the weakly bound {sup 6,7}Li+{sup 144}Sm systems were measured with high accuracy at bombarding energies from 85% up to 170% of the Coulomb barrier. An optical model analysis was performed, and the relevant parameters of the real and imaginary parts of the optical potential were extracted. The results are compared with those previously published for the tightly bound {sup 12}C+{sup 144}Sm and {sup 16}O+{sup 144}Sm systems. The usual threshold anomaly observed in the behavior of the potential of tightly bound systems was not observed for either weakly bound system. This absence is attributed to the repulsion due to breakup coupling which cancels the attraction arising from couplings with bound channels.

  10. MSM Self-Energies at Finite Temperature in the Presence of Weak Magnetic Fields: Towards a Full Symmetry Restoration Study

    SciTech Connect (OSTI)

    Tejeda-Yeomans, Maria Elena; Navarro, Jorge; Sanchez, Angel; Piccinelli, Gabriella

    2008-07-02

    The study of the universe's primordial plasma at high temperature plays an important role when tackling different questions in cosmology, such as the origin of the matter-antimatter asymmetry. In the Minimal Standard Model (MSM) neither the amount of CP violation nor the strength of the phase transition are enough to produce and preserve baryon number during the Electroweak Phase Transition (EWPT), which are two of the three ingredients needed to develop baryon asymmetry. In this talk we present the first part of the analysis done within a scenario where it is viable to have improvements to the aforementioned situation: we work with the degrees of freedom in the broken symmetry phase of the MSM and analyze the development of the EWPT in the presence of a weak magnetic field. More specifically, we calculate the particle self-energies that include the effects of the weak magnetic field, needed for the MSM effective potential up to ring diagrams.

  11. Collisions induced by halo and weakly bound nuclei around the Coulomb barrier: Results at INFN-LNS Catania

    SciTech Connect (OSTI)

    Figuera, Pierpaolo

    2012-10-20

    The study of collisions around the Coulomb barrier induced by halo and/or weakly bound nuclei has been the object of many publications in the last years, since the peculiar structure of such nuclei can strongly affect the reaction dynamics. In this paper we will summarize some results on the above topic obtained by our group at INFN-LNS Catania. Results concerning the study of elastic scattering and different reaction mechanisms in collisions induced by the halo nuclei {sup 11}Be and {sup 6}He and by the weakly bound stable nuclei {sup 6,7}Li on a {sup 64}Zn target, at energies around the Coulomb barrier, will be presented. The conclusions of our studies will be compared with the ones of other authors, in order to show if clear systematic conclusions can be drawn from the different papers published in the literature so far.

  12. Applications of exact linearization techniques for steady-state stability enhancement in a weak ac/dc system

    SciTech Connect (OSTI)

    Kaprielian, S.; Clements, K. ); Turi, J. )

    1992-05-01

    A nonlinear control strategy to improve the steady-state stability of a weak AC/DC power system is presented. The approach described in this paper is based on the extension of feedback linearization techniques to nonlinear descriptor system models. This method produces a nonlinear control strategy which is capable of enhancing system performance for various system operating conditions. This claim is supported with simulation results.

  13. Weak links and critical current anisotropy in melt-textured HTSC ceramics studied by magneto-optical express control

    SciTech Connect (OSTI)

    Belyaeva, A.I.; Eremenko, V.V.; Nastenko, V.A.

    1997-06-01

    YBa{sub 2}Cu{sub 3}O{sub 7{minus}x} ceramics were prepared by the modified melt textured process on the polycrystalline substrate of the YBaCuO{sub 5} composition. Magneto-optical technique with the ferrogarnet films as sensor was used for visualization of magnetic flux distribution and their evaluation under remagnetization of specimens. The pictures of weak links visualized by the magneto-optical technique were correlated with the sample macro- and microstructure, studied by X-ray topography electron (SEM) and polarization fight microscopy. The role of different details of the structural peculiarities of the specimens in the weak links formation was analyzed and the problem of critical current anisotropy was reviewed. The weak links behavior under the magnetic field variation was studied in the details. The pinning centers, weak links, its dependence upon the (211) concentration, the particle size as well as its role in J{sub c} value formation were discussed. Experimental values of the critical current density varied from 2 10{sup 4} up to (5{divided_by}8) 10{sup 5} A cm{sup {minus}2} for the regions of specimen with the different structures. The authors report the first real time direct magneto-optic images of the isotropic magnetic flux distribution in the area of the sample which initially was substrate 211. The principal possibility of their modified method for obtaining highly textured isotropic Y-Ba-Cu-O ceramics capable of carrying current density up to 10{sup 6} A cm{sup {minus}2} was discussed.

  14. Methods of use of cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1997-09-23

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  15. A probabilistic approach to microRNA-target binding

    SciTech Connect (OSTI)

    Ogul, Hasan; Umu, Sinan U.; Bioinformatics Program, Informatics Institute, Middle East Technical University, Cankaya TR-06800, Ankara ; Tuncel, Y. Yener; Akkaya, Mahinur S.

    2011-09-16

    Highlights: {yields} A new probabilistic model is introduced for microRNA-target binding. {yields} The new model significantly outperforms RNAHybrid and miRTif. {yields} The experiments can unveil the effects of the type and directions of distinct base pairings. -- Abstract: Elucidation of microRNA activity is a crucial step in understanding gene regulation. One key problem in this effort is how to model the pairwise interactions of microRNAs with their targets. As this interaction is strongly mediated by their sequences, it is desired to set-up a probabilistic model to explain the binding preferences between a microRNA sequence and the sequence of a putative target. To this end, we introduce a new model of microRNA-target binding, which transforms an aligned duplex to a new sequence and defines the likelihood of this sequence using a Variable Length Markov Chain. It offers a complementary representation of microRNA-mRNA pairs for microRNA target prediction tools or other probabilistic frameworks of integrative gene regulation analysis. The performance of present model is evaluated by its ability to predict microRNA-target mRNA interaction given a mature microRNA sequence and a putative mRNA binding site. In regard to classification accuracy, it outperforms two recent methods based on thermodynamic stability and sequence complementarity. The experiments can also unveil the effects of base pairing types and non-seed region in duplex formation.

  16. Methods of use of cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1997-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  17. Methods of detection using a cellulose binding domain fusion product

    DOE Patents [OSTI]

    Shoseyov, Oded (Shimshon, IL); Shpiegl, Itai (North Gallilea, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1999-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  18. Inhibition of cell-cell binding by lipid assemblies

    DOE Patents [OSTI]

    Nagy, Jon O. (Rodeo, CA); Bargatze, Robert F. (Bozeman, MT)

    2001-05-22

    This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

  19. Methods of detection using a cellulose binding domain fusion product

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1999-01-05

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 34 figs.

  20. Inhibition Of Call-Cell Binding By Kipid Assemblies

    DOE Patents [OSTI]

    Nagy, Jon O. (Rodeo, CA), Bargatze, Robert F. (Bozeman, MT)

    2003-12-16

    This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

  1. Workshop on gate valve pressure locking and thermal binding

    SciTech Connect (OSTI)

    Brown, E.J.

    1995-07-01

    The purpose of the Workshop on Gate Valve Pressure Locking and Thermal Binding was to discuss pressure locking and thermal binding issues that could lead to inoperable gate valves in both boiling water and pressurized water reactors. The goal was to foster exchange of information to develop the technical bases to understand the phenomena, identify the components that are susceptible, discuss actual events, discuss the safety significance, and illustrate known corrective actions that can prevent or limit the occurrence of pressure locking or thermal binding. The presentations were structured to cover U.S. Nuclear Regulatory Commission staff evaluation of operating experience and planned regulatory activity; industry discussions of specific events, including foreign experience, and efforts to determine causes and alleviate the affects; and valve vendor experience and recommended corrective action. The discussions indicated that identifying valves susceptible to pressure locking and thermal binding was a complex process involving knowledge of components, systems, and plant operations. The corrective action options are varied and straightforward.

  2. Beam Normal Single Spin Asymmetry in Forward Angle Inelastic Electron-Proton Scattering using the Q-Weak Apparatus

    SciTech Connect (OSTI)

    Nuruzzaman, nfn

    2014-12-01

    The Q-weak experiment in Hall-C at the Thomas Jefferson National Accelerator Facility has made the first direct measurement of the weak charge of the proton through the precision measurement of the parity-violating asymmetry in elastic electron-proton scattering at low momentum transfer. There is also a parity conserving Beam Normal Single Spin Asymmetry or transverse asymmetry (B_n) on H_2 with a sin(phi)-like dependence due to two-photon exchange. If the size of elastic B_n is a few ppm, then a few percent residual transverse polarization in the beam, combined with small broken azimuthal symmetries in the detector, would require a few ppb correction to the Q-weak data. As part of a program of B_n background studies, we made the first measurement of B_n in the N-to-Delta(1232) transition using the Q-weak apparatus. The final transverse asymmetry, corrected for backgrounds and beam polarization, was found to be B_n = 42.82 ± 2.45 (stat) ± 16.07 (sys) ppm at beam energy E_beam = 1.155 GeV, scattering angle theta = 8.3 deg, and missing mass W = 1.2 GeV. B_n from electron-nucleon scattering is a unique tool to study the gamma^* Delta Delta form factors, and this measurement will help to improve the theoretical models on beam normal single spin asymmetry and thereby our understanding of the doubly virtual Compton scattering process. To help correct false asymmetries from beam noise, a beam modulation system was implemented to induce small position, angle, and energy changes at the target to characterize detector response to the beam jitter. Two air-core dipoles separated by ~10 m were pulsed at a time to produce position and angle changes at the target, for virtually any tune of the beamline. The beam energy was modulated using an SRF cavity. The hardware and associated control instrumentation will be described in this dissertation. Preliminary detector sensitivities were extracted which helped to reduce the width of the measured asymmetry. The beam modulation system has also proven valuable for tracking changes in the beamline optics, such as dispersion at the target.

  3. Binding Behavior of Dopamine Transporter Key to Understanding Chemical

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Reactions in the Brain Binding Behavior of Dopamine Transporter Key to Understanding Chemical Reactions in the Brain Print Most people have heard of adrenaline, the chemical that causes the "fight or flight" reaction in humans. Most people have also heard of the chemical substances cocaine and methamphetamine, which also elicit a particular (perhaps desired) human response. What most people do not know is that the same receptors in the human brain recognize the natural, or

  4. Binding Behavior of Dopamine Transporter Key to Understanding Chemical

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Reactions in the Brain Binding Behavior of Dopamine Transporter Key to Understanding Chemical Reactions in the Brain Print Most people have heard of adrenaline, the chemical that causes the "fight or flight" reaction in humans. Most people have also heard of the chemical substances cocaine and methamphetamine, which also elicit a particular (perhaps desired) human response. What most people do not know is that the same receptors in the human brain recognize the natural, or

  5. Binding Behavior of Dopamine Transporter Key to Understanding Chemical

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Reactions in the Brain Binding Behavior of Dopamine Transporter Key to Understanding Chemical Reactions in the Brain Print Most people have heard of adrenaline, the chemical that causes the "fight or flight" reaction in humans. Most people have also heard of the chemical substances cocaine and methamphetamine, which also elicit a particular (perhaps desired) human response. What most people do not know is that the same receptors in the human brain recognize the natural, or

  6. Reversible Acid Gas Capture Using CO2-Binding Organic Liquids

    SciTech Connect (OSTI)

    Heldebrant, David J.; Koech, Phillip K.; Yonker, Clement R.; Rainbolt, James E.; Zheng, Feng

    2010-08-31

    Acid gas scrubbing technology is predominantly aqueous alkanolamine based. Of the acid gases, CO2, H2S and SO2 have been shown to be reversible, however there are serious disadvantages with corrosion and high regeneration costs. The primary scrubbing system composed of monoethanolamine is limited to 30% by weight because of the highly corrosive solution. This gravimetric limitation limits the CO2 volumetric (?108 g/L) and gravimetric capacity (?7 wt%) of the system. Furthermore the scrubbing system has a large energy penalty from pumping and heating the excess water required to dissolve the MEA bicarbonate salt. Considering the high specific heat of water (4 j/g-1K-1), low capacities and the high corrosion we set out to design a fully organic solvent that can chemically bind all acid gases i.e. CO2 as reversible alkylcarbonate ionic liquids or analogues thereof. Having a liquid acid gas carrier improves process economics because there is no need for excess solvent to pump and to heat. We have demonstrated illustrated in Figure 1, that CO2-binding organic liquids (CO2BOLs) have a high CO2 solubility paired with a much lower specific heat (<1.5 J/g-1K-1) than aqueous systems. CO2BOLs are a subsection of a larger class of materials known as Binding Organic Liquids (BOLs). Our BOLs have been shown to reversibly bind and release COS, CS2, and SO2, which we denote COSBOLS, CS2BOLs and SO2BOLs. Our BOLs are highly tunable and can be designed for post or pre-combustion gas capture. The design and testing of the next generation zwitterionic CO2BOLs and SO2BOLs are presented.

  7. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere

  8. Characterization of Selective Binding of Alkali Cations with Carboxylate

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Characterization of Selective Binding of Alkali Cations with Carboxylate Print During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions

  9. Characterization of Selective Binding of Alkali Cations with Carboxylate

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Characterization of Selective Binding of Alkali Cations with Carboxylate Print During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions

  10. Characterization of Selective Binding of Alkali Cations with Carboxylate

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Characterization of Selective Binding of Alkali Cations with Carboxylate Print During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions

  11. Binding Behavior of Dopamine Transporter Key to Understanding Chemical

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Reactions in the Brain Binding Behavior of Dopamine Transporter Key to Understanding Chemical Reactions in the Brain Print Most people have heard of adrenaline, the chemical that causes the "fight or flight" reaction in humans. Most people have also heard of the chemical substances cocaine and methamphetamine, which also elicit a particular (perhaps desired) human response. What most people do not know is that the same receptors in the human brain recognize the natural, or

  12. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere

  13. Characterization of Selective Binding of Alkali Cations with Carboxylate

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Characterization of Selective Binding of Alkali Cations with Carboxylate Print During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions

  14. Characterization of Selective Binding of Alkali Cations with Carboxylate

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Characterization of Selective Binding of Alkali Cations with Carboxylate Print During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions

  15. Protein Immobilization in Metal-Organic Frameworks by Covalent Binding |

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Protein Immobilization in Metal-Organic Frameworks by Covalent Binding Previous Next List Xuan Wang, Trevor A. Makal and Hong-Cai Zhou, Aust. J. Chem. 67, 1629-1631 (2014) DOI: 10.1071/CH14104 CH14104_TOC Abstract: Metal-organic frameworks (MOFs), possessing a well defined system of pores, demonstrate extensive potential serving as a platform in biological catalysis. Successful immobilization of enzymes in a

  16. High molecular weight polysaccharide that binds and inhibits virus

    DOE Patents [OSTI]

    Konowalchuk, Thomas W

    2014-01-14

    This invention provides a high molecular weight polysaccharide capable of binding to and inhibiting virus and related pharmaceutical formulations and methods on inhibiting viral infectivity and/or pathogenicity, as well as immunogenic compositions. The invention further methods of inhibiting the growth of cancer cells and of ameliorating a symptom of aging. Additionally, the invention provides methods of detecting and/or quantifying and/or isolating viruses.

  17. Gold Binding by Native and Chemically Modified Hops Biomasses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    López, M. Laura; Gardea-Torresdey, J. L.; Peralta-Videa, J. R.; de la Rosa, G.; Armendáriz, V.; Herrera, I.; Troiani, H.; Henning, J.

    2005-01-01

    Heavy metals from mining, smelting operations and other industrial processing facilities pollute wastewaters worldwide. Extraction of metals from industrial effluents has been widely studied due to the economic advantages and the relative ease of technical implementation. Consequently, the search for new and improved methodologies for the recovery of gold has increased. In this particular research, the use of cone hops biomass ( Humulus lupulus ) was investigated as a new option for gold recovery. The results showed that the gold binding to native hops biomass was pH dependent from pH 2 to pH 6, with a maximum percentage bindingmore » at pH 3. Time dependency studies demonstrated that Au(III) binding to native and modified cone hops biomasses was found to be time independent at pH 2 while at pH 5, it was time dependent. Capacity experiments demonstrated that at pH 2, esterified hops biomass bound 33.4 mg Au/g of biomass, while native and hydrolyzed hops biomasses bound 28.2 and 12.0 mg Au/g of biomass, respectively. However, at pH 5 the binding capacities were 38.9, 37.8 and 11.4 mg of Au per gram of native, esterified and hydrolyzed hops biomasses, respectively.« less

  18. Two-photon Absorption In Quantum Dots,quantum Dashes And Related Materials

    SciTech Connect (OSTI)

    Jain, Ravinder

    2009-08-31

    We have proposed the use of USQDs for various deep-tissue biological imaging applications, notably wavelength-multiplexed multicolor imaging and intra-nuclear studies such as those involving cell apoptosis, and have studied the issue of maximizing two-photon absorption-induced fluorescence (TPAF) signals from CdSe/ZnS USQDs to be used for this application. In particular, using 2 nm USQDs, we have shown that the TPAF signal at 780 nm is ~ 8 times that at 850 nm and 68 times that at 900 nm, two wavelengths that have been used in previous studies using CdSe/ZnS SQDs for deep-tissue imaging of biological studies via TPAF .

  19. Demonstration of Datacenter Automation Software and Hardware (DASH) at the California Franchise Tax Board

    SciTech Connect (OSTI)

    Bell, Geoffrey C.; Federspiel, Clifford

    2009-12-18

    Control software and wireless sensors designed for closed-loop, monitoring and control of IT equipment's inlet air temperatures in datacenters were evaluated and tested while other datacenter cooling best practices were implemented. The controls software and hardware along with each best practice were installed sequentially and evaluated using a measurement and verification procedure between each measure. The results show that the overall project eliminates 475,239 kWh per year, which is 21.3percent of the baseline energy consumption of the data center. The total project, including the best practices will save $42,772 per year and cost $134,057 yielding a simple payback of 3.1 years. However, the control system alone eliminates 59.6percent of the baseline energy used to move air in the datacenter and 13.6percent of the baseline cooling energy, which is 15.2percent of the baseline energy consumption (see Project Approach, Task 1, below, for additional information) while keeping temperatures substantially within the limits recommended by ASHRAE. Savings attributed to the control system are $30,564 per year with a cost $56,824 for a simple payback of 1.9 years.

  20. V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote...

  1. New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities...

    Office of Scientific and Technical Information (OSTI)

    New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins Citation Details In-Document Search Title: New Insights into the RNA-Binding and E3 Ubiquitin Ligase...

  2. Plasticity of the Quinone-binding Site of the Complex II Homolog...

    Office of Scientific and Technical Information (OSTI)

    Plasticity of the Quinone-binding Site of the Complex II Homolog Quinol:Fumarate Reductase Citation Details In-Document Search Title: Plasticity of the Quinone-binding Site of the...

  3. Discovery of a new ATP-binding motif involved in peptidic azoline...

    Office of Scientific and Technical Information (OSTI)

    Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis Citation Details In-Document Search Title: Discovery of a new ATP-binding motif involved in peptidic ...

  4. Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site

    SciTech Connect (OSTI)

    Yang, Jingsong; Campobasso, Nino; Biju, Mangatt P.; Fisher, Kelly; Pan, Xiao-Qing; Cottom, Josh; Galbraith, Sarah; Ho, Thau; Zhang, Hong; Hong, Xuan; Ward, Paris; Hofmann, Glenn; Siegfried, Brett; Zappacosta, Francesca; Washio, Yoshiaki; Cao, Ping; Qu, Junya; Bertrand, Sophie; Wang, Da-Yuan; Head, Martha S.; Li, Hu; Moores, Sheri; Lai, Zhihong; Johanson, Kyung; Burton, George; Erickson-Miller, Connie; Simpson, Graham; Tummino, Peter; Copeland, Robert A.; Oliff, Allen

    2014-10-02

    c-Abl kinase activity is regulated by a unique mechanism involving the formation of an autoinhibited conformation in which the N-terminal myristoyl group binds intramolecularly to the myristoyl binding site on the kinase domain and induces the bending of the {alpha}I helix that creates a docking surface for the SH2 domain. Here, we report a small-molecule c-Abl activator, DPH, that displays potent enzymatic and cellular activity in stimulating c-Abl activation. Structural analyses indicate that DPH binds to the myristoyl binding site and prevents the formation of the bent conformation of the {alpha}I helix through steric hindrance, a mode of action distinct from the previously identified allosteric c-Abl inhibitor, GNF-2, that also binds to the myristoyl binding site. DPH represents the first cell-permeable, small-molecule tool compound for c-Abl activation.

  5. Reversible CO Binding in Metal-Organic Frameworks | Center for Gas

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Reversible CO Binding in Metal-Organic Frameworks

  6. Diamonds in the rough: a strong case for the inclusion of weak-intensity X-ray diffraction data

    SciTech Connect (OSTI)

    Wang, Jimin; Wing, Richard A.

    2014-05-01

    Here, new evidence is provided to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry averaging. Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperature B factors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individual B factors of atomic models cannot be refined. Here, new evidence is provided to show that the inclusion of these data helps to improve the quality of experimental phases by imposing proper constraints on electron-density models during noncrystallographic symmetry (NCS) averaging. Using electron-density correlation coefficients as criteria, the resolution of data has successfully been extended from 3.1 to 2.5 Å resolution with redundancy-independent merging R factors from below 100% to about 310%. It is further demonstrated that phase information can be fully extracted from observed amplitudes through de novo NCS averaging. Averaging starts with uniform density inside double-shelled spherical masks and NCS matrices that are derived from bound heavy-atom clusters at the vertices of cuboctahedrally symmetric protein particles.

  7. Effect of the radio frequency discharge on the dust charging process in a weakly collisional and fully ionized plasma

    SciTech Connect (OSTI)

    Motie, Iman; Bokaeeyan, Mahyar

    2015-02-15

    A close analysis of dust charging process in the presence of radio frequency (RF) discharge on low pressure and fully ionized plasma for both weak and strong discharge's electric field is considered. When the electromagnetic waves pass throughout fully ionized plasma, the collision frequency of the plasma is derived. Moreover, the disturbed distribution function of plasma particles in the presence of the RF discharge is obtained. In this article, by using the Krook model, we separate the distribution function in two parts, the Maxwellian part and the perturbed part. The perturbed part of distribution can make an extra current, so-called the accretion rate of electron (or ion) current, towards a dust particle as a function of the average electron-ion collision frequency. It is proven that when the potential of dust grains increases, the accretion rate of electron current experiences an exponential reduction. Furthermore, the accretion rate of electron current for a strong electric field is relatively smaller than that for a weak electric field. The reasons are elaborated.

  8. Analytical models of calcium binding in a calcium channel

    SciTech Connect (OSTI)

    Liu, Jinn-Liang; Eisenberg, Bob

    2014-08-21

    The anomalous mole fraction effect of L-type calcium channels is analyzed using a Fermi like distribution with the experimental data of Almers and McCleskey [J. Physiol. 353, 585 (1984)] and the atomic resolution model of Lipkind and Fozzard [Biochemistry 40, 6786 (2001)] of the selectivity filter of the channel. Much of the analysis is algebraic, independent of differential equations. The Fermi distribution is derived from the configuration entropy of ions and water molecules with different sizes, different valences, and interstitial voids between particles. It allows us to calculate potentials and distances (between the binding ion and the oxygen ions of the glutamate side chains) directly from the experimental data using algebraic formulas. The spatial resolution of these results is comparable with those of molecular models, but of course the accuracy is no better than that implied by the experimental data. The glutamate side chains in our model are flexible enough to accommodate different types of binding ions in different bath conditions. The binding curves of Na{sup +} and Ca{sup 2+} for [CaCl{sub 2}] ranging from 10{sup −8} to 10{sup −2} M with a fixed 32 mM background [NaCl] are shown to agree with published Monte Carlo simulations. The Poisson-Fermi differential equation—that includes both steric and correlation effects—is then used to obtain the spatial profiles of energy, concentration, and dielectric coefficient from the solvent region to the filter. The energy profiles of ions are shown to depend sensitively on the steric energy that is not taken into account in the classical rate theory. We improve the rate theory by introducing a steric energy that lumps the effects of excluded volumes of all ions and water molecules and empty spaces between particles created by Lennard-Jones type and electrostatic forces. We show that the energy landscape varies significantly with bath concentrations. The energy landscape is not constant.

  9. Hydroxyapatite-binding peptides for bone growth and inhibition

    DOE Patents [OSTI]

    Bertozzi, Carolyn R. (Berkeley, CA); Song, Jie (Shrewsbury, MA); Lee, Seung-Wuk (Walnut Creek, CA)

    2011-09-20

    Hydroxyapatite (HA)-binding peptides are selected using combinatorial phage library display. Pseudo-repetitive consensus amino acid sequences possessing periodic hydroxyl side chains in every two or three amino acid sequences are obtained. These sequences resemble the (Gly-Pro-Hyp).sub.x repeat of human type I collagen, a major component of extracellular matrices of natural bone. A consistent presence of basic amino acid residues is also observed. The peptides are synthesized by the solid-phase synthetic method and then used for template-driven HA-mineralization. Microscopy reveal that the peptides template the growth of polycrystalline HA crystals .about.40 nm in size.

  10. Functionalized polymers for binding to solutes in aqueous solutions

    DOE Patents [OSTI]

    Smith, Barbara F.; Robison, Thomas W.

    2006-11-21

    A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. The polymer has a backbone polymer to which one or more functional groups are covalently linked. The backbone polymer can be such polymers as polyethylenimine, polyvinylamine, polyallylamine, and polypropylamine. These polymers are generally water-soluble, but can be insoluble when cross-linked. The functional group can be for example diol derivatives, polyol derivatives, thiol and dithiol derivatives, guest-host groups, affinity groups, beta-diphosphonic acids, and beta-diamides

  11. Breaking the ties that bind: New hope for biomass fuels

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    New hope for biomass fuels Breaking the ties that bind: New hope for biomass fuels Researchers have discovered a potential chink in the armor of fibers that make the cell walls of certain inedible plant materials so tough. April 22, 2009 Los Alamos National Laboratory sits on top of a once-remote mesa in northern New Mexico with the Jemez mountains as a backdrop to research and innovation covering multi-disciplines from bioscience, sustainable energy sources, to plasma physics and new materials.

  12. Climate change: Clinton affirms binding emissions reduction policy

    SciTech Connect (OSTI)

    Fairley, P.

    1996-12-04

    In Australia last month President Clinton called for an international agreement to negotiate {open_quotes}legally binding commitments to fight climate change.{close_quotes} His comments affirmed the line the Administration adopted in July and lent prominence to the effort to bring about a treaty by December 1997. Environmentalists welcomed Clinton`s comments, but industry response is divided. The Global Climate Coalition (Washington), of which CMA is a member, has tried to slow negotiations by questioning the scientific consensus on climate change and suggesting {open_quotes}serious damage to the American economy{close_quotes} could result from emissions reduction.

  13. Highly-Selective and Reversible O2 Binding in

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Cr3(1,3,5-benzenetricarboxylate)2 | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Highly-Selective and Reversible O2 Binding in Cr3(1,3,5-benzenetricarboxylate)2 Previous Next List Leslie J. Murray, Mircea Dinca, Junko Yano, Sachin Chavan, Silvia Bordiga, Craig M. Brown and Jeffrey R. Long, J. Am. Chem. Soc., 2010, 132 (23), pp 7856-7857 DOI: 10.1021/ja1027925 Abstract Image Abstract: Reaction of Cr(CO)6 with trimesic acid in DMF affords the metal-organic

  14. Grain in weakly ionized plasma in the presence of an external magnetic field: Charging by plasma currents and effective potential

    SciTech Connect (OSTI)

    Momot, A. I.; M.M. Bogolubov Institute for Theoretical Physics, Nat. Acad. Sci. of Ukraine, 14b, Metrologichna Str., Kyiv, 03680

    2013-07-15

    The problem of grain screening is solved numerically for the case of weakly ionized plasma in the presence of an external magnetic field. The plasma dynamics is described within the drift-diffusion approximation under the assumption that the grain absorbs all encountered electrons and ions. We also assume that the plasma current through the grain surface is equal to zero in the stationary state. This condition is used to perform self-consistent calculations of the grain charge. The spatial distribution of the screened grain potential is studied and compared with the analytical estimates. It is shown that at the distances larger than the Debye length such potential has the Coulomb-like asymptotics with the effective charge dependent on the angle between the radius vector and the external magnetic field direction. The numerical solutions show that in the direction parallel to the external magnetic field the effective potential can have nonmonotonic behavior.

  15. Probing neutrino physics with a self-consistent treatment of the weak decoupling, nucleosynthesis, and photon decoupling epochs

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Grohs, E.; Fuller, George M.; Kishimoto, Chad T.; Paris, Mark W.

    2015-05-11

    In this study, we show that a self-consistent and coupled treatment of the weak decoupling, big bang nucleosynthesis, and photon decoupling epochs can be used to provide new insights and constraints on neutrino sector physics from high-precision measurements of light element abundances and Cosmic Microwave Background observables. Implications of beyond-standard-model physics in cosmology, especially within the neutrino sector, are assessed by comparing predictions against five observables: the baryon energy density, helium abundance, deuterium abundance, effective number of neutrinos, and sum of the light neutrino mass eigenstates. We give examples for constraints on dark radiation, neutrino rest mass, lepton numbers, andmore » scenarios for light and heavy sterile neutrinos.« less

  16. Probing neutrino physics with a self-consistent treatment of the weak decoupling, nucleosynthesis, and photon decoupling epochs

    SciTech Connect (OSTI)

    Grohs, E.; Fuller, George M.; Kishimoto, Chad T.; Paris, Mark W.

    2015-05-11

    In this study, we show that a self-consistent and coupled treatment of the weak decoupling, big bang nucleosynthesis, and photon decoupling epochs can be used to provide new insights and constraints on neutrino sector physics from high-precision measurements of light element abundances and Cosmic Microwave Background observables. Implications of beyond-standard-model physics in cosmology, especially within the neutrino sector, are assessed by comparing predictions against five observables: the baryon energy density, helium abundance, deuterium abundance, effective number of neutrinos, and sum of the light neutrino mass eigenstates. We give examples for constraints on dark radiation, neutrino rest mass, lepton numbers, and scenarios for light and heavy sterile neutrinos.

  17. INFLUENCE OF MAGNETOROTATIONAL INSTABILITY ON NEUTRINO HEATING: A NEW MECHANISM FOR WEAKLY MAGNETIZED CORE-COLLAPSE SUPERNOVAE

    SciTech Connect (OSTI)

    Sawai, Hidetomo; Yamada, Shoichi

    2014-03-20

    We investigated the impact of magnetorotational instability (MRI) on the dynamics of weakly magnetized, rapidly rotating core-collapse supernovae by conducting high-resolution axisymmetric MHD simulations with simplified neutrino transfer. We found that an initially sub-magnetar-class magnetic field is drastically amplified by MRI and substantially affects the dynamics thereafter. Although the magnetic pressure is not strong enough to eject matter, the amplified magnetic field efficiently transfers angular momentum from small to large radii and from higher to lower latitudes, which causes the expansion of the heating region due to the extra centrifugal force. This then enhances the efficiency of neutrino heating and eventually leads to neutrino-driven explosion. This is a new scenario of core-collapse supernovae that has never been demonstrated by past numerical simulations.

  18. Dynamical mean-field theory and weakly non-linear analysis for the phase separation of active Brownian particles

    SciTech Connect (OSTI)

    Speck, Thomas; Menzel, Andreas M.; Bialké, Julian; Löwen, Hartmut

    2015-06-14

    Recently, we have derived an effective Cahn-Hilliard equation for the phase separation dynamics of active Brownian particles by performing a weakly non-linear analysis of the effective hydrodynamic equations for density and polarization [Speck et al., Phys. Rev. Lett. 112, 218304 (2014)]. Here, we develop and explore this strategy in more detail and show explicitly how to get to such a large-scale, mean-field description starting from the microscopic dynamics. The effective free energy emerging from this approach has the form of a conventional Ginzburg-Landau function. On the coarsest scale, our results thus agree with the mapping of active phase separation onto that of passive fluids with attractive interactions through a global effective free energy (motility-induced phase transition). Particular attention is paid to the square-gradient term necessary for the phase separation kinetics. We finally discuss results from numerical simulations corroborating the analytical results.

  19. Enhanced collective focusing of intense neutralized ion beam pulses in the presence of weak solenoidal magnetic fields

    SciTech Connect (OSTI)

    Dorf, Mikhail A. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Davidson, Ronald C.; Kaganovich, Igor D.; Startsev, Edward A. [Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States)

    2012-05-15

    The design of ion drivers for warm dense matter and high energy density physics applications and heavy ion fusion involves transverse focusing and longitudinal compression of intense ion beams to a small spot size on the target. To facilitate the process, the compression occurs in a long drift section filled with a dense background plasma, which neutralizes the intense beam self-fields. Typically, the ion bunch charge is better neutralized than its current, and as a result a net self-pinching (magnetic) force is produced. The self-pinching effect is of particular practical importance, and is used in various ion driver designs in order to control the transverse beam envelope. In the present work we demonstrate that this radial self-focusing force can be significantly enhanced if a weak (B {approx} 100 G) solenoidal magnetic field is applied inside the neutralized drift section, thus allowing for substantially improved transport. It is shown that in contrast to magnetic self-pinching, the enhanced collective self-focusing has a radial electric field component and occurs as a result of the overcompensation of the beam charge by plasma electrons, whereas the beam current becomes well-neutralized. As the beam leaves the neutralizing drift section, additional transverse focusing can be applied. For instance, in the neutralized drift compression experiments (NDCX) a strong (several Tesla) final focus solenoid is used for this purpose. In the present analysis we propose that the tight final focus in the NDCX experiments may possibly be achieved by using a much weaker (few hundred Gauss) magnetic lens, provided the ion beam carries an equal amount of co-moving neutralizing electrons from the preceding drift section into the lens. In this case the enhanced focusing is provided by the collective electron dynamics strongly affected by a weak applied magnetic field.

  20. Weak-link capacitor

    DOE Patents [OSTI]

    Dirk, Shawn M. (Albuquerque, NM); Johnson, Ross S. (Albuquerque, NM); Wheeler, David R. (Albuquerque, NM); Bogart, Gregory R. (Corrales, NM)

    2011-06-07

    A process for making a dielectric material where a precursor polymer selected from poly(phenylene vinylene) polyacetylene, poly(p-phenylene), poly(thienylene vinylene), poly(1,4-naphthylene vinylene), and poly(p-pyridine vinylene) is energized said by exposure by radiation or increase in temperature to a level sufficient to eliminate said leaving groups contained within the precursor polymer, thereby transforming the dielectric material into a conductive polymer. The leaving group in the precursor polymer can be a chloride, a bromide, an iodide, a fluoride, an ester, an xanthate, a nitrile, an amine, a nitro group, a carbonate, a dithiocarbamate, a sulfonium group, an oxonium group, an iodonium group, a pyridinium group, an ammonium group, a borate group, a borane group, a sulphinyl group, or a sulfonyl group.

  1. Weak-link capacitor

    DOE Patents [OSTI]

    Dirk, Shawn M.; Johnson, Ross S.; Wheeler, David R.; Bogart, Gregory R.

