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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

    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. 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...

  6. 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...

  7. 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.; Hfling, 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.

  8. 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.; Alf, 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.

  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.; Michaelides, Angelos; Alf, 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.

  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. Weak Interactions

    DOE R&D Accomplishments [OSTI]

    Lee, T. D.

    1957-06-01

    Experimental results on the non-conservation of parity and charge conservation in weak interactions are reviewed. The two-component theory of the neutrino is discussed. Lepton reactions are examined under the assumption of the law of conservation of leptons and that the neutrino is described by a two- component theory. From the results of this examination, the universal Fermi interactions are analyzed. Although reactions involving the neutrino can be described, the same is not true of reactions which do not involve the lepton, as the discussion of the decay of K mesons and hyperons shows. The question of the invariance of time reversal is next examined. (J.S.R.)

  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.; Hfling, 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. Weakly relativistic plasma expansion

    SciTech Connect (OSTI)

    Fermous, Rachid Djebli, Mourad

    2015-04-15

    Plasma expansion is an important physical process that takes place in laser interactions with solid targets. Within a self-similar model for the hydrodynamical multi-fluid equations, we investigated the expansion of both dense and under-dense plasmas. The weakly relativistic electrons are produced by ultra-intense laser pulses, while ions are supposed to be in a non-relativistic regime. Numerical investigations have shown that relativistic effects are important for under-dense plasma and are characterized by a finite ion front velocity. Dense plasma expansion is found to be governed mainly by quantum contributions in the fluid equations that originate from the degenerate pressure in addition to the nonlinear contributions from exchange and correlation potentials. The quantum degeneracy parameter profile provides clues to set the limit between under-dense and dense relativistic plasma expansions at a given density and temperature.

  17. Multiple weak-link SQUID

    SciTech Connect (OSTI)

    Kroger, H.

    1980-09-23

    The disclosed SQUID (Superconducting quantum interference device) comprises two superposed superconductive layers with an insulating layer therebetween. A plurality of holes through the insulating layer filled with superconductive material form weak links between the superconductive layers. One or more control lines superposed with respect to the superconductive layers provide magnetic flux through the area between the weak links to control the zero voltage supercurrent flowing through the weak links from one of the superconductive layers to the other thereby providing the switching function for Josephson superconductive circuits.

  18. Magnetic field control of the neutral and charged exciton fine structure in single quantum dashes emitting at 1.55 μm

    SciTech Connect (OSTI)

    Mrowiński, P.; Musiał, A.; Maryński, A.; Syperek, M.; Misiewicz, J.; Sęk, G.; Somers, A.; Reithmaier, J. P.; Höfling, S.

    2015-02-02

    We investigated the neutral and charged exciton fine structure in single InAs/InGaAlAs/InP quantum dashes emitting at 1.55 μm using polarization-resolved microphotoluminescence in a magnetic field. Inverted spin configuration of horizontally [1–10] and vertically [110] polarized transitions has been observed. An in-plane magnetic field of up to 5 Tesla has been applied to tailor the fine structure, and eventually to reduce the splitting of the bright exciton states down to zero. This inverted structure has been observed for all the investigated excitons, making it a characteristic feature for this class of nanostructures with the largest splitting reduction of 170 μeV.

  19. 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.

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

    Office of Scientific and Technical Information (OSTI)

    Corrigendum and addendum. Modeling weakly nonlinear acoustic wave propagation Citation Details In-Document Search Title: Corrigendum and addendum. Modeling weakly nonlinear ...

  1. 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.

  2. 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.

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

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

    Probing the Proton's Weak Side Probing the Proton's Weak Side Scientists know that the sun gets its shine through the actions of a little-understood fundamental force of nature called the weak force. But there's a lot that they don't know about the weak force. So for the first time, researchers at the U.S. Department of Energy's Jefferson Lab are trying to precisely measure the weak force's grasp on the ubiquitous proton. The weak force is one of four fundamental forces, which include

  4. High Energy Electromagnetic and Weak Interaction Processes

    DOE R&D Accomplishments [OSTI]

    Lee, T. D.

    1972-01-11

    This talk reviews some known features of the high energy electromagnetic and weak interaction processes and then tries to speculate on some particular aspects of their future possibilities.

  5. 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.

  6. 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.