    2013-04-23

    A process for making a dielectric material where a precursor polymer selected from poly(phenylene vinylene)polyacetylene, poly(p-phenylene), poly(thienylene vinylene), poly(1,4-naphthylene vinylene), and poly(p-pyridine vinylene) is energized said by exposure by radiation or increase in temperature to a level sufficient to eliminate said leaving groups contained within the precursor polymer, thereby transforming the dielectric material into a conductive polymer. The leaving group in the precursor polymer can be a chloride, a bromide, an iodide, a fluoride, an ester, an xanthate, a nitrile, an amine, a nitro group, a carbonate, a dithiocarbamate, a sulfonium group, an oxonium group, an iodonium group, a pyridinium group, an ammonium group, a borate group, a borane group, a sulphinyl group, or a sulfonyl group.

  2. Extremely weak hydrogen flames

    SciTech Connect (OSTI)

    Lecoustre, V.R.; Sunderland, P.B. [Department of Fire Protection Engineering, University of Maryland, College Park, MD 20742 (United States); Chao, B.H. [Department of Mechanical Engineering, University of Hawaii, Honolulu, HI 96822 (United States); Axelbaum, R.L. [Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130 (United States)

    2010-11-15

    Hydrogen jet diffusion flames were observed near their quenching limits. These involved downward laminar flow of hydrogen from a stainless steel hypodermic tube with an inside diameter of 0.15 mm. Near their quenching limits these flames had hydrogen flow rates of 3.9 and 2.1 {mu}g/s in air and oxygen, respectively. Assuming complete combustion, the associated heat release rates are 0.46 and 0.25 W. To the authors' knowledge, these are the weakest self-sustaining steady flames ever observed. (author)

  3. Stabilization of weak ferromagnetism ...

    Office of Scientific and Technical Information (OSTI)

    coopervr@ornl.gov Abstract: Multiferroic BiFeO3 exhibits excellent magnetoelectric coupling critical for magnetic information processing with minimal power consumption. ...

  4. Development of Gamma-Emitting Receptor Binding Radiopharmace

    SciTech Connect (OSTI)

    Reba, Richard

    2003-02-20

    The long-term objective is to develop blood-brain barrier (BBB) permeable m2-selective (relative to m1, m3, and m4) receptor-binding radiotracers and utilize these radiotracers for quantifying receptor concentrations obtained from PET or SPECT images of human brain. In initial studies, we concluded that the lipophilicity and high affinity prevented (R,S)-I-QNB from reaching a flow-independent and receptor-dependent state in a reasonable time. Thus, it was clear that (R,S)-I-QNB should be modified. Therefore, during the last portion of this funded research, we proposed that more polar heterocycles should help accomplish that. Since reports of others concluded that radiobromination and radiofluorination of the unactivated phenyl ring is not feasible (Newkome et al,,1982), we, therefore, explored during this grant period a series of analogues of (R)-QNB in which one or both of the six-membered phenyl rings is replaced by a five-membered thienyl (Boulay et al., 1995), or furyl ring. The chemistry specific aims were to synthesize novel compounds designed to be m2-selective mAChR ligands capable of penetrating into the CNS, and develop methods for efficient radiolabeling of promising m2-selective muscarinic ligands. The pharmacology specific aims were to determine the affinity and subtype-selectivity of the novel compounds using competition binding studies with membranes from cells that express each of the five muscarinic receptor subtypes, to determine the ability of the promising non-radioactive compounds and radiolabeled novel compounds to cross the BBB, to determine the biodistribution, in-vivo pharmacokinetics, and in-vitm kinetics of promising m2-selective radioligands and to determine the distribution of receptors for the novel m2-selective radioligands using quantitative autoradiography of rat brain, and compare this distribution to the distribution of known m2-selective compounds.

  5. Coexistence of Weak Ferromagnetism and Polar Lattice Distortion in Epitaxial NiTiO3 thin films of the LiNbO3-Type Structure

    SciTech Connect (OSTI)

    Varga, Tamas; Droubay, Timothy C.; Bowden, Mark E.; Colby, Robert J.; Manandhar, Sandeep; Shutthanandan, V.; Hu, Dehong; Kabius, Bernd C.; Apra, Edoardo; Shelton, William A.; Chambers, Scott A.

    2013-04-15

    We report the magnetic and structural characteristics of epitaxial NiTiO3 films grown by pulsed laser deposition that are isostructural with acentric LiNbO3 (space group R3c). Optical second harmonic generation and magnetometry demonstrate lattice polarization at room temperature and weak ferromagnetism below 250 K, respectively. These results appear to be consistent with earlier predictions from first-principles calculations of the coexistence of ferroelectricity and weak ferromagnetism in a series of transition metal titanates crystallizing in the LiNbO3 structure. This acentric form of NiTiO3 is believed to be one of the rare examples of ferroelectrics exhibiting weak ferromagnetism generated by a Dzyaloshinskii-Moriya interaction.

  6. Measurement of the weak mixing angle with the Drell-Yan process in proton-proton collisions at the LHC

    SciTech Connect (OSTI)

    Chatrchyan, S.; et al.,

    2011-12-01

    A multivariate likelihood method to measure electroweak couplings with the Drell-Yan process at the LHC is presented. The process is described by the dilepton rapidity, invariant mass, and decay angle distributions. The decay angle ambiguity due to the unknown assignment of the scattered constituent quark and antiquark to the two protons in a collision is resolved statistically using correlations between the observables. The method is applied to a sample of dimuon events from proton-proton collisions at sqrt(s) = 7 TeV collected by the CMS experiment at the LHC, corresponding to an integrated luminosity of 1.1 inverse femtobarns. From the dominant u-ubar, d-dbar to gamma*/Z to opposite sign dimuons process, the effective weak mixing angle parameter is measured to be sin^2(theta[eff]) = 0.2287 +/- 0.0020 (stat.) +/- 0.0025 (syst.). This result is consistent with measurements from other processes, as expected within the standard model.

  7. New perspective on glycoside hydrolase binding to lignin from pretreated corn stover

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Yarbrough, John M.; Mittal, Ashutosh; Mansfield, Elisabeth; Taylor, II, Larry E.; Hobdey, Sarah E.; Sammond, Deanne W.; Bomble, Yannick J.; Crowley, Michael F.; Decker, Stephen R.; Himmel, Michael E.; et al

    2015-12-18

    In this study, non-specific binding of cellulases to lignin has been implicated as a major factor in the loss of cellulase activity during biomass conversion to sugars. It is believed that this binding may strongly impact process economics through loss of enzyme activities during hydrolysis and enzyme recycling scenarios. The current model suggests glycoside hydrolase activities are lost though non-specific/non-productive binding of carbohydrate-binding domains to lignin, limiting catalytic site access to the carbohydrate components of the cell wall.

  8. U-227: bind-dyndb-ldap DN Escaping Flaw Lets Remote Users Deny Service

    Broader source: Energy.gov [DOE]

    A vulnerability has been reported in bind-dyndb-ldap, which can be exploited by malicious people to cause a DoS (Denial of Service).

  9. V-172: ISC BIND RUNTIME_CHECK Error Lets Remote Users Deny Service Against Recursive Resolvers

    Broader source: Energy.gov [DOE]

    A defect exists which allows an attacker to crash a BIND 9 recursive resolver with a RUNTIME_CHECK error in resolver.c

  10. Unraveling a Hotspot for TCR Recognition on HLA-A2: Evidence Against the Existence of Peptide-independent TCR Binding Determinants

    SciTech Connect (OSTI)

    Gagnon, Susan J.; Borbulevych, Oleg Y.; Davis-Harrison, Rebecca L.; Baxter, Tiffany K.; Clemens, John R.; Armstrong, Kathryn M.; Turner, Richard V.; Damirjian, Marale; Biddison, William E.; Baker, Brian M.

    2010-07-19

    T cell receptor (TCR) recognition of peptide takes place in the context of the major histocompatibility complex (MHC) molecule, which accounts for approximately two-thirds of the peptide/MHC buried surface. Using the class I MHC HLA-A2 and a large panel of mutants, we have previously shown that surface mutations that disrupt TCR recognition vary with the identity of the peptide. The single exception is Lys66 on the HLA-A2 {alpha}1 helix, which when mutated to alanine disrupts recognition for 93% of over 250 different T cell clones or lines, independent of which peptide is bound. Thus, Lys66 could serve as a peptide-independent TCR binding determinant. Here, we have examined the role of Lys66 in TCR recognition of HLA-A2 in detail. The structure of a peptide/HLA-A2 molecule with the K66A mutation indicates that although the mutation induces no major structural changes, it results in the exposure of a negatively charged glutamate (Glu63) underneath Lys66. Concurrent replacement of Glu63 with glutamine restores TCR binding and function for T cells specific for five different peptides presented by HLA-A2. Thus, the positive charge on Lys66 does not serve to guide all TCRs onto the HLA-A2 molecule in a manner required for productive signaling. Furthermore, electrostatic calculations indicate that Lys66 does not contribute to the stability of two TCR-peptide/HLA-A2 complexes. Our findings are consistent with the notion that each TCR arrives at a unique solution of how to bind a peptide/MHC, most strongly influenced by the chemical and structural features of the bound peptide. This would not rule out an intrinsic affinity of TCRs for MHC molecules achieved through multiple weak interactions, but for HLA-A2 the collective mutational data place limits on the role of any single MHC amino acid side-chain in driving TCR binding in a peptide-independent fashion.

  11. Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition

    SciTech Connect (OSTI)

    Wang, Jin; Lu, Qiang N.; Lu, H PETER.

    2006-07-01

    The study of associations between two biomolecules is the key to understand molecular recognition and function. Molecular function is often thought to be determined by the underlying structures. Here, combining single molecule study of protein binding with an energy landscape inspired microscopic model, we found strong evidences that bio-molecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse grained molecular dynamics performed on the residue level with the energy function biased towards the native binding structure (Go model). With our model, the underlying free energy landscape of the binding can be explored. Two distinct conformational states as free energy minimum, one with partially folding of CBD and significant binding of CBD to CDC42, and another with native folding of CBD and native binding of CBD to CDC42, are clearly seen. This shows the binding process proceeds with significant interface binding of CBD with CDC42 first without complete folding of CBD. Finally binding and folding are coupled with each other cooperatively to reach the native binding state. The single molecule experimental finding of the dynamic fluctuations between the loosely bound and closely bound conformational states can be identified with theoretically calculated free energy minimum and quantitatively explained in our model as a result of binding associated with large conformational changes. Theoretical predictions have identified certain key residues for binding which are consistent with mutational experiments. The combined study provides a test ground for fundamental mechanisms as well as insights into design and further explorations on biomolecular recognition with large conformational changes.

  12. A comparative study of lock-in-amplifiers and improved duffing chaotic oscillators for the detection and processing of weak signals

    SciTech Connect (OSTI)

    Tang, Yanmei; Li, Xinli; Bai, Yan

    2014-04-11

    The measurement of multiphase flow parameters is of great importance in a wide range of industries. In the measurement of multiphase, the signals from the sensors are extremely weak and often buried in strong background noise. It is thus desirable to develop effective signal processing techniques that can detect the weak signal from the sensor outputs. In this paper, two methods, i.e., lock-in-amplifier (LIA) and improved Duffing chaotic oscillator are compared to detect and process the weak signal. For sinusoidal signal buried in noise, the correlation detection with sinusoidal reference signal is simulated by using LIA. The improved Duffing chaotic oscillator method, which based on the Wigner transformation, can restore the signal waveform and detect the frequency. Two methods are combined to detect and extract the weak signal. Simulation results show the effectiveness and accuracy of the proposed improved method. The comparative analysis shows that the improved Duffing chaotic oscillator method can restrain noise strongly since it is sensitive to initial conditions.

  13. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

    SciTech Connect (OSTI)

    Knott, Michael [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom)] [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Best, Robert B., E-mail: robertbe@helix.nih.gov [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States)

    2014-05-07

    Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

  14. Distinct p53 genomic binding patterns in normal and cancer-derived human cells

    SciTech Connect (OSTI)

    Botcheva K.; McCorkle S. R.; McCombie W. R.; Dunn J. J.; Anderson C. W.

    2011-12-15

    We report here genome-wide analysis of the tumor suppressor p53 binding sites in normal human cells. 743 high-confidence ChIP-seq peaks representing putative genomic binding sites were identified in normal IMR90 fibroblasts using a reference chromatin sample. More than 40% were located within 2 kb of a transcription start site (TSS), a distribution similar to that documented for individually studied, functional p53 binding sites and, to date, not observed by previous p53 genome-wide studies. Nearly half of the high-confidence binding sites in the IMR90 cells reside in CpG islands, in marked contrast to sites reported in cancer-derived cells. The distinct genomic features of the IMR90 binding sites do not reflect a distinct preference for specific sequences, since the de novo developed p53 motif based on our study is similar to those reported by genome-wide studies of cancer cells. More likely, the different chromatin landscape in normal, compared with cancer-derived cells, influences p53 binding via modulating availability of the sites. We compared the IMR90 ChIPseq peaks to the recently published IMR90 methylome1 and demonstrated that they are enriched at hypomethylated DNA. Our study represents the first genome-wide, de novo mapping of p53 binding sites in normal human cells and reveals that p53 binding sites reside in distinct genomic landscapes in normal and cancer-derived human cells.

  15. ON THE WEAK-WIND PROBLEM IN MASSIVE STARS: X-RAY SPECTRA REVEAL A MASSIVE HOT WIND IN {mu} COLUMBAE

    SciTech Connect (OSTI)

    Huenemoerder, David P.; Oskinova, Lidia M.; Todt, Helge; Ignace, Richard; Waldron, Wayne L.; Hamaguchi, Kenji

    2012-09-10

    {mu} Columbae is a prototypical weak-wind O star for which we have obtained a high-resolution X-ray spectrum with the Chandra LETG/ACIS instrument and a low-resolution spectrum with Suzaku. This allows us, for the first time, to investigate the role of X-rays on the wind structure in a bona fide weak-wind system and to determine whether there actually is a massive hot wind. The X-ray emission measure indicates that the outflow is an order of magnitude greater than that derived from UV lines and is commensurate with the nominal wind-luminosity relationship for O stars. Therefore, the {sup w}eak-wind problem{sup -}identified from cool wind UV/optical spectra-is largely resolved by accounting for the hot wind seen in X-rays. From X-ray line profiles, Doppler shifts, and relative strengths, we find that this weak-wind star is typical of other late O dwarfs. The X-ray spectra do not suggest a magnetically confined plasma-the spectrum is soft and lines are broadened; Suzaku spectra confirm the lack of emission above 2 keV. Nor do the relative line shifts and widths suggest any wind decoupling by ions. The He-like triplets indicate that the bulk of the X-ray emission is formed rather close to the star, within five stellar radii. Our results challenge the idea that some OB stars are 'weak-wind' stars that deviate from the standard wind-luminosity relationship. The wind is not weak, but it is hot and its bulk is only detectable in X-rays.

  16. Expression, purification, crystallization and structure of human adipocyte lipid-binding protein (aP2)

    SciTech Connect (OSTI)

    Marr, Eric; Tardie, Mark; Carty, Maynard; Brown Phillips, Tracy; Wang, Ing-Kae; Soeller, Walt; Qiu, Xiayang Karam, George

    2006-11-01

    The crystal structure of human adipocyte lipid-binding protein (aP2) with a bound palmitate is reported at 1.5 Å resolution. Human adipocyte lipid-binding protein (aP2) belongs to a family of intracellular lipid-binding proteins involved in the transport and storage of lipids. Here, the crystal structure of human aP2 with a bound palmitate is described at 1.5 Å resolution. Unlike the known crystal structure of murine aP2 in complex with palmitate, this structure shows that the fatty acid is in a folded conformation and that the loop containing Phe57 acts as a lid to regulate ligand binding by excluding solvent exposure to the central binding cavity.

  17. Efficiencies and Optimization of Weak Base Anion Ion-Exchange Resin for Groundwater Hexavalent Chromium Removal at Hanford

    SciTech Connect (OSTI)

    Nesham, Dean O.; Ivarson, Kristine A.; Hanson, James P.; Miller, Charles W.; Meyers, P.; Jaschke, Naomi M.

    2014-02-03

    The U.S. Department of Energy’s (DOE’s) contractor, CH2M HILL Plateau Remediation Company, has successfully converted a series of groundwater treatment facilities to use a new treatment resin that is delivering more than $3 million in annual cost savings and efficiency in treating groundwater contamination at the DOE Hanford Site in southeastern Washington State. During the production era, the nuclear reactors at the Hanford Site required a continuous supply of high-quality cooling water during operations. Cooling water consumption ranged from about 151,417 to 378,541 L/min (40,000 to 100,000 gal/min) per reactor, depending on specific operating conditions. Water from the Columbia River was filtered and treated chemically prior to use as cooling water, including the addition of sodium dichromate as a corrosion inhibitor. Hexavalent chromium was the primary component of the sodium dichromate and was introduced into the groundwater at the Hanford Site as a result of planned and unplanned discharges from the reactors starting in 1944. Groundwater contamination by hexavalent chromium and other contaminants related to nuclear reactor operations resulted in the need for groundwater remedial actions within the Hanford Site reactor areas. Beginning in 1995, groundwater treatment methods were evaluated, leading to the use of pump-and-treat facilities with ion exchange using Dowex™ 21K, a regenerable, strong-base anion exchange resin. This required regeneration of the resin, which was performed offsite. In 2008, DOE recognized that regulatory agreements would require significant expansion for the groundwater chromium treatment capacity. As a result, CH2M HILL performed testing at the Hanford Site in 2009 and 2010 to demonstrate resin performance in the specific groundwater chemistry at different waste sites. The testing demonstrated that a weak-base anion, single-use resin, specifically ResinTech SIR-700 ®, was effective at removing chromium, had a significantly higher capacity, could be disposed of efficiently onsite, and would eliminate the complexities and programmatic risks from sampling, packaging, transportation, and return of resin for regeneration.

  18. Areas of Weakly Anomalous to Anomalous Surface Temperature in Routt County, Colorado, as Identified from ASTER Thermal Data

    SciTech Connect (OSTI)

    Hussein, Khalid

    2012-02-01

    Citation Information: Originator: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Publication Date: 2012 Title: Warm Modeled Temperature Routt Edition: First Note: This “Weakly Anomalous to Anomalous Surface Temperature” dataset differs from the “Anomalous Surface Temperature” dataset for this county (another remotely sensed CIRES product) by showing areas of modeled temperatures between 1? and 2? above the mean, as opposed to the greater than 2? temperatures contained in the “Anomalous Surface Temperature” dataset. Publication Information: Publication Place: Earth Science & Observation Center, Cooperative Institute for Research in Environmental Science (CIRES), University of Colorado, Boulder Publisher: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Description: This layer contains areas of anomalous surface temperature in Routt County identified from ASTER thermal data and spatial based insolation model. The temperature is calculated using the Emissivity Normalization Algorithm that separate temperature from emissivity. The incoming solar radiation was calculated using spatial based insolation model developed by Fu and Rich (1999). Then the temperature due to solar radiation was calculated using emissivity derived from ASTER data. The residual temperature, i.e. temperature due to solar radiation subtracted from ASTER temperature was used to identify thermally anomalous areas. Areas that had temperature between 1? and 2? were considered ASTER modeled warm surface exposures (thermal anomalies) Spatial Domain: Extent: Top: 4501071.574000 m Left: 311351.975000 m Right: 359411.975000 m Bottom: 4447521.574000 m Contact Information: Contact Organization: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Contact Person: Khalid Hussein Address: CIRES, Ekeley Building Earth Science & Observation Center (ESOC) 216 UCB City: Boulder State: CO Postal Code: 80309-0216 Country: USA Contact Telephone: 303-492-6782 Spatial Reference Information: Coordinate System: Universal Transverse Mercator (UTM) WGS’1984 Zone 13N False Easting: 500000.00000000 False Northing: 0.00000000 Central Meridian: -105.00000000 Scale Factor: 0.99960000 Latitude of Origin: 0.00000000 Linear Unit: Meter Datum: World Geodetic System ’1984 (WGS ’1984) Prime Meridian: Greenwich Angular Unit: Degree Digital Form: Format Name: Shape file

  19. Areas of Weakly Anomalous to Anomalous Surface Temperature in Chaffee County, Colorado, as Identified from ASTER Thermal Data

    SciTech Connect (OSTI)

    Hussein, Khalid

    2012-02-01

    Citation Information: Originator: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Publication Date: 2012 Title: Very Warm Modeled Temperature Chaffee Edition: First Note: This “Weakly Anomalous to Anomalous Surface Temperature” dataset differs from the “Anomalous Surface Temperature” dataset for this county (another remotely sensed CIRES product) by showing areas of modeled temperatures between 1? and 2? above the mean, as opposed to the greater than 2? temperatures contained in the “Anomalous Surface Temperature” dataset. Publication Information: Publication Place: Earth Science & Observation Center, Cooperative Institute for Research in Environmental Science (CIRES), University of Colorado, Boulder Publisher: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Description: This layer contains areas of anomalous surface temperature in Chaffee County identified from ASTER thermal data and spatial based insolation model. The temperature is calculated using the Emissivity Normalization Algorithm that separate temperature from emissivity. The incoming solar radiation was calculated using spatial based insolation model developed by Fu and Rich (1999). Then the temperature due to solar radiation was calculated using emissivity derived from ASTER data. The residual temperature, i.e. temperature due to solar radiation subtracted from ASTER temperature was used to identify thermally anomalous areas. Areas that had temperature greater than 2? were considered ASTER modeled very warm surface exposures (thermal anomalies) Spatial Domain: Extent: Top: 4333432.368072 m Left: 366907.700763 m Right: 452457.816015 m Bottom: 4208271.566715 m Contact Information: Contact Organization: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Contact Person: Khalid Hussein Address: CIRES, Ekeley Building Earth Science & Observation Center (ESOC) 216 UCB City: Boulder State: CO Postal Code: 80309-0216 Country: USA Contact Telephone: 303-492-6782 Spatial Reference Information: Coordinate System: Universal Transverse Mercator (UTM) WGS’1984 Zone 13N False Easting: 500000.00000000 False Northing: 0.00000000 Central Meridian: -105.00000000 Scale Factor: 0.99960000 Latitude of Origin: 0.00000000 Linear Unit: Meter Datum: World Geodetic System ’1984 (WGS ’1984) Prime Meridian: Greenwich Angular Unit: Degree Digital Form: Format Name: Shape file

  20. Areas of Weakly Anomalous to Anomalous Surface Temperature in Archuleta County, Colorado, as Identified from ASTER Thermal Data

    SciTech Connect (OSTI)

    Hussein, Khalid

    2012-02-01

    Citation Information: Originator: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Publication Date: 2012 Title: Warm Modeled Temperature Archuleta Note: This “Weakly Anomalous to Anomalous Surface Temperature” dataset differs from the “Anomalous Surface Temperature” dataset for this county (another remotely sensed CIRES product) by showing areas of modeled temperatures between 1? and 2? above the mean, as opposed to the greater than 2? temperatures contained in the “Anomalous Surface Temperature” dataset. Edition: First Publication Information: Publication Place: Earth Science & Observation Center, Cooperative Institute for Research in Environmental Science (CIRES), University of Colorado, Boulder Publisher: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Description: This layer contains areas of anomalous surface temperature in Archuleta County identified from ASTER thermal data and spatial based insolation model. The temperature is calculated using the Emissivity Normalization Algorithm that separate temperature from emissivity. The incoming solar radiation was calculated using spatial based insolation model developed by Fu and Rich (1999). Then the temperature due to solar radiation was calculated using emissivity derived from ASTER data. The residual temperature, i.e. temperature due to solar radiation subtracted from ASTER temperature was used to identify thermally anomalous areas. Areas that had temperature between 1? and 2? were considered ASTER modeled warm surface exposures (thermal anomalies). Spatial Domain: Extent: Top: 4144825.235807 m Left: 285446.256851 m Right: 350577.338852 m Bottom: 4096962.250137 m Contact Information: Contact Organization: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Contact Person: Khalid Hussein Address: CIRES, Ekeley Building Earth Science & Observation Center (ESOC) 216 UCB City: Boulder State: CO Postal Code: 80309-0216 Country: USA Contact Telephone: 303-492-6782 Spatial Reference Information: Coordinate System: Universal Transverse Mercator (UTM) WGS’1984 Zone 13N False Easting: 500000.00000000 False Northing: 0.00000000 Central Meridian: -105.00000000 Scale Factor: 0.99960000 Latitude of Origin: 0.00000000 Linear Unit: Meter Datum: World Geodetic System ’1984 (WGS ’1984) Prime Meridian: Greenwich Angular Unit: Degree Digital Form: Format Name: Shape file

  1. Areas of Weakly Anomalous to Anomalous Surface Temperature in Alamosa and Saguache Counties, Colorado, as Identified from ASTER Thermal Data

    SciTech Connect (OSTI)

    Hussein, Khalid

    2012-02-01

    Citation Information: Originator: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Publication Date: 2012 Title: Very Warm Modeled Temperature Alamosa Saguache Edition: First Note: This “Weakly Anomalous to Anomalous Surface Temperature” dataset differs from the “Anomalous Surface Temperature” dataset for this county (another remotely sensed CIRES product) by showing areas of modeled temperatures between 1? and 2? above the mean, as opposed to the greater than 2? temperatures contained in the “Anomalous Surface Temperature” dataset. Publication Information: Publication Place: Earth Science & Observation Center, Cooperative Institute for Research in Environmental Science (CIRES), University of Colorado, Boulder Publisher: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Description: This layer contains areas of anomalous surface temperature in Alamosa and Saguache Counties identified from ASTER thermal data and spatial based insolation model. The temperature is calculated using the Emissivity Normalization Algorithm that separate temperature from emissivity. The incoming solar radiation was calculated using spatial based insolation model developed by Fu and Rich (1999). Then the temperature due to solar radiation was calculated using emissivity derived from ASTER data. The residual temperature, i.e. temperature due to solar radiation subtracted from ASTER temperature was used to identify thermally anomalous areas. Areas that had temperature greater than 2? were considered ASTER modeled very warm surface exposures (thermal anomalies) Spatial Domain: Extent: Top: 4217727.601630 m Left: 394390.400264 m Right: 460179.841813 m Bottom: 4156258.036086 m Contact Information: Contact Organization: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Contact Person: Khalid Hussein Address: CIRES, Ekeley Building Earth Science & Observation Center (ESOC) 216 UCB City: Boulder State: CO Postal Code: 80309-0216 Country: USA Contact Telephone: 303-492-6782 Spatial Reference Information: Coordinate System: Universal Transverse Mercator (UTM) WGS’1984 Zone 13N False Easting: 500000.00000000 False Northing: 0.00000000 Central Meridian: -105.00000000 Scale Factor: 0.99960000 Latitude of Origin: 0.00000000 Linear Unit: Meter Datum: World Geodetic System ’1984 (WGS ’1984) Prime Meridian: Greenwich Angular Unit: Degree Digital Form: Format Name: Shape file

  2. Areas of Weakly Anomalous to Anomalous Surface Temperature in Dolores County, Colorado, as Identified from ASTER Thermal Data

    SciTech Connect (OSTI)

    Hussein, Khalid

    2012-02-01

    Citation Information: Originator: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Publication Date: 2012 Title: Very Warm Modeled Temperature Dolores Edition: First Note: This “Weakly Anomalous to Anomalous Surface Temperature” dataset differs from the “Anomalous Surface Temperature” dataset for this county (another remotely sensed CIRES product) by showing areas of modeled temperatures between 1? and 2? above the mean, as opposed to the greater than 2? temperatures contained in the “Anomalous Surface Temperature” dataset. Publication Information: Publication Place: Earth Science & Observation Center, Cooperative Institute for Research in Environmental Science (CIRES), University of Colorado, Boulder Publisher: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Description: This layer contains areas of anomalous surface temperature in Dolores County identified from ASTER thermal data and spatial based insolation model. The temperature is calculated using the Emissivity Normalization Algorithm that separate temperature from emissivity. The incoming solar radiation was calculated using spatial based insolation model developed by Fu and Rich (1999). Then the temperature due to solar radiation was calculated using emissivity derived from ASTER data. The residual temperature, i.e. temperature due to solar radiation subtracted from ASTER temperature was used to identify thermally anomalous areas. Areas that had temperature greater than 2? were considered ASTER modeled very warm surface exposures (thermal anomalies) Spatial Domain: Extent: Top: 4186234.213315 m Left: 212558.673056 m Right: 232922.811862 m Bottom: 4176781.467043 m Contact Information: Contact Organization: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Contact Person: Khalid Hussein Address: CIRES, Ekeley Building Earth Science & Observation Center (ESOC) 216 UCB City: Boulder State: CO Postal Code: 80309-0216 Country: USA Contact Telephone: 303-492-6782 Spatial Reference Information: Coordinate System: Universal Transverse Mercator (UTM) WGS’1984 Zone 13N False Easting: 500000.00000000 False Northing: 0.00000000 Central Meridian: -105.00000000 Scale Factor: 0.99960000 Latitude of Origin: 0.00000000 Linear Unit: Meter Datum: World Geodetic System ’1984 (WGS ’1984) Prime Meridian: Greenwich Angular Unit: Degree Digital Form: Format Name: Shape file

  3. Areas of Weakly Anomalous to Anomalous Surface Temperature in Garfield County, Colorado, as Identified from ASTER Thermal Data

    SciTech Connect (OSTI)

    Hussein, Khalid

    2012-02-01

    Citation Information: Originator: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Publication Date: 2012 Title: Warm Modeled Temperature Garfield Edition: First Note: This “Weakly Anomalous to Anomalous Surface Temperature” dataset differs from the “Anomalous Surface Temperature” dataset for this county (another remotely sensed CIRES product) by showing areas of modeled temperatures between 1? and 2? above the mean, as opposed to the greater than 2? temperatures contained in the “Anomalous Surface Temperature” dataset. Publication Information: Publication Place: Earth Science & Observation Center, Cooperative Institute for Research in Environmental Science (CIRES), University of Colorado, Boulder Publisher: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Description: This layer contains areas of anomalous surface temperature in Garfield County identified from ASTER thermal data and spatial based insolation model. The temperature is calculated using the Emissivity Normalization Algorithm that separate temperature from emissivity. The incoming solar radiation was calculated using spatial based insolation model developed by Fu and Rich (1999). Then the temperature due to solar radiation was calculated using emissivity derived from ASTER data. The residual temperature, i.e. temperature due to solar radiation subtracted from ASTER temperature was used to identify thermally anomalous areas. Areas that had temperature between 1? and 2? were considered ASTER modeled warm surface exposures (thermal anomalies) Spatial Domain: Extent: Top: 4442180.552290 m Left: 268655.053363 m Right: 359915.053363 m Bottom: 4312490.552290 m Contact Information: Contact Organization: Earth Science &Observation Center (ESOC), CIRES, University of Colorado at Boulder Contact Person: Khalid Hussein Address: CIRES, Ekeley Building Earth Science & Observation Center (ESOC) 216 UCB City: Boulder State: CO Postal Code: 80309-0216 Country: USA Contact Telephone: 303-492-6782 Spatial Reference Information: Coordinate System: Universal Transverse Mercator (UTM) WGS’1984 Zone 13N False Easting: 500000.00000000 False Northing: 0.00000000 Central Meridian: -105.00000000 Scale Factor: 0.99960000 Latitude of Origin: 0.00000000 Linear Unit: Meter Datum: World Geodetic System ’1984 (WGS ’1984) Prime Meridian: Greenwich Angular Unit: Degree Digital Form: Format Name: Shape file

  4. NMR studies of DNA oligomers and their interactions with minor groove binding ligands

    SciTech Connect (OSTI)

    Fagan, P A

    1996-05-01

    The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I{center_dot}C base pairs are functional analogs of A{center_dot}T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1 ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.

  5. Assessing Energetic Contributions to Binding from a Disordered Region in a Protein-Protein Interaction

    SciTech Connect (OSTI)

    S Cho; C Swaminathan; D Bonsor; M Kerzic; R Guan; J Yang; C Kieke; P Anderson; D Kranz; et al.

    2011-12-31

    Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Through X-ray structure determination of the protein binding partners before and after complex formation and isothermal titration calorimetry of the interactions, we observe a correlation between protein ordering and binding affinity for complexes along this affinity maturation pathway. Additionally, we show that discrepancies between observed and calculated heat capacities based on buried surface area changes in the protein complexes can be explained largely by heat capacity changes that would result solely from folding the locally disordered region. Previously developed algorithms for predicting binding energies of protein-protein interactions, however, are unable to correctly model the energetic contributions of the structural transitions in our model system. While this highlights the shortcomings of current computational methods in modeling conformational flexibility, it suggests that the experimental methods used here could provide training sets of molecular interactions for improving these algorithms and further rationalizing molecular recognition in protein-protein interactions.

  6. Method for detecting binding events using micro-X-ray fluorescence spectrometry

    DOE Patents [OSTI]

    Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Mann, Grace (Hong Kong, HK)

    2010-12-28

    Method for detecting binding events using micro-X-ray fluorescence spectrometry. Receptors are exposed to at least one potential binder and arrayed on a substrate support. Each member of the array is exposed to X-ray radiation. The magnitude of a detectable X-ray fluorescence signal for at least one element can be used to determine whether a binding event between a binder and a receptor has occurred, and can provide information related to the extent of binding between the binder and receptor.

  7. X-ray crystallographic analysis of adipocyte fatty acid binding protein

    Office of Scientific and Technical Information (OSTI)

    (aP2) modified with 4-hydroxy-2-nonenal (Journal Article) | SciTech Connect X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal Citation Details In-Document Search Title: X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal Fatty acid binding proteins (FABP) have been characterized as facilitating the intracellular solubilization and transport of long-chain fatty acyl

  8. Data Plots of Run I - III Results from SLAC E-158: A precision Measurement of the Weak Mixing Angle in Moller Scattering

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Three physics runs were made in 2002 and 2003 by E-158. As a result, the E-158 Collaboration announced that it had made "the first observation of Parity Violation in electron-electron (Moller) scattering). This precise Parity Violation measurement gives the best determination of the electron's weak charge at low energy (low momentum transfer between interacting particles). E158's measurement tests the predicted running (or evolution) of this weak charge with energy, and searches for new phenomena at TeV energy scales (one thousand times the proton-mass energy scale).[Copied from the experiment's public home page at http://www-project slac.stanford.edu/3158/Default.htm] See also the E158 page for collaborators at http://www.slac.stanford.edu/exp/e158/. Both websites provide data and detailed information.

  9. A Measurement of the Weak Charge of the Proton through Parity Violating Electron Scattering using the Qweak Apparatus: A 21% Result

    SciTech Connect (OSTI)

    Beminiwattha, Rakitha

    2013-08-01

    After a decade of preparations, the Qweak experiment at Jefferson Lab is making the first direct measurement of the weak charge of the proton, Q^p_W. This quantity is suppressed in the Standard Model making a good candidate for search for new physics beyond the SM at the TeV scale. Operationally, we measure a small (about -0.200 ppm) parity-violating asymmetry in elastic electron-proton scattering in integrating mode while flipping the helicity of the electrons 1000 times per second. Commissioning took place Fall 2010, and we finished taking data in early summer 2012. This dissertation is based on the data taken on an initial two weeks period (Wien0). It will provide an overview of the Qweak apparatus, description of the data acquisition and analysis software systems, and final analysis and results from the Wien0 data set. The result is a 16% measurement of the parity violating electron-proton scattering asymmetry, A = -0.2788 +/- 0.0348 (stat.) +/- 0.0290 (syst.) ppm at Q^2 = 0.0250 +/- 0.0006 (GeV)^2. From this a 21% measurement of the weak charge of the proton, Q_w^p(msr)= +0.0952 +/- 0.0155 (stat.) +/- 0.0131 (syst.) +/- 0.0015 (theory) is extracted. From this a 2% measurement of the weak mixing angle, sin^2theta_W(msr)= +0.2328 +/- 0.0039 (stat.) +/- 0.0033 (syst.) +/- 0.0004 (theory) and improved constraints on isoscalar/isovector effective coupling constants of the weak neutral hadronic currents are extracted. These results deviate from the Standard Model by one standard deviation. The Wien0 results are a proof of principle of the Qweak data analysis and a highlight of the road ahead for obtaining full results.

  10. Comparison of galaxy clusters selected by weak-lensing, optical spectroscopy, and X-rays in the deep lens survey F2 field

    SciTech Connect (OSTI)

    Starikova, Svetlana; Jones, Christine; Forman, William R.; Vikhlinin, Alexey; Kurtz, Michael J.; Fabricant, Daniel G.; Murray, Stephen S.; Geller, Margaret J.; Dell'Antonio, Ian P.

    2014-05-10

    We compare galaxy clusters selected in Chandra and XMM-Newton X-ray observations of the 4 deg{sup 2} Deep Lens Survey (DLS) F2 field to the cluster samples previously selected in the same field from a sensitive weak-lensing shear map derived from the DLS and from a detailed galaxy redshift survey—the Smithsonian Hectospec Lensing Survey (SHELS). Our Chandra and XMM-Newton observations cover 1.6 deg{sup 2} of the DLS F2 field, including all 12 weak-lensing peaks above a signal-to-noise ratio of 3.5, along with 16 of the 20 SHELS clusters with published velocity dispersions >500 km s{sup –1}. We detect 26 extended X-ray sources in this area and confirm 23 of them as galaxy clusters using the optical imaging. Approximately 75% of clusters detected in either X-ray or spectroscopic surveys are found in both; these follow the previously established scaling relations between velocity dispersion, L {sub X}, and T {sub X}. A lower percentage, 60%, of clusters are in common between X-ray and DLS samples. With the exception of a high false-positive rate in the DLS weak-lensing search (5 out of 12 DLS candidates appear to be false), differences between the three cluster detection methods can be attributed primarily to observational uncertainties and intrinsic scatter between different observables and cluster mass.

  11. A NOVEL APPROACH IN THE WEAKLY INTERACTING MASSIVE PARTICLE QUEST: CROSS-CORRELATION OF GAMMA-RAY ANISOTROPIES AND COSMIC SHEAR

    SciTech Connect (OSTI)

    Camera, Stefano; Fornasa, Mattia; Fornengo, Nicolao; Regis, Marco

    2013-07-01

    Both cosmic shear and cosmological gamma-ray emission stem from the presence of dark matter (DM) in the universe: DM structures are responsible for the bending of light in the weak-lensing regime and those same objects can emit gamma rays, either because they host astrophysical sources (active galactic nuclei or star-forming galaxies) or directly by DM annihilations (or decays, depending on the properties of the DM particle). Such gamma rays should therefore exhibit strong correlation with the cosmic shear signal. In this Letter, we compute the cross-correlation angular power spectrum of cosmic shear and gamma rays produced by the annihilation/decay of weakly interacting massive particle DM, as well as by astrophysical sources. We show that this observable provides novel information on the composition of the extragalactic gamma-ray background (EGB), since the amplitude and shape of the cross-correlation signal strongly depend on which class of sources is responsible for the gamma-ray emission. If the DM contribution to the EGB is significant (at least in a definite energy range), although compatible with current observational bounds, its strong correlation with the cosmic shear makes such signal potentially detectable by combining Fermi Large Area Telescope data with forthcoming galaxy surveys, like the Dark Energy Survey and Euclid. At the same time, the same signal would demonstrate that the weak-lensing observables are indeed due to particle DM matter and not to possible modifications of general relativity.

  12. Investigation of the mode of binding of a novel series ofN-benzyl...

    Office of Scientific and Technical Information (OSTI)

    of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select...

  13. Structure of Human Toll-like Receptor 3 (TLR3) Ligand-binding...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain Jungwoo Choe1, Matthew S. Kelker1, and Ian A. Wilson1 1Department of Molecular Biology and The Skaggs Institute for Chemical...

  14. Novel CO2 Binding Mechanism Determined via in-situ Absorption Spectroscopy

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    & Theory | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Novel CO2 Binding Mechanism Determined via in-situ Absorption Spectroscopy & Theory

  15. Metal binding in an aluminum based metal-organic framework for carbon

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    dioxide capture | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Metal binding in an aluminum based metal-organic framework for carbon dioxide capture

  16. Developing Adnectins That Target SRC Co-Activator Binding to PXR: A

    Office of Scientific and Technical Information (OSTI)

    Structural Approach toward Understanding Promiscuity of PXR (Journal Article) | SciTech Connect Developing Adnectins That Target SRC Co-Activator Binding to PXR: A Structural Approach toward Understanding Promiscuity of PXR Citation Details In-Document Search Title: Developing Adnectins That Target SRC Co-Activator Binding to PXR: A Structural Approach toward Understanding Promiscuity of PXR Authors: Khan, Javed A. ; Camac, Daniel M. ; Low, Simon ; Tebben, Andrew J. ; Wensel, David L. ;

  17. Discovery of a new ATP-binding motif involved in peptidic azoline

    Office of Scientific and Technical Information (OSTI)

    biosynthesis (Journal Article) | SciTech Connect Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis Citation Details In-Document Search Title: Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis Authors: Dunbar, Kyle L. ; Chekan, Jonathan R. ; Cox, Courtney L. ; Burkhart, Brandon J. ; Nair, Satish K. ; Mitchell , Douglas A. [1] + Show Author Affiliations (UIUC) Publication Date: 2014-11-20 OSTI Identifier: 1163365 Resource Type: Journal

  18. Memo Is Homologous to Nonheme Iron Dioxygenases and Binds an ErbB2-derived

    Office of Scientific and Technical Information (OSTI)

    Phosphopeptide in Its Vestigial Active Site (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Memo Is Homologous to Nonheme Iron Dioxygenases and Binds an ErbB2-derived Phosphopeptide in Its Vestigial Active Site Citation Details In-Document Search Title: Memo Is Homologous to Nonheme Iron Dioxygenases and Binds an ErbB2-derived Phosphopeptide in Its Vestigial Active Site Authors: Qiu, Chen ; Lienhard, Susanne ; Hynes, Nancy E. ; Badache, Ali ; Leahy, Daniel

  19. The same pocket in menin binds both MLL and JUND but has opposite effects

    Office of Scientific and Technical Information (OSTI)

    on transcription (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: The same pocket in menin binds both MLL and JUND but has opposite effects on transcription Citation Details In-Document Search Title: The same pocket in menin binds both MLL and JUND but has opposite effects on transcription Menin is a tumour suppressor protein whose loss or inactivation causes multiple endocrine neoplasia 1 (MEN1), a hereditary autosomal dominant tumour syndrome that is

  20. A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type

    Office of Scientific and Technical Information (OSTI)

    Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2 (Journal Article) | SciTech Connect A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2 Citation Details In-Document Search Title: A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2 Authors: Jégouzo, Sabine A.F. ; Feinberg, Hadar ; Dungarwalla,

  1. Designing artificial metal binding peptides | Center for Bio-Inspired Solar

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Fuel Production artificial metal binding peptides 24 Oct 2012 Dong Wang is a graduate student in the Department of Chemistry and Biochemistry at Arizona State University. He is working in the lab of Professor James Allen, who is leading the Subtask 2 of the Bisfuel Center (Water oxidation catalysts). Dong's research project is focused on design and characterization of artificial peptides capable of binding divalent metals with the aim to construct an efficient water oxidation catalyst that

  2. U-039: ISC Update: BIND 9 Resolver crashes after logging an error in query.c

    Broader source: Energy.gov [DOE]

    A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and working to produce patches which avoid the crash.

  3. U-038: BIND 9 Resolver crashes after logging an error in query.c

    Broader source: Energy.gov [DOE]

    A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and working to produce patches which avoid the crash.

  4. Oligomycin frames a common drug-binding site in the ATP synthase

    SciTech Connect (OSTI)

    Symersky, Jindrich; Osowski, Daniel; Walters, D. Eric; Mueller, David M.

    2015-12-01

    We report the high-resolution (1.9 {angstrom}) crystal structure of oligomycin bound to the subunit c10 ring of the yeast mitochondrial ATP synthase. Oligomycin binds to the surface of the c10 ring making contact with two neighboring molecules at a position that explains the inhibitory effect on ATP synthesis. The carboxyl side chain of Glu59, which is essential for proton translocation, forms an H-bond with oligomycin via a bridging water molecule but is otherwise shielded from the aqueous environment. The remaining contacts between oligomycin and subunit c are primarily hydrophobic. The amino acid residues that form the oligomycin-binding site are 100% conserved between human and yeast but are widely different from those in bacterial homologs, thus explaining the differential sensitivity to oligomycin. Prior genetics studies suggest that the oligomycin-binding site overlaps with the binding site of other antibiotics, including those effective against Mycobacterium tuberculosis, and thereby frames a common 'drug-binding site.' We anticipate that this drug-binding site will serve as an effective target for new antibiotics developed by rational design.

  5. Elevated epidermal growth factor receptor binding in plutonium-induced lung tumors from dogs

    SciTech Connect (OSTI)

    Leung, F.C.; Bohn, L.R.; Dagle, G.E. )

    1991-04-01

    The objective of this study is to examine and characterize epidermal growth factor receptor (EGF-R) binding in inhaled plutonium-induced canine lung-tumor tissue and to compare it with that in normal canine lung tissue. Crude membrane preparations from normal and lung-tumor tissue from beagle dogs were examined in a radioreceptor assay, using {sup 125}I-labeled epidermal growth factor (EGF) as a ligand. Specific EGF receptor binding was determined in the presence of excess unlabeled EGF. We have examined EGF receptor binding in eight lung-tumor samples obtained from six dogs. Epidermal growth factor receptor binding was significantly greater in lung-tumor samples (31.38%) compared with that in normal lung tissue (3.76%). Scatchard plot analysis from the displacement assay revealed that there was no statistical difference in the binding affinity but significantly higher concentration of EGF-R sites in the lung-tumor tissue (619 fmol/mg) than in normal lung tissue (53 fmol/mg). The increase in EGF-R number in plutonium-induced dog lung tumors does not seem to correlate with increase in the initial lung burden exposure to plutonium. Our results demonstrate that there is a significant increase in EGF-R binding in inhaled plutonium-induced dog lung tumors.

  6. In silico identification of anthropogenic chemicals as ligands of zebrafish sex hormone binding globulin

    SciTech Connect (OSTI)

    Thorsteinson, Nels; Ban, Fuqiang; Santos-Filho, Osvaldo; Tabaei, Seyed M.H. [Prostate Centre at the Vancouver General Hospital, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6 (Canada); Miguel-Queralt, Solange; Underhill, Caroline [Department of Obstetrics and Gynecology, University of British Columbia, Child and Family Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4 (Canada); Cherkasov, Artem [Prostate Centre at the Vancouver General Hospital, University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6 (Canada)], E-mail: artc@interchange.ubc.ca; Hammond, Geoffrey L. [Department of Obstetrics and Gynecology, University of British Columbia, Child and Family Research Institute, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4 (Canada)

    2009-01-01

    Anthropogenic compounds with the capacity to interact with the steroid-binding site of sex hormone binding globulin (SHBG) pose health risks to humans and other vertebrates including fish. Building on studies of human SHBG, we have applied in silico drug discovery methods to identify potential binders for SHBG in zebrafish (Danio rerio) as a model aquatic organism. Computational methods, including; homology modeling, molecular dynamics simulations, virtual screening, and 3D QSAR analysis, successfully identified 6 non-steroidal substances from the ZINC chemical database that bind to zebrafish SHBG (zfSHBG) with low-micromolar to nanomolar affinities, as determined by a competitive ligand-binding assay. We also screened 80,000 commercial substances listed by the European Chemicals Bureau and Environment Canada, and 6 non-steroidal hits from this in silico screen were tested experimentally for zfSHBG binding. All 6 of these compounds displaced the [{sup 3}H]5{alpha}-dihydrotestosterone used as labeled ligand in the zfSHBG screening assay when tested at a 33 {mu}M concentration, and 3 of them (hexestrol, 4-tert-octylcatechol, and dihydrobenzo(a)pyren-7(8H)-one) bind to zfSHBG in the micromolar range. The study demonstrates the feasibility of large-scale in silico screening of anthropogenic compounds that may disrupt or highjack functionally important protein:ligand interactions. Such studies could increase the awareness of hazards posed by existing commercial chemicals at relatively low cost.

  7. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This alsomore » represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.« less

  8. Statistical and systematic errors in the measurement of weak-lensing Minkowski functionals: Application to the Canada-France-Hawaii Lensing Survey

    SciTech Connect (OSTI)

    Shirasaki, Masato; Yoshida, Naoki

    2014-05-01

    The measurement of cosmic shear using weak gravitational lensing is a challenging task that involves a number of complicated procedures. We study in detail the systematic errors in the measurement of weak-lensing Minkowski Functionals (MFs). Specifically, we focus on systematics associated with galaxy shape measurements, photometric redshift errors, and shear calibration correction. We first generate mock weak-lensing catalogs that directly incorporate the actual observational characteristics of the Canada-France-Hawaii Lensing Survey (CFHTLenS). We then perform a Fisher analysis using the large set of mock catalogs for various cosmological models. We find that the statistical error associated with the observational effects degrades the cosmological parameter constraints by a factor of a few. The Subaru Hyper Suprime-Cam (HSC) survey with a sky coverage of ?1400 deg{sup 2} will constrain the dark energy equation of the state parameter with an error of ?w {sub 0} ? 0.25 by the lensing MFs alone, but biases induced by the systematics can be comparable to the 1? error. We conclude that the lensing MFs are powerful statistics beyond the two-point statistics only if well-calibrated measurement of both the redshifts and the shapes of source galaxies is performed. Finally, we analyze the CFHTLenS data to explore the ability of the MFs to break degeneracies between a few cosmological parameters. Using a combined analysis of the MFs and the shear correlation function, we derive the matter density ?{sub m0}=0.256±{sub 0.046}{sup 0.054}.

  9. Development of finite local perturbations of electrical conductivity in the flow of a weakly-conducting gas when a magnetic field is present

    SciTech Connect (OSTI)

    Zaklyaz'minskiy, L.; Sokolov, V.; Degtyarev, L.; Kurdyusov, S.; Samarskiy, A.

    1988-08-08

    A study has been made of the possibility of development of a T-layer from local finite perturbation of electrical conductivity, introduced artificially into a steady-state flow of a weakly conducting gas. The analysis is made with the help of a numerical solution of equations of magnetic hydrodynamics, formulated in the assumption that the electron, ion and neutral components of the medium are found in thermodynamic equilibrium; the viscosity, Hall effect and transfer of energy by radiation are not taken into account.

  10. Modulation of FadR Binding Capacity for Acyl-CoA Fatty Acids Through Structure-Guided Mutagenesis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bacik, John-Paul; Yeager, Chris M.; Twary, Scott N.; Martí-Arbona, Ricardo

    2015-09-18

    FadR is a versatile global regulator in Escherichia coli that controls fatty acid metabolism and thereby modulates the ability of this bacterium to grow using fatty acids or acetate as the sole carbon source. FadR regulates fatty acid metabolism in response to intra-cellular concentrations of acyl-CoA lipids. The ability of FadR to bind acyl-CoA fatty acids is hence of significant interest for the engineering of biosynthetic pathways for the production of lipid-based biofuels and commodity chemicals. Based on the available crystal structure of E. coli bound to myristoyl- CoA, we predicted amino acid positions within the effector binding pocket thatmore » would alter the ability of FadR to bind acyl-CoA fatty acids without affecting DNA binding. We utilized fluorescence polarization to characterize the in-vitro binding properties of wild type and mutant FadR. We found that a Leu102Ala mutant enhanced binding of the effector, likely by increasing the size of the binding pocket for the acyl moiety of the molecule. Conversely, the elimination of the guanidine side chain (Arg213Ala and Arg213Met mutants) of the CoA moiety binding site severely diminished the ability of FadR to bind the acyl-CoA effector. These results demonstrate the ability to fine tune FadR binding capacity. The validation of an efficient method to fully characterize all the binding events involved in the specific activity (effector and DNA operator binding) of FadR has allowed us to increase our understanding of the role of specific amino acids in the binding and recognition of acyl-CoA fatty acids and will greatly facilitate efforts aimed at engineering tunable FadR regulators for synthetic biology.« less

  11. Beyond the detergent effect: a binding site for sodium dodecyl sulfate (SDS) in mammalian apoferritin

    SciTech Connect (OSTI)

    Liu, Renyu Bu, Weiming; Xi, Jin; Mortazavi, Shirin R.; Cheung-Lau, Jasmina C.; Dmochowski, Ivan J.; Loll, Patrick J.

    2012-05-01

    Using X-ray crystallography and isothermal titration calorimetry, we show that sodium dodecyl sulfate (SDS) binds specifically to a pre-formed internal cavity in horse-spleen apoferritin. Although sodium dodecyl sulfate (SDS) is widely used as an anionic detergent, it can also exert specific pharmacological effects that are independent of the surfactant properties of the molecule. However, structural details of how proteins recognize SDS are scarce. Here, it is demonstrated that SDS binds specifically to a naturally occurring four-helix bundle protein: horse apoferritin. The X-ray crystal structure of the apoferritin–SDS complex was determined at a resolution of 1.9 Å and revealed that the SDS binds in an internal cavity that has previously been shown to recognize various general anesthetics. A dissociation constant of 24 ± 9 µM at 293 K was determined by isothermal titration calorimetry. SDS binds in this cavity by bending its alkyl tail into a horseshoe shape; the charged SDS head group lies in the opening of the cavity at the protein surface. This crystal structure provides insights into the protein–SDS interactions that give rise to binding and may prove useful in the design of novel SDS-like ligands for some proteins.

  12. Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh

    SciTech Connect (OSTI)

    Ramirez, Ursula D.; Focia, Pamela J.; Freymann, Douglas M.

    2008-10-01

    Crystal structures of the Ffh NG GTPase domain at < 1.24 Å resolution reveal multiple overlapping nucleotide binding modes. Two structures of the nucleotide-bound NG domain of Ffh, the GTPase subunit of the bacterial signal recognition particle (SRP), have been determined at ultrahigh resolution in similar crystal forms. One is GDP-bound and one is GMPPCP-bound. The asymmetric unit of each structure contains two protein monomers, each of which exhibits differences in nucleotide-binding conformation and occupancy. The GDP-bound Ffh NG exhibits two binding conformations in one monomer but not the other and the GMPPCP-bound protein exhibits full occupancy of the nucleotide in one monomer but only partial occupancy in the other. Thus, under the same solution conditions, each crystal reveals multiple binding states that suggest that even when nucleotide is bound its position in the Ffh NG active site is dynamic. Some differences in the positioning of the bound nucleotide may arise from differences in the crystal-packing environment and specific factors that have been identified include the relative positions of the N and G domains, small conformational changes in the P-loop, the positions of waters buried within the active site and shifts in the closing loop that packs against the guanine base. However, ‘loose’ binding may have biological significance in promoting facile nucleotide exchange and providing a mechanism for priming the SRP GTPase prior to its activation in its complex with the SRP receptor.

  13. Protein binding studies of technetium-99m-labeled phosphine and isocyanide cationic complexes

    SciTech Connect (OSTI)

    Zanelli, G.D.; Cook, N.; Lahiri, A.; Ellison, D.; Webbon, P.; Woolley, G.

    1988-01-01

    Most /sup 99m/Tc/phosphine/isocyanide complexes synthesized to date show preferential uptake by the myocardium of many animal species but not in man. A new complex has been synthesized, (/sup 99m/Tc(DEPE)2(CNR)2), +(DEPIC), where R = t - butyl isocyanide, which in three animal species images the myocardium very well, but in humans it remains primarily in the blood pool. One reason for the difference in the behavior of these complexes in different species could be the characteristics of their binding to plasma proteins. The protein binding characteristics of DEPIC and two other well-known complexes have therefore been studied. Whereas the other complexes bind nonspecifically to many proteins both in animal and human plasma, DEPIC binds almost exclusively to prealbumin in humans but nonspecifically to other proteins in the rabbit. The binding sites in human plasma appear to be those normally occupied by thyroxine on the prealbumin tetramer and these can be blocked by sodium salicylate.

  14. Measurements and modeling of the impact of weak magnetic fields on the plasma properties of a planar slot antenna driven plasma source

    SciTech Connect (OSTI)

    Yoshikawa, Jun Susa, Yoshio; Ventzek, Peter L. G.

    2015-05-15

    The radial line slot antenna plasma source is a type of surface wave plasma source driven by a planar slot antenna. Microwave power is transmitted through a slot antenna structure and dielectric window to a plasma characterized by a generation zone adjacent to the window and a diffusion zone that contacts a substrate. The diffusion zone is characterized by a very low electron temperature. This renders the source useful for soft etch applications and thin film deposition processes requiring low ion energy. Another property of the diffusion zone is that the plasma density tends to decrease from the axis to the walls under the action of ambipolar diffusion at distances far from where the plasma is generated. A previous simulation study [Yoshikawa and. Ventzek, J. Vac. Sci. Technol. A 31, 031306 (2013)] predicted that the anisotropy in transport parameters due to weak static magnetic fields less than 50 G could be leveraged to manipulate the plasma profile in the radial direction. These simulations motivated experimental tests in which weak magnetic fields were applied to a radial line slot antenna source. Plasma absorption probe measurements of electron density and etch rate showed that the magnetic fields remote from the wafer were able to manipulate both parameters. A summary of these results is presented in this paper. Argon plasma simulation trends are compared with experimental plasma and etch rate measurements. A test of the impact of magnetic fields on charge up damage showed no perceptible negative effect.

  15. Stellar yields of rotating first stars. I. Yields of weak supernovae and abundances of carbon-enhanced hyper-metal-poor stars

    SciTech Connect (OSTI)

    Takahashi, Koh; Umeda, Hideyuki [Department of Astronomy, The University of Tokyo, Bunkyo, Tokyo 113-0033 (Japan); Yoshida, Takashi, E-mail: ktakahashi@astron.s.u-tokyo.ac.jp [Yukawa Institute for Theoretical Physics, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502 (Japan)

    2014-10-10

    We perform a stellar evolution simulation of first stars and calculate stellar yields from the first supernovae. The initial masses are taken from 12 to 140 M {sub ?} to cover the whole range of core-collapse supernova progenitors, and stellar rotation is included, which results in efficient internal mixing. A weak explosion is assumed in supernova yield calculations, thus only outer distributed matter, which is not affected by the explosive nucleosynthesis, is ejected in the models. We show that the initial mass and the rotation affect the explosion yield. All the weak explosion models have abundances of [C/O] larger than unity. Stellar yields from massive progenitors of >40-60 M {sub ?} show enhancement of Mg and Si. Rotating models yield abundant Na and Al, and Ca is synthesized in nonrotating heavy massive models of >80 M {sub ?}. We fit the stellar yields to the three most iron-deficient stars and constrain the initial parameters of the mother progenitor stars. The abundance pattern in SMSS 0313–6708 is well explained by 50-80 M {sub ?} nonrotating models, rotating 30-40 M {sub ?} models well fit the abundance of HE 0107-5240, and both nonrotating and rotating 15-40 M {sub ?} models explain HE 1327-2326. The presented analysis will be applicable to other carbon-enhanced hyper-metal-poor stars observed in the future. The abundance analyses will give valuable information about the characteristics of the first stars.

  16. Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

    SciTech Connect (OSTI)

    Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven

    2014-10-02

    Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

  17. Beta-endorphin and alpha-n-acetyl beta-endorphin; synthesis, conformation and binding parameter

    SciTech Connect (OSTI)

    Lovegren, E.S.

    1986-01-01

    Beta-endorphin (EP) is a 31-residue opioid peptide found in many tissues, including the pituitary, brain and reproductive tract. Alpha-amino-acetyl beta-endorphin (AcEP) was characterized spectroscopically by proton nuclear magnetic resonance (NMR) and circular dichroism in deuterated water and trifluoroethanol (TFE). Both EP and AcEP bind to neuroblastoma N2a cells. This binding was not mediated through opiate receptors, and both peptides seemed to bind at common sites. Ovarian immunoreactive-EP levels were determined for immature and mature rates. These levels were found to be responsive to exogenous gonadotropin treatment in immature animals. A large percentage of the immunoreactive-EP is present in follicular fluid, and most of the endorphin-like peptides were acetylated, as measured by radioimmunoassay. Chromatogaphic analysis suggested at least three EP-like species: EP, a carboxy-terminally cleaved and an amino-terminally acetylated EP.

  18. LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins

    SciTech Connect (OSTI)

    Sosa, Brian A.; Rothballer, Andrea; Kutay, Ulrike; Schwartz, Thomas U.

    2012-08-31

    Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansive grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.

  19. Crystal Structure of the HP1-EMSY Complex Reveals an Unusual Mode of HP1 Binding

    SciTech Connect (OSTI)

    Huang,Y.; Myers, M.; Xu, R.

    2006-01-01

    Heterochromatin protein-1 (HP1) plays an essential role in both the assembly of higher-order chromatin structure and epigenetic inheritance. The C-terminal chromo shadow domain (CSD) of HP1 is responsible for homodimerization and interaction with a number of chromatin-associated nonhistone proteins, including EMSY, which is a BRCA2-interacting protein that has been implicated in the development of breast and ovarian cancer. We have determined the crystal structure of the HP1{beta} CSD in complex with the N-terminal domain of EMSY at 1.8 Angstroms resolution. Surprisingly, the structure reveals that EMSY is bound by two HP1 CSD homodimers, and the binding sequences differ from the consensus HP1 binding motif PXVXL. This structural information expands our understanding of HP1 binding specificity and provides insights into interactions between HP1 homodimers that are likely to be important for heterochromatin formation.

  20. T-662: ISC BIND Packet Processing Flaw Lets Remote Users Deny Service

    Broader source: Energy.gov [DOE]

    A defect in the affected BIND 9 versions allows an attacker to remotely cause the "named" process to exit using a specially crafted packet. This defect affects both recursive and authoritative servers. The code location of the defect makes it impossible to protect BIND using ACLs configured within named.conf or by disabling any features at compile-time or run-time. A remote attacker would need to be able to send a specially crafted packet directly to a server running a vulnerable version of BIND. There is also the potential for an indirect attack via malware that is inadvertently installed and run, where infected machines have direct access to an organization's nameservers.

  1. Ligand-induced conformational changes in a thermophilic ribose-binding protein

    SciTech Connect (OSTI)

    Cuneo, Matthew J.; Beese, Lorena S.; Hellinga, Homme W.

    2009-05-21

    Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (appTm value is 108 C) than the mesophilic Escherichia coli homolog (ecRBP) (appTm value is 56 C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.

  2. Binding of formyl peptides to Walker 256 carcinosarcoma cells and the chemotactic response of these cells

    SciTech Connect (OSTI)

    Rayner, D.C.; Orr, F.W.; Shiu, R.P.

    1985-05-01

    N-Formylmethionylleucylphenylalanine (fMLP) induces chemotaxis in leukocytes, the response being mediated by peptide binding to a receptor on the plasma membrane. In tumor cells, this peptide has been reported to induce cellular swelling and chemotaxis in vitro and to enhance the localization of circulating tumor cells in vivo. In the Boyden chamber, the authors evaluated the migratory responses of Walker carcinosarcoma 256 cells to varying concentrations of fMLP. Sigmoidal dose-response curves were obtained with the dose of chemotactic factor that elicits a half-maximal chemotactic response of 5.0 +/- 2.5 X 10(-8) M. Checkerboard analysis indicated that these responses were dependent upon a concentration gradient of fMLP with increases in migration of circa 2 to 2.5 times that of random movement. To examine the binding of fMLP, the tumor cells were incubated with 5 X 10(-9) M fML-(/sup 3/H)P in Hanks balanced salt solution. Specific binding (0.5 to 1% of total radioligand, to whole cells inhibited by 5 X 10(-6) M fMLP) approached equilibrium after 4 to 6 h at 4 degrees C and after 6 to 10 h at 22 degrees C. Autoradiographic studies demonstrated heterogeneous binding of the peptide by tumor cells and also showed its intracellular localization. In homogenates of Walker cells prepared in 0.1 M Tris HCl, pH 7.4, with 10 mM MgCl2 and bovine serum albumin (1 mg/ml), specific binding of approximately 0.5% of total fML-(/sup 3/H)P reached equilibrium after 60 min at 4 degrees C. In whole cells and homogenates, binding was reversible by addition of unlabeled fMLP.

  3. Photoelectron Spectroscopy and Theoretical Studies of Anion-pi Interactions: Binding Strength and Anion Specificity

    SciTech Connect (OSTI)

    Zhang, Jian; Zhou, Bin; Sun, Zhenrong; Wang, Xue B.

    2015-01-01

    Proposed in theory and confirmed to exist, anion–? interactions have been recognized as new and important non-covalent binding forces. Despite extensive theoretical studies, numerous crystal structural identifications, and a plethora of solution phase investigations, intrinsic anion–? interaction strengths that are free from complications of condensed phases’ environments, have not been directly measured in the gas phase. Herein we present a joint photoelectron spectroscopic and theoretical study on this subject, in which tetraoxacalix[2]arene[2]triazine 1, an electron-deficient and cavity self-tunable macrocyclic was used as a charge-neutral molecular host to probe its interactions with a series of anions with distinctly different shapes and charge states (spherical halides Cl?, Br?, I?, linear thiocyanate SCN?, trigonal planar nitrate NO??, pyramidic iodate IO??, and tetrahedral sulfate SO?²?). The binding energies of the resultant gaseous 1:1 complexes (1•Cl?,1•Br?, 1•I?, 1•SCN?, 1•NO??, 1•IO?? and 1•SO?²?) were directly measured experimentally, exhibiting substantial non-covalent interactions with pronounced anion specific effects. The binding strengths of Cl?, NO??, IO?? with 1 are found to be strongest among all singly charged anions, amounting to ca. 30 kcal/mol, but only about 40% of that between 1 and SO?²?. Quantum chemical calculations reveal that all anions reside in the center of the cavity of 1 with anion–? binding motif in the complexes’ optimized structures, where 1 is seen to be able to self-regulate its cavity structure to accommodate anions of different geometries and three-dimensional shapes. Electron density surface and natural bond orbital charge distribution analysis further support anion–? binding formation. The calculated binding energies of the anions and 1 nicely reproduce the experimentally estimated electron binding energy increase. This work illustrates that size-selective photoelectron spectroscopy combined with theoretical calculations represent a powerful technique to probe intrinsic anion–? interactions and has potential to provide quantitative guest-host molecular binding strengths and unravel fundamental insights in specific anion recognitions.

  4. De novo Design of an Artificial bis-[4Fe4S] Binding Protein

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    De novo Design of an Artificial bis-[4Fe4S] Binding Protein Authors: Roy, A,, Sarrou, I., Vaughn, M.D., Astashkin, A.V., and Ghirlanda, G. Title: De novo Design of an Artificial bis-[4Fe4S] Binding Protein Source: Biochemistry Year: 2013 Volume: 52 Pages: 7586-7594 ABSTRACT: In nature, protein subunits containing multiple iron-sulfur clusters often mediate the delivery of reducing equivalents from metabolic pathways to the active site of redox proteins. The de novo design of redox active

  5. Structural Basis of Wnt Signaling Inhibition by Dickkopf Binding to LRP5/6

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Basis of Wnt Signaling Inhibition by Dickkopf Binding to LRP5/6 Citation Details In-Document Search Title: Structural Basis of Wnt Signaling Inhibition by Dickkopf Binding to LRP5/6 Authors: Ahn, Victoria E. ; Chu, Matthew Ling-Hon ; Choi, Hee-Jung ; Tran, Denise ; Abo, Arie ; Weis, William I. Publication Date: 2011-11-01 OSTI Identifier: 1198118 Type: Published Article Journal Name: Developmental Cell Additional Journal Information: Journal Volume: 21;

  6. Structural Studies of Wnts and Identification of an LRP6 Binding Site

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Structural Studies of Wnts and Identification of an LRP6 Binding Site Citation Details In-Document Search Title: Structural Studies of Wnts and Identification of an LRP6 Binding Site Authors: Chu, Matthew Ling-Hon ; Ahn, Victoria E. ; Choi, Hee-Jung ; Daniels, Danette L. ; Nusse, Roel ; Weis, William I. ; , Publication Date: 2014-05-13 OSTI Identifier: 1131442 Report Number(s): SLAC-REPRINT-2014-111 DOE Contract Number: AC02-76SF00515 Resource Type:

  7. Structure and Ca[superscript 2+]-Binding Properties of the Tandem

    Office of Scientific and Technical Information (OSTI)

    C[subscript 2] Domains of E-Syt2 (Journal Article) | SciTech Connect and Ca[superscript 2+]-Binding Properties of the Tandem C[subscript 2] Domains of E-Syt2 Citation Details In-Document Search Title: Structure and Ca[superscript 2+]-Binding Properties of the Tandem C[subscript 2] Domains of E-Syt2 Authors: Xu, Junjie ; Bacaj, Taulant ; Zhou, Amy ; Tomchick, Diana R. ; Südhof, Thomas C. ; Rizo, Josep [1] ; UTSMC) [2] + Show Author Affiliations (Stanford-MED) ( Publication Date: 2014-12-23

  8. Syntaxin 1a Variants Lacking an N-peptide or Bearing the LE Mutation Bind

    Office of Scientific and Technical Information (OSTI)

    to Munc18a in a Closed Conformation (Journal Article) | SciTech Connect Syntaxin 1a Variants Lacking an N-peptide or Bearing the LE Mutation Bind to Munc18a in a Closed Conformation Citation Details In-Document Search Title: Syntaxin 1a Variants Lacking an N-peptide or Bearing the LE Mutation Bind to Munc18a in a Closed Conformation Authors: Colbert, Karen N. ; Hattendorf, Douglas A. ; Weiss, Thomas M. ; Burkhardt, Pawel ; Fasshauer, Dirk ; Weis, William I. Publication Date: 2014-05-13 OSTI

  9. Mass calibration of galaxy clusters at redshift 0.1–1.0 using weak lensing in the Sloan Digital Sky Survey Stripe 82 co-add

    SciTech Connect (OSTI)

    Wiesner, Matthew P.; Lin, Huan; Soares-Santos, Marcelle

    2015-07-08

    We present galaxy cluster mass–richness relations found in the Sloan Digital Sky Survey Stripe 82 co-add using clusters found using a Voronoi tessellation cluster finder. These relations were found using stacked weak lensing shear observed in a large sample of galaxy clusters. These mass–richness relations are presented for four redshift bins, 0.1 < z ? 0.4, 0.4 < z ? 0.7, 0.7 < z ? 1.0 and 0.1 < z ? 1.0. We describe the sample of galaxy clusters and explain how these clusters were found using a Voronoi tessellation cluster finder. We fit a Navarro-Frenk-White profile to the stacked weak lensing shear signal in redshift and richness bins in order to measure virial mass (M200). We describe several effects that can bias weak lensing measurements, including photometric redshift bias, the effect of the central BCG, halo miscentering, photometric redshift uncertainty and foreground galaxy contamination. We present mass–richness relations using richness measure NVT with each of these effects considered separately as well as considered altogether. We also examine redshift evolution of the mass–richness relation. As a result, we present measurements of the mass coefficient (M200|20) and the power-law slope (?) for power-law fits to the mass and richness values in each of the redshift bins. We find values of the mass coefficient of 8.49 ± 0.526, 14.1 ± 1.78, 30.2 ± 8.74 and 9.23 ± 0.525 × 1013 h–1 M? for each of the four redshift bins, respectively. As a result, we find values of the power-law slope of 0.905 ± 0.0585, 0.948 ± 0.100, 1.33 ± 0.260 and 0.883 ± 0.0500, respectively.