  7. Reversing entanglement change by a weak measurement

    SciTech Connect (OSTI)

    Sun Qingqing; Zubairy, M. Suhail; Al-Amri, M.; Davidovich, Luiz

    2010-11-15

    Entanglement of a system changes due to interactions with the environment. A typical type of interaction is amplitude damping. If we add a detector to monitor the environment and only select the no-damping outcome, this amplitude damping is modified into a weak measurement. Here we show that the entanglement change of a two-qubit state due to amplitude damping or weak measurement can be probabilistically reversed. For the amplitude-damping case, the entanglement partially recovers under most conditions. For the weak-measurement case, the recovery of the initial entangled state is exact. The reversal procedure involves another weak measurement, preceded and followed by bit flips applied to both qubits. We propose a linear optics scheme for the experimental demonstration of these procedures.

  8. 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 Proton's 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

  9. 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 ...

  10. 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...

  11. 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...

  12. From weak discontinuities to nondissipative shock waves

    SciTech Connect (OSTI)

    Garifullin, R. N. Suleimanov, B. I.

    2010-01-15

    An analysis is presented of the effect of weak dispersion on transitions from weak to strong discontinuities in inviscid fluid dynamics. In the neighborhoods of transition points, this effect is described by simultaneous solutions to the Korteweg-de Vries equation u{sub t}'+ uu{sub x}' + u{sub xxx}' = 0 and fifth-order nonautonomous ordinary differential equations. As x{sup 2} + t{sup 2} {yields}{infinity}, the asymptotic behavior of these simultaneous solutions in the zone of undamped oscillations is given by quasi-simple wave solutions to Whitham equations of the form r{sub i}(t, x) = tl{sub i} x/t{sup 2}.

  13. 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 etal. 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-systems 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 behaviorand also thereby reveal the non-local dependence of sub-system state functions on distant interventionsare 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. Magnetic reconnection in a weakly ionized plasma

    SciTech Connect (OSTI)

    Leake, James E.; Lukin, Vyacheslav S.; Linton, Mark G.

    2013-06-15

    Magnetic reconnection in partially ionized plasmas is a ubiquitous phenomenon spanning the range from laboratory to intergalactic scales, yet it remains poorly understood and relatively little studied. Here, we present results from a self-consistent multi-fluid simulation of magnetic reconnection in a weakly ionized reacting plasma with a particular focus on the parameter regime of the solar chromosphere. The numerical model includes collisional transport, interaction and reactions between the species, and optically thin radiative losses. This model improves upon our previous work in Leake et al.[“Multi-fluid simulations of chromospheric magnetic reconnection in a weakly ionized reacting plasma,” Astrophys. J. 760, 109 (2012)] by considering realistic chromospheric transport coefficients, and by solving a generalized Ohm's law that accounts for finite ion-inertia and electron-neutral drag. We find that during the two dimensional reconnection of a Harris current sheet with an initial width larger than the neutral-ion collisional coupling scale, the current sheet thins until its width becomes less than this coupling scale, and the neutral and ion fluids decouple upstream from the reconnection site. During this process of decoupling, we observe reconnection faster than the single-fluid Sweet-Parker prediction, with recombination and plasma outflow both playing a role in determining the reconnection rate. As the current sheet thins further and elongates, it becomes unstable to the secondary tearing instability, and plasmoids are seen. The reconnection rate, outflows, and plasmoids observed in this simulation provide evidence that magnetic reconnection in the chromosphere could be responsible for jet-like transient phenomena such as spicules and chromospheric jets.

  20. 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

  1. Characterization of a novel weak interaction between MUC1 and Src-SH3 using nuclear magnetic resonance spectroscopy

    SciTech Connect (OSTI)