  10. Mass calibration of galaxy clusters at redshift 0.1–1.0 using weak lensing in the Sloan Digital Sky Survey Stripe 82 co-add

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wiesner, Matthew P.; Lin, Huan; Soares-Santos, Marcelle

    2015-07-08

    We present galaxy cluster mass–richness relations found in the Sloan Digital Sky Survey Stripe 82 co-add using clusters found using a Voronoi tessellation cluster finder. These relations were found using stacked weak lensing shear observed in a large sample of galaxy clusters. These mass–richness relations are presented for four redshift bins, 0.1 < z ≤ 0.4, 0.4 < z ≤ 0.7, 0.7 < z ≤ 1.0 and 0.1 < z ≤ 1.0. We describe the sample of galaxy clusters and explain how these clusters were found using a Voronoi tessellation cluster finder. We fit a Navarro-Frenk-White profile to the stackedmore » weak lensing shear signal in redshift and richness bins in order to measure virial mass (M200). We describe several effects that can bias weak lensing measurements, including photometric redshift bias, the effect of the central BCG, halo miscentering, photometric redshift uncertainty and foreground galaxy contamination. We present mass–richness relations using richness measure NVT with each of these effects considered separately as well as considered altogether. We also examine redshift evolution of the mass–richness relation. As a result, we present measurements of the mass coefficient (M200|20) and the power-law slope (α) for power-law fits to the mass and richness values in each of the redshift bins. We find values of the mass coefficient of 8.49 ± 0.526, 14.1 ± 1.78, 30.2 ± 8.74 and 9.23 ± 0.525 × 1013 h–1 M⊙ for each of the four redshift bins, respectively. As a result, we find values of the power-law slope of 0.905 ± 0.0585, 0.948 ± 0.100, 1.33 ± 0.260 and 0.883 ± 0.0500, respectively.« less

  11. JOINT ANALYSIS OF CLUSTER OBSERVATIONS. II. CHANDRA/XMM-NEWTON X-RAY AND WEAK LENSING SCALING RELATIONS FOR A SAMPLE OF 50 RICH CLUSTERS OF GALAXIES

    SciTech Connect (OSTI)

    Mahdavi, Andisheh [Department of Physics and Astronomy, San Francisco State University, San Francisco, CA 94131 (United States); Hoekstra, Henk [Leiden Observatory, Leiden University, Niels Bohrweg 2, NL-2333 CA Leiden (Netherlands); Babul, Arif; Bildfell, Chris [Department of Physics and Astronomy, University of Victoria, Victoria, BC V8W 3P6 (Canada); Jeltema, Tesla [Santa Cruz Institute for Particle Physics, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 (United States); Henry, J. Patrick [Institute for Astronomy, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States)

    2013-04-20

    We present a study of multiwavelength X-ray and weak lensing scaling relations for a sample of 50 clusters of galaxies. Our analysis combines Chandra and XMM-Newton data using an energy-dependent cross-calibration. After considering a number of scaling relations, we find that gas mass is the most robust estimator of weak lensing mass, yielding 15% {+-} 6% intrinsic scatter at r{sub 500}{sup WL} (the pseudo-pressure Y{sub X} yields a consistent scatter of 22% {+-} 5%). The scatter does not change when measured within a fixed physical radius of 1 Mpc. Clusters with small brightest cluster galaxy (BCG) to X-ray peak offsets constitute a very regular population whose members have the same gas mass fractions and whose even smaller (<10%) deviations from regularity can be ascribed to line of sight geometrical effects alone. Cool-core clusters, while a somewhat different population, also show the same (<10%) scatter in the gas mass-lensing mass relation. There is a good correlation and a hint of bimodality in the plane defined by BCG offset and central entropy (or central cooling time). The pseudo-pressure Y{sub X} does not discriminate between the more relaxed and less relaxed populations, making it perhaps the more even-handed mass proxy for surveys. Overall, hydrostatic masses underestimate weak lensing masses by 10% on the average at r{sub 500}{sup WL}; but cool-core clusters are consistent with no bias, while non-cool-core clusters have a large and constant 15%-20% bias between r{sub 2500}{sup WL} and r{sub 500}{sup WL}, in agreement with N-body simulations incorporating unthermalized gas. For non-cool-core clusters, the bias correlates well with BCG ellipticity. We also examine centroid shift variance and power ratios to quantify substructure; these quantities do not correlate with residuals in the scaling relations. Individual clusters have for the most part forgotten the source of their departures from self-similarity.

  12. Kits and methods of detection using cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, O.; Yosef, K.

    1998-04-14

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  13. Kits and methods of detection using cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL)

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  14. Structure of the Escherichia coli Phosphonate Binding Protein PhnD and Rationally Optimized Phosphonate Biosensors

    SciTech Connect (OSTI)

    Alicea, Ismael; Marvin, Jonathan S.; Miklos, Aleksandr E.; Ellington, Andrew D.; Looger, Loren L.; Schreiter, Eric R.

    2012-09-17

    The phnD gene of Escherichia coli encodes the periplasmic binding protein of the phosphonate (Pn) uptake and utilization pathway. We have crystallized and determined structures of E. coli PhnD (EcPhnD) in the absence of ligand and in complex with the environmentally abundant 2-aminoethylphosphonate (2AEP). Similar to other bacterial periplasmic binding proteins, 2AEP binds near the center of mass of EcPhnD in a cleft formed between two lobes. Comparison of the open, unliganded structure with the closed 2AEP-bound structure shows that the two lobes pivot around a hinge by {approx}70{sup o} between the two states. Extensive hydrogen bonding and electrostatic interactions stabilize 2AEP, which binds to EcPhnD with low nanomolar affinity. These structures provide insight into Pn uptake by bacteria and facilitated the rational design of high signal-to-noise Pn biosensors based on both coupled small-molecule dyes and autocatalytic fluorescent proteins.

  15. Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh

    SciTech Connect (OSTI)

    Ramirez, U.D.; Focia, P.J.; Freymann, D.M.

    2008-10-24

    Two structures of the nucleotide-bound NG domain of Ffh, the GTPase subunit of the bacterial signal recognition particle (SRP), have been determined at ultrahigh resolution in similar crystal forms. One is GDP-bound and one is GMPPCP-bound. The asymmetric unit of each structure contains two protein monomers, each of which exhibits differences in nucleotide-binding conformation and occupancy. The GDP-bound Ffh NG exhibits two binding conformations in one monomer but not the other and the GMPPCP-bound protein exhibits full occupancy of the nucleotide in one monomer but only partial occupancy in the other. Thus, under the same solution conditions, each crystal reveals multiple binding states that suggest that even when nucleotide is bound its position in the Ffh NG active site is dynamic. Some differences in the positioning of the bound nucleotide may arise from differences in the crystal-packing environment and specific factors that have been identified include the relative positions of the N and G domains, small conformational changes in the P-loop, the positions of waters buried within the active site and shifts in the closing loop that packs against the guanine base. However, 'loose' binding may have biological significance in promoting facile nucleotide exchange and providing a mechanism for priming the SRP GTPase prior to its activation in its complex with the SRP receptor.

  16. NRC staff review of licensee responses to pressure-locking and thermal-binding issue

    SciTech Connect (OSTI)

    Rathbun, H.J.

    1996-12-01

    Commercial nuclear power plant operating experience has indicated that pressure locking and thermal binding represent potential common mode failure mechanisms that can cause safety-related power-operated gate valves to fail in the closed position, thus rendering redundant safety-related systems incapable of performing their safety functions. In Generic Letter (GL) 95-07, {open_quotes}Pressure Locking and Thermal Binding of Safety-Related Power-Operated Gate Valves,{close_quotes} the U.S. Nuclear Regulatory Commission (NRC) staff requested that nuclear power plant licensees take certain actions to ensure that valves susceptible to pressure locking or thermal binding are capable of performing their safety functions within the current licensing bases of the facility. The NRC staff has received summary information from licensees in response to GL 95-07 describing actions they have taken to prevent the occurrence of pressure locking and thermal binding. The NRC staff has developed a systematic process to help ensure uniform and consistent review of licensee submittals in response to GL 95-07.

  17. Methanobactin: a copper binding compound having antibiotic and antioxidant activity isolated from methanotrophic bacteria

    DOE Patents [OSTI]

    DiSpirito, Alan A. (Ames, IA); Zahn, James A. (Harbor Beach, MI); Graham, David W. (Lawrence, KS); Kim, Hyung J. (St. Paul, MN); Alterman, Michail (Lawrence, KS); Larive, Cynthia (Lawrence, KS)

    2007-04-03

    A means and method for treating bacterial infection, providing antioxidant activity, and chelating copper using a copper binding compound produced by methanotrophic bacteria is described. The compound, known as methanobactin, is the first of a new class of antibiotics having gram-positive activity. Methanobactin has been sequenced, and its structural formula determined.

  18. Tumor necrosis factor: specific binding and internalization in sensitive and resistant cells

    SciTech Connect (OSTI)

    Tsujimoto, M.; Yip, Y.K.; Vilcek, J.

    1985-11-01

    Highly purified, Escherichia coli-derived recombinant human tumor necrosis factor (TNF) was labeled with /sup 125/I and employed to determine receptor binding, internalization, and intracellular degradation in murine L929 cells (highly sensitive to the cytotoxic action of TNF) and in diploid human FS-4 cells (resistant to TNF cytotoxicity). /sup 125/I-labeled TNF bound specifically to high-affinity receptors on both L929 and FS-4 cells. Scatchard analysis of the binding data indicated the presence of 2200 binding sites per L929 cell and 7500 binding sites per FS-4 cell. The calculated dissociation constants are 6.1 x 10/sup -10/ M and 3.2 x 10/sup -10/ M for L929 and FS-4 cells, respectively. In both L929 and FS-4 cells, incubation at 37/sup 0/C resulted in a rapid internalization of the bulk of the cell-bound TNF, followed by the appearance of trichloroacetic acid-soluble /sup 125/I radioactivity in the tissue culture medium, due to degradation of TNF. Degradation but not cellular uptake of TNF was inhibited in the presence of chloroquine (an inhibitor of lysosomal proteases) in both L929 and FS-4 cells, suggesting that degradation occurs intracellularly, probably within lysosomes. These results show that resistance of FS-4 cells to TNF cytotoxicity is not due to a lack of receptors or their inability to internalize and degrade TNF.

  19. Measurement of the second-order Zeeman effect on the sodium clock transition in the weak-magnetic-field region using the scalar Aharonov-Bohm phase

    SciTech Connect (OSTI)

    Numazaki, Kazuya; Imai, Hiromitsu; Morinaga, Atsuo [Department of Physics, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510 (Japan)

    2010-03-15

    The second-order Zeeman effect of the sodium clock transition in a weak magnetic field of less than 50 {mu}T was measured as the scalar Aharonov-Bohm phase by two-photon stimulated Raman atom interferometry. The ac Stark effect of the Raman pulse was canceled out by adopting an appropriate intensity ratio of two photons in the Raman pulse. The Ramsey fringes for the pulse separation of 7 ms were obtained with a phase uncertainty of {pi}/200 rad. The nondispersive feature of the scalar Aharonov-Bohm phase was clearly demonstrated through 18 fringes with constant amplitude. The Breit-Rabi formula of the sodium clock transition was verified to be {Delta}{nu}=(0.222{+-}0.003)x10{sup 12}xB{sup 1.998{+-}0.004} in a magnetic field of less than 50 {mu}T.

  20. The nonlinear Schrödinger equation and the propagation of weakly nonlinear waves in optical fibers and on the water surface

    SciTech Connect (OSTI)

    Chabchoub, A.; Kibler, B.; Finot, C.; Millot, G.; Onorato, M.; Dudley, J.M.; Babanin, A.V.

    2015-10-15

    The dynamics of waves in weakly nonlinear dispersive media can be described by the nonlinear Schrödinger equation (NLSE). An important feature of the equation is that it can be derived in a number of different physical contexts; therefore, analogies between different fields, such as for example fiber optics, water waves, plasma waves and Bose–Einstein condensates, can be established. Here, we investigate the similarities between wave propagation in optical Kerr media and water waves. In particular, we discuss the modulation instability (MI) in both media. In analogy to the water wave problem, we derive for Kerr-media the Benjamin–Feir index, i.e. a nondimensional parameter related to the probability of formation of rogue waves in incoherent wave trains.

  1. Equation of state of a weakly interacting two-dimensional Bose gas studied at zero temperature by means of quantum Monte Carlo methods

    SciTech Connect (OSTI)

    Astrakharchik, G. E.; Boronat, J.; Casulleras, J.; Kurbakov, I. L.; Lozovik, Yu. E.

    2009-05-15

    The equation of state of a weakly interacting two-dimensional Bose gas is studied at zero temperature by means of quantum Monte Carlo methods. Going down to as low densities as na{sup 2}{proportional_to}10{sup -100} permits us to obtain agreement on beyond mean-field level between predictions of perturbative methods and direct many-body numerical simulation, thus providing an answer to the fundamental question of the equation of state of a two-dimensional dilute Bose gas in the universal regime (i.e., entirely described by the gas parameter na{sup 2}). We also show that the measure of the frequency of a breathing collective oscillation in a trap at very low densities can be used to test the universal equation of state of a two-dimensional Bose gas.

  2. Population studies. XIII. A new analysis of the Bidelman-Macconnell 'weak-metal' stars - confirmation of metal-poor stars in the thick disk of the galaxy

    SciTech Connect (OSTI)

    Beers, Timothy C.; Norris, John E.; Placco, Vinicius M.; Lee, Young Sun; Rossi, Silvia; Carollo, Daniela; Masseron, Thomas E-mail: jen@mso.anu.edu.au E-mail: youngsun@cnu.ac.kr E-mail: daniela.carollo@mq.edu.au

    2014-10-10

    A new set of very high signal-to-noise (S/N > 100/1), medium-resolution (R ? 3000) optical spectra have been obtained for 302 of the candidate 'weak-metal' stars selected by Bidelman and MacConnell. We use these data to calibrate the recently developed generalization of the Sloan Extension for Galactic Exploration and Understanding and Exploration (SEGUE) Stellar Parameter Pipeline, and obtain estimates of the atmospheric parameters (T {sub eff}, log g, and [Fe/H]) for these non-Sloan Digital Sky Survey/SEGUE data; we also obtain estimates of [C/Fe]. The new abundance measurements are shown to be consistent with available high-resolution spectroscopic determinations, and represent a substantial improvement over the accuracies obtained from the previous photometric estimates reported in Paper I of this series. The apparent offset in the photometric abundances of the giants in this sample noted by several authors is confirmed by our new spectroscopy; no such effect is found for the dwarfs. The presence of a metal-weak thick-disk (MWTD) population is clearly supported by these new abundance data. Some 25% of the stars with metallicities –1.8 < [Fe/H] ?–0.8 exhibit orbital eccentricities e < 0.4, yet are clearly separated from members of the inner-halo population with similar metallicities by their location in a Lindblad energy versus angular momentum diagram. A comparison is made with recent results for a similar-size sample of Radial Velocity Experiment stars from Ruchti et al. We conclude, based on both of these samples, that the MWTD is real, and must be accounted for in discussions of the formation and evolution of the disk system of the Milky Way.

  3. Calculation of positron binding energies using the generalized any particle propagator theory

    SciTech Connect (OSTI)

    Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Márcio T. do N.; Reyes, Andrés

    2014-09-21

    We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ?0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.

  4. Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B)

    SciTech Connect (OSTI)

    Lerch, Thomas F.; Chapman, Michael S.

    2012-02-05

    Adeno-associated virus is a promising vector for gene therapy. In the current study, the binding site on AAV serotype 3B for the heparan sulfate proteoglycan (HSPG) receptor has been characterized. X-ray diffraction identified a disaccharide binding site at the most positively charged region on the virus surface. The contributions of basic amino acids at this and other sites were characterized using site-directed mutagenesis. Both heparin and cell binding are correlated to positive charge at the disaccharide binding site, and transduction is significantly decreased in AAV-3B vectors mutated at this site to reduce heparin binding. While the receptor attachment sites of AAV-3B and AAV-2 are both in the general vicinity of the viral spikes, the exact amino acids that participate in electrostatic interactions are distinct. Diversity in the mechanisms of cell attachment by AAV serotypes will be an important consideration for the rational design of improved gene therapy vectors.

  5. Identification of the heparin binding site on adeno-associated virus serotype 3B (AAV-3B)

    SciTech Connect (OSTI)

    Lerch, Thomas F.; Chapman, Michael S.

    2012-05-24

    Adeno-associated virus is a promising vector for gene therapy. In the current study, the binding site on AAV serotype 3B for the heparan sulfate proteoglycan (HSPG) receptor has been characterized. X-ray diffraction identified a disaccharide binding site at the most positively charged region on the virus surface. The contributions of basic amino acids at this and other sites were characterized using site-directed mutagenesis. Both heparin and cell binding are correlated to positive charge at the disaccharide binding site, and transduction is significantly decreased in AAV-3B vectors mutated at this site to reduce heparin binding. While the receptor attachment sites of AAV-3B and AAV-2 are both in the general vicinity of the viral spikes, the exact amino acids that participate in electrostatic interactions are distinct. Diversity in the mechanisms of cell attachment by AAV serotypes will be an important consideration for the rational design of improved gene therapy vectors.

  6. Elementary Particles and Weak Interactions

    DOE R&D Accomplishments [OSTI]

    Lee, T. D.; Yang, C. N.

    1957-01-01

    Some general patterns of interactions between various elementary particles are reviewed and some general questions concerning the symmetry properties of these particles are studied. Topics are included on the theta-tau puzzle, experimental limits on the validity of parity conservation, some general discussions on the consequences due to possible non-invariance under P, C, and T, various possible experimental tests on invariance under P, C, and T, a two-component theory of the neutrino, a possible law of conservation of leptons and the universal Fermi interactions, and time reversal invariance and Mach's principle. (M.H.R.)

  7. Conservation Laws in Weak Interactions

    DOE R&D Accomplishments [OSTI]

    Lee, T. D.

    1957-03-01

    Notes are presented on four lectures given at Harvard University in March 1957 on elementary particle physics, the theta-tau problem, validity of parity conservation, tests for invariance under P, C, and T, and the two-component theory of the neutrino. (W.D.M.)

  8. High-Affinity and Cooperative Binding of Oxidized Calmodulin by Methionine Sulfoxide Reductase

    SciTech Connect (OSTI)

    Xiong, Yijia; Chen, Baowei; Smallwood, Heather S.; Urbauer, Ramona J.; Markillie, Lye Meng; Galeva, Nadezhda A.; Williams, Todd D.; Squier, Thomas C.

    2006-12-12

    Methionines play an important role in modulating protein-protein interactions associated with intracellular signaling, and their reversible oxidation to form methionine sulfoxides [Met(O)] in calmodulin (CaM) and other signaling proteins has been suggested to couple cellular redox changes to protein function changes through the action of methionine sulfoxide reductases (Msr). Prior measurements indicate the full recovery of target protein activation upon the stereospecific reduction of oxidized CaM by MsrA, where the formation of the S-stereoisomer of Met(O) selectively inhibits the CaM-dependent activation of the Ca-ATPase. However, the physiological substrates of MsrA remain unclear, as neither the binding specificities nor affinities of protein targets have been measured. To assess the specificity of binding and its possible importance in the maintenance of CaM function, we have measured the kinetics of repair and the binding affinity between oxidized CaM and MsrA. Reduction of Met(O) in fully oxidized CaM by MsrA is sensitive to protein folding, as repair of the intact protein is incomplete, with > 6 Met(O) remaining in each CaM following MsrA reduction. In contrast, following proteolytic digestion, MsrA is able to fully reduce one-half of the oxidized methionines, indicating that Met(O) within folded proteins are not substrates for MsrA repair. Further, in comparison to free Met(O), the turnover number and Km for oxidized CaM (CaMox) are substantially smaller, indicating that the binding interaction retards Msr recycling to reduce steady-state enzyme activity. Mutation of the active site (i.e., C72S) in MsrA permitted equilibrium-binding measurements using both ensemble and single-molecule measurements obtained by fluorescence correlation spectroscopy (FCS). Multiple MsrA bind tightly to CaMox (Kd = 70 +- 10 nM) with an affinity that is three orders of magnitude greater than the Michaelis constant (KM = 71 +- 8 micromolar). These results indicate that MsrA selectively reduces surface-exposed Met(O) within unstructured sequences and suggest that only a small subset of oxidized proteins are substrates for MsrA, which may selectively modulate the function of key signaling proteins as part of an adaptive response to oxidative stress.

  9. Structural determinants of nuclear export signal orientation in binding to exportin CRM1

    SciTech Connect (OSTI)

    Fung, Ho Yee Joyce; Fu, Szu -Chin; Brautigam, Chad A.; Chook, Yuh Min

    2015-09-08

    The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). A comparison of minus and plus NESs identified structural and sequence determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.

  10. Structural determinants of nuclear export signal orientation in binding to exportin CRM1

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Fung, Ho Yee Joyce; Fu, Szu -Chin; Brautigam, Chad A.; Chook, Yuh Min

    2015-09-08

    The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). A comparison of minus and plus NESs identified structural and sequencemore » determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.« less

  11. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

  12. Quenching methods for background reduction in luminescence-based probe-target binding assays

    DOE Patents [OSTI]

    Cai, Hong (Los Alamos, NM); Goodwin, Peter M (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Nolan, Rhiannon L. (Santa Fe, NM)

    2007-04-10

    Background luminescence is reduced from a solution containing unbound luminescent probes, each having a first molecule that attaches to a target molecule and having an attached luminescent moiety, and luminescent probe/target adducts. Quenching capture reagent molecules are formed that are capable of forming an adduct with the unbound luminescent probes and having an attached quencher material effective to quench luminescence of the luminescent moiety. The quencher material of the capture reagent molecules is added to a solution of the luminescent probe/target adducts and binds in a proximity to the luminescent moiety of the unbound luminescent probes to quench luminescence from the luminescent moiety when the luminescent moiety is exposed to exciting illumination. The quencher capture reagent does not bind to probe molecules that are bound to target molecules and the probe/target adduct emission is not quenched.

  13. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; et al

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobicmore » environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.« less

  14. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

    SciTech Connect (OSTI)

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology.

  15. Nucleic acids encoding phloem small RNA-binding proteins and transgenic plants comprising them

    DOE Patents [OSTI]

    Lucas, William J.; Yoo, Byung-Chun; Lough, Tony J.; Varkonyi-Gasic, Erika

    2007-03-13

    The present invention provides a polynucleotide sequence encoding a component of the protein machinery involved in small RNA trafficking, Cucurbita maxima phloem small RNA-binding protein (CmPSRB 1), and the corresponding polypeptide sequence. The invention also provides genetic constructs and transgenic plants comprising the polynucleotide sequence encoding a phloem small RNA-binding protein to alter (e.g., prevent, reduce or elevate) non-cell autonomous signaling events in the plants involving small RNA metabolism. These signaling events are involved in a broad spectrum of plant physiological and biochemical processes, including, for example, systemic resistance to pathogens, responses to environmental stresses, e.g., heat, drought, salinity, and systemic gene silencing (e.g., viral infections).

  16. Ritonavir binds to and downregulates estrogen receptors: Molecular mechanism of promoting early atherosclerosis

    SciTech Connect (OSTI)

    Xiang, Jin; Wang, Ying; Su, Ke; Liu, Min; Hu, Peng-Chao; Ma, Tian; Li, Jia-Xi; Wei, Lei; Zheng, Zhongliang; Yang, Fang

    2014-10-01

    Estrogenic actions are closely related to cardiovascular disease. Ritonavir (RTV), a human immunodeficiency virus (HIV) protease inhibitor, induces atherosclerosis in an estrogen-related manner. However, how RTV induce pathological phenotypes through estrogen pathway remains unclear. In this study, we found that RTV increases thickness of coronary artery walls of Sprague Dawley rats and plasma free fatty acids (FFA) levels. In addition, RTV could induce foam cell formation, downregulate both estrogen receptor ? (ER?) and ER? expression, upregulate G protein-coupled estrogen receptor (GPER) expression, and all of them could be partially blocked by 17?-estradiol (E2), suggesting RTV acts as an antagonist for E2. Computational modeling shows a similar interaction with ER? between RTV and 2-aryl indoles, which are highly subtype-selective ligands for ER?. We also found that RTV directly bound to ER? and selectively inhibited the nuclear localization of ER?, and residue Leu536 in the hydrophobic core of ligand binding domain (LBD) was essential for the interaction with RTV. In addition, RTV did not change the secondary structure of ER?-LBD like E2, which explained how ER? lost the capacity of nuclear translocation under the treatment of RTV. All of the evidences suggest that ritonavir acts as an antagonist for 17?-estradiol in regulating ? subtype estrogen receptor function and early events of atherosclerosis. - Graphical abstract: RTV directly binds to ER? and Leu536 in the hydrophobic core of ligand binding domain is essential for the interaction. - Highlights: • RTV increases the thickness of rat coronary artery wall and foam cell formation. • RTV downregulates the expression of ER? and ER?. • RTV inhibits ER? promoter activity. • RTV directly binds to ER? and the key amino acid is Leu536. • RTV inhibits the nuclear translocation of ER? and GPER.

  17. Reversible CO-binding to the Active Site of Nitrogenase | Stanford

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Synchrotron Radiation Lightsource Reversible CO-binding to the Active Site of Nitrogenase Tuesday, March 31, 2015 All living organisms depend on the availability of nitrogen for incorporation into the basic biological building blocks such as amino acids and DNA. Globally the largest reservoir for nitrogen is the atmosphere, with an N2 content of roughly 78%. However, as a highly unreactive gas, most organisms are unable to directly utilize dinitrogen due to the severe energy barrier required

  18. Model for Eukaryotic Tail-anchored Protein Binding Based on the Structure

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of Get3 Model for Eukaryotic Tail-anchored Protein Binding Based on the Structure of Get3 Targeting of newly synthesized membrane proteins to the endoplasmic reticulum (ER) is an important cellular process. Most membrane proteins are recognized and targeted co-translationally by the signal recognition particle (SRP). A number of membrane proteins (eg. SNAREs, apoptosis factors, and protein translocation components) are 'tail-anchored' by a single carboxy-terminal transmembrane domain. Due to

  19. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; et al

    2015-01-09

    The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes withmore » different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.« less

  20. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Prigozhin, Daniil M.; Krieger, Inna V.; Huizar, John P.; Mavrici, Daniela; Waldo, Geoffrey S.; Hung, Li -Wei; Sacchettini, James C.; Terwilliger, Thomas C.; Alber, Tom; Mayer, Claudine

    2014-12-31

    Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows thatmore » Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.« less

  1. Identification of FAM96B as a novel prelamin A binding partner

    SciTech Connect (OSTI)

    Xiong, Xing-Dong; Wang, Junwen; Zheng, Huiling; Jing, Xia; Liu, Zhenjie; Institute of Biochemistry and Molecular Biology, Guangdong Medical College, Zhanjiang 524023; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808 ; Zhou, Zhongjun; Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong ; Liu, Xinguang; Institute of Biochemistry and Molecular Biology, Guangdong Medical College, Zhanjiang 524023; Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan 523808

    2013-10-11

    Highlights: •We screen the binding protein of prelamin A by yeast two-hybrid screen. •FAM96B colocalizes with prelamin A in HEK-293 cells. •FAM96B physically interacts with prelamin A. -- Abstract: Prelamin A accumulation causes nuclear abnormalities, impairs nuclear functions, and eventually promotes cellular senescence. However, the underlying mechanism of how prelamin A promotes cellular senescence is still poorly understood. Here we carried out a yeast two-hybrid screen using a human skeletal muscle cDNA library to search for prelamin A binding partners, and identified FAM96B as a prelamin A binding partner. The interaction of FAM96B with prelamin A was confirmed by GST pull-down and co-immunoprecipitation experiments. Furthermore, co-localization experiments by fluorescent confocal microscopy revealed that FAM96B colocalized with prelamin A in HEK-293 cells. Taken together, our data demonstrated the physical interaction between FAM96B and prelamin A, which may provide some clues to the mechanisms of prelamin A in premature aging.

  2. Protein arginine deiminase 2 binds calcium in an ordered fashion: Implications for inhibitor design

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Slade, Daniel J.; Fang, Pengfei; Dreyton, Christina J.; Zhang, Ying; Fuhrmann, Jakob; Rempel, Don; Bax, Benjamin D.; Coonrod, Scott A.; Lewis, Huw D.; Guo, Min; et al

    2015-01-26

    Protein arginine deiminases (PADs) are calcium-dependent histone-modifying enzymes whose activity is dysregulated in inflammatory diseases and cancer. PAD2 functions as an Estrogen Receptor (ER) coactivator in breast cancer cells via the citrullination of histone tail arginine residues at ER binding sites. Although an attractive therapeutic target, the mechanisms that regulate PAD2 activity are largely unknown, especially the detailed role of how calcium facilitates enzyme activation. To gain insights into these regulatory processes, we determined the first structures of PAD2 (27 in total), and through calcium-titrations by X-ray crystallography, determined the order of binding and affinity for the six calcium ionsmore » that bind and activate this enzyme. These structures also identified several PAD2 regulatory elements, including a calcium switch that controls proper positioning of the catalytic cysteine residue, and a novel active site shielding mechanism. Additional biochemical and mass-spectrometry-based hydrogen/deuterium exchange studies support these structural findings. The identification of multiple intermediate calcium-bound structures along the PAD2 activation pathway provides critical insights that will aid the development of allosteric inhibitors targeting the PADs.« less

  3. A Novel, ;Double-Clamp; Binding Mode for Human Heme Oxygenase-1 Inhibition

    SciTech Connect (OSTI)

    Rahman, Mona N.; Vlahakis, Jason Z.; Vukomanovic, Dragic; Lee, Wallace; Szarek, Walter A.; Nakatsu, Kanji; Jia, Zongchao

    2012-08-01

    The development of heme oxygenase (HO) inhibitors is critical in dissecting and understanding the HO system and for potential therapeutic applications. We have established a program to design and optimize HO inhibitors using structure-activity relationships in conjunction with X-ray crystallographic analyses. One of our previous complex crystal structures revealed a putative secondary hydrophobic binding pocket which could be exploited for a new design strategy by introducing a functional group that would fit into this potential site. To test this hypothesis and gain further insights into the structural basis of inhibitor binding, we have synthesized and characterized 1-(1H-imidazol-1-yl)-4,4-diphenyl-2-butanone (QC-308). Using a carbon monoxide (CO) formation assay on rat spleen microsomes, the compound was found to be {approx}15 times more potent (IC{sub 50} = 0.27{+-}0.07 {mu}M) than its monophenyl analogue, which is already a potent compound in its own right (QC-65; IC{sub 50} = 4.0{+-}1.8 {mu}M). The crystal structure of hHO-1 with QC-308 revealed that the second phenyl group in the western region of the compound is indeed accommodated by a definitive secondary proximal hydrophobic pocket. Thus, the two phenyl moieties are each stabilized by distinct hydrophobic pockets. This 'double-clamp' binding offers additional inhibitor stabilization and provides a new route for improvement of human heme oxygenase inhibitors.

  4. Structural and Energetic Analysis of Activiation by a Cyclic Nucleotide Binding Domain

    SciTech Connect (OSTI)

    Altieri,S.; Clayton, G.; Silverman, W.; Olivares, A.; De La Cruz, E.; Thomas, L.; Morais-Cabral, J.

    2008-01-01

    MlotiK1 is a prokaryotic homolog of cyclic-nucleotide-dependent ion channels that contains an intracellular C-terminal cyclic nucleotide binding (CNB) domain. X-ray structures of the CNB domain have been solved in the absence of ligand and bound to cAMP. Both the full-length channel and CNB domain fragment are easily expressed and purified, making MlotiK1 a useful model system for dissecting activation by ligand binding. We have used X-ray crystallography to determine three new MlotiK1 CNB domain structures: a second apo configuration, a cGMP-bound structure, and a second cAMP-bound structure. In combination, the five MlotiK1 CNB domain structures provide a unique opportunity for analyzing, within a single protein, the structural differences between the apo state and the bound state, and the structural variability within each state. With this analysis as a guide, we have probed the nucleotide selectivity and importance of specific residue side chains in ligand binding and channel activation. These data help to identify ligand-protein interactions that are important for ligand dependence in MlotiK1 and, more globally, in the class of nucleotide-dependent proteins.

  5. Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition

    SciTech Connect (OSTI)

    Sigalov, Alexander B., E-mail: Alexander.sigalov@umassmed.edu [University of Massachusetts Medical School, Worcester, MA 01655 (United States); Hendricks, Gregory M. [University of Massachusetts Medical School, Worcester, MA 01655 (United States)] [University of Massachusetts Medical School, Worcester, MA 01655 (United States)

    2009-11-13

    Intrinsically disordered cytoplasmic domains of T cell receptor (TCR) signaling subunits including {zeta}{sub cyt} and CD3{epsilon}{sub cyt} all contain one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor triggering. Membrane binding-induced helical folding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} ITAMs is thought to control TCR activation. However, the question whether or not lipid binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} is necessarily accompanied by a folding transition of ITAMs remains open. In this study, we investigate whether the membrane binding mechanisms of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depend on the membrane model used. Circular dichroic and fluorescence data indicate that binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} to detergent micelles and unstable vesicles is accompanied by a disorder-to-order transition, whereas upon binding to stable vesicles these proteins remain unfolded. Using electron microscopy and dynamic light scattering, we show that upon protein binding, unstable vesicles fuse and rupture. In contrast, stable vesicles remain intact under these conditions. This suggests different membrane binding modes for {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depending on the bilayer stability: (1) coupled binding and folding, and (2) binding without folding. These findings explain the long-standing puzzle in the literature and highlight the importance of the choice of an appropriate membrane model for protein-lipid interactions studies.

  6. Evidence for a particle produced in association with weak bosons and decaying to a bottom-antibottom quark pair in Higgs boson searches at the Tevatron

    SciTech Connect (OSTI)

    Aaltonen, T.; Abazov, V.M.; Abbott, B.; Acharya, B.S.; Adams, M.; Adams, T.; Alexeev, G.D.; Alkhazov, G.; Alton, A.; Alvarez Gonzalez, B.; Alverson, G.; /Northeastern U. /INFN, Padua

    2012-07-01

    We combine searches by the CDF and D0 Collaborations for the associated production of a Higgs boson with a W or Z boson and subsequent decay of the Higgs boson to a bottom-antibottom quark pair. The data, originating from Fermilab Tevatron p{bar p} collisions at {radical}s=1.96 TeV, correspond to integrated luminosities of up to 9.7 fb{sup -1}. The searches are conducted for a Higgs boson with mass in the range 100-150 GeV/c{sup 2}. We observe an excess of events in the data compared with the background predictions, which is most significant in the mass range between 120 and 135 GeV/c{sup 2}. The largest local significance is 3.3 standard deviations, corresponding to a global significance of 3.1 standard deviations. We interpret this as evidence for the presence of a new particle consistent with the standard model Higgs boson, which is produced in association with a weak vector boson and decays to a bottom-antibottom quark pair.