    Gunasekara, Nirosha; Sykes, Brian; Hugh, Judith

    2012-05-18

    Highlights: Black-Right-Pointing-Pointer MUC1 binds the Src-SH3 domain potentially triggering Src dependent cell migration. Black-Right-Pointing-Pointer NMR Spectroscopy was used to monitor MUC1-CD and Src SH3 domain titrations. Black-Right-Pointing-Pointer MUC1-CD peptides bind with a low affinity (K{sub d} of 2-3 mM) to a non-canonical site. Black-Right-Pointing-Pointer Weak interactions may mediate dynamic processes like migration. Black-Right-Pointing-Pointer The MUC1-CD and Src-SH3 interaction may be a prime target to inhibit cell migration. -- Abstract: Breast cancer causes death through cancer cell migration and subsequent metastasis to distant organs. In vitro, the MUC1 mucin can mediate breast cancer cell migration by binding to intercellular adhesion molecule-1 (ICAM-1). This migration is dependent on MUC1 cytoplasmic domain (MUC1-CD) activation of the non-receptor tyrosine kinase, Src, possibly through competitive displacement of an inhibitory Src intramolecular SH3 binding. Therefore, we characterized the binding site and affinity of the MUC1-CD for Src-SH3 using multidimensional nuclear magnetic resonance (NMR) spectroscopy to monitor the titration of the {sup 15}N labeled Src-SH3 domain with synthetic native and mutant peptides of MUC1-CD. The results revealed that the dissociation constant (K{sub d}) for the interaction of the native MUC1-CD peptides and Src-SH3 domain was weak with a K{sub d} of 2-3 mM. Notably, the SH3 residues most perturbed upon peptide binding were located outside the usual hydrophobic binding cleft in a previously described alternate binding site on the Src-SH3, suggesting that MUC1-CD binds to a non-canonical site. The binding characteristics outlined here suggest that the interaction between Src-SH3 and MUC1-CD represents a novel weak electrostatic interaction of the type which is increasingly recognized as important in transient and dynamic protein complexes required for cell migration and signal transduction. As such, this

  2. Inhibition of selectin binding

    DOE Patents [OSTI]

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Caroline

    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.

  3. Inhibition of selectin binding

    DOE Patents [OSTI]

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Caroline

    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.

  4. Inhibition of selectin binding

    DOE Patents [OSTI]

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Carolyn

    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.

  5. 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.

  6. Cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    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.

  7. Weak interactions of supersymmetric staus at high energies (Journal...

    Office of Scientific and Technical Information (OSTI)

    Neutrino telescopes may have the potential to detect the quasistable staus predicted by ... We show that the neutral-current weak interaction contribution is much smaller than ...

  8. 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:...

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

    Office of Scientific and Technical Information (OSTI)

    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 ...

  10. Van der Waals metal-semiconductor junction: Weak Fermi level...

    Office of Scientific and Technical Information (OSTI)

    Van der Waals metal-semiconductor junction: Weak Fermi level pinning enables effective tuning of Schottky barrier Citation Details In-Document Search Title: Van der Waals ...

  11. 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 ...

  12. 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

  13. 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.

  14. 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.

  15. The Impact of Camera Optical Alignments on Weak Lensing Measures...

    Office of Scientific and Technical Information (OSTI)

    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 ...

  16. 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...

  17. 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.

  18. Proton Delivery and Removal in [Ni(PR2N...

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

    ... The total binding energy (E bind , solid line) is broken down into two components: distortion energy (E dis , dashed ... complemented by harmonic thermal and entropic ...

  19. Identification and characterization of riboflavin-binding proteins in human circulation

    SciTech Connect (OSTI)

    Innis-Whitehouse, W.S.A.

    1988-01-01

    Riboflavin binding by plasma proteins from healthy human subjects was examined by equilibrium dialysis and binding was observed to vary over a greater than 10-fold range. Upon fractionation of plasma by gel filtration, the major riboflavin-binding components eluted with albumin and gamma-globulins. Albumin was purified and found to bind riboflavin only very weakly, although FMN and photo-chemical degradation products were more tightly bound. Most of the binding occurred in the gamma-globulin fraction and was attributed to immunoglobulins because the binding proteins and immunoglobulins copurified using various methods, were removed by treatment of plasma with protein A-agarose, and were coincident upon immuno-electrophoresis followed by autoradiography to detect (2-{sup 14}C)-riboflavin. Binding differences among plasma samples were reflected in the binding recovered with the immunoglobulin fractions; however, there was not a direct relationship between the amount of immunoglobulin and the amount of (2-{sup 14}C)riboflavin bound. Hence, it appeared that the binding was due to a subfraction of immunoglobulins.

  20. Mechanical and acoustic properties of weakly cemented granular rocks

    SciTech Connect (OSTI)

    Nakagawa, S.; Myer, L.R.

    2001-05-09

    This paper presents the results of laboratory measurements on the mechanical and acoustic properties of weakly cemented granular rock. Artificial rock samples were fabricated by cementing sand and glass beads with sodium silicate binder. During uniaxial compression tests, the rock samples showed stress-strain behavior which was more similar to that of soils than competent rocks, exhibiting large permanent deformations with frictional slip. The mechanical behavior of the samples approached that of competent rocks as the amount of binder was increased. For very weak samples, acoustic waves propagating in these rocks showed very low velocities of less than 1000 m/sec for compressional waves. A borehole made within this weakly cemented rock exhibited a unique mode of failure that is called ''anti-KI mode fracture'' in this paper. The effect of cementation, grain type, and boundary conditions on this mode of failure was also examined experimentally.