  7. Study of dust particle charging in weakly ionized inert gases taking into account the nonlocality of the electron energy distribution function

    SciTech Connect (OSTI)

    Filippov, A. V. Dyatko, N. A.; Kostenko, A. S.

    2014-11-15

    The charging of dust particles in weakly ionized inert gases at atmospheric pressure has been investigated. The conditions under which the gas is ionized by an external source, a beam of fast electrons, are considered. The electron energy distribution function in argon, krypton, and xenon has been calculated for three rates of gas ionization by fast electrons: 10{sup 13}, 10{sup 14}, and 10{sup 15} cm{sup ?1}. A model of dust particle charging with allowance for the nonlocal formation of the electron energy distribution function in the region of strong plasma quasi-neutrality violation around the dust particle is described. The nonlocality is taken into account in an approximation where the distribution function is a function of only the total electron energy. Comparative calculations of the dust particle charge with and without allowance for the nonlocality of the electron energy distribution function have been performed. Allowance for the nonlocality is shown to lead to a noticeable increase in the dust particle charge due to the influence of the group of hot electrons from the tail of the distribution function. It has been established that the screening constant virtually coincides with the smallest screening constant determined according to the asymptotic theory of screening with the electron transport and recombination coefficients in an unperturbed plasma.

  8. Investigation of mechanisms for He-I emission radial profile broadening in a weakly ionized cylindrical helium plasma with recombining edge

    SciTech Connect (OSTI)

    Hollmann, E. M.; Brandt, C.; Hudson, B.; Nishijima, D.; Pigarov, A. Yu.; Kumar, D.

    2013-09-15

    Spatially resolved spectroscopic measurements of He-I line emission are used to study the causes of emission profile broadening radially across the cylinder of a weakly ionized helium plasma. The plasma consists of an ionizing core (r < 2 cm) surrounded by a recombining edge (r > 2 cm) plasma. The brightness profiles of low-n EUV He-I resonance lines are shown to be strongly radially broadened due to opacity. The brightness profiles of high-n visible lines are also found to be strongly radially broadened, but dominantly due to edge recombination. Visible low-n lines are less strongly radially broadened, apparently by a combination of both recombination and EUV opacity. The low-n visible He-I line ratio method with central opacity correction is found to calculate central electron density and temperature well, with poor agreement at the edge, as expected for recombining plasma. In the recombining edge, high-n Boltzmann analysis is found to accurately measure the cold (T{sub e} < 0.2 eV) edge temperature. Near the core, however, high-n Boltzmann analysis can be complicated by electron-impact excitation, giving incorrect (T{sub e}? 0.1 eV) apparent temperatures. Probe measurements were not able to capture the cold edge temperature accurately, probably due to large potential fluctuations, even when using fast triple probe measurements. Fast spectroscopic measurements show that this discrepancy is not explained by recombining plasma alternating with ionizing plasma in the edge region.

  9. Weak ferromagnetism and temperature dependent dielectric properties of Zn{sub 0.9}Ni{sub 0.1}O diluted magnetic semiconductor

    SciTech Connect (OSTI)

    Ahmed, Raju; Moslehuddin, A.S.M.; Mahmood, Zahid Hasan; Hossain, A.K.M. Akther

    2015-03-15

    Highlights: • Single phase wurtzite structure was confirmed from XRD analysis. • Weak ferromagnetic behaviour at room temperature. • Pure semiconducting properties confirmed from temperature dependent conductivity. • Smaller dielectric properties at higher frequency. • Possible potential application in high frequency spintronic devices. - Abstract: In this study the room temperature ferromagnetic behaviour and dielectric properties of ZnO based diluted magnetic semiconductor (DMS) have been investigated using nominal chemical composition Zn{sub 0.9}Ni{sub 0.1}O. The X-ray diffraction analysis confirmed formation of single phase hexagonal wurtzite structure. An increase in grain size with increasing sintering temperature was observed from scanning electron microscopy. Field dependent DC magnetization values indicated dominant paramagnetic ordering along with a slight ferromagnetic behaviour at room temperature. Frequency dependent complex initial permeability showed some positive values around 12 at room temperature. In dielectric measurement, an increasing trend of complex permittivity, loss tangent and ac conductivity with increasing temperature were observed. The temperature dependent dispersion curves of dielectric properties revealed clear relaxation at higher temperature. Frequency dependent ac conductivity was found to increase with frequency whereas complex permittivity and loss tangent showed an opposite trend.

  10. AN INDIRECT SEARCH FOR WEAKLY INTERACTING MASSIVE PARTICLES IN THE SUN USING 3109.6 DAYS OF UPWARD-GOING MUONS IN SUPER-KAMIOKANDE

    SciTech Connect (OSTI)

    Tanaka, T.; Abe, K.; Hayato, Y.; Iida, T.; Kameda, J.; Koshio, Y.; Kouzuma, Y.; Miura, M.; Moriyama, S.; Nakahata, M.; Nakayama, S.; Obayashi, Y.; Sekiya, H.; Shiozawa, M.; Suzuki, Y.; Takeda, A.; Takenaga, Y.; Ueno, K.; Ueshima, K.; Yamada, S.; Collaboration: Super-Kamiokande Collaboration; and others

    2011-12-01

    We present the result of an indirect search for high energy neutrinos from Weakly Interacting Massive Particle (WIMP) annihilation in the Sun using upward-going muon (upmu) events at Super-Kamiokande. Data sets from SKI-SKIII (3109.6 days) were used for the analysis. We looked for an excess of neutrino signal from the Sun as compared with the expected atmospheric neutrino background in three upmu categories: stopping, non-showering, and showering. No significant excess was observed. The 90% C.L. upper limits of upmu flux induced by WIMPs of 100 GeV c{sup -2} were 6.4 Multiplication-Sign 10{sup -15} cm{sup -2} s{sup -1} and 4.0 Multiplication-Sign 10{sup -15} cm{sup -2} s{sup -1} for the soft and hard annihilation channels, respectively. These limits correspond to upper limits of 4.5 Multiplication-Sign 10{sup -39} cm{sup -2} and 2.7 Multiplication-Sign 10{sup -40} cm{sup -2} for spin-dependent WIMP-nucleon scattering cross sections in the soft and hard annihilation channels, respectively.

  11. 6-D weak-strong beam-beam simulation study of proton lifetime in presence of head-on beam-beam compensation in the RHIC

    SciTech Connect (OSTI)

    Luo, Y.; Fischer, W.

    2010-08-01

    In this note we summarize the calculated particle loss of a proton bunch in the presence of head-on beam-beam compensation in the Relativistic Heavy Ion Collider (RHIC). To compensate the head-on beam-beam effect in the RHIC 250 GeV polarized proton run, we are introducing a DC electron beam with the same transverse profile as the proton beam to collide with the proton beam. Such a device is called an electron lens (e-lens). In this note we first present the optics and beam parameters and the tracking setup. Then we calculate and compare the particle loss of a proton bunch with head-on beam-beam compensation, phase advance of k{pi} between IP8 and the center of the e-lens and second order chromaticity correction. We scanned the proton beam's linear chromaticity, working point and bunch intensity. We also scanned the electron beam's intensity, transverse beam size. The effect of the electron-proton transverse offset in the e-lens was studied. In the study 6-D weak-strong beam-beam interaction model a la Hirata is used for proton collisions at IP6 and IP8. The e-lens is modeled as 8 slices. Each slice is modeled with as drift - (4D beam-beam kick) - drift.

  12. Search for neutral color-octet weak-triplet scalar particles in proton-proton collisions at √s = 8 TeV

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Khachatryan, Vardan

    2015-09-29

    A search for pair production of neutral color-octet weak-triplet scalar particles (Θ0) is performed in processes where one Θ0 decays to a pair of b quark jets and the other to a Z boson plus a jet, with the Z boson decaying to a pair of electrons or muons. The search is performed with data collected by the CMS experiment at the CERN LHC corresponding to an integrated luminosity of 19.7 fb–1 of proton-proton collisions at √s = 8 TeV. The number of observed events is found to be in agreement with the standard model predictions. The 95% confidence levelmore » upper limit on the product of the cross section and branching fraction is obtained as a function of the Θ0 mass. The 95% confidence level lower bounds on the Θ0 mass are found to be 623 and 426 GeV, for two different octo-triplet theoretical scenarios. These are the first direct experimental bounds on particles predicted by the octo-triplet model.« less

  13. Search for neutral color-octet weak-triplet scalar particles in proton-proton collisions at √s = 8 TeV

    SciTech Connect (OSTI)

    Khachatryan, Vardan

    2015-09-29

    A search for pair production of neutral color-octet weak-triplet scalar particles (Θ0) is performed in processes where one Θ0 decays to a pair of b quark jets and the other to a Z boson plus a jet, with the Z boson decaying to a pair of electrons or muons. The search is performed with data collected by the CMS experiment at the CERN LHC corresponding to an integrated luminosity of 19.7 fb–1 of proton-proton collisions at √s = 8 TeV. The number of observed events is found to be in agreement with the standard model predictions. The 95% confidence level upper limit on the product of the cross section and branching fraction is obtained as a function of the Θ0 mass. The 95% confidence level lower bounds on the Θ0 mass are found to be 623 and 426 GeV, for two different octo-triplet theoretical scenarios. These are the first direct experimental bounds on particles predicted by the octo-triplet model.

  14. Optical energy storage and reemission based weak localization of light and accompanying random lasing action in disordered Nd{sup 3+} doped (Pb, La)(Zr, Ti)O{sub 3} ceramics

    SciTech Connect (OSTI)

    Xu, Long; Zhao, Hua; Xu, Caixia; Zhang, Siqi; Zhang, Jingwen

    2014-08-14

    Multi-mode random lasing action and weak localization of light were evidenced and studied in normally transparent but disordered Nd{sup 3+} doped (Pb,La)(Zr,Ti)O{sub 3} ceramics. Noticeable localized zone and multi-photon process were observed under strong pumping power. A tentative phenomenological physical picture was proposed by taking account of diffusive process, photo-induced scattering, and optical energy storage process as dominant factors in elucidating the weak localization of light observed. Both the decreased transmittance (increased reflectivity) of light and the observed long lasting fading-off phenomenon supported the physical picture proposed by us.

  15. Kinetic and Crystallgraphic Studies of a Redesigned Manganese-Binding Site in Cytochrome c Peroxidase

    SciTech Connect (OSTI)

    Pfister,T.; Mirarefi, A.; Gengenbach, A.; Zhao, X.; Danstrom , C.; Conatser, N.; Gao, Y.; Robinson, H.; Zukoski, C.; et al.

    2007-01-01

    Manganese peroxidase (MnP) from the white rot fungus Phanerochaete chrysosporium contains a manganese-binding site that plays a critical role in its function. Previously, a Mn{sup II}-binding site was designed into cytochrome c peroxidase (CcP) based on sequence homology (Yeung et al. in Chem. Biol. 4:215-222, 1997; Gengenbach et al. in Biochemistry 38:11425-11432, 1999). Here, we report a redesign of this site based on X-ray structural comparison of MnP and CcP. The variant, CcP(D37E, V45E, H181E), displays 2.5-fold higher catalytic efficiency (k{sub cat}/k{sub M}) than the variant in the original design, mostly due to a stronger k{sub M} of 1.9 mM (vs. 4.1 mM). High-resolution X-ray crystal structures of a metal-free form and a form with Co{sup II} at the designed Mn{sup II} site were also obtained. The metal ion in the engineered metal-binding site overlays well with Mn{sup II} bound in MnP, suggesting that this variant is the closest structural model of the Mn{sup II}-binding site in MnP for which a crystal structure exists. A major difference arises in the distances of the ligands to the metal; the metal-ligand interactions in the CcP variant are much weaker than the corresponding interactions in MnP, probably owing to partial occupancy of metal ion at the designed site, difference in the identity of metal ions (Co{sup II} rather than Mn{sup II}) and other interactions in the second coordination sphere. These results indicate that the metal ion, the ligands, and the environment around the metal-binding site play important roles in tuning the structure and function of metalloenzymes.

  16. Influence of a Weak Field of Pulsed DC Electricity on the Behavior and Incidence of Injury in Adult Steelhead and Pacific Lamprey, Final Report.

    SciTech Connect (OSTI)

    Mesa, Matthew

    2009-02-13

    Predation by pinnipeds, such as California sea lions Zalophus californianus, Pacific harbor seals Phoca vitulina, and Stellar sea lions Eumetopias jubatus on adult Pacific salmon Oncorhynchus spp in the lower Columbia River has become a serious concern for fishery managers trying to conserve and restore runs of threatened and endangered fish. As a result, Smith-Root, Incorporated (SRI; Vancouver, Washington), manufacturers of electrofishing and closely-related equipment, proposed a project to evaluate the potential of an electrical barrier to deter marine mammals and reduce the amount of predation on adult salmonids (SRI 2007). The objectives of their work were to develop, deploy, and evaluate a passive, integrated sonar and electric barrier that would selectively inhibit the upstream movements of marine mammals and reduce predation, but would not injure pinnipeds or impact anadromous fish migrations. However, before such a device could be deployed in the field, concerns by regional fishery managers about the potential effects of such a device on the migratory behavior of Pacific salmon, steelhead O. mykiss, Pacific lampreys Entoshpenus tridentata, and white sturgeon Acipenser transmontanus, needed to be addressed. In this report, we describe the results of laboratory research designed to evaluate the effects of prototype electric barriers on adult steelhead and Pacific lampreys. The effects of electricity on fish have been widely studied and include injury or death (e.g., Sharber and Carothers 1988; Dwyer et al. 2001; Snyder 2003), physiological dysfunction (e.g., Schreck et al. 1976; Mesa and Schreck 1989), and altered behavior (Mesa and Schreck 1989). Much of this work was done to investigate the effects of electrofishing on fish in the wild. Because electrofishing operations would always use more severe electrical settings than those proposed for the pinniped barrier, results from these studies are probably not relevant to the work proposed by SRI. Field electrofishing operations typically use high voltage and amperage settings and a variety of waveforms, pulse widths (PW), and pulse frequencies (PF), depending on conditions and target species. For example, when backpack electrofishing for trout in a small stream, one might use settings such as 500 V pulsed DC, a PW of 1 ms, and a PF of 60 Hz. In contrast, the electrical barrier proposed by SRI will produce electrical conditions significantly lower than those used in electrofishing, particularly for PW and PF (e.g., PW ranging from 300-1,000 {micro}s and PF from 2-3 Hz). Further, voltage gradients (in V/cm) are predicted to be lower in the electric barrier than those produced during typical electrofishing. Although the relatively weak, pulsed DC electric fields to be produced by the barrier may be effective at deterring pinnipeds, little, if anything, is known about the effects of such low intensity electrical fields on fish behavior. For this research, we evaluated the effects of weak, pulsed DC electric currents on the behavior of adult steelhead and Pacific lamprey and the incidence of injury in steelhead only. In a series of laboratory experiments, we: (1) documented the rate of passage of fish over miniature, prototype electric barriers when they were on and off; (2) determined some electric thresholds beyond which fish would not pass over the barrier; and (3) assessed the incidence and severity of injury in steelhead exposed to relatively severe electrical conditions. The results of this study should be useful for making decisions about whether to install electrical barriers in the lower Columbia River, or elsewhere, to reduce predation on upstream migrating salmonids and other fishes by marine pinnipeds.

  17. Particle trap to sheath non-binding contact for a gas-insulated transmission line having a corrugated outer conductor

    DOE Patents [OSTI]

    Fischer, William H. (Pittsburgh, PA)

    1984-04-24

    A non-binding particle trap to outer sheath contact for use in gas insulated transmission lines having a corrugated outer conductor. The non-binding feature of the contact according to the teachings of the invention is accomplished by having a lever arm rotatably attached to a particle trap by a pivot support axis disposed parallel to the direction of travel of the inner conductor/insulator/particle trap assembly.

  18. More light on the 2?{sub 5} Raman overtone of SF{sub 6}: Can a weak anisotropic spectrum be due to a strong transition anisotropy?

    SciTech Connect (OSTI)

    Kremer, D.; Rachet, F.; Chrysos, M.

    2014-01-21

    Long known as a fully polarized band with a near vanishing depolarization ratio [?{sub s} = 0.05, W. Holzer and R. Ouillon, Chem. Phys. Lett. 24, 589 (1974)], the 2?{sub 5} Raman overtone of SF{sub 6} has so far been considered as of having a prohibitively weak anisotropic spectrum [D. P. Shelton and L. Ulivi, J. Chem. Phys. 89, 149 (1988)]. Here, we report the first anisotropic spectrum of this overtone, at room temperature and for 13 gas densities ranging between 2 and 27 amagat. This spectrum is 10 times broader and 50 times weaker than the isotropic counterpart of the overtone [D. Kremer, F. Rachet, and M. Chrysos, J. Chem. Phys. 138, 174308 (2013)] and its profile much more sensitive to pressure effects than the profile of the isotropic spectrum. From our measurements an accurate value for the anisotropy matrix-element |?000020|??|000000?| was derived and this value was found to be comparable to that of the mean-polarizability ((000020), ?{sup ¯} (000000)). Among other conclusions our study offers compelling evidence that, in Raman spectroscopy, highly polarized bands or tiny depolarization ratios are not necessarily incompatible with large polarizability anisotropy transition matrix-elements. Our findings and the way to analyze them suggest that new strategies should be developed on the basis of the complementarity inherent in independent incoherent Raman experiments that run with two different incident-beam polarizations, and on concerted efforts to ab initio calculate accurate data for first and second polarizability derivatives. Values for these derivatives are still rarities in the literature of SF{sub 6}.

  19. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

    SciTech Connect (OSTI)

    Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; Joachimiak, Andrzej

    2015-01-09

    The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.

  20. Fluorinated Calixpyrroles: Anion-Binding Extractants that Reduce the Hofmeister Bias

    SciTech Connect (OSTI)

    Levitskaia, Tatiana G.; Marquez, Manuel; Sessler, Jonathan L.; Shriver, James A.; Vercouter, Thomas; Moyer, Bruce A.

    2003-04-30

    b-Fluorinated calix[4]pyrrole 1 and calix[5]pyrrole 2, strong, neutral anion-binding agents, were found to transport small anions effectively while overcoming the classical solvation-based Hofmeister anion bias selectivity. These two receptors showed an ability to extract smaller anions (bromide and chloride for 1 and nitrate and fluoride for 2) as effectively as iodide anion into nitrobenzene (NB). The present results also represent a rare example of liquid-liquid extraction of inorganic salts effected using an anion receptor in the absence of a cation co-extractant.

  1. Determination of the Exciton Binding Energy in CdSe Quantum Dots

    SciTech Connect (OSTI)

    Meulenberg, R; Lee, J; Wolcott, A; Zhang, J; Terminello, L; van Buuren, T

    2009-10-27

    The exciton binding energy (EBE) in CdSe quantum dots (QDs) has been determined using x-ray spectroscopy. Using x-ray absorption and photoemission spectroscopy, the conduction band (CB) and valence band (VB) edge shifts as a function of particle size have been determined and combined to obtain the true band gap of the QDs (i.e. without and exciton). These values can be compared to the excitonic gap obtained using optical spectroscopy to determine the EBE. The experimental EBE results are compared with theoretical calculations on the EBE and show excellent agreement.

  2. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Loots, Gabriela G. [LLNL; Ovcharenko, I. [LLNL

    Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. This database of evolutionary conserved regions (ECRs) in vertebrate genomes features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and fugu genomes. (taken from paper in Journal: Bioinformatics, November 7, 2006, pp. 122-124

  3. Binding Energies and Melting Temperatures of Heavy Hadrons in Quark-Gluon Plasma

    SciTech Connect (OSTI)

    Narodetskii, I. M.; Simonov, Yu. A.; Veselov, A. I.

    2011-05-23

    We discuss the consequences of the suggestion that the non-perturbative quark-antiquark potential at T{>=}T{sub c}, where T{sub c} is a temperature of a deconfinement phase transition in QCD can be studied through the modification of the correlation functions, which define the quadratic field correlators of the nonperturbative vaccuum fields. We use the non-perturbative quark-antiquark potential derived within the Field Correlator Method and the screened Coulomb potential with T-dependent Debye mass to calculate J/{psi}, {Upsilon} and {Omega}{sub bbb} binding energies and melting temperatures in the deconfined phase of QCD.

  4. Reversible CO Binding Enables Tunable CO/H2 and CO/N2 Separations in

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Metal-Organic Frameworks with Exposed Divalent Metal Cations | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Reversible CO Binding Enables Tunable CO/H2 and CO/N2 Separations in Metal-Organic Frameworks with Exposed Divalent Metal Cations Previous Next List Eric D. Bloch, Matthew R. Hudson, Jarad A. Mason, Sachin Chavan, Valentina Crocellà, Joshua D. Howe, Kyuho Lee, Allison L. Dzubak, Wendy L. Queen, Joseph M. Zadrozny, Stephen J. Geier, Li-Chiang Lin,

  5. Strong and Reversible Binding of Carbon Dioxide in a Green Metal-Organic

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Framework | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Strong and Reversible Binding of Carbon Dioxide in a Green Metal-Organic Framework Previous Next List Jeremiah J. Gassensmith, Hiroyasu Furukawa, Ronald A. Smaldone, Ross S. Forgan, Youssry Y. Botros, Omar M. Yaghi, and J. Fraser Stoddart, J. Am. Chem. Soc., 2011, 133 (39), pp 15312-15315 DOI: 10.1021/ja206525x Abstract Image Abstract: The efficient capture and storage of gaseous CO2 is a pressing

  6. Nuclear binding energy and symmetry energy of nuclear matter with modern nucleon-nucleon potentials

    SciTech Connect (OSTI)

    Hassaneen, Kh.S.A.; Abo-Elsebaa, H.M.; Sultan, E.A.; Mansour, H.M.M.

    2011-03-15

    Research Highlights: > The nuclear matter is studied within the Brueckner-Hartree-Fock (BHF) approach employing the most recent accurate nucleon-nucleon potentials. > The results come out by approximating the single particle self-consistent potential with a parabolic form. > We discuss the current status of the Coester line, i.e., density and energy of the various saturation points being strongly linearly correlated. > The nuclear symmetry energy is calculated as the difference between the binding energy of pure neutron matter and that of symmetric nuclear matter. - Abstract: The binding energy of nuclear matter at zero temperature in the Brueckner-Hartree-Fock approximation with modern nucleon-nucleon potentials is studied. Both the standard and continuous choices of single particle energies are used. These modern nucleon-nucleon potentials fit the deuteron properties and are phase shifts equivalent. Comparison with other calculations is made. In addition we present results for the symmetry energy obtained with different potentials, which is of great importance in astrophysical calculation.

  7. Structural Insights into the Cooperative Binding of SeqA to a Tandem GATC Repeat

    SciTech Connect (OSTI)

    Chung, Y.; Brendler, T; Austin, S; Guarne, A

    2009-01-01

    SeqA is a negative regulator of DNA replication in Escherichia coli and related bacteria that functions by sequestering the origin of replication and facilitating its resetting after every initiation event. Inactivation of the seqA gene leads to unsynchronized rounds of replication, abnormal localization of nucleoids and increased negative superhelicity. Excess SeqA also disrupts replication synchrony and affects cell division. SeqA exerts its functions by binding clusters of transiently hemimethylated GATC sequences generated during replication. However, the molecular mechanisms that trigger formation and disassembly of such complex are unclear. We present here the crystal structure of a dimeric mutant of SeqA [SeqA{Delta}(41-59)-A25R] bound to tandem hemimethylated GATC sites. The structure delineates how SeqA forms a high-affinity complex with DNA and it suggests why SeqA only recognizes GATC sites at certain spacings. The SeqA-DNA complex also unveils additional protein-protein interaction surfaces that mediate the formation of higher ordered complexes upon binding to newly replicated DNA. Based on this data, we propose a model describing how SeqA interacts with newly replicated DNA within the origin of replication and at the replication forks.

  8. Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Qiu, Wei; Lam, Robert; Voytyuk, Oleksandr; Romanov, Vladimir; Gordon, Roni; Gebremeskel, Simon; Vodsedalek, Jakub; Thompson, Christine; Beletskaya, Irina; Battaile, Kevin P.; et al

    2014-07-31

    The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated β-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members. Here, themore » high-resolution crystal structures of the human TNKS2 PARP domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials. These structures provide insight into the inhibitor-binding modes for the tankyrase PARP domain and valuable information to guide the rational design of future tankyrase-specific inhibitors.« less

  9. Tight binding prediction of the {alpha}-Gd{sub 2}S{sub 3} magnetic structure

    SciTech Connect (OSTI)

    Roy, Lindsay E.; Hughbanks, Timothy

    2007-03-15

    Spin-dependent extended Hueckel tight binding (EHTB) calculations were carried out for the magnetic solid Gd{sub 2}S{sub 3} by considering 20 different variations in the ordering of the 4f {sup 7} moments. The tight-binding calculations are used to interpolate the band structure of a nonmagnetic congener (Y{sub 2}S{sub 3}) and the 4f/5d,6s exchange interactions are introduced as perturbations via the introduction of spin-dependent H{sub dd} and H{sub ss} parameters. The calculations predict that Gd{sub 2}S{sub 3} adopts an antiferromagnetic ordering of the 4f {sup 7} moments that is consistent with published neutron diffraction results. Our attempt to account for the calculated energies of the spin patterns using an Ising model was unsuccessful. - Graphical abstract: The spin-dependent EHTB method correctly predicts the magnetic structure of {alpha}-Gd{sub 2}S{sub 3} determined from neutron diffraction experiments.

  10. Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2

    SciTech Connect (OSTI)

    Qiu, Wei; Lam, Robert; Voytyuk, Oleksandr; Romanov, Vladimir; Gordon, Roni; Gebremeskel, Simon; Vodsedalek, Jakub; Thompson, Christine; Beletskaya, Irina; Battaile, Kevin P.; Pai, Emil F.; Rottapel, Robert; Chirgadze, Nickolay Y.

    2014-07-31

    The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated ?-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members. Here, the high-resolution crystal structures of the human TNKS2 PARP domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials. These structures provide insight into the inhibitor-binding modes for the tankyrase PARP domain and valuable information to guide the rational design of future tankyrase-specific inhibitors.

  11. The structure of the SBP-Tag–streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits

    SciTech Connect (OSTI)

    Barrette-Ng, Isabelle H.; Wu, Sau-Ching; Tjia, Wai-Mui; Wong, Sui-Lam; Ng, Kenneth K. S.

    2013-05-01

    The structure of the SBP-Tag–streptavidin complex reveals a novel mode of peptide recognition in which a single peptide binds simultaneously to biotin-binding pockets from adjacent subunits of streptavidin. The molecular details of peptide recognition suggest how the SBP-Tag can be further modified to become an even more useful tag for a wider range of biotechnological applications. The 38-residue SBP-Tag binds to streptavidin more tightly (K{sub d} ? 2.5–4.9 nM) than most if not all other known peptide sequences. Crystallographic analysis at 1.75 Å resolution shows that the SBP-Tag binds to streptavidin in an unprecedented manner by simultaneously interacting with biotin-binding pockets from two separate subunits. An N-terminal HVV peptide sequence (residues 12–14) and a C-terminal HPQ sequence (residues 31–33) form the bulk of the direct interactions between the SBP-Tag and the two biotin-binding pockets. Surprisingly, most of the peptide spanning these two sites (residues 17–28) adopts a regular ?-helical structure that projects three leucine side chains into a groove formed at the interface between two streptavidin protomers. The crystal structure shows that residues 1–10 and 35–38 of the original SBP-Tag identified through in vitro selection and deletion analysis do not appear to contact streptavidin and thus may not be important for binding. A 25-residue peptide comprising residues 11–34 (SBP-Tag2) was synthesized and shown using surface plasmon resonance to bind streptavidin with very similar affinity and kinetics when compared with the SBP-Tag. The SBP-Tag2 was also added to the C-terminus of ?-lactamase and was shown to be just as effective as the full-length SBP-Tag in affinity purification. These results validate the molecular structure of the SBP-Tag–streptavidin complex and establish a minimal bivalent streptavidin-binding tag from which further rational design and optimization can proceed.

  12. Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy

    SciTech Connect (OSTI)

    Sheng, WC; Zhuang, ZB; Gao, MR; Zheng, J; Chen, JGG; Yan, YS

    2015-01-08

    The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearly increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.

  13. Operating experience feedback report -- Pressure locking and thermal binding of gate valves. Commercial power reactors: Volume 9

    SciTech Connect (OSTI)

    Hsu, C.

    1993-03-01

    The potential for valve inoperability caused by pressure locking and thermal binding has been known for many years in the nuclear industry. Pressure locking or thermal binding is a common-mode failure mechanism that can prevent a gate valve from opening, and could render redundant trains of safety systems or multiple safety systems inoperable. In spite of numerous generic communications issued in the past by the Nuclear Regulatory Commission (NRC) and industry, pressure locking and thermal binding continues to occur to gate valves installed in safety-related systems of both boding water reactors (BWRs) and pressurized water reactors (PWRs). The generic communications to date have not led to effective industry action to fully identify, evaluate, and correct the problem. This report provides a review of operating events involving these failure mechanisms. As a result of this review this report: (1) identifies conditions when the failure mechanisms have occurred, (2) identifies the spectrum of safety systems that have been subjected to the failure mechanisms, and (3) identifies conditions that may introduce the failure mechanisms under both normal and accident conditions. On the basis of the evaluation of the operating events, the Office for Analysis and Evaluation of Operational Data (AEOD) of the NRC concludes that the binding problems with gate valves are an important safety issue that needs priority NRC and industry attention. This report also provides AEOD`s recommendation for actions to effectively prevent the occurrence of valve binding failures.

  14. Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm

    SciTech Connect (OSTI)

    Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard; Nix, David; Pollard, Daniel A.; Iyer, Venky N.; Hechmer, Aaron; Simirenko, Lisa; Stapleton, Mark; Luengo Hendriks, Cris L.; Chu, Hou Cheng; Ogawa, Nobuo; Inwood, William; Sementchenko, Victor; Beaton, Amy; Weiszmann, Richard; Celniker, Susan E.; Knowles, David W.; Gingeras, Tom; Speed, Terence P.; Eisen, Michael B.; Biggin, Mark D.

    2008-01-10

    Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly-bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.

  15. Cationic Gold Clusters Ligated with Differently Substituted Phosphines: Effect of Substitution on Ligand Reactivity and Binding

    SciTech Connect (OSTI)

    Johnson, Grant E.; Olivares, Astrid M.; Hill, David E.; Laskin, Julia

    2015-01-01

    We present a systematic study of the effect of the number of methyl (Me) and cyclohexyl (Cy) functional groups in monodentate phosphine ligands on the solution-phase synthesis of ligated sub-nanometer gold clusters and their gas-phase fragmentation pathways. Small mixed ligand cationic gold clusters were synthesized using ligand exchange reactions between pre-formed triphenylphosphine ligated (PPh3) gold clusters and monodentate Me- and Cy-substituted ligands in solution and characterized using electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation (CID) experiments. Under the same experimental conditions, larger gold-PPh3 clusters undergo efficient exchange of unsubstituted PPh3 ligands for singly Me- and Cy-substituted PPh2Me and PPh2Cy ligands. The efficiency of ligand exchange decreases with an increasing number of Me or Cy groups in the substituted phosphine ligands. CID experiments performed for a series of ligand-exchanged gold clusters indicate that loss of a neutral Me-substituted ligand is preferred over loss of a neutral PPh¬3 ligand while the opposite trend is observed for Cy-substituted ligands. The branching ratio of the competing ligand loss channels is strongly correlated with the electron donating ability of the phosphorous lone pair as determined by the relative proton affinity of the ligand. The results indicate that the relative ligand binding energies increase in the order PMe3 < PPhMe2 < PPh2Me < PPh3< PPh2Cy < PPhCy2< PCy3. Furthermore, the difference in relative ligand binding energies increases with the number of substituted PPh3-mMem or PPh3-mCym ligands (L) exchanged onto each cluster. This study provides the first experimental determination of the relative binding energies of ligated gold clusters containing differently substituted monophosphine ligands, which are important to controlling their synthesis and reactivity in solution. The results also indicate that ligand substitution is an important parameter that must be considered in theoretical modeling of these complex systems

  16. Two-dimensional weak anti-localization in Bi{sub 2}Te{sub 3} thin film grown on Si(111)-(7 Multiplication-Sign 7) surface by molecular beam epitaxy

    SciTech Connect (OSTI)

    Roy, Anupam; Guchhait, Samaresh; Sonde, Sushant; Dey, Rik; Pramanik, Tanmoy; Rai, Amritesh; Movva, Hema C. P.; Banerjee, Sanjay K. [Microelectronics Research Center, The University of Texas at Austin, Austin, Texas 78758 (United States)] [Microelectronics Research Center, The University of Texas at Austin, Austin, Texas 78758 (United States); Colombo, Luigi [Texas Instruments, 12500 TI Boulevard, Dallas, Texas 75266 (United States)] [Texas Instruments, 12500 TI Boulevard, Dallas, Texas 75266 (United States)

    2013-04-22

    We report on low temperature transport studies of Bi{sub 2}Te{sub 3} topological insulator thin films grown on Si(111)-(7 Multiplication-Sign 7) surface by molecular beam epitaxy. A sharp increase in the magnetoresistance with magnetic field at low temperature indicates the existence of weak anti-localization. The measured weak anti-localization effect agrees well with the Hikami-Larkin-Nagaoka model, and the extracted phase coherence length shows a power-law dependence with temperature indicating the existence of a two-dimensional system. An insulating ground state has also been observed at low temperature showing a logarithmic divergence of the resistance that appears to be the influence of electron-electron interaction in a two-dimensional system.

  17. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study

    SciTech Connect (OSTI)

    Arnold, John

    2015-01-21

    The uranyl cation (UO?²?) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due to the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration.

  18. CO2 Binding Organic Liquids Gas Capture with Polarity Swing Assisted Regeneration

    SciTech Connect (OSTI)

    Heldebrant, David

    2014-05-31

    This report outlines the comprehensive bench-scale testing of the CO2-binding organic liquids (CO2BOLs) solvent platform and its unique Polarity Swing Assisted Regeneration (PSAR). This study outlines all efforts on a candidate CO2BOL solvent molecule, including solvent synthesis, material characterization, preliminary toxicology studies, and measurement of all physical, thermodynamic and kinetic data, including bench-scale testing. Equilibrium and kinetic models and analysis were made using Aspen Plus™. Preliminary process configurations, a technoeconomic assessment and solvent performance projections for separating CO2 from a subcritical coal-fired power plant are compared to the U.S. Department of Energy's Case 10 monoethanolamine baseline.

  19. Benchmark Theoretical Study of the ?–? Binding Energy in the Benzene Dimer

    SciTech Connect (OSTI)

    Miliordos, Evangelos; Apra, Edoardo; Xantheas, Sotiris S.

    2014-09-04

    We establish a new estimate for the interaction energy between two benzene molecules in the parallel displaced (PD) conformation by systematically converging (i) the intra- and intermolecular geometry at the minimum geometry, (ii) the expansion of the orbital basis set and (iii) the level of electron correlation. The calculations were performed at the second order Møller - Plesset perturbation (MP2) and the Coupled Cluster including Singles, Doubles and a perturbative estimate of Triples replacements [CCSD(T)] levels of electronic structure theory. At both levels of theory, by including results corrected for Basis Set Superposition Error (BSSE), we have estimated the Complete Basis Set (CBS) limit by employing the family of Dunning’s correlation consistent polarized valence basis sets. The largest MP2 calculation was performed with the cc-pV6Z basis set (2,772 basis functions), whereas the largest CCSD(T) calculation with the cc-pV5Z basis set (1,752 basis functions). The cluster geometries were optimized with basis sets up to quadruple-? quality, observing that both its intra- and inter-molecular parts have practically converged with the triple-? quality sets. The use of converged geometries was found to play an important role for obtaining accurate estimates for the CBS limits. Our results demonstrate that the binding energies with the families of the plain (cc-pVnZ) and augmented (aug-cc-pVnZ) sets converge [to within < 0.01 kcal/mol for MP2 and < 0.15 kcal/mol for CCSD(T)] to the same CBS limit. In addition, the average of the uncorrected and BSSEcorrected binding energies was found to converge to the same CBS limit must faster than either of the two constituents (uncorrected or BSSE-corrected binding energies). Due to the fact that the family of augmented basis sets (especially for the larger sets) causes serious linear dependency problems, the plain basis sets (for which no linear dependencies were found) are deemed as a more efficient and straightforward path for obtaining an accurate CBS limit. We considered extrapolations of the uncorrected (?𝐸) and BSSE-corrected (?𝐸!") binding energies, their average value (?𝐸!"#) as well as the average of the latter over the plain and augmented sets (?𝐸!"#) with the cardinal number of the basis set n. Our best estimate of the CCSD(T)/CBS limit for the ?-? interaction energy in the PD benzene dimer is De = 2.65 ± 0.02 kcal/mol. The best CCSD(T)/cc-pV5Z calculated value is 2.62 kcal/mol, just 0.03 kcal/mol away from the CBS limit. For comparison, the MP2/CBS limit estimate is 5.00 ± 0.01 kcal/mol, demonstrating a 90% overbinding with respect to CCSD(T). The Spin-Component-Scaled (SCS) MP2 variant was found to closely reproduce the CCSD(T) results for each basis set, while Scaled-Opposite-Spin (SOS) yielded results that are too low when compared to CCSD(T).

  20. Method for nucleic acid hybridization using single-stranded DNA binding protein

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1996-01-01

    Method of nucleic acid hybridization for detecting the presence of a specific nucleic acid sequence in a population of different nucleic acid sequences using a nucleic acid probe. The nucleic acid probe hybridizes with the specific nucleic acid sequence but not with other nucleic acid sequences in the population. The method includes contacting a sample (potentially including the nucleic acid sequence) with the nucleic acid probe under hybridizing conditions in the presence of a single-stranded DNA binding protein provided in an amount which stimulates renaturation of a dilute solution (i.e., one in which the t.sub.1/2 of renaturation is longer than 3 weeks) of single-stranded DNA greater than 500 fold (i.e., to a t.sub.1/2 less than 60 min, preferably less than 5 min, and most preferably about 1 min.) in the absence of nucleotide triphosphates.

  1. High throughput screening of ligand binding to macromolecules using high resolution powder diffraction

    DOE Patents [OSTI]

    Von Dreele, Robert B.; D'Amico, Kevin

    2006-10-31

    A process is provided for the high throughput screening of binding of ligands to macromolecules using high resolution powder diffraction data including producing a first sample slurry of a selected polycrystalline macromolecule material and a solvent, producing a second sample slurry of a selected polycrystalline macromolecule material, one or more ligands and the solvent, obtaining a high resolution powder diffraction pattern on each of said first sample slurry and the second sample slurry, and, comparing the high resolution powder diffraction pattern of the first sample slurry and the high resolution powder diffraction pattern of the second sample slurry whereby a difference in the high resolution powder diffraction patterns of the first sample slurry and the second sample slurry provides a positive indication for the formation of a complex between the selected polycrystalline macromolecule material and at least one of the one or more ligands.

  2. CO2-Binding Organic Liquids, an Integrated Acid Gas Capture System

    SciTech Connect (OSTI)

    Heldebrant, David J.; Koech, Phillip K.; Rainbolt, James E.; Zheng, Feng

    2011-04-01

    Amine systems are effective for CO2 capture, but they are still inefficient because the solvent regeneration energy is largely defined by the amount of water in the process. Most amines form heat-stable salts with SO2 and COS resulting in parasitic solvent loss and degradation. Stripping the CO2-rich solvent is energy intensive it requires temperatures above 100 ?C due to the high specific heat and heat of vaporization of water. CO2-capture processes could be much more energy efficient in a water free amine process. In addition, if the capture-material is chemically compatible with other acid gases, less solvent would be lost to heat-stable salts and the process economics would be further improved. One such system that can address these concerns is Binding Organic Liquids (BOLs), a class of switchable ionic liquids.

  3. Ab initio study of formation, migration and binding properties of helium-vacancy clusters in aluminum

    SciTech Connect (OSTI)

    Yang, Li; Zu, Xiaotao T.; Gao, Fei

    2008-08-01

    Ab initio calculations based on density functional theory have been performed to study the dissolution and migration of helium, and the stability of small helium-vacancy clusters HenVm (n, m=0 to 4) in aluminum. The results indicate that the octahedral configuration is more stable than the tetrahedral. Interstitial helium atoms are predicted to have attractive interactions and jump between two octahedral sites via an intermediate tetrahedral site with low migration energy of 0.10 eV. The binding energies of an interstitial He atom and an isolated vacancy to a HenVm cluster are also obtained from the calculated formation energies of the clusters. We find that the divacancy and tri--vacancy clusters are not stable, but He atoms can increase the stability of vacancy clusters. The interactions of He atoms with a vacancy are found to be in good agreement with the experimental results.

  4. BuD, a helix–loop–helix DNA-binding domain for genome modification

    SciTech Connect (OSTI)

    Stella, Stefano; Molina, Rafael; López-Méndez, Blanca; Juillerat, Alexandre; Bertonati, Claudia; Daboussi, Fayza; Campos-Olivas, Ramon; Duchateau, Phillippe; Montoya, Guillermo

    2014-07-01

    Crystal structures of BurrH and the BurrH–DNA complex are reported. DNA editing offers new possibilities in synthetic biology and biomedicine for modulation or modification of cellular functions to organisms. However, inaccuracy in this process may lead to genome damage. To address this important problem, a strategy allowing specific gene modification has been achieved through the addition, removal or exchange of DNA sequences using customized proteins and the endogenous DNA-repair machinery. Therefore, the engineering of specific protein–DNA interactions in protein scaffolds is key to providing ‘toolkits’ for precise genome modification or regulation of gene expression. In a search for putative DNA-binding domains, BurrH, a protein that recognizes a 19 bp DNA target, was identified. Here, its apo and DNA-bound crystal structures are reported, revealing a central region containing 19 repeats of a helix–loop–helix modular domain (BurrH domain; BuD), which identifies the DNA target by a single residue-to-nucleotide code, thus facilitating its redesign for gene targeting. New DNA-binding specificities have been engineered in this template, showing that BuD-derived nucleases (BuDNs) induce high levels of gene targeting in a locus of the human haemoglobin ? (HBB) gene close to mutations responsible for sickle-cell anaemia. Hence, the unique combination of high efficiency and specificity of the BuD arrays can push forward diverse genome-modification approaches for cell or organism redesign, opening new avenues for gene editing.

  5. Surface structural ion adsorption modeling of competitive binding of oxyanions by metal (hydr)oxides

    SciTech Connect (OSTI)

    Hiemstra, T.; Riemsdijk, W.H. van

    1999-02-01

    An important challenge in surface complexation models (SCM) is to connect the molecular microscopic reality to macroscopic adsorption phenomena. This study elucidates the primary factor controlling the adsorption process by analyzing the adsorption and competition of PO{sub 4}, AsO{sub 4}, and SeO{sub 3}. The authors show that the structure of the surface-complex acting in the dominant electrostatic field can be ascertained as the primary controlling adsorption factor. The surface species of arsenate are identical with those of phosphate and the adsorption behavior is very similar. On the basis of the selenite adsorption, The authors show that the commonly used 1pK models are incapable to incorporate in the adsorption modeling the correct bidentate binding mechanism found by spectroscopy. The use of the bidentate mechanism leads to a proton-oxyanion ratio and corresponding pH dependence that are too large. The inappropriate intrinsic charge attribution to the primary surface groups and the condensation of the inner sphere surface complex to a point charge are responsible for this behavior of commonly used 2pK models. Both key factors are differently defined in the charge distributed multi-site complexation (CD-MUSIC) model and are based in this model on a surface structural approach. The CD-MUSIC model can successfully describe the macroscopic adsorption phenomena using the surface speciation and binding mechanisms as found by spectroscopy. The model is also able to predict the anion competition well. The charge distribution in the interface is in agreement with the observed structure of surface complexes.

  6. Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module

    SciTech Connect (OSTI)

    Deshpande, Chandrika N.; Harrop, Stephen J.; Boucher, Yan; Hassan, Karl A.; Di Leo, Rosa; Xu, Xiaohui; Cui, Hong; Savchenko, Alexei; Chang, Changsoo; Labbate, Maurizio; Paulsen, Ian T.; Stokes, H.W.; Curmi, Paul M.G.; Mabbutt, Bridget C.

    2012-02-15

    The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes. We report the 1.8 {angstrom} crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators. Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.

  7. The impacts of electronic state hybridization on the binding energy of single phosphorus donor electrons in extremely downscaled silicon nanostructures

    SciTech Connect (OSTI)

    The Anh, Le Manoharan, Muruganathan; Moraru, Daniel; Tabe, Michiharu; Mizuta, Hiroshi

    2014-08-14

    We present the density functional theory calculations of the binding energy of the Phosphorus (P) donor electrons in extremely downscaled single P-doped Silicon (Si) nanorods. In past studies, the binding energy of donor electrons was evaluated for the Si nanostructures as the difference between the ionization energy for the single P-doped Si nanostructures and the electron affinity for the un-doped Si nanostructures. This definition does not take into account the strong interaction of donor electron states and Si electron states explicitly at the conductive states and results in a monotonous increase in the binding energy by reducing the nanostructure's dimensions. In this paper, we introduce a new approach to evaluate the binding energy of donor electrons by combining the projected density of states (PDOS) analysis and three-dimensional analysis of associated electron wavefunctions. This enables us to clarify a gradual change of the spatial distribution of the 3D electron wavefunctions (3DWFs) from the donor electron ground state, which is fully localized around the P donor site to the first conductive state, which spreads over the outer Si nanorods contributing to current conduction. We found that the energy of the first conductive state is capped near the top of the atomistic effective potential at the donor site with respect to the surrounding Si atoms in nanorods smaller than about 27 a{sub 0}. This results in the binding energy of approximately 1.5?eV, which is virtually independent on the nanorod's dimensions. This fact signifies a good tolerance of the binding energy, which governs the operating temperature of the single dopant-based transistors in practice. We also conducted the computationally heavy transmission calculations of the single P-doped Si nanorods connected to the source and drain electrodes. The calculated transmission spectra are discussed in comparison with the atomistic effective potential distributions and the PDOS-3DWFs method.

  8. Crystal and solution structures of an odorant-binding protein from the southern house mosquito complexed with an oviposition pheromone

    SciTech Connect (OSTI)

    Mao, Yang; Xu, Xianzhong; Xu, Wei; Ishida, Yuko; Leal, Walter S.; Ames, James B.; Clardy, Jon

    2010-11-15

    Culex mosquitoes introduce the pathogens responsible for filariasis, West Nile virus, St. Louis encephalitis, and other diseases into humans. Currently, traps baited with oviposition semiochemicals play an important role in detection efforts and could provide an environmentally friendly approach to controlling their populations. The odorant binding proteins (OBPs) in the female's antenna play a crucial, if yet imperfectly understood, role in sensing oviposition cues. Here, we report the X-ray crystallography and NMR 3D structures of OBP1 for Culex quinquefasciatus (CquiOBP1) bound to an oviposition pheromone (5R,6S)-6-acetoxy-5-hexadecanolide (MOP). In both studies, CquiOBP1 had the same overall six-helix structure seen in other insect OBPs, but a detailed analysis revealed an important previously undescribed feature. There are two models for OBP-mediated signal transduction: (i) direct release of the pheromone from an internal binding pocket in a pH-dependent fashion and (ii) detection of a pheromone-induced conformational change in the OBP {center_dot} pheromone complex. Although CquiOBP1 binds MOP in a pH-dependent fashion, it lacks the C terminus required for the pH-dependent release model. This study shows that CquiOBP binds MOP in an unprecedented fashion using both a small central cavity for the lactone head group and a long hydrophobic channel for its tail.

  9. Minimal Determinants for Binding Activated G alpha from the Structure of a G alpha i1-Peptide Dimer

    SciTech Connect (OSTI)

    Johnston,C.; Lobanova, E.; Shavkunov, A.; Low, J.; Ramer, J.; Blasesius, R.; Fredericks, Z.; willard, F.; Kuhlman, B.; et al.

    2006-01-01

    G-Proteins cycle between an inactive GDP-bound state and an active GTP-bound state, serving as molecular switches that coordinate cellular signaling. We recently used phage display to identify a series of peptides that bind G{alpha}subunits in a nucleotide-dependent manner [Johnston, C. A., Willard, F. S., Jezyk, M. R., Fredericks, Z., Bodor, E. T., Jones, M. B., Blaesius, R., Watts, V. J., Harden, T. K., Sondek, J., Ramer, J. K., and Siderovski, D. P. (2005) Structure 13, 1069-1080]. Here we describe the structural features and functions of KB-1753, a peptide that binds selectively to GDP{center_dot}AlF{sub 4{sup -}}- and GTP{gamma}S-bound states of G{alpha}{sup i} subunits. KB-1753 blocks interaction of G{alpha}{sub transducin} with its effector, cGMP phosphodiesterase, and inhibits transducin-mediated activation of cGMP degradation. Additionally, KB-1753 interferes with RGS protein binding and resultant GAP activity. A fluorescent KB-1753 variant was found to act as a sensor for activated G{alpha} in vitro. The crystal structure of KB-1753 bound to G{alpha}{sub i1}-GDP{center_dot}AlF{sub 4{sup -}} reveals binding to a conserved hydrophobic groove between switch II and 3 helices and, along with supporting biochemical data and previous structural analyses, supports the notion that this is the site of effector interactions for G{alpha}i subunits.

  10. Use of Cre/loxP recombination to swap cell binding motifs on the adenoviral capsid protein IX

    SciTech Connect (OSTI)

    Poulin, Kathy L.; Tong, Grace; Vorobyova, Olga; Pool, Madeline; Kothary, Rashmi; Parks, Robin J.

    2011-11-25

    We used Cre/loxP recombination to swap targeting ligands present on the adenoviral capsid protein IX (pIX). A loxP-flanked sequence encoding poly-lysine (pK-binds heparan sulfate proteoglycans) was engineered onto the 3'-terminus of pIX, and the resulting fusion protein allowed for routine virus propagation. Growth of this virus on Cre-expressing cells removed the pK coding sequence, generating virus that could only infect through alternative ligands, such as a tyrosine kinase receptor A (TrkA)-binding motif engineered into the capsid fibre protein for enhanced infection of neuronal cells. We used a similar approach to swap the pK motif on pIX for a sequence encoding a single-domain antibody directed towards CD66c for targeted infection of cancer cells; Cre-mediated removal of the pK-coding sequence simultaneously placed the single-domain antibody coding sequence in frame with pIX. Thus, we have developed a simple method to propagate virus lacking native viral tropism but containing cell-specific binding ligands. - Highlights: > We describe a method to grow virus lacking native tropism but containing novel cell-binding ligands. > Cre/loxP recombination was used to modify the adenovirus genome. > A targeting ligand present on capsid protein IX was removed or replaced using recombination. > Cre-loxP was also used to 'swap' the identity of the targeting ligand present on pIX.

  11. Structure of N-Terminal Domain of NPC1 Reveals Distinct Subdomains for Binding and Transfer of Cholesterol

    SciTech Connect (OSTI)

    Kwon, Hyock Joo; Abi-Mosleh, Lina; Wang, Michael L.; Deisenhofer, Johann; Goldstein, Joseph L.; Brown, Michael S.; Infante, Rodney E.

    2010-09-21

    LDL delivers cholesterol to lysosomes by receptor-mediated endocytosis. Exit of cholesterol from lysosomes requires two proteins, membrane-bound Niemann-Pick C1 (NPC1) and soluble NPC2. NPC2 binds cholesterol with its isooctyl side chain buried and its 3{beta}-hydroxyl exposed. Here, we describe high-resolution structures of the N-terminal domain (NTD) of NPC1 and complexes with cholesterol and 25-hydroxycholesterol. NPC1(NTD) binds cholesterol in an orientation opposite to NPC2: 3{beta}-hydroxyl buried and isooctyl side chain exposed. Cholesterol transfer from NPC2 to NPC1(NTD) requires reorientation of a helical subdomain in NPC1(NTD), enlarging the opening for cholesterol entry. NPC1 with point mutations in this subdomain (distinct from the binding subdomain) cannot accept cholesterol from NPC2 and cannot restore cholesterol exit from lysosomes in NPC1-deficient cells. We propose a working model wherein after lysosomal hydrolysis of LDL-cholesteryl esters, cholesterol binds NPC2, which transfers it to NPC1(NTD), reversing its orientation and allowing insertion of its isooctyl side chain into the outer lysosomal membranes.

  12. Binding and Recognition in the Assembly of an Active BRCA1/BARD1 Ubiquitin-Ligase Complex

    SciTech Connect (OSTI)

    Brzovic, Peter S.; Keeffe, Jennifer R.; Nishikawa, Hiroyuki; Miyamoto, Keiko; Fox, David; Fukuda, Mamoru; Ohta, Tomohiko; Klevit, Rachel E.

    2003-05-13

    BRCA1 is a breast and ovarian cancer tumor suppressor protein that associates with BARD1 to form a RING/RING heterodimer. The BRCA1/BARD1 RING complex functions as an ubiquitin (Ub) ligase with activity substantially greater than individual BRCA1 or BARD1 subunits. By using NMR spectroscopy and site-directed mutagenesis, we have mapped the binding site on the BRCA1/BARD1 heterodimer for the Ub-conjugating enzyme UbcH5c. The results demonstrate that UbcH5c binds only to the BRCA1 RING domain and not the BARD1 RING. The binding interface is formed by the first and second Zn2+-loops and central -helix of the BRCA1 RING domain, a region disrupted by cancer-predisposing mutations. Unexpectedly, a second Ub-conjugating enzyme, UbcH7, also interacts with the BRCA1/BARD1 complex with similar affinity, although it is not active in Ub-ligase activity assays. Thus, binding alone is not sufficient for BRCA1-dependent Ub-ligase activity.

  13. Analysis of hydrogen adsorption and surface binding configuration on tungsten using direct recoil spectrometry

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kolasinski, R. D.; Hammond, K. D.; Whaley, J. A.; Buchenauer, D. A.; Wirth, B. D.

    2014-12-03

    In our work, we apply low energy ion beam analysis to examine directly how the adsorbed hydrogen concentration and binding configuration on W(1 0 0) depend on temperature. We exposed the tungsten surface to fluxes of both atomic and molecular H and D. We then probed the H isotopes adsorbed along different crystal directions using 1–2 keV Ne+ ions. At saturation coverage, H occupies two-fold bridge sites on W(1 0 0) at 25 °C. Moreover, the H coverage dramatically changes the behavior of channeled ions, as does reconstruction of the surface W atoms. For the exposure conditions examined here, wemore » find that surface sites remain populated with H until the surface temperature reaches 200 °C. Then, we observe H rapidly desorbing until only a residual concentration remains at 450 °C. Development of an efficient atomistic model that accurately reproduces the experimental ion energy spectra and azimuthal variation of recoiled H is underway.« less

  14. An Insertion Mutation That Distorts Antibody Binding Site Architecture Enhances Function of a Human Antibody

    SciTech Connect (OSTI)

    Krause, Jens C.; Ekiert, Damian C.; Tumpey, Terrence M.; Smith, Patricia B.; Wilson, Ian A.; Crowe, Jr., James E.

    2011-09-02

    The structural and functional significance of somatic insertions and deletions in antibody chains is unclear. Here, we demonstrate that a naturally occurring three-amino-acid insertion within the influenza virus-specific human monoclonal antibody 2D1 heavy-chain variable region reconfigures the antibody-combining site and contributes to its high potency against the 1918 and 2009 pandemic H1N1 influenza viruses. The insertion arose through a series of events, including a somatic point mutation in a predicted hot-spot motif, introduction of a new hot-spot motif, a molecular duplication due to polymerase slippage, a deletion due to misalignment, and additional somatic point mutations. Atomic resolution structures of the wild-type antibody and a variant in which the insertion was removed revealed that the three-amino-acid insertion near the base of heavy-chain complementarity-determining region (CDR) H2 resulted in a bulge in that loop. This enlarged CDR H2 loop impinges on adjacent regions, causing distortion of the CDR H1 architecture and its displacement away from the antigen-combining site. Removal of the insertion restores the canonical structure of CDR H1 and CDR H2, but binding, neutralization activity, and in vivo activity were reduced markedly because of steric conflict of CDR H1 with the hemagglutinin antigen.

  15. On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

    SciTech Connect (OSTI)

    Brokaw, Jason B.; Chu, Jhih-wei

    2010-11-17

    We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.

  16. The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

    SciTech Connect (OSTI)

    Stella, Stefano; Cascio, Duilio; Johnson, Reid C.

    2010-06-21

    The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNA-dependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high- and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of {approx}65{sup o}, and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.

  17. A Rac1--GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium

    SciTech Connect (OSTI)

    Prehna, G.; Stebbins, C

    2007-01-01

    The Rho family of small GTPases represent well characterized signaling molecules that regulate many cellular functions such as actin cytoskeletal arrangement and the cell cycle by acting as molecular switches. A Rac1-GDP-Zn complex has been crystallized in space group P3221 and its crystal structure has been solved at 1.9 {angstrom} resolution. These trigonal crystals reveal the unexpected ability of Rac1 to coordinate Zn atoms in a tetrahedral fashion by use of its biologically relevant switch I and switch II regions. Upon coordination of zinc, the switch I region is stabilized in the GDP-bound conformation and contributes to a Rac1 trimer in the asymmetric unit. Zinc coordination causes switch II to adopt a novel conformation with a symmetry-related molecule. Additionally, zinc was found to displace magnesium from its octahedral coordination at switch I, although GDP binding remained stable. This structure represents the first reported Rac1-GDP-Zn complex, which further underscores the conformational flexibility and versatility of the small GTPase switch regions.

  18. A Rac1-GDP Trimer Complex Binds Zinc with Tetrahedral and Octahedral Coordination, Displacing Magnesium

    SciTech Connect (OSTI)

    Prehna,G.; Stebbins, E.

    2007-01-01

    The Rho family of small GTPases represent well characterized signaling molecules that regulate many cellular functions such as actin cytoskeletal arrangement and the cell cycle by acting as molecular switches. A Rac1-GDP-Zn complex has been crystallized in space group P3{sub 2}21 and its crystal structure has been solved at 1.9 {angstrom} resolution. These trigonal crystals reveal the unexpected ability of Rac1 to coordinate Zn atoms in a tetrahedral fashion by use of its biologically relevant switch I and switch II regions. Upon coordination of zinc, the switch I region is stabilized in the GDP-bound conformation and contributes to a Rac1 trimer in the asymmetric unit. Zinc coordination causes switch II to adopt a novel conformation with a symmetry-related molecule. Additionally, zinc was found to displace magnesium from its octahedral coordination at switch I, although GDP binding remained stable. This structure represents the first reported Rac1-GDP-Zn complex, which further underscores the conformational flexibility and versatility of the small GTPase switch regions.

  19. cAMP-response-element-binding protein positively regulates breast cancer metastasis and subsequent bone destruction

    SciTech Connect (OSTI)

    Son, Jieun; Lee, Jong-Ho; Kim, Ha-Neui; Ha, Hyunil Lee, Zang Hee

    2010-07-23

    Research highlights: {yields} CREB is highly expressed in advanced breast cancer cells. {yields} Tumor-related factors such as TGF-{beta} further elevate CREB expression. {yields} CREB upregulation stimulates metastatic potential of breast cancer cells. {yields} CREB signaling is required for breast cancer-induced bone destruction. -- Abstract: cAMP-response-element-binding protein (CREB) signaling has been reported to be associated with cancer development and poor clinical outcome in various types of cancer. However, it remains to be elucidated whether CREB is involved in breast cancer development and osteotropism. Here, we found that metastatic MDA-MB-231 breast cancer cells exhibited higher CREB expression than did non-metastatic MCF-7 cells and that CREB expression was further increased by several soluble factors linked to cancer progression, such as IL-1, IGF-1, and TGF-{beta}. Using wild-type CREB and a dominant-negative form (K-CREB), we found that CREB signaling positively regulated the proliferation, migration, and invasion of MDA-MB-231 cells. In addition, K-CREB prevented MDA-MB-231 cell-induced osteolytic lesions in a mouse model of cancer metastasis. Furthermore, CREB signaling in cancer cells regulated the gene expression of PTHrP, MMPs, and OPG, which are closely involved in cancer metastasis and bone destruction. These results indicate that breast cancer cells acquire CREB overexpression during their development and that this CREB upregulation plays an important role in multiple steps of breast cancer bone metastasis.

  20. The PDZ-binding motif of Yes-associated protein is required for its co-activation of TEAD-mediated CTGF transcription and oncogenic cell transforming activity

    SciTech Connect (OSTI)

    Shimomura, Tadanori; Miyamura, Norio; Hata, Shoji; Miura, Ryota; Hirayama, Jun Nishina, Hiroshi

    2014-01-17

    Highlights: •Loss of the PDZ-binding motif inhibits constitutively active YAP (5SA)-induced oncogenic cell transformation. •The PDZ-binding motif of YAP promotes its nuclear localization in cultured cells and mouse liver. •Loss of the PDZ-binding motif inhibits YAP (5SA)-induced CTGF transcription in cultured cells and mouse liver. -- Abstract: YAP is a transcriptional co-activator that acts downstream of the Hippo signaling pathway and regulates multiple cellular processes, including proliferation. Hippo pathway-dependent phosphorylation of YAP negatively regulates its function. Conversely, attenuation of Hippo-mediated phosphorylation of YAP increases its ability to stimulate proliferation and eventually induces oncogenic transformation. The C-terminus of YAP contains a highly conserved PDZ-binding motif that regulates YAP’s functions in multiple ways. However, to date, the importance of the PDZ-binding motif to the oncogenic cell transforming activity of YAP has not been determined. In this study, we disrupted the PDZ-binding motif in the YAP (5SA) protein, in which the sites normally targeted by Hippo pathway-dependent phosphorylation are mutated. We found that loss of the PDZ-binding motif significantly inhibited the oncogenic transformation of cultured cells induced by YAP (5SA). In addition, the increased nuclear localization of YAP (5SA) and its enhanced activation of TEAD-dependent transcription of the cell proliferation gene CTGF were strongly reduced when the PDZ-binding motif was deleted. Similarly, in mouse liver, deletion of the PDZ-binding motif suppressed nuclear localization of YAP (5SA) and YAP (5SA)-induced CTGF expression. Taken together, our results indicate that the PDZ-binding motif of YAP is critical for YAP-mediated oncogenesis, and that this effect is mediated by YAP’s co-activation of TEAD-mediated CTGF transcription.

  1. Superdeformed band up to spin approx. (127/2 in /sup 149/Gd

    SciTech Connect (OSTI)

    Haas, B.; Taras, P.; Flibotte, S.; Banville, F.; Gascon, J.; Cournoyer, S.; Monaro, S.; Nadon, N.; Prevost, D.; Thibault, D.; and others

    1988-02-08

    A rotational band of nineteen transitions, extending to spinapprox.(127/2h-dash-bar and with an average moment of inertia scrI/sup (2)/ of 77 h-dash-bar/sup 2/ MeV/sup -1/, has been observed in /sup 149/Gd. Its intensity accounts for approximately (1/2% of the total fusion cross section. Lifetime measurements yielded an average quadrupole moment of 17 +- 2 e-b, in excellent agreement with the value calculated microscopically for a superdeformed shape. The trends in scrI/sup (1)/ and scrI/sup (2)/ are consistent with very weak pairing effects. The data also suggest that to populate superdeformed bands significantly one must form cold residual nuclei.

  2. Evaluation of polyacrylonitrile (PAN) as a binding polymer for absorbers used to treat liquid radioactive wastes

    SciTech Connect (OSTI)

    Sebesta, F.; John, J.; Motl, A.; Stamberg, K.

    1995-11-01

    The chemical and radiation stability of polyacrylonitrile (PAN) in the form of beads (B-PAN), similar to the beads of composite absorbers, and one selected composite absorber (ammonium molybdophosphate, the active component in PAN binder [AMP-PAN], a prospective candidate for the treatment of acidic wastes) were studied. Aqueous 1M HNO{sub 3} + 1M NaNO{sub 3}, 1M NaOH + 1M NaNO{sub 3}, and 1M NaOH were chosen as simulants of DOE acidic and alkaline wastes. In addition,radiation stability was determined indistilled water. The chemical stability of B-PAN and AMP-PAN beads was tested for a period up to one month of contact with the solution at ambient temperature. The radiation stability of the beads was checked in a radiation dose range 10{sup 3}--10{sup 6} Gy (10{sup 5}--10{sup 8} rads). In acidic solutions the stability of PAN binder was proved not to be limited by either chemical or radiation decomposition. PAN binder may thus be used for preparing composite absorbers for treatment of acid wastes from DOE facilities. The same conclusion is valid for alkaline solutions with pH up to 13. In highly alkaline solutions (concentration of NAOH higher than I M) and in the presence of NaNO{sub 3}, the stability of the tested polyacrylonitrile polymer was sufficient for applications not extending over 10 days. Cross-linking of the polymer caused by ionizing radiation was found to have a positive influence on chemical stability. This effect enables a longer period of applicability of PAN-based composite absorbers. Because of the high sorption rate achievable with PAN-based absorbers, the stability achieved is sufficient for most applications in the DOE complex. The chemical stability of binding polymer may also be further improved by testing another, more suitable type of polymer from the broad family of polyacrylonitrile polymers.

  3. Anion Binding in Metal-Organic Frameworks Functionalized with Urea Hydrogen-Bonding Groups

    SciTech Connect (OSTI)

    Custelcean, Radu; Moyer, Bruce A; Bryantsev, Vyacheslav S.; Hay, Benjamin P.

    2006-01-01

    A series of metal-organic frameworks (MOFs) functionalized with urea hydrogen-bonding groups has been synthesized and structurally analyzed by single-crystal X-ray diffraction to evaluate the efficacy of anion coordination by urea within the structural constraints of the MOFs. We found that urea-based functionalities may be used for anion binding within metal-organic frameworks when the tendency for urea{hor_ellipsis}urea self-association is decreased by strengthening the intramolecular CH{hor_ellipsis}O hydrogen bonding of N-phenyl substituents to the carbonyl oxygen atom. Theoretical calculations indicate that N,N'-bis(m-pyridyl)urea (BPU) and N,N'-bis(m-cyanophenyl)urea (BCPU) should have enhanced hydrogen-bonding donor abilities toward anions and decreased tendencies to self-associate into hydrogen-bonded tapes compared to other disubstituted ureas. Accordingly, BPU and BCPU were incorporated in MOFs as linkers through coordination of various Zn, Cu, and Ag transition metal salts, including Zn(ClO{sub 4}){sub 2}, ZnSO{sub 4}, Cu(NO{sub 3}){sub 2}, Cu(CF{sub 3}SO{sub 3}){sub 2}, AgNO{sub 3}, and AgSO{sub 3}CH{sub 3}. Structural analysis by single-crystal X-ray diffraction showed that these linkers are versatile anion binders, capable of chelate hydrogen bonding to all of the oxoanions explored. Anion coordination by the urea functionalities was found to successfully compete with urea self-association in all cases except for that of charge-diffuse perchlorate.

  4. Apoferritin-based nanomedicine platform for drug delivery: equilibrium binding study of daunomycin with DNA

    SciTech Connect (OSTI)

    Ma Ham, Aihui; Wu, Hong J.; Wang, Jun; Kang, Xinhuang; Zhang, Youyu; Lin, Yuehe

    2011-05-11

    Apoferritin is a nanostructured material with a uniform size and spherical structure, and it has excellent bio-compatibility. In this work, we report the use of apoferritin as a novel and biocompatible carrier for stabilizing enzymes and their activities. We used glucose oxidase (GOx) as a model enzyme. GOx was immobilized on the surface of the apoferritin through a green synthetic approach taking advantage of bioaffinity binding between streptavidin and biotin. As a result, a glucose oxidase-biotin/streptavidin/biotin-apoferritin conjugate (Apo-GOx) was prepared using streptavidin as a bridge. The synthesized Apo-GOx was characterized with transmission electron microscopy, ultraviolet, and fluorescence spectroscopy. The activity and stability of GOx on the surface of the apoferritin were studied in different environments, such as temperature, chemicals, and pH, in comparison with the biotinylated GOx (B-GOx). The results showed that the activity of GOx on the apoferritin surface was significantly enhanced. The thermal and chemical stability of the GOx on the apoferritin was also greatly improved compared to free B-GOx in a solution. It was found that the activity of the GOx on the apoferritin only lost 30% in comparison to a 70% loss of free B-GOx after a 2-hr incubation at 50oC. There was almost no decrease in activity for the GOx on the apoferritin as compared to an 80% activity decrease for free B-GOx after 30 minutes of incubation in a 5 M urea solution. The GOx immobilized apoferritin nanoparticles exhibited high sensitivity for glucose detection with a detection limit of 3 nM glucose. This work offers a novel approach for immobilizing enzymes with enhanced stability and activity, and this method may find a number of applications, such as in catalysis and bioassys/biosensors.

  5. Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate

    SciTech Connect (OSTI)

    Pazy, Y.; Motaleb, M.A.; Guarnieri, M.T.; Charon, N.W.; Zhao, R.; Silversmith, R.E.

    2010-04-05

    Two-component signal transduction systems are widespread in prokaryotes and control numerous cellular processes. Extensive investigation of sensor kinase and response regulator proteins from many two-component systems has established conserved sequence, structural, and mechanistic features within each family. In contrast, the phosphatases which catalyze hydrolysis of the response regulator phosphoryl group to terminate signal transduction are poorly understood. Here we present structural and functional characterization of a representative of the CheC/CheX/FliY phosphatase family. The X-ray crystal structure of Borrelia burgdorferi CheX complexed with its CheY3 substrate and the phosphoryl analogue BeF{sub 3}{sup -} reveals a binding orientation between a response regulator and an auxiliary protein different from that shared by every previously characterized example. The surface of CheY3 containing the phosphoryl group interacts directly with a long helix of CheX which bears the conserved (E - X{sub 2} - N) motif. Conserved CheX residues Glu96 and Asn99, separated by a single helical turn, insert into the CheY3 active site. Structural and functional data indicate that CheX Asn99 and CheY3 Thr81 orient a water molecule for hydrolytic attack. The catalytic residues of the CheX-CheY3 complex are virtually superimposable on those of the Escherichia coli CheZ phosphatase complexed with CheY, even though the active site helices of CheX and CheZ are oriented nearly perpendicular to one other. Thus, evolution has found two structural solutions to achieve the same catalytic mechanism through different helical spacing and side chain lengths of the conserved acid/amide residues in CheX and CheZ.