  1. Variance control in weak-value measurement pointers

    SciTech Connect (OSTI)

    Parks, A. D.; Gray, J. E.

    2011-07-15

    The variance of an arbitrary pointer observable is considered for the general case that a complex weak value is measured using a complex valued pointer state. For the typical cases where the pointer observable is either its position or momentum, the associated expressions for the pointer's variance after the measurement contain a term proportional to the product of the weak value's imaginary part with the rate of change of the third central moment of position relative to the initial pointer state just prior to the time of the measurement interaction when position is the observable--or with the initial pointer state's third central moment of momentum when momentum is the observable. These terms provide a means for controlling pointer position and momentum variance and identify control conditions which, when satisfied, can yield variances that are smaller after the measurement than they were before the measurement. Measurement sensitivities which are useful for estimating weak-value measurement accuracies are also briefly discussed.

  2. Resurgence and holomorphy: From weak to strong coupling

    SciTech Connect (OSTI)

    Cherman, Aleksey; Koroteev, Peter; Ünsal, Mithat

    2015-05-15

    We analyze the resurgence properties of finite-dimensional exponential integrals which are prototypes for partition functions in quantum field theories. In these simple examples, we demonstrate that perturbation theory, even at arbitrarily weak coupling, fails as the argument of the coupling constant is varied. It is well-known that perturbation theory also fails at stronger coupling. We show that these two failures are actually intimately related. The formalism of resurgent transseries, which takes into account global analytic continuation properties, fixes both problems and provides an arbitrarily accurate description of exact result for any value of coupling. This means that strong coupling results can be deduced by using merely weak coupling data. Finally, we give another perspective on resurgence theory by showing that the monodromy properties of the weak coupling results are in precise agreement with the monodromy properties of the strong-coupling expansions, obtained using analysis of the holomorphy structure of Picard-Fuchs equations.

  3. 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

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

    SciTech Connect (OSTI)

    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.

  5. 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...

  6. 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...

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

    Office of Environmental Management (EM)

    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 ...

  8. 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,

  9. 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.

  10. The DES Science Verification Weak Lensing Shear Catalogs

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

    Jarvis, M.

    2016-05-01

    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 SVmore » 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.« less

  11. 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.

  12. 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.

  13. Weak and strong coupling equilibration in nonabelian gauge theories

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

    Keegan, Liam; Kurkela, Aleksi; Romatschke, Paul; van der Schee, Wilke; Zhu, Yan

    2016-04-06

    In this study, we present a direct comparison studying equilibration through kinetic theory at weak coupling and through holography at strong coupling in the same set-up. The set-up starts with a homogeneous thermal state, which then smoothly transitions through an out-of-equilibrium phase to an expanding system undergoing boost-invariant flow. This first apples-to-apples comparison of equilibration provides a benchmark for similar equilibration processes in heavy-ion collisions, where the equilibration mechanism is still under debate. We find that results at weak and strong coupling can be smoothly connected by simple, empirical power-laws for the viscosity, equilibration time and entropy production of themore » system.« less

  14. Weak-interaction processes in core-collapse supernovae

    SciTech Connect (OSTI)

    Langanke, K.

    2015-02-24

    Weak interaction processes play an important role for the dynamics of a core-collapse supernova. Due to progress of nuclear modeling and constrained by data it has been possible to improve the rates of these processes for supernova conditions decisively. This manuscript describes the recent advances and the current status in deriving electron capture rates on nuclei and of inelastic neutrino-nucleus scattering for applications in supernova simulations and briefly discusses their impact on such studies.

  15. On quasilinear perpendicular diffusion of cosmic rays in weak turbulence

    SciTech Connect (OSTI)

    Schlickeiser, R.; Shalchi, A.

    2004-09-15

    The quasilinear calculation of perpendicular diffusion of cosmic ray particles for weak dynamical magnetic turbulence of arbitrary geometry is presented. Starting from the equations of motion a detailed point-by-point derivation of quasilinear Fokker-Planck coefficients is given. It is shown that, in order to have diffusive behaviour of the Fokker-Planck coefficients, the existence of a finite correlation time of the magnetic fluctuations is essential.

  16. 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.

  17. Effective Supergravity from the Weakly Coupled HeteroticString

    SciTech Connect (OSTI)

    Gaillard, Mary K.