  6. The R6A-1 peptide binds to switch II of G{alpha}{sub i1} but is not a GDP-dissociation inhibitor

    SciTech Connect (OSTI)

    Willard, Francis S. . E-mail: fwillard@med.unc.edu; Siderovski, David P.

    2006-01-27

    Heterotrimeric G-proteins are molecular switches that convert signals from membrane receptors into changes in intracellular physiology. Recently, several peptides that bind heterotrimeric G-protein {alpha} subunits have been isolated including the novel G{alpha}{sub i1} . GDP binding peptides R6A and KB-752. The R6A peptide and its minimized derivative R6A-1 interact with G{alpha}{sub i1} . GDP. Based on spectroscopic analysis of BODIPYFL-GTP{gamma}S binding to G{alpha}{sub i1}, it has been reported that R6A-1 has guanine nucleotide dissociation inhibitor (GDI) activity against G{alpha}{sub i1} [W.W. Ja, R.W. Roberts, Biochemistry 43 (28) (2004) 9265-9275]. Using radioligand binding, we show that R6A-1 is not a GDI for G{alpha}{sub i1} subunits. Furthermore, we demonstrate that R6A-1 reduces the fluorescence quantum yield of the G{alpha}{sub i1}-BODIPYFL-GTP{gamma}S complex, thus explaining the previously reported GDI activity as a fluorescence artifact. We further show that R6A-1 has significant sequence similarity to the guanine nucleotide exchange factor peptide KB-752 that binds to switch II of G{alpha}{sub i1}. We use competitive binding analysis to show that R6A-1 also binds to switch II of G{alpha} subunits.

  7. Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pan, Wenxiao; Daily, Michael; Baker, Nathan A.

    2015-05-07

    Background: The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. Methods: We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. This new BC treatment allows for the analysis of enzymes with “imperfect” reaction rates. Results: The numerical method is first verified in simple systems and thenmore » applied to the calculation of ligand binding to a mouse acetylcholinesterase (mAChE) monomer. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates. Conclusions: Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.« less

  8. Quantification of the epitope diversity of HIV-1-specific binding antibodies by peptide microarrays for global HIV-1 vaccine development

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Stephenson, Kathryn E.; Neubauer, George H.; Reimer, Ulf; Pawlowski, Nikolaus; Knaute, Tobias; Zerweck, Johannes; Korber, Bette T.; Barouch, Dan H.

    2014-11-14

    An effective vaccine against human immunodeficiency virus type 1 (HIV-1) will have to provide protection against a vast array of different HIV-1 strains. Current methods to measure HIV-1-specific binding antibodies following immunization typically focus on determining the magnitude of antibody responses, but the epitope diversity of antibody responses has remained largely unexplored. Here we describe the development of a global HIV-1 peptide microarray that contains 6564 peptides from across the HIV-1 proteome and covers the majority of HIV-1 sequences in the Los Alamos National Laboratory global HIV-1 sequence database. Using this microarray, we quantified the magnitude, breadth, and depth ofmore » IgG binding to linear HIV-1 sequences in HIV-1-infected humans and HIV-1-vaccinated humans, rhesus monkeys and guinea pigs. The microarray measured potentially important differences in antibody epitope diversity, particularly regarding the depth of epitope variants recognized at each binding site. Our data suggest that the global HIV-1 peptide microarray may be a useful tool for both preclinical and clinical HIV-1 research.« less

  9. Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics

    SciTech Connect (OSTI)

    Pan, Wenxiao; Daily, Michael; Baker, Nathan A.

    2015-05-07

    Background: The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. Methods: We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. This new BC treatment allows for the analysis of enzymes with “imperfect” reaction rates. Results: The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to a mouse acetylcholinesterase (mAChE) monomer. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates. Conclusions: Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.

  10. Electronic Structures, Bonding Configurations, and Band-Gap-Opening Properties of Graphene Binding with Low-Concentration Fluorine

    SciTech Connect (OSTI)

    Duan, Yuhua; Stinespring, Charter D.; Chorpening, Benjamin

    2015-06-18

    To better understand the effects of low-level fluorine in graphene-based sensors, first-principles density functional theory (DFT) with van der Waals dispersion interactions has been employed to investigate the structure and impact of fluorine defects on the electrical properties of single-layer graphene films. The results show that both graphite-2H and graphene have zero band gaps. When fluorine bonds to a carbon atom, the carbon atom is pulled slightly above the graphene plane, creating what is referred to as a CF defect. The lowest-binding energy state is found to correspond to two CF defects on nearest neighbor sites, with one fluorine above the carbon plane and the other below the plane. Overall this has the effect of buckling the graphene. The results further show that the addition of fluorine to graphene leads to the formation of an energy band (BF) near the Fermi level, contributed mainly from the 2p orbitals of fluorine with a small contribution from the porbitals of the carbon. Among the 11 binding configurations studied, our results show that only in two cases does the BF serve as a conduction band and open a band gap of 0.37 eV and 0.24 eV respectively. The binding energy decreases with decreasing fluorine concentration due to the interaction between neighboring fluorine atoms. The obtained results are useful for sensor development and nanoelectronics.

  11. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis

    SciTech Connect (OSTI)

    Prigozhin, Daniil M. [Univ. of California, Berkeley, CA (United States); Krieger, Inna V. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Texas A & M Univ., College Station, TX (United States); Huizar, John P. [Univ. of California, Berkeley, CA (United States); Mavrici, Daniela [Univ. of California, Berkeley, CA (United States); Waldo, Geoffrey S. [Univ. of California, Berkeley, CA (United States); Hung, Li -Wei [Univ. of California, Berkeley, CA (United States); Sacchettini, James C. [Texas A & M Univ., College Station, TX (United States); Terwilliger, Thomas C. [Univ. of California, Berkeley, CA (United States); Alber, Tom [Univ. of California, Berkeley, CA (United States); Mayer, Claudine [Institut Pasteur, Paris (France)

    2014-12-31

    Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.

  12. Electronic Structures, Bonding Configurations, and Band-Gap-Opening Properties of Graphene Binding with Low-Concentration Fluorine

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Duan, Yuhua; Stinespring, Charter D.; Chorpening, Benjamin

    2015-06-18

    To better understand the effects of low-level fluorine in graphene-based sensors, first-principles density functional theory (DFT) with van der Waals dispersion interactions has been employed to investigate the structure and impact of fluorine defects on the electrical properties of single-layer graphene films. The results show that both graphite-2H and graphene have zero band gaps. When fluorine bonds to a carbon atom, the carbon atom is pulled slightly above the graphene plane, creating what is referred to as a CF defect. The lowest-binding energy state is found to correspond to two CF defects on nearest neighbor sites, with one fluorine abovemore » the carbon plane and the other below the plane. Overall this has the effect of buckling the graphene. The results further show that the addition of fluorine to graphene leads to the formation of an energy band (BF) near the Fermi level, contributed mainly from the 2p orbitals of fluorine with a small contribution from the porbitals of the carbon. Among the 11 binding configurations studied, our results show that only in two cases does the BF serve as a conduction band and open a band gap of 0.37 eV and 0.24 eV respectively. The binding energy decreases with decreasing fluorine concentration due to the interaction between neighboring fluorine atoms. The obtained results are useful for sensor development and nanoelectronics.« less

  13. Studying the Solar System's Chemical Recipe

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    silicates and other minerals, forming the chondrules found in early meteoroids (dashed black circles). Beyond the "snowline" (dashed white curves), water, methane, and other...

  14. Searching for the Solar System's Chemical Recipe

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    silicates and other minerals, forming the chondrules found in early meteoroids (dashed black circles). Beyond the "snowline" (dashed white curves), water, methane, and other...

  15. New experimental possibility to search for the ratio of a possible T-violating amplitude to the weak-interaction amplitude in polarized neutron transmission through a polarized nuclear target

    SciTech Connect (OSTI)

    Lukashevich, V. V.; Aldushchenkov, A. V.; Dallman, D. [St. Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina 188350 (Russian Federation); CERN, Geneva (Switzerland)

    2011-03-15

    This paper considers a spin-dependent neutron interaction with optical potentials (fields) from the strong interaction, the weak interaction, and an assumed T-violating interaction. The vector sum of these fields and their interferences determines an effective field of the target with an angular position in space due to polar and azimuthal angles. The phase of the azimuthal component is found to be the sum of two angles. The tangent of the first angle is equal to the ratio of the T-violating forward-scattering amplitude D to the weak-interaction amplitude C. The quantity is of interest. The tangent of the second angle depends on the spin rotation in the residual pseudomagnetic field of the target, and it can be treated as a background effect. This paper shows that the second angle has different signs in measurements with polarized and unpolarized neutrons; thus, two measurements allow it to be compensated for. In addition, the use of the Ramsey method of separated oscillatory fields for measurement of the neutron spin rotation angle, depending on the phase of the rf field in the Ramsey cell, allows a cosine-like spectrum to be measured. This spectrum is called a phase spectrum. The phase spectra measured with polarized and unpolarized targets have a phase shift. The measurements of this phase shift with polarized and nonpolarized neutrons at a p-wave resonance enable the ratio D/C to be isolated. We also describe the algorithm for separating the ratio D/C, taking into account the influence of the fringing fields of the Ramsey coil magnet and the target magnet.

  16. Insights on the binding of thioflavin derivative markers to amyloid fibril models and A?{sub 1-40} fibrils from computational approaches

    SciTech Connect (OSTI)

    Alí-Torres, Jorge; Rimola, Albert; Sodupe, Mariona; Rodriguez-Rodríguez, Cristina

    2014-10-06

    The present contribution analyzes the binding of ThT and neutral ThT derivatives to a ?-sheet model by means of quantum chemical calculations. In addition, we study the properties of four molecules: (2-(2-hydroxyphenyl)benzoxazole (HBX), 2-(2-hydroxyphenyl)benzothiazole (HBT) and their respective iodinated compounds, HBXI and HBTI, in binding to amyloid fibril models and A?{sub 1-40}fibrils by using a combination of docking, molecular dynamics and quantum mechanics calculations.

  17. Near-infrared fluorescence glucose sensing based on glucose/galactose-binding protein coupled to 651-Blue Oxazine

    SciTech Connect (OSTI)

    Khan, Faaizah; Pickup, John C.

    2013-08-30

    Highlights: •We showed that the NIR fluorophore, 651-Blue Oxazine, is solvatochromic (polarity sensitive). •Blue Oxazine was covalently attached to mutants of glucose/galactose-binding protein (GBP). •Fluorescence intensity of GBP-Blue Oxazine increased with addition of glucose. •Fluorescence from bead-immobilised GBP-Blue Oxazine was detectable through skin in vitro. •This shows proof-of-concept for non-invasive glucose sensing using GBP-Blue Oxazine. -- Abstract: Near-infrared (NIR) fluorescent dyes that are environmentally sensitive or solvatochromic are useful tools for protein labelling in in vivo biosensor applications such as glucose monitoring in diabetes since their spectral properties are mostly independent of tissue autofluorescence and light scattering, and they offer potential for non-invasive analyte sensing. We showed that the fluorophore 651-Blue Oxazine is polarity-sensitive, with a marked reduction in NIR fluorescence on increasing solvent polarity. Mutants of glucose/galactose-binding protein (GBP) used as the glucose receptor were site-specifically and covalently labelled with Blue Oxazine using click chemistry. Mutants H152C/A213R and H152C/A213R/L238S showed fluorescence increases of 15% and 21% on addition of saturating glucose concentrations and binding constants of 6 and 25 mM respectively. Fluorescence responses to glucose were preserved when GBP-Blue Oxazine was immobilised to agarose beads, and the beads were excited by NIR light through a mouse skin preparation studied in vitro. We conclude GBP-Blue Oxazine shows proof-of-concept as a non-invasive continuous glucose sensing system.

  18. Binding energies and spatial structures of small carrier complexes in monolayer transition-metal dichalcogenides via diffusion Monte Carlo

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mayers, Matthew Z.; Berkelbach, Timothy C.; Hybertsen, Mark S.; Reichman, David R.

    2015-10-09

    Ground-state diffusion Monte Carlo is used to investigate the binding energies and intercarrier radial probability distributions of excitons, trions, and biexcitons in a variety of two-dimensional transition-metal dichalcogenide materials. We compare these results to approximate variational calculations, as well as to analogous Monte Carlo calculations performed with simplified carrier interaction potentials. Our results highlight the successes and failures of approximate approaches as well as the physical features that determine the stability of small carrier complexes in monolayer transition-metal dichalcogenide materials. In conclusion, we discuss points of agreement and disagreement with recent experiments.

  19. Selective Binding of O2 over N2 in a Redox-Active Metal-Organic Framework

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    with Open Iron(II) Coordination Sites | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Selective Binding of O2 over N2 in a Redox-Active Metal-Organic Framework with Open Iron(II) Coordination Sites Previous Next List E. D. Bloch, L. J. Murray, W. L. Queen, S. Chavan, S. N. Maximoff, J. P. Bigi, R. Krishna, V. K. Peterson, F. Grandjean, G. J. Long, B. Smit, S. Bordiga, C. M. Brown, and J. R. Long, J. Am. Chem. Soc. 133 (37), 14814 (2011) DOI:

  20. The role of amino acid electron-donor/acceptor atoms in host-cell binding peptides is associated with their 3D structure and HLA-binding capacity in sterile malarial immunity induction

    SciTech Connect (OSTI)

    Patarroyo, Manuel E.; Almonacid, Hannia; Moreno-Vranich, Armando

    2012-01-20

    Highlights: Black-Right-Pointing-Pointer Fundamental residues located in some HABPs are associated with their 3D structure. Black-Right-Pointing-Pointer Electron-donor atoms present in {beta}-turn, random, distorted {alpha}-helix structures. Black-Right-Pointing-Pointer Electron-donor atoms bound to HLA-DR53. Black-Right-Pointing-Pointer Electron-acceptor atoms present in regular {alpha}-helix structure bound to HLA-DR52. -- Abstract: Plasmodium falciparum malaria continues being one of the parasitic diseases causing the highest worldwide mortality due to the parasite's multiple evasion mechanisms, such as immunological silence. Membrane and organelle proteins are used during invasion for interactions mediated by high binding ability peptides (HABPs); these have amino acids which establish hydrogen bonds between them in some of their critical binding residues. Immunisation assays in the Aotus model using HABPs whose critical residues had been modified have revealed a conformational change thereby enabling a protection-inducing response. This has improved fitting within HLA-DR{beta}1{sup Asterisk-Operator} molecules where amino acid electron-donor atoms present in {beta}-turn, random or distorted {alpha}-helix structures preferentially bound to HLA-DR53 molecules, whilst HABPs having amino acid electron-acceptor atoms present in regular {alpha}-helix structure bound to HLA-DR52. This data has great implications for vaccine development.

  1. Steven Weinberg, Weak Interactions, and Electromagnetic Interactions

    Office of Scientific and Technical Information (OSTI)

    Symmetries; Physical Review D, Vol. 7, Issue 4: 1068-1082, February 15, 1973 Current Algebra and Gauge Theories. I; Physical Review D, Vol. 8, Issue 2: 605-625, July 15, 1973...

  2. Modeling the Interaction between Integrin-Binding Peptide (RGD) and Rutile Surface: The Effect of Na+ on Peptide Adsorption

    SciTech Connect (OSTI)

    Wu, Chunya; Skelton, Adam; Chen, Mingjun; Vlcek, Lukas; Cummings, Peter T

    2011-01-01

    The dynamics of a single tripeptide Arg-Gly-Asp (RGD) adsorbing onto negatively charged hydroxylated rutile (110) surface in aqueous solution was studied using molecular dynamics (MD) simulations. The results indicate that the adsorbed Na{sup +} ions play an important role in determining the binding geometry of RGD. With an initial 'horseshoe' configuration, the charged side groups (COO{sup -} and NH{sub 2}) of the peptide are able to interact with the surface through direct hydrogen bonds (H bonds) in the very early stage of adsorption. The Na{sup +} ions approach the positively charged Arg side chain, competing with the Arg side chain for adsorption to the negatively charged hydroxyl oxygen. In coordination with the structural adjustment of the peptide, the Arg residue is driven to detach from the rutile surface. In contrast, the Na+ ions in close proximity to the negatively charged Asp side chain contribute to the binding of the COO{sup -} group on the surface, helping the carboxyl oxygen not involved in COO{sup -}-surface H bonds to orientate toward the hydroxyl hydrogens. Once both carboxyl oxygens form enough H bonds with the hydroxyl hydrogens, the redundant ions move toward a more favorable adsorption site.

  3. Functional glass slides for in vitro evaluation of interactions between osteosarcoma TE85 cells and mineral-binding ligands

    SciTech Connect (OSTI)

    Song, Jie; Chen, Julia; Klapperich, Catherine M.; Eng, Vincent; Bertozzi, Carolyn R.

    2004-07-20

    Primary amine-functionalized glass slides obtained through a multi-step plasma treatment were conjugated with anionic amino acids that are frequently found as mineral binding elements in acidic extracellular matrix components of natural bone. The modified glass surfaces were characterized by X-ray photoelectron spectroscopy (XPS) and contact angle measurements. Human osteosarcoma TE85 cells were cultured on these functionalized slides and analyses on both protein and gene expression levels were performed to probe the ''biocompatibility'' of the surface ligands. Cell attachment and proliferation on anionic surfaces were either better than or comparable to those of cells cultured on tissue culture polystyrene (TCPS). The modified glass surfaces promoted the expression of osteocalcin, alkaline phosphatase activity and ECM proteins such as fibronectin and vitronectin under differentiation culture conditions. Transcript analysis using gene chip microarrays confirmed that culturing TE85 cells on anionic surfaces did not activate apoptotic pathways. Collectively, these results suggest that the potential mineral-binding anionic ligands examined here do not exert significant adverse effects on the expression of important osteogenic markers of TE85 cells. This work paves the way for the incorporation of these ligands into 3-dimensional artificial bone-like scaffolds.

  4. Non-binding conductor load bearing roller for a gas-insulated transmission line having a corrugated outer conductor

    DOE Patents [OSTI]

    Fischer, William H. (Pittsburgh, PA)

    1984-01-01

    A gas-insulated transmission line includes a corrugated outer conductor, an inner conductor disposed within and insulated from the outer conductor by means of support insulators and an insulating gas, and a non-binding transport device for supporting and permitting movement of the inner conductor/insulating support assembly axially along the corrugated outer conductor without radial displacement and for moving without binding along corrugations of any slope less than vertical. The transport device includes two movable contacts, such as skids or rollers, supported on a common pivot lever, the pivot lever being rotatably disposed about a pivot lever axis, which pivot lever axis is in turn disposed on the periphery of a support insulator or particle trap if one is used. The movable contacts are separated axially a distance equal to the axial distance between the peaks and valleys of the corrugations of the outer conductor and separated radially a distance equal to the radial distance between the peaks and valleys of the corrugations of the outer conductor. The transport device has the pivot lever axis disposed parallel to the motion of travel of the inner conductor/insulating support assembly.

  5. Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smooth particle hydrodynamics

    SciTech Connect (OSTI)

    Pan, Wenxiao; Daily, Michael D.; Baker, Nathan A.

    2015-12-01

    We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to an acetylcholinesterase monomer. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) boundary condition, is considered on the reactive boundaries. This new boundary condition treatment allows for the analysis of enzymes with "imperfect" reaction rates. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates. Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.

  6. Structure-Based Design of Robust Glucose Biosensors using a Thermotoga maritima Periplasmic Glucose-Binding Protein

    SciTech Connect (OSTI)

    Tian,Y.; Cunco, M.; Changela, A.; Hocker, B.; Beese, L.; Hellinga, H.

    2007-01-01

    We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Angstroms resolution by X-ray crystallography. TmGBP is specific for glucose and exhibits high thermostability (midpoint of thermal denaturation is 119 {+-} 1 C and 144 {+-} 2 C in the absence and presence of 1 mM glucose, respectively). A series of fluorescent conjugates was constructed by coupling single, environmentally sensitive fluorophores to unique cysteines introduced by site-specific mutagenesis at positions predicted to be responsive to ligand-induced conformational changes based on the structure. These conjugates were screened to identify engineered tmGBPs that function as reagentless fluorescent glucose biosensors. The Y13C Cy5 conjugate is bright, gives a large response to glucose over concentration ranges appropriate for in vivo monitoring of blood glucose levels (1-30 mM), and can be immobilized in an orientation-specific manner in microtiter plates to give a reversible response to glucose. The immobilized protein retains its response after long-term storage at room temperature.

  7. H2-M polymorphism in mice susceptible to collagen-induced arthritis involves the peptide binding groove

    SciTech Connect (OSTI)

    Walter, W.; Loos, M.; Maeurer, M.J.

    1996-12-31

    The ability to develop type II collagen (CII)-induced arthritis (CIA) in mice is associated with the major histocompatibility I-A gene and with as yet poorly defined regulatory molecules of the major histocompatibility complex (MHC) class II antigen processing and presentation pathway. H2-M molecules are thought to be involved in the loading of antigenic peptides into the MHC class II binding cleft. We sequenced H2-Ma, H2-Mb1, and H2-Mb2 genes from CIA-susceptible and -resistant mouse strains and identified four different Ma and Mb2 alleles, and three different Mb1 alleles defined by polymorphic residues within the predicted peptide binding groove. Most CIA-resistant mouse strains share common Ma, Mb1, and Mb2 alleles. In contrast, H2-M alleles designated Ma-III, Ma-IV, Mb1-III, and Mb2-IV could be exclusively identified in the CIA-susceptible H2{sup r} and H2{sup q} haplotypes, suggesting that allelic H2-M molecules may modulate the composition of different CII peptides loaded onto MHC class II molecules, presumably presenting {open_quotes}arthritogenic{close_quotes} epitopes to T lymphocytes. 42 refs., 4 figs., 3 tabs.

  8. Search for long-lived, weakly interacting particles that decay to displaced hadronic jets in proton-proton collisions at s=8  TeV with the ATLAS detector

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Aad, G.; Abbott, B.; Abdallah, J.; Abdinov, O.; Aben, R.; Abolins, M.; AbouZeid, O. S.; Abramowicz, H.; Abreu, H.; Abreu, R.; et al

    2015-07-17

    A search for the decay of neutral, weakly interacting, long-lived particles using data collected by the ATLAS detector at the LHC is presented. This analysis uses the full data set recorded in 2012: 20.3 fb-1 of proton-proton collision data at √s = 8 TeV. The search employs techniques for reconstructing decay vertices of long-lived particles decaying to jets in the inner tracking detector and muon spectrometer. Signal events require at least two reconstructed vertices. No significant excess of events over the expected background is found, and limits as a function of proper lifetime are reported for the decay of themore » Higgs boson and other scalar bosons to long-lived particles and for Hidden Valley Z' and Stealth SUSY benchmark models. The first search results for displaced decays in Z' and Stealth SUSY models are presented. The upper bounds of the excluded proper lifetimes are the most stringent to date.« less

  9. Dimorphism in iron(II) methylphosphonate: Low-temperature crystal structure and temperature-dependent Mossbauer studies of a new form of the layered weak ferromagnet Fe[(CH{sub 3}PO{sub 3})(H{sub 2}O)

    SciTech Connect (OSTI)

    Leone, Philippe . E-mail: philippe.leone@cnrs-imn.fr; Palvadeau, Pierre; Boubekeur, Kamal; Meerschaut, Alain; Bellitto, Carlo; Bauer, Elvira M.; Righini, Guido; Fabritchnyi, Pavel

    2005-04-15

    A second form of the literature-known layered weak ferromagnet Fe[(CH{sub 3}PO{sub 3})(H{sub 2}O)] has been isolated. The crystal structure determination of this new form (2) has been carried out at T=300, 200 and 130K. It crystallizes in the orthorhombic space group Pmn2{sub 1}: a=5.7177(11), b=8.8093(18), c=4.8154(10)A, while form (1) crystallizes in the space group Pna2{sub 1}: a=17.58(2), b=4.814(1), c=5.719(1)A. Moessbauer spectroscopy on form (2) has been performed in the temperature range 4-300K; and, at T{approx}160K, a drastic change in the quadrupole splitting ({delta}E) and a broadening of the doublet components is noticed. But surprisingly, on cooling the crystal, no structural change is observed, which could account for the increase in {delta}E. Below T=25K, {sup 57}Fe spectra transform into hyperfine splitting patterns which reveal a magnetically ordered state in agreement with the results of earlier magnetic susceptibility studies.

  10. Molecular-Scale Features that Govern the Effects of O-Glycosylation on a Carbohydrate-Binding Module

    SciTech Connect (OSTI)

    Guan, Xiaoyang; Chaffey, Patrick K.; Zeng, Chen; Greene, Eric R.; Chen, Liqun; Drake, Matthew R.; Chen, Claire; Groobman, Ari; Resch, Michael G.; Himmel, Michael E.; Beckham, Gregg T.; Tan, Zhongping

    2015-09-21

    The protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of O-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of O-glycosylation in this system. This study suggests the possibility of designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site.

  11. Molecular-Scale Features that Govern the Effects of O-Glycosylation on a Carbohydrate-Binding Module

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Guan, Xiaoyang; Chaffey, Patrick K.; Zeng, Chen; Greene, Eric R.; Chen, Liqun; Drake, Matthew R.; Chen, Claire; Groobman, Ari; Resch, Michael G.; Himmel, Michael E.; et al

    2015-09-21

    The protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of O-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of O-glycosylation in this system. This study suggests the possibility ofmore » designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site.« less

  12. Communication: Towards the binding energy and vibrational red shift of the simplest organic hydrogen bond: Harmonic constraints for methanol dimer

    SciTech Connect (OSTI)

    Heger, Matthias; Suhm, Martin A.; Mata, Ricardo A.

    2014-09-14

    The discrepancy between experimental and harmonically predicted shifts of the OH stretching fundamental of methanol upon hydrogen bonding to a second methanol unit is too large to be blamed mostly on diagonal and off-diagonal anharmonicity corrections. It is shown that a decisive contribution comes from post-MP2 electron correlation effects, which appear not to be captured by any of the popular density functionals. We also identify that the major deficiency is in the description of the donor OH bond. Together with estimates for the electronic and harmonically zero-point corrected dimer binding energies, this work provides essential constraints for a quantitative description of this simple hydrogen bond. The spectroscopic dissociation energy is predicted to be larger than 18 kJ/mol and the harmonic OH-stretching fundamental shifts by about ?121 cm{sup ?1} upon dimerization, somewhat more than in the anharmonic experiment (?111 cm{sup ?1})

  13. Binding-induced folding of prokaryotic ubiquitin-like protein on the mycobacterium proteasomal ATPase targets substrates for degradation

    SciTech Connect (OSTI)

    Wang, T.; Li, H.; Darwin, K. H.

    2010-11-01

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  14. Binding-induced Folding of Prokaryotic Ubiquitin-like Protein on the Mycobacterium Proteasomal ATPase Targets Substrates for Degradation

    SciTech Connect (OSTI)

    T Wang; K Heran Darwin; H Li

    2011-12-31

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.

  15. Depletion of cellular poly (A) binding protein prevents protein synthesis and leads to apoptosis in HeLa cells

    SciTech Connect (OSTI)

    Thangima Zannat, Mst.; Bhattacharjee, Rumpa B.; Bag, Jnanankur

    2011-05-13

    Highlights: {yields} Depletion of cellular PABP level arrests mRNA translation in HeLa cells. {yields} PABP knock down leads to apoptotic cell death. {yields} PABP depletion does not affect transcription. {yields} PABP depletion does not lead to nuclear accumulation of mRNA. -- Abstract: The cytoplasmic poly (A) binding protein (PABP) is important in mRNA translation and stability. In yeast, depletion of PABP leads to translation arrest. Similarly, the PABP gene in Drosophila is important for proper development. It is however uncertain, whether mammalian PABP is essential for mRNA translation. Here we showed the effect of PABP depletion on mRNA metabolism in HeLa cells by using a small interfering RNA. Our results suggest that depletion of PABP prevents protein synthesis and consequently leads to cell death through apoptosis. Interestingly, no detectable effect of PABP depletion on transcription, transport and stability of mRNA was observed.

  16. Atomic evidence that modification of H-bonds established with amino acids critical for host-cell binding induces sterile immunity against malaria

    SciTech Connect (OSTI)

    Patarroyo, Manuel E.; Cifuentes, Gladys; Universidad del Rosario, Bogota ; Pirajan, Camilo; Moreno-Vranich, Armando; Vanegas, Magnolia; Universidad Nacional de Colombia, Bogota; Universidad del Rosario, Bogota

    2010-04-09

    Based on the 3D X-ray crystallographic structures of relevant proteins of the malaria parasite involved in invasion to host cells and 3D NMR structures of High Activity Binding Peptides (HABPs) and their respective analogues, it was found that HABPs are rendered into highly immunogenic and sterile immunity inducers in the Aotus experimental model by modifying those amino acids that establish H-bonds with other HABPs or binding to host's cells. This finding adds striking and novel physicochemical principles, at the atomic level, for a logical and rational vaccine development methodology against infectious disease, among them malaria.

  17. Observations of the scale-dependent turbulence and evaluation of the flux-gradient relationship for sensible heat for a closed Douglas-Fir canopy in very weak wind conditions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Vickers, D.; Thomas, C.

    2014-05-13

    Observations of the scale-dependent turbulent fluxes and variances above, within and beneath a tall closed Douglas-Fir canopy in very weak winds are examined. The daytime subcanopy vertical velocity spectra exhibit a double-peak structure with peaks at time scales of 0.8 s and 51.2 s. A double-peak structure is also observed in the daytime subcanopy heat flux cospectra. The daytime momentum flux cospectra inside the canopy and in the subcanopy are characterized by a relatively large cross-wind component, likely due to the extremely light and variable winds, such that the definition of a mean wind direction, and subsequent partitioning of themore »momentum flux into along- and cross-wind components, has little physical meaning. Positive values of both momentum flux components in the subcanopy contribute to upward transfer of momentum, consistent with the observed mean wind speed profile. In the canopy at night at the smallest resolved scales, we find relatively large momentum fluxes (compared to at larger scales), and increasing vertical velocity variance with decreasing time scale, consistent with very small eddies likely generated by wake shedding from the canopy elements that transport momentum but not heat. We find unusually large values of the velocity aspect ratio within the canopy, consistent with enhanced suppression of the horizontal wind components compared to the vertical by the canopy. The flux-gradient approach for sensible heat flux is found to be valid for the subcanopy and above-canopy layers when considered separately; however, single source approaches that ignore the canopy fail because they make the heat flux appear to be counter-gradient when in fact it is aligned with the local temperature gradient in both the subcanopy and above-canopy layers. Modeled sensible heat fluxes above dark warm closed canopies are likely underestimated using typical values of the Stanton number.« less

  18. First-principles investigation on the electronic efficiency and binding energy of the contacts formed by graphene and poly-aromatic hydrocarbon anchoring groups

    SciTech Connect (OSTI)

    Li, Yang; Tu, Xingchen; Wang, Hao; Hou, Shimin; Sanvito, Stefano

    2015-04-28

    The electronic efficiency and binding energy of contacts formed between graphene electrodes and poly-aromatic hydrocarbon (PAH) anchoring groups have been investigated by the non-equilibrium Green’s function formalism combined with density functional theory. Our calculations show that PAH molecules always bind in the interior and at the edge of graphene in the AB stacking manner, and that the binding energy increases following the increase of the number of carbon and hydrogen atoms constituting the PAH molecule. When we move to analyzing the electronic transport properties of molecular junctions with a six-carbon alkyne chain as the central molecule, the electronic efficiency of the graphene-PAH contacts is found to depend on the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the corresponding PAH anchoring group, rather than its size. To be specific, the smaller is the HOMO-LUMO gap of the PAH anchoring group, the higher is the electronic efficiency of the graphene-PAH contact. Although the HOMO-LUMO gap of a PAH molecule depends on its specific configuration, PAH molecules with similar atomic structures show a decreasing trend for their HOMO-LUMO gap as the number of fused benzene rings increases. Therefore, graphene-conjugated molecule-graphene junctions with high-binding and high-conducting graphene-PAH contacts can be realized by choosing appropriate PAH anchor groups with a large area and a small HOMO-LUMO gap.

  19. Observations of the scale-dependent turbulence and evaluation of the flux–gradient relationship for sensible heat for a closed Douglas-fir canopy in very weak wind conditions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Vickers, D.; Thomas, C. K.

    2014-09-16

    Observations of the scale-dependent turbulent fluxes, variances, and the bulk transfer parameterization for sensible heat above, within, and beneath a tall closed Douglas-fir canopy in very weak winds are examined. The daytime sub-canopy vertical velocity spectra exhibit a double-peak structure with peaks at timescales of 0.8 s and 51.2 s. A double-peak structure is also observed in the daytime sub-canopy heat flux co-spectra. The daytime momentum flux co-spectra in the upper bole space and in the sub-canopy are characterized by a relatively large cross-wind component, likely due to the extremely light and variable winds, such that the definition of amore »mean wind direction, and subsequent partitioning of the momentum flux into along- and cross-wind components, has little physical meaning. Positive values of both momentum flux components in the sub-canopy contribute to upward transfer of momentum, consistent with the observed sub-canopy secondary wind speed maximum. For the smallest resolved scales in the canopy at nighttime, we find increasing vertical velocity variance with decreasing timescale, consistent with very small eddies possibly generated by wake shedding from the canopy elements that transport momentum, but not heat. Unusually large values of the velocity aspect ratio within the canopy were observed, consistent with enhanced suppression of the horizontal wind components compared to the vertical by the very dense canopy. The flux–gradient approach for sensible heat flux is found to be valid for the sub-canopy and above-canopy layers when considered separately in spite of the very small fluxes on the order of a few W m−2 in the sub-canopy. However, single-source approaches that ignore the canopy fail because they make the heat flux appear to be counter-gradient when in fact it is aligned with the local temperature gradient in both the sub-canopy and above-canopy layers. While sub-canopy Stanton numbers agreed well with values typically reported in the literature, our estimates for the above-canopy Stanton number were much larger, which likely leads to underestimated modeled sensible heat fluxes above dark warm closed canopies.« less

  20. Correlating the hydrogen evolution reaction activity in alkaline electrolytes with the hydrogen binding energy on monometallic surfaces

    SciTech Connect (OSTI)

    Sheng, WC; Myint, M; Chen, JGG; Yan, YS

    2013-05-01

    The slow reaction kinetics of the hydrogen evolution and oxidation reactions (HER/HOR) on platinum in alkaline electrolytes hinders the development of alkaline electrolysers, solar hydrogen cells and alkaline fuel cells. A fundamental understanding of the exchange current density of the HER/HOR in alkaline media is critical for the search and design of highly active electrocatalysts. By studying the HER on a series of monometallic surfaces, we demonstrate that the HER exchange current density in alkaline solutions can be correlated with the calculated hydrogen binding energy (HBE) on the metal surfaces via a volcano type of relationship. The HER activity varies by several orders of magnitude from Pt at the peak of the plot to W and Au located on the bottom of each side of the plot, similar to the observation in acids. Such a correlation suggests that the HBE can be used as a descriptor for identifying electrocatalysts for HER/HOR in alkaline media, and that the HER exchange current density can be tuned by modifying the surface chemical properties.