    2005-05-01

    The motivation for Calabi-Yau-like compactifications of the weakly coupled E{sub 8} {circle_times} E{sub 8} heterotic string theory, its particle spectrum and the issue of dilaton stabilization are briefly reviewed. Modular invariant models for hidden sector condensation and supersymmetry breaking are described at the quantum level of the effective field theory. Their phenomenological and cosmological implications, including a possible origin for R-parity, are discussed.

  18. 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

  19. Optimizing weak lensing mass estimates for cluster profile uncertainty

    SciTech Connect (OSTI)

    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. Depending 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.

  20. 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.

  1. 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

  2. Photochemically enhanced binding of small molecules to the tumor necrosis factor receptor-1 inhibits the binding of TNF-[alpha

    SciTech Connect (OSTI)

    Carter, Percy H.; Scherle, Peggy A.; Muckelbauer, Jodi K.; Voss, Matthew E.; Liu, Rui-qin; Thompson III, Lorin A.; Xu, Meizhong; Lo, Yvonne C.; Li, Zhong; Strzemienski, Paul; Yang, Gengjie; Falahatpishen, Nikoo; Farrow, Neil A.; Tebben, Andrew J.; Underwood, Denis; Trzaskos, James M.; Friedman, Steven M.; Newton, Robert C.; Decicco, Carl P.

    2010-03-05

    The binding of tumor necrosis factor alpha (TNF-{alpha}) to the type-1 TNF receptor (TNFRc1) plays an important role in inflammation. Despite the clinical success of biologics (antibodies, soluble receptors) for treating TNF-based autoimmune conditions, no potent small molecule antagonists have been developed. Our screening of chemical libraries revealed that N-alkyl 5-arylidene-2-thioxo-1,3-thiazolidin-4-ones were antagonists of this protein-protein interaction. After chemical optimization, we discovered IW927, which potently disrupted the binding of TNF-{alpha} to TNFRc1 (IC{sub 50} = 50 nM) and also blocked TNF-stimulated phosphorylation of I{kappa}-B in Ramos cells (IC{sub 50} = 600 nM). This compound did not bind detectably to the related cytokine receptors TNFRc2 or CD40, and did not display any cytotoxicity at concentrations as high as 100 {micro}M. Detailed evaluation of this and related molecules revealed that compounds in this class are 'photochemically enhanced' inhibitors, in that they bind reversibly to the TNFRc1 with weak affinity (ca. 40-100 mM) and then covalently modify the receptor via a photochemical reaction. We obtained a crystal structure of IV703 (a close analog of IW927) bound to the TNFRc1. This structure clearly revealed that one of the aromatic rings of the inhibitor was covalently linked to the receptor through the main-chain nitrogen of Ala-62, a residue that has already been implicated in the binding of TNF-{alpha} to the TNFRc1. When combined with the fact that our inhibitors are reversible binders in light-excluded conditions, the results of the crystallography provide the basis for the rational design of nonphotoreactive inhibitors of the TNF-{alpha}-TNFRc1 interaction.

  3. 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.

  4. Neutrino energy transport in weak decoupling and big bang nucleosynthesis

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

    Grohs, Evan Bradley; Paris, Mark W.; Kishimoto, Chad T.; Fuller, George M.; Vlasenko, Alexey

    2016-04-21

    In this study, we calculate the evolution of the early universe through the epochs of weak decoupling, weak freeze-out and big bang nucleosynthesis (BBN) by simultaneously coupling a full strong, electromagnetic, and weak nuclear reaction network with a multienergy group Boltzmann neutrino energy transport scheme. The modular structure of our code provides the ability to dissect the relative contributions of each process responsible for evolving the dynamics of the early universe in the absence of neutrino flavor oscillations. Such an approach allows a detailed accounting of the evolution of the νe, ν¯e, νμ, ν¯μ, ντ, ν¯τ energy distribution functions alongsidemore » and self-consistently with the nuclear reactions and entropy/heat generation and flow between the neutrino and photon/electron/positron/baryon plasma components. This calculation reveals nonlinear feedback in the time evolution of neutrino distribution functions and plasma thermodynamic conditions (e.g., electron-positron pair densities), with implications for the phasing between scale factor and plasma temperature; the neutron-to-proton ratio; light-element abundance histories; and the cosmological parameter Neff. We find that our approach of following the time development of neutrino spectral distortions and concomitant entropy production and extraction from the plasma results in changes in the computed value of the BBN deuterium yield. For example, for particular implementations of quantum corrections in plasma thermodynamics, our calculations show a 0.4% increase in deuterium. These changes are potentially significant in the context of anticipated improvements in observational and nuclear physics uncertainties.« less

  5. 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

  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 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

  7. 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.

  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. Bending of solitons in weak and slowly varying inhomogeneous plasma

    SciTech Connect (OSTI)

    Mukherjee, Abhik Janaki, M. S. Kundu, Anjan

    2015-12-15

    The bending of solitons in two dimensional plane is presented in the presence of weak and slowly varying inhomogeneous ion density for the propagation of ion acoustic soliton in unmagnetized cold plasma with isothermal electrons. Using reductive perturbation technique, a modified Kadomtsev-Petviashvili equation is obtained with a chosen unperturbed ion density profile. The exact solution of the equation shows that the phase of the solitary wave gets modified by a function related to the unperturbed inhomogeneous ion density causing the soliton to bend in the two dimensional plane, while the amplitude of the soliton remains constant.

  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. 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.

  15. Cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    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.

  16. 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.

  17. 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.

  18. 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.

  19. XRD acquisition parameters for detection of weak peaks

    SciTech Connect (OSTI)

    Seabaugh, P.W.; Sullenger, D.B.; Hudgens, C.R.; Nichols, M.C.; Boehme, D.R.; Sandia National Labs., Albuquerque, NM )

    1989-01-01

    The use of high intensity x-ray sources provides opportunities as well as special problems in the detection of minor XRD peaks. Scattering contributions from slits along with other factors can become important and may interfere with the analysis. This further complexity can best be resolved by using nonconventional data collection and analysis strategies. To study these factors, an experimental design plan was formulated and implemented which was used to determine operating parameters for a high intensity x-ray diffraction unit. Major issues studied included the extraction of a weak signal from a noisy background, the reduction of background noise, the volume of data to be collected, the time allocated for background characterization, the control sample, and the impact of the quality'' of the sample. 4 figs.

  20. 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

  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. 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.

  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. 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.

  11. 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

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

    SciTech Connect (OSTI)

    Gruen, D.; Friedrich, O.; Amara, A.; Bacon, D.; Bonnett, C.; Hartley, W.; Jain, B.; M. Jarvis; Kavprzak, T.; Krause, E.; Mana, A.; Rozo, E.; Rykoff, E. S.; Seitz, S.; Sheldon, E.; Troxel, M. A.; Vikram, V.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Banerji, M.; Bauer, A. H.; Becker, M. R.; Benoit-Levy, A.; Bernstein, G. M.; Bernstein, R. A.; Bertin, E.; Bridle, S. L.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Rosell, A. Carnero; Carretero, J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Eifler, T. F.; Neto, A. Fausti; Fernandez, E.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gerdes, D. W.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; Maia, M. A. G.; March, M.; Martini, P.; Melchior, P.; Miller, C. J.; Miguel, R.; Mohr, J. J.; Nord, B.; Orgando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Roodman, A.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, D.; Walker, A. R.; Wechsler, R. H.; Weller, J.; Zhang, Y.; Zuntz, J.

    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 of 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.

  13. 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 (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 of the matter density with Poissonian noise, we find agreement of our measurements with predictions in a fiducial Λ 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.

  14. 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

  15. Weak Lensing by Galaxy Clusters: from Pixels to Cosmology

    SciTech Connect (OSTI)

    Gruen, Daniel

    2015-03-11

    The story of the origin and evolution of our Universe is told, equivalently, by space-time itself and by the structures that grow inside of it. Clusters of galaxies are the frontier of bottom-up structure formation. They are the most massive objects to have collapsed at the present epoch. By that virtue, their abundance and structural parameters are highly sensitive to the composition and evolution of the Universe. The most common probe of cluster cosmology, abundance, uses samples of clusters selected by some observable. Applying a mass-observable relation (MOR), cosmological parameters can be constrained by comparing the sample to predicted cluster abundances as a function of observable and redshift. Arguably, however, cluster probes have not yet entered the era of per cent level precision cosmology. The primary reason for this is our imperfect understanding of the MORs. The overall normalization, the slope of mass vs. observable, the redshift evolution, and the degree and correlation of intrinsic scatters of observables at fixed mass have to be constrained for interpreting abundances correctly. Mass measurement of clusters by means of the differential deflection of light from background sources in their gravitational field, i.e. weak lensing, is a powerful approach for achieving this. This thesis presents new methods for and scientific results of weak lensing measurements of clusters of galaxies. The former include, on the data reduction side, (i) the correction of CCD images for non-linear effects due to the electric fields of accumulated charges and (ii) a method for masking artifact features in sets of overlapping images of the sky by comparison to the median image. Also, (iii) I develop a method for the selection of background galaxy samples based on their color and apparent magnitude that includes a new correction for contamination with cluster member galaxies. The main scientific results are the following. (i) For the Hubble Frontier Field cluster RXC J