  1. Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action

    SciTech Connect (OSTI)

    Baram, David; Pyetan, Erez; Sittner, Assa; Auerbach-Nevo, Tamar; Bashan, Anat; Yonath, Ada (WIS-I)

    2010-07-13

    Trigger factor (TF), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. Here, we present the 3.5-{angstrom} crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with the N-terminal domain of TF (TFa) from the same organism. For anchoring, TFa exploits a small ribosomal surface area in the vicinity of proteins L23 and L29, by using its 'signature motif' as well as additional structural elements. The molecular details of TFa interactions reveal that L23 is essential for the association of TF with the ribosome and may serve as a channel of communication with the nascent chain progressing in the tunnel. L29 appears to induce a conformational change in TFa, which results in the exposure of TFa hydrophobic patches to the opening of the ribosomal exit tunnel, thus increasing its affinity for hydrophobic segments of the emerging nascent polypeptide. This observation implies that, in addition to creating a protected folding space for the emerging nascent chain, TF association with the ribosome prevents aggregation by providing a competing hydrophobic environment and may be critical for attaining the functional conformation necessary for chaperone activity.

  2. Insights into Regulated Ligand Binding Sites from the Structure of ZO-1 Src Homology 3-Guanylate Kinase Module

    SciTech Connect (OSTI)

    Lye, Ming F.; Fanning, Alan S.; Su, Ying; Anderson, James M.; Lavie, Arnon (UNC); (UIC)

    2010-11-09

    Tight junctions are dynamic components of epithelial and endothelial cells that regulate the paracellular transport of ions, solutes, and immune cells. The assembly and permeability of these junctions is dependent on the zonula occludens (ZO) proteins, members of the membrane-associated guanylate kinase homolog (MAGUK) protein family, which are characterized by a core Src homology 3 (SH3)-GUK module that coordinates multiple protein-protein interactions. The structure of the ZO-1 SH3-GUK domain confirms that the interdependent folding of the SH3 and GUK domains is a conserved feature of MAGUKs, but differences in the orientation of the GUK domains in three different MAGUKs reveal interdomain flexibility of the core unit. Using pull-down assays, we show that an effector loop, the U6 region in ZO-1, forms a novel intramolecular interaction with the core module. This interaction is divalent cation-dependent and overlaps with the binding site for the regulatory molecule calmodulin on the GUK domain. These findings provide insight into the previously observed ability of the U6 region to regulate TJ assembly in vivo and the structural basis for the complex protein interactions of the MAGUK family.

  3. Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses

    SciTech Connect (OSTI)

    Moody, M.  Anthony; Gao, Feng; Gurley, Thaddeus  C.; Amos, Joshua  D.; Kumar, Amit; Hora, Bhavna; Marshall, Dawn  J.; Whitesides, John  F.; Xia, Shi-Mao; Parks, Robert; Lloyd, Krissey  E.; Hwang, Kwan-Ki; Lu, Xiaozhi; Bonsignori, Mattia; Finzi, Andrés; Vandergrift, Nathan  A.; Alam, S.  Munir; Ferrari, Guido; Shen, Xiaoying; Tomaras, Georgia  D.; Kamanga, Gift; Cohen, Myron  S.; Sam, Noel  E.; Kapiga, Saidi; Gray, Elin S.; Tumba, Nancy  L.; Morris, Lynn; Zolla-Pazner, Susan; Gorny, Miroslaw  K.; Mascola, John  R.; Hahn, Beatrice H.; Shaw, George  M.; Sodroski, Joseph  G.; Liao, Hua-Xin; Montefiori, David C.; Hraber, Peter T.; Korber, Bette T.; Haynes, Barton F.

    2015-09-09

    The third variable (V3) loop and the CD4 binding site (CD4bs) of the viral envelope are frequently targeted by neutralizing antibodies (nAbs) in HIV-1-infected individuals. In chronic infection, virus escape mutants repopulate the plasma and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize, but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tier 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.

  4. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

    SciTech Connect (OSTI)

    Henke, Paul S.; Mak, Chi H.

    2014-08-14

    The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg{sup 2+} that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.

  5. Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Moody, M.  Anthony; Gao, Feng; Gurley, Thaddeus  C.; Amos, Joshua  D.; Kumar, Amit; Hora, Bhavna; Marshall, Dawn  J.; Whitesides, John  F.; Xia, Shi-Mao; Parks, Robert; et al

    2015-09-09

    The third variable (V3) loop and the CD4 binding site (CD4bs) of the viral envelope are frequently targeted by neutralizing antibodies (nAbs) in HIV-1-infected individuals. In chronic infection, virus escape mutants repopulate the plasma and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize, but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tiermore » 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.« less

  6. hnRNP L binds to CA repeats in the 3'UTR of bcl-2 mRNA

    SciTech Connect (OSTI)

    Lee, Dong-Hyoung; Lim, Mi-Hyun; Youn, Dong-Ye [Department of Biochemistry, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-gu, Seoul 137-701 (Korea, Republic of)] [Department of Biochemistry, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-gu, Seoul 137-701 (Korea, Republic of); Jung, Seung Eun [Department of Medical Science, The Graduate School, Yonsei University, Seoul (Korea, Republic of)] [Department of Medical Science, The Graduate School, Yonsei University, Seoul (Korea, Republic of); Ahn, Young Soo [Brain Korea 21 Project for Medical Science, Brain Research Institute, Department of Pharmacology, Yonsei University College of Medicine, Seoul (Korea, Republic of)] [Brain Korea 21 Project for Medical Science, Brain Research Institute, Department of Pharmacology, Yonsei University College of Medicine, Seoul (Korea, Republic of); Tsujimoto, Yoshihide [Department of Medical Genetics, Laboratory of Molecular Genetics, Osaka University Medical School, Osaka (Japan)] [Department of Medical Genetics, Laboratory of Molecular Genetics, Osaka University Medical School, Osaka (Japan); Lee, Jeong-Hwa, E-mail: leejh@catholic.ac.kr [Department of Biochemistry, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-gu, Seoul 137-701 (Korea, Republic of)] [Department of Biochemistry, College of Medicine, The Catholic University of Korea, 505 Banpo-Dong, Seocho-gu, Seoul 137-701 (Korea, Republic of)

    2009-05-08

    We previously reported that the CA-repeat sequence in the 3'-untranslated region (3'UTR) of bcl-2 mRNA is involved in the decay of bcl-2 mRNA. However, the trans-acting factor for the CA element in bcl-2 mRNA remains unidentified. The heterogeneous nuclear ribonucleoprotein L (hnRNP L), an intron splicing factor, has been reported to bind to CA repeats and CA clusters in the 3'UTR of several genes. We reported herein that the CA repeats of bcl-2 mRNA have the potential to form a distinct ribonuclear protein complex in cytoplasmic extracts of MCF-7 cells, as evidenced by RNA electrophoretic mobility shift assays (REMSA). A super-shift assay using the hnRNP L antibody completely shifted the complex. Immunoprecipitation with the hnRNP L antibody and MCF-7 cells followed by RT-PCR revealed that hnRNP L interacts with endogenous bcl-2 mRNA in vivo. Furthermore, the suppression of hnRNP L in MCF-7 cells by the transfection of siRNA for hnRNP L resulted in a delay in the degradation of RNA transcripts including CA repeats of bcl-2 mRNA in vitro, suggesting that the interaction between hnRNPL and CA repeats of bcl-2 mRNA participates in destabilizing bcl-2 mRNA.

  7. Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved ?-helix for Act1 binding and IL-17 signaling

    SciTech Connect (OSTI)

    Zhang, Bing [Oklahoma State University, Stillwater, OK 74078 (United States); Liu, Caini; Qian, Wen [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Han, Yue [Oklahoma State University, Stillwater, OK 74078 (United States); Li, Xiaoxia, E-mail: lix@ccf.org [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Deng, Junpeng, E-mail: lix@ccf.org [Oklahoma State University, Stillwater, OK 74078 (United States)

    2014-05-01

    Crystal structure of the SEFIR domain from human IL-17 receptor A provides new insights into IL-17 signaling. Interleukin 17 (IL-17) cytokines play a crucial role in mediating inflammatory and autoimmune diseases. A unique intracellular signaling domain termed SEFIR is found within all IL-17 receptors (IL-17Rs) as well as the key adaptor protein Act1. SEFIR-mediated protein–protein interaction is a crucial step in IL-17 cytokine signaling. Here, the 2.3 Å resolution crystal structure of the SEFIR domain of IL-17RA, the most commonly shared receptor for IL-17 cytokine signaling, is reported. The structure includes the complete SEFIR domain and an additional ?-helical C-terminal extension, which pack tightly together to form a compact unit. Structural comparison between the SEFIR domains of IL-17RA and IL-17RB reveals substantial differences in protein topology and folding. The uniquely long insertion between strand ?C and helix ?C in IL-17RA SEFIR is mostly well ordered, displaying a helix (?CC?{sub ins}) and a flexible loop (CC?). The DD? loop in the IL-17RA SEFIR structure is much shorter; it rotates nearly 90° with respect to the counterpart in the IL-17RB SEFIR structure and shifts about 12 Å to accommodate the ?CC?{sub ins} helix without forming any knots. Helix ?C was identified as critical for its interaction with Act1 and IL-17-stimulated gene expression. The data suggest that the heterotypic SEFIR–SEFIR association via helix ?C is a conserved and signature mechanism specific for IL-17 signaling. The structure also suggests that the downstream motif of IL-17RA SEFIR together with helix ?C could provide a composite ligand-binding surface for recruiting Act1 during IL-17 signaling.

  8. Atomic nuclei decay modes by spontaneous emission of heavy ions

    SciTech Connect (OSTI)

    Poenaru, D.N.; Ivascu, M.; Sndulescu, A.; Greiner, W.

    1985-08-01

    The great majority of the known nuclides with Z>40, including the so-called stable nuclides, are metastable with respect to several modes of spontaneous superasymmetric splitting. A model extended from the fission theory of alpha decay allows one to estimate the lifetimes and the branching ratios relative to the alpha decay for these natural radioactivities. From a huge amount of systematic calculations it is concluded that the process should proceed with maximum intensity in the trans-lead nuclei, where the minimum lifetime is obtained from parent-emitted heavy ion combinations leading to a magic (/sup 208/Pb) or almost magic daughter nucleus. More than 140 nuclides with atomic number smaller than 25 are possible candidates to be emitted from heavy nuclei, with half-lives in the range of 10/sup 10/--10/sup 30/ s: /sup 5/He, /sup 8en-dash10/Be, /sup 11,12/B, /sup 12en-dash16/C, /sup 13en-dash17/N, /sup 15en-dash22/O, /sup 18en-dash23/F, /sup 20en-dash26/Ne, /sup 23en-dash28/Na, /sup 23en-dash30/Mg, /sup 27en-dash32/Al, /sup 28en-dash36/Si, /sup 31en-dash39/P, /sup 32en-dash42/S, /sup 35en-dash45/Cl, /sup 37en-dash47/Ar, /sup 40en-dash49/ K, . .Ca, /sup 44en-dash53/ Sc, /sup 46en-dash53/Ti, /sup 48en-dash54/V, and /sup 49en-dash55/ Cr. The shell structure and the pairing effects are clearly manifested in these new decay modes.

  9. Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor, P

    SciTech Connect (OSTI)

    Green, Todd J.; Luo, Ming

    2009-10-05

    The negative-strand RNA viruses (NSRVs) are unique because their nucleocapsid, not the naked RNA, is the active template for transcription and replication. The viral polymerase of nonsegmented NSRVs contains a large polymerase catalytic subunit (L) and a nonenzymatic cofactor, the phosphoprotein (P). Insight into how P delivers the polymerase complex to the nucleocapsid has long been pursued by reverse genetics and biochemical approaches. Here, we present the X-ray crystal structure of the C-terminal domain of P of vesicular stomatitis virus, a prototypic nonsegmented NSRV, bound to nucleocapsid-like particles. P binds primarily to the C-terminal lobe of 2 adjacent N proteins within the nucleocapsid. This binding mode is exclusive to the nucleocapsid, not the nucleocapsid (N) protein in other existing forms. Localization of phosphorylation sites within P and their proximity to the RNA cavity give insight into how the L protein might be oriented to access the RNA template.

  10. Binding of the Respiratory Chain Inhibitor Antimycin to theMitochondrial bc1 Complex: A New Crystal Structure Reveals an AlteredIntramolecular Hydrogen-Bonding Pattern

    SciTech Connect (OSTI)

    Huang, Li-shar; Cobessi, David; Tung, Eric Y.; Berry, Edward A.

    2005-05-10

    Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex.Structure-activity-relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28Angstrom resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cyt b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alpha-A helix.

  11. Binding of flexible and constrained ligands to the Grb2 SH2 domain: structural effects of ligand preorganization

    SciTech Connect (OSTI)

    Clements, John H.; DeLorbe, John E.; Benfield, Aaron P.; Martin, Stephen F.

    2010-10-01

    Structures of the Grb2 SH2 domain complexed with a series of flexible and constrained replacements of the phosphotyrosine residue in tripeptides derived from Ac-pYXN (where X = V, I, E and Q) were compared to determine what, if any, structural differences arise as a result of ligand preorganization. Structures of the Grb2 SH2 domain complexed with a series of pseudopeptides containing flexible (benzyl succinate) and constrained (aryl cyclopropanedicarboxylate) replacements of the phosphotyrosine (pY) residue in tripeptides derived from Ac-pYXN-NH{sub 2} (where X = V, I, E and Q) were elucidated by X-ray crystallography. Complexes of flexible/constrained pairs having the same pY + 1 amino acid were analyzed in order to ascertain what structural differences might be attributed to constraining the phosphotyrosine replacement. In this context, a given structural dissimilarity between complexes was considered to be significant if it was greater than the corresponding difference in complexes coexisting within the same asymmetric unit. The backbone atoms of the domain generally adopt a similar conformation and orientation relative to the ligands in the complexes of each flexible/constrained pair, although there are some significant differences in the relative orientations of several loop regions, most notably in the BC loop that forms part of the binding pocket for the phosphate group in the tyrosine replacements. These variations are greater in the set of complexes of constrained ligands than in the set of complexes of flexible ligands. The constrained ligands make more direct polar contacts to the domain than their flexible counterparts, whereas the more flexible ligand of each pair makes more single-water-mediated contacts to the domain; there was no correlation between the total number of protein–ligand contacts and whether the phosphotyrosine replacement of the ligand was preorganized. The observed differences in hydrophobic interactions between the complexes of each flexible/constrained ligand pair were generally similar to those observed upon comparing such contacts in coexisting complexes. The average adjusted B factors of the backbone atoms of the domain and loop regions are significantly greater in the complexes of constrained ligands than in the complexes of the corresponding flexible ligands, suggesting greater thermal motion in the crystalline state in the former complexes. There was no apparent correlation between variations in crystal packing and observed structural differences or similarities in the complexes of flexible and constrained ligands, but the possibility that crystal packing might result in structural variations cannot be rigorously excluded. Overall, it appears that there are more variations in the three-dimensional structure of the protein and the ligand in complexes of the constrained ligands than in those of their more flexible counterparts.

  12. Measurement of the Effective Weak Mixing Angle inpp¯?Z/?*?e+e-Events

    SciTech Connect (OSTI)

    Abazov, V.? M.; Abbott, B.; Acharya, B.? S.; Adams, M.; Adams, T.; Agnew, J.? P.; Alexeev, G.? D.; Alkhazov, G.; Alton, A.; Askew, A.; Atkins, S.; Augsten, K.; Avila, C.; Badaud, F.; Bagby, L.; Baldin, B.; Bandurin, D. ?V.; Banerjee, S.; Barberis, E.; Baringer, P.; Bartlett, J. ?F.; Bassler, U.; Bazterra, V.; Bean, A.; Begalli, M.; Bellantoni, L.; Beri, S.? B.; Bernardi, G.; Bernhard, R.; Bertram, I.; Besançon, M.; Beuselinck, R.; Bhat, P.? C.; Bhatia, S.; Bhatnagar, V.; Blazey, G.; Blessing, S.; Bloom, K.; Boehnlein, A.; Boline, D.; Boos, E.? E.; Borissov, G.; Borysova, M.; Brandt, A.; Brandt, O.; Brock, R.; Bross, A.; Brown, D.; Bu, X. ?B.; Buehler, M.; Buescher, V.; Bunichev, V.; Burdin, S.; Buszello, C.? P.; Camacho-Pérez, E.; Casey, B.? C.?K.; Castilla-Valdez, H.; Caughron, S.; Chakrabarti, S.; Chan, K.? M.; Chandra, A.; Chapon, E.; Chen, G.; Cho, S.? W.; Choi, S.; Choudhary, B.; Cihangir, S.; Claes, D.; Clutter, J.; Cooke, M.; Cooper, W. ?E.; Corcoran, M.; Couderc, F.; Cousinou, M. -C.; Cutts, D.; Das, A.; Davies, G.; de Jong, S. ?J.; De La Cruz-Burelo, E.; Déliot, F.; Demina, R.; Denisov, D.; Denisov, S.? P.; Desai, S.; Deterre, C.; DeVaughan, K.; Diehl, H.? T.; Diesburg, M.; Ding, P. ?F.; Dominguez, A.; Dubey, A.; Dudko, L.? V.; Duperrin, A.; Dutt, S.; Eads, M.; Edmunds, D.; Ellison, J.; Elvira, V. ?D.; Enari, Y.; Evans, H.; Evdokimov, V.? N.; Fauré, A.; Feng, L.; Ferbel, T.; Fiedler, F.; Filthaut, F.; Fisher, W.; Fisk, H.? E.; Fortner, M.; Fox, H.; Fuess, S.; Garbincius, P. ?H.; Garcia-Bellido, A.; García-González, J. ?A.; Gavrilov, V.; Geng, W.; Gerber, C.? E.; Gershtein, Y.; Ginther, G.; Gogota, O.; Golovanov, G.; Grannis, P. ?D.; Greder, S.; Greenlee, H.; Grenier, G.; Gris, Ph.; Grivaz, J. -F.; Grohsjean, A.; Grünendahl, S.; Grünewald, M.? W.; Guillemin, T.; Gutierrez, G.; Gutierrez, P.; Haley, J.; Han, L.; Harder, K.; Harel, A.; Hauptman, J.? M.; Hays, J.; Head, T.; Hebbeker, T.; Hedin, D.; Hegab, H.; Heinson, A. ?P.; Heintz, U.; Hensel, C.; Heredia-De La Cruz, I.; Herner, K.; Hesketh, G.; Hildreth, M.? D.; Hirosky, R.; Hoang, T.; Hobbs, J. ?D.; Hoeneisen, B.; Hogan, J.; Hohlfeld, M.; Holzbauer, J.? L.; Howley, I.; Hubacek, Z.; Hynek, V.; Iashvili, I.; Ilchenko, Y.; Illingworth, R.; Ito, A.? S.; Jabeen, S.; Jaffré, M.; Jayasinghe, A.; Jeong, M.? S.; Jesik, R.; Jiang, P.; Johns, K.; Johnson, E.; Johnson, M.; Jonckheere, A.; Jonsson, P.; Joshi, J.; Jung, A.? W.; Juste, A.; Kajfasz, E.; Karmanov, D.; Katsanos, I.; Kaur, M.; Kehoe, R.; Kermiche, S.; Khalatyan, N.; Khanov, A.; Kharchilava, A.; Kharzheev, Y. ?N.; Kiselevich, I.; Kohli, J.? M.; Kozelov, A.? V.; Kraus, J.; Kumar, A.; Kupco, A.; Kur?a, T.; Kuzmin, V. ?A.; Lammers, S.; Lebrun, P.; Lee, H.? S.; Lee, S.? W.; Lee, W. ?M.; Lei, X.; Lellouch, J.; Li, D.; Li, H.; Li, L.; Li, Q.? Z.; Lim, J.? K.; Lincoln, D.; Linnemann, J.; Lipaev, V.? V.; Lipton, R.; Liu, H.; Liu, Y.; Lobodenko, A.; Lokajicek, M.; Lopes de Sa, R.; Luna-Garcia, R.; Lyon, A.? L.; Maciel, A. ?K.?A.; Madar, R.; Magaña-Villalba, R.; Malik, S.; Malyshev, V.? L.; Mansour, J.; Martínez-Ortega, J.; McCarthy, R.; McGivern, C. ?L.; Meijer, M.? M.; Melnitchouk, A.; Menezes, D.; Mercadante, P. ?G.; Merkin, M.; Meyer, A.; Meyer, J.; Miconi, F.; Mondal, N.? K.; Mulhearn, M.; Nagy, E.; Narain, M.; Nayyar, R.; Neal, H.? A.; Negret, J.? P.; Neustroev, P.; Nguyen, H.? T.; Nunnemann, T.; Orduna, J.; Osman, N.; Osta, J.; Pal, A.; Parashar, N.; Parihar, V.; Park, S. ?K.; Partridge, R.; Parua, N.; Patwa, A.; Penning, B.; Perfilov, M.; Peters, Y.; Petridis, K.; Petrillo, G.; Pétroff, P.; Pleier, M. -A.; Podstavkov, V. ?M.; Popov, A.? V.; Prewitt, M.; Price, D.; Prokopenko, N.; Qian, J.; Quadt, A.; Quinn, B.; Ratoff, P.? N.; Razumov, I.; Ripp-Baudot, I.; Rizatdinova, F.; Rominsky, M.; Ross, A.; Royon, C.; Rubinov, P.; Ruchti, R.; Sajot, G.; Sánchez-Hernández, A.; Sanders, M.? P.; Santos, A. ?S.; Savage, G.; Savitskyi, M.; Sawyer, L.; Scanlon, T.; Schamberger, R. ?D.; Scheglov, Y.; Schellman, H.; Schwanenberger, C.; Schwienhorst, R.; Sekaric, J.; Severini, H.; Shabalina, E.; Shary, V.; Shaw, S.; Shchukin, A. ?A.; Simak, V.; Skubic, P.; Slattery, P.; Smirnov, D.; Snow, G.? R.; Snow, J.; Snyder, S.; Söldner-Rembold, S.; Sonnenschein, L.; Soustruznik, K.; Stark, J.; Stoyanova, D.? A.; Strauss, M.; Suter, L.; Svoisky, P.; Titov, M.; Tokmenin, V.? V.; Tsai, Y. -T.; Tsybychev, D.; Tuchming, B.; Tully, C.; Uvarov, L.; Uvarov, S.; Uzunyan, S.; Van Kooten, R.; van Leeuwen, W.? M.; Varelas, N.; Varnes, E.? W.; Vasilyev, I.? A.; Verkheev, A. ?Y.; Vertogradov, L. ?S.; Verzocchi, M.; Vesterinen, M.; Vilanova, D.

    2015-07-22

    We present a measurement of the fundamental parameter of the standard model, the weak mixing angle sin2??eff which determines the relative strength of weak and electromagnetic interactions, in pp¯?Z/?*?e+e- events at a center of mass energy of 1.96 TeV, using data corresponding to 9.7 fb-1 of integrated luminosity collected by the D0 detector at the Fermilab Tevatron. The effective weak mixing angle is extracted from the forward-backward charge asymmetry as a function of the invariant mass around the Z boson pole. The measured value of sin2??eff=0.23147±0.00047 is the most precise measurement from light quark interactions to date, with a precision close to the best LEP and SLD results.

  13. Preferential selection of isomer binding from chiral mixtures: alternate binding modes observed for the E and Z isomers of a series of 5-substituted 2,4-diaminofuro[2,3-d]pyrimidines as ternary complexes with NADPH and human dihydrofolate reductase

    SciTech Connect (OSTI)

    Cody, Vivian; Piraino, Jennifer; Pace, Jim; Li, Wei; Gangjee, Aleem

    2010-12-01

    The structures of six chirally mixed E/Z-isomers of 5-substituted 2,4-diaminofuro[2,3-d]pyrimidines reveals only one isomer is bound in the active site of human DHFR. The configuration of all but one C9-analogue is observed as the E-isomer. The crystal structures of six human dihydrofolate reductase (hDHFR) ternary complexes with NADPH and a series of mixed E/Z isomers of 5-substituted 5-[2-(2-methoxyphenyl)-prop-1-en-1-yl]furo[2,3-d]pyrimidine-2,4-diamines substituted at the C9 position with propyl, isopropyl, cyclopropyl, butyl, isobutyl and sec-butyl (E2–E7, Z3) were determined and the results were compared with the resolved E and Z isomers of the C9-methyl parent compound. The configuration of all of the inhibitors, save one, was observed as the E isomer, in which the binding of the furopyrimidine ring is flipped such that the 4-amino group binds in the 4-oxo site of folate. The Z3 isomer of the C9-isopropyl analog has the normal 2,4-diaminopyrimidine ring binding geometry, with the furo oxygen near Glu30 and the 4-amino group interacting near the cofactor nicotinamide ring. Electron-density maps for these structures revealed the binding of only one isomer to hDHFR, despite the fact that chiral mixtures (E:Z ratios of 2:1, 3:1 and 3:2) of the inhibitors were incubated with hDHFR prior to crystallization. Superposition of the hDHFR complexes with E2 and Z3 shows that the 2?-methoxyphenyl ring of E2 is perpendicular to that of Z3. The most potent inhibitor in this series is the isopropyl analog Z3 and the least potent is the isobutyl analog E6, consistent with data that show that the Z isomer makes the most favorable interactions with the active-site residues. The isobutyl moiety of E6 is observed in two orientations and the resultant steric crowding of the E6 analog is consistent with its weaker activity. The alternative binding modes observed for the furopyrimidine ring in these E/Z isomers suggest that new templates can be designed to probe these binding regions of the DHFR active site.

  14. The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors

    SciTech Connect (OSTI)

    Lin, David Yin-wei; Tanaka, Yoshimasa; Iwasaki, Masashi; Gittis, Apostolos G.; Su, Hua-Poo; Mikami, Bunzo; Okazaki, Taku; Honjo, Tasuku; Minato, Nagahiro; Garboczi, David N. (NIH); (Kyoto)

    2008-07-29

    Signaling through the programmed death 1 (PD-1) inhibitory receptor upon binding its ligand, PD-L1, suppresses immune responses against autoantigens and tumors and plays an important role in the maintenance of peripheral immune tolerance. Release from PD-1 inhibitory signaling revives 'exhausted' virus-specific T cells in chronic viral infections. Here we present the crystal structure of murine PD-1 in complex with human PD-L1. PD-1 and PD-L1 interact through the conserved front and side of their Ig variable (IgV) domains, as do the IgV domains of antibodies and T cell receptors. This places the loops at the ends of the IgV domains on the same side of the PD-1/PD-L1 complex, forming a surface that is similar to the antigen-binding surface of antibodies and T cell receptors. Mapping conserved residues allowed the identification of residues that are important in forming the PD-1/PD-L1 interface. Based on the structure, we show that some reported loss-of-binding mutations involve the PD-1/PD-L1 interaction but that others compromise protein folding. The PD-1/PD-L1 interaction described here may be blocked by antibodies or by designed small-molecule drugs to lower inhibitory signaling that results in a stronger immune response. The immune receptor-like loops offer a new surface for further study and potentially the design of molecules that would affect PD-1/PD-L1 complex formation and thereby modulate the immune response.

  15. The Structure of the MUR1 GDP-mannose 4,67-deydratase from A. thaliana: Implications for Ligand Binding Specificity

    SciTech Connect (OSTI)

    Mulichak, A.M.; Bonin, C.P.; Reiter, W.-D.; Garavito, R.M.

    2010-03-08

    GDP-D-mannose 4,6-dehydratase catalyzes the first step in the de novo synthesis of GDP-L-fucose, the activated form of L-fucose, which is a component of glycoconjugates in plants known to be important to the development and strength of stem tissues. We have determined the three-dimensional structure of the MUR1 dehydratase isoform from Arabidopsis thaliana complexed with its NADPH cofactor as well as with the ligands GDP and GDP-D-rhamnose. MUR1 is a member of the nucleoside-diphosphosugar modifying subclass of the short-chain dehydrogenase/reductase enzyme family, having homologous structures and a conserved catalytic triad of Lys, Tyr, and Ser/Thr residues. MUR1 is the first member of this subfamily to be observed as a tetramer, the interface of which reveals a close and intimate overlap of neighboring NADP{sup +}-binding sites. The GDP moiety of the substrate also binds in an unusual syn conformation. The protein-ligand interactions around the hexose moiety of the substrate support the importance of the conserved triad residues and an additional Glu side chain serving as a general base for catalysis. Phe and Arg side chains close to the hexose ring may serve to confer substrate specificity at the O2 position. In the MUR1/GDP-D-rhamnose complex, a single unique monomer within the protein tetramer that has an unoccupied substrate site highlights the conformational changes that accompany substrate binding and may suggest the existence of negative cooperativity in MUR1 function.

  16. Changes in the Zero-Point Energy of the Protons as the Source of the Binding Energy of Water to A-Phase DNA

    SciTech Connect (OSTI)

    Reiter, G. F.; Senesi, R.; Mayers, J.

    2010-10-01

    The measured changes in the zero-point kinetic energy of the protons are entirely responsible for the binding energy of water molecules to A phase DNA at the concentration of 6 water molecules/base pair. The changes in kinetic energy can be expected to be a significant contribution to the energy balance in intracellular biological processes and the properties of nano-confined water. The shape of the momentum distribution in the dehydrated A phase is consistent with coherent delocalization of some of the protons in a double well potential, with a separation of the wells of 0.2 Angst .

  17. X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal

    SciTech Connect (OSTI)

    Hellberg, Kristina; Grimsrud, Paul A.; Kruse, Andrew C.; Banaszak, Leonard J.; Ohlendorf, Douglas H.; Bernlohr, David A.

    2012-07-11

    Fatty acid binding proteins (FABP) have been characterized as facilitating the intracellular solubilization and transport of long-chain fatty acyl carboxylates via noncovalent interactions. More recent work has shown that the adipocyte FABP is also covalently modified in vivo on Cys117 with 4-hydroxy-2-nonenal (4-HNE), a bioactive aldehyde linked to oxidative stress and inflammation. To evaluate 4-HNE binding and modification, the crystal structures of adipocyte FABP covalently and noncovalently bound to 4-HNE have been solved to 1.9 {angstrom} and 2.3 {angstrom} resolution, respectively. While the 4-HNE in the noncovalently modified protein is coordinated similarly to a carboxylate of a fatty acid, the covalent form show a novel coordination through a water molecule at the polar end of the lipid. Other defining features between the two structures with 4-HNE and previously solved structures of the protein include a peptide flip between residues Ala36 and Lys37 and the rotation of the side chain of Phe57 into its closed conformation. Representing the first structure of an endogenous target protein covalently modified by 4-HNE, these results define a new class of in vivo ligands for FABPs and extend their physiological substrates to include bioactive aldehydes.

  18. The nuclear localization of low risk HPV11 E7 protein mediated by its zinc binding domain is independent of nuclear import receptors

    SciTech Connect (OSTI)

    Piccioli, Zachary; McKee, Courtney H.; Leszczynski, Anna; Onder, Zeynep; Hannah, Erin C.; Mamoor, Shahan; Crosby, Lauren; Moroianu, Junona

    2010-11-10

    We investigated the nuclear import of low risk HPV11 E7 protein using 1) transfection assays in HeLa cells with EGFP fusion plasmids containing 11E7 and its domains and 2) nuclear import assays in digitonin-permeabilized HeLa cells with GST fusion proteins containing 11E7 and its domains. The EGFP-11E7 and EGFP-11cE7{sub 39-98} localized mostly to the nucleus. The GST-11E7 and GST-11cE7{sub 39-98} were imported into the nuclei in the presence of either Ran-GDP or RanG19V-GTP mutant and in the absence of nuclear import receptors. This suggests that 11E7 enters the nucleus via a Ran-dependent pathway, independent of nuclear import receptors, mediated by a nuclear localization signal located in its C-terminal domain (cNLS). This cNLS contains the zinc binding domain consisting of two copies of Cys-X-X-Cys motif. Mutagenesis of Cys residues in these motifs changed the localization of the EGFP-11cE7/-11E7 mutants to cytoplasmic, suggesting that the zinc binding domain is essential for nuclear localization of 11E7.

  19. Activated RhoA Binds to the Pleckstrin Homology (PH) Domain of PDZ-RhoGEF, a Potential Site for Autoregulation

    SciTech Connect (OSTI)

    Chen, Zhe; Medina, Frank; Liu, Mu-ya; Thomas, Celestine; Sprang, Stephen R.; Sternweis, Paul C.

    2010-07-19

    Guanine nucleotide exchange factors (GEFs) catalyze exchange of GDP for GTP by stabilizing the nucleotide-free state of the small GTPases through their Dbl homology/pleckstrin homology (DH {center_dot} PH) domains. Unconventionally, PDZ-RhoGEF (PRG), a member of the RGS-RhoGEFs, binds tightly to both nucleotide-free and activated RhoA (RhoA {center_dot} GTP). We have characterized the interaction between PRG and activated RhoA and determined the structure of the PRG-DH {center_dot} PH-RhoA {center_dot} GTP{gamma}S (guanosine 5{prime}-O-[{gamma}-thio]triphosphate) complex. The interface bears striking similarity to a GTPase-effector interface and involves the switch regions in RhoA and a hydrophobic patch in PRG-PH that is conserved among all Lbc RhoGEFs. The two surfaces that bind activated and nucleotide-free RhoA on PRG-DH {center_dot} PH do not overlap, and a ternary complex of PRG-DH {center_dot} PH bound to both forms of RhoA can be isolated by size-exclusion chromatography. This novel interaction between activated RhoA and PH could play a key role in regulation of RhoGEF activity in vivo.

  20. Ion binding compounds, radionuclide complexes, methods of making radionuclide complexes, methods of extracting radionuclides, and methods of delivering radionuclides to target locations

    DOE Patents [OSTI]

    Chen, Xiaoyuan (Syracuse, NY); Wai, Chien M. (Moscow, ID); Fisher, Darrell R. (Richland, WA)

    2000-01-01

    The invention pertains to compounds for binding lanthanide ions and actinide ions. The invention further pertains to compounds for binding radionuclides, and to methods of making radionuclide complexes. Also, the invention pertains to methods of extracting radionuclides. Additionally, the invention pertains to methods of delivering radionuclides to target locations. In one aspect, the invention includes a compound comprising: a) a calix[n]arene group, wherein n is an integer greater than 3, the calix[n]arene group comprising an upper rim and a lower rim; b) at least one ionizable group attached to the lower rim; and c) an ion selected from the group consisting of lanthanide and actinide elements bound to the ionizable group. In another aspect, the invention includes a method of extracting a radionuclide, comprising: a) providing a sample comprising a radionuclide; b) providing a calix[n]arene compound in contact with the sample, wherein n is an integer greater than 3; and c) extracting radionuclide from the sample into the calix[n]arene compound. In yet another aspect, the invention includes a method of delivering a radionuclide to a target location, comprising: a) providing a calix[n]arene compound, wherein n is an integer greater than 3, the calix[n]arene compound comprising at least one ionizable group; b) providing a radionuclide bound to the calix[n]arene compound; and c) providing an antibody attached to the calix[n]arene compound, the antibody being specific for a material found at the target location.