  16. Compaction localization and constitutive behavior of weak porous sandstone.

    SciTech Connect (OSTI)

    Holcomb, David Joseph; Dewers, Thomas A.; Issen, Kathleen

    2009-06-01

    A combined experimental and constitutive modeling program for weak porous sandstone deformation is described. A series of axisymmetric compression tests were performed over a range of mean stresses to study dilatational, compactional and transitional regimes. Experimental results were used both to derive constitutive parameters for testing localization theory and to parameterize a poroelastic-plastic model. Observed strain localization, imaged syn-deformationally using acoustic emissions, includes high- and low-angle shear and low angle compactional features or 'bands'. Isotropic elastic moduli measured via unloading loops show a progressive degradation pre-failure as decreasing functions of work-conjugate plastic strains and increasing functions of stress magnitude. The degradation pathway is unique for samples which underwent localization versus those that underwent spatially pervasive pore collapse. Total shear and volume strains are partitioned into elastic and plastic portions including the ''coupling'' strain associated with modulus degradation. Plastic strain calculated with and without the coupling term is compared with regard to localization predictions. Both coupled and uncoupled cases predict high angle shear bands for uniaxial and low mean stress conditions on the dilatational side of the yield surface. Uncoupled predictions show progressively lower angle shear bands approaching the transitional regime (stress conditions approaching the 'cap' surface). When elastic-plastic coupling is accounted for, compaction bands are predicted for the transitional regime, as are observed in the experiments. Finite element modeling efforts are described using a 3-invariant, mixed-hardening, continuous yield surface, elasto-plasticity model that includes several features important for porous sandstone constitutive behavior and observed experimentally, including non-associativity, nonlinear elasticity, elastic-plastic coupling, and kinematic hardening. Modeled

  17. Sample variance in weak lensing: How many simulations are required?

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

    Petri, Andrea; May, Morgan; Haiman, Zoltan

    2016-03-24

    Constraining cosmology using weak gravitational lensing consists of comparing a measured feature vector of dimension Nb with its simulated counterpart. An accurate estimate of the Nb × Nb feature covariance matrix C is essential to obtain accurate parameter confidence intervals. When C is measured from a set of simulations, an important question is how large this set should be. To answer this question, we construct different ensembles of Nr realizations of the shear field, using a common randomization procedure that recycles the outputs from a smaller number Ns ≤ Nr of independent ray-tracing N-body simulations. We study parameter confidence intervalsmore » as a function of (Ns, Nr) in the range 1 ≤ Ns ≤ 200 and 1 ≤ Nr ≲ 105. Previous work [S. Dodelson and M. D. Schneider, Phys. Rev. D 88, 063537 (2013)] has shown that Gaussian noise in the feature vectors (from which the covariance is estimated) lead, at quadratic order, to an O(1/Nr) degradation of the parameter confidence intervals. Using a variety of lensing features measured in our simulations, including shear-shear power spectra and peak counts, we show that cubic and quartic covariance fluctuations lead to additional O(1/N2r) error degradation that is not negligible when Nr is only a factor of few larger than Nb. We study the large Nr limit, and find that a single, 240 Mpc/h sized 5123-particle N-body simulation (Ns = 1) can be repeatedly recycled to produce as many as Nr = few × 104 shear maps whose power spectra and high-significance peak counts can be treated as statistically independent. Lastly, a small number of simulations (Ns = 1 or 2) is sufficient to forecast parameter confidence intervals at percent accuracy.« less

  18. 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.

  19. Supramolecular binding and separation of hydrocarbons within a functionalized porous metal–organic framework

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

    Yang, Sihai; Ramirez-Cuesta, Anibal J.; Newby, Ruth; Garcia-Sakai, Victoria; Manuel, Pascal; Callear, Samantha K.; Campbell, Stuart I.; Tang, Chiu C.; Schröder, Martin

    2014-12-01

    Supramolecular interactions are fundamental to host–guest binding in many chemical and biological processes. Direct visualization of such supramolecular interactions within host–guest systems is extremely challenging, but crucial to understanding their function. Within this paper, we report a comprehensive study that combines neutron scattering, synchrotron X-ray and neutron diffraction, and computational modelling to define the detailed binding at a molecular level of acetylene, ethylene and ethane within the porous host NOTT-300. This study reveals simultaneous and cooperative hydrogen-bonding, π···π stacking interactions and intermolecular dipole interactions in the binding of acetylene and ethylene to give up to 12 individual weak supramolecular interactionsmore » aligned within the host to form an optimal geometry for the selective binding of hydrocarbons. In addition, we also report the cooperative binding of a mixture of acetylene and ethylene within the porous host, together with the corresponding breakthrough experiments and analysis of adsorption isotherms of gas mixtures.« less

  20. 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

  1. Combining weak-lensing tomography and spectroscopic redshift surveys

    SciTech Connect (OSTI)

    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 same 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

  2. 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

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. 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)

  8. Dash for Bikes, Walk for Trikes | National Nuclear Security Administra...

    National Nuclear Security Administration (NNSA)

    thousands of dollars each year for the Savannah River Site's annual Toys for Tots campaign. The fun is profitable enough to raise a significant amount of money to surprise...

  9. 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:...

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

    DOE Patents [OSTI]

    Wachter, Eric A.; Fisher, Walter G.

    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.

  11. Optimal preselection and postselection in weak measurements for observing photonic spin Hall effect

    SciTech Connect (OSTI)

    Zhou, Xinxing; Li, Xing; Luo, Hailu Wen, Shuangchun

    2014-02-03

    Photonic spin Hall effect (SHE) holds great potential applications in precision metrology. How to obtain a high measurement precision is an important issue to detect the photonic SHE. In this Letter, we propose using optimal preselection and postselection in weak measurements to enhance the measurement precision. We find that the maximum weak value and pointer shift can be obtained with an optimal overlap of preselection and postselection states. These findings offer the possibility for improving the precision of weak measurements and thereby have possible applications for accurately characterizing the parameters of nanostructures.

  12. 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.

  13. 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.

  14. Coupled ion Binding and Structural Transitions Along the Transport...

    Office of Scientific and Technical Information (OSTI)

    binding primes the transport domain to accept its substrate and triggers extracellular gate opening, which prevents inward domain translocation until substrate binding takes place. ...

  15. 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 ...

  16. A Story of Q-weak at Jefferson Lab (On YouTube) | Jefferson Lab

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

    A Story of Q-weak at Jefferson Lab (On YouTube) External Link: http://www.youtube.com/watch?v=WhYb53Kkl9k By jlab_admin on Sun, 2012-02-05

  17. Process for loading weak-acid ion exchange resin with uranium

    DOE Patents [OSTI]

    Notz, Karl J.

    1976-01-01

    A method for loading ion exchange resins is described. The process comprises contacting a weak acid cation exchange resin in the ammonium form with a uranyl fluoride salt solution.

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

    Broader source: Energy.gov [DOE]

    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.

  19. Method of Control o Multiple Contraction in the volume of Weakly Ionized

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

    Plasma by Standing Acoustic Wave Excitation. | Princeton Plasma Physics Lab 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 in the volume of weakly ionized plasma to control the initiation of contraction (transition to arc) in certain designated places - the antimodes of the standing wave. No.: M-876 Inventor(s): Igor Kaganovich

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Flow cytometer measurement of binding assays

    DOE Patents [OSTI]

    Saunders, George C.

    1987-01-01

    A method of measuring the result of a binding assay that does not require separation of fluorescent smaller particles is disclosed. In a competitive binding assay the smaller fluorescent particles coated with antigen compete with antigen in the sample being analyzed for available binding sites on larger particles. In a sandwich assay, the smaller, fluorescent spheres coated with antibody attach themselves to molecules containing antigen that are attached to larger spheres coated with the same antibody. The separation of unattached, fluorescent smaller particles is made unnecessary by only counting the fluorescent events triggered by the laser of a flow cytometer when the event is caused by a particle with a light scatter measurement within a certain range corresponding to the presence of larger particles.

  7. A DETECTION OF WEAK-LENSING MAGNIFICATION USING GALAXY SIZES AND MAGNITUDES

    SciTech Connect (OSTI)

    Schmidt, Fabian; Rhodes, Jason; Leauthaud, Alexie; Tanaka, Masayuki; Massey, Richard; George, Matthew R.; Koekemoer, Anton M.; Finoguenov, Alexis

    2012-01-10

    Weak lensing is commonly measured using shear through galaxy ellipticities or using the effect of magnification bias on galaxy number densities. Here, we report on the first detection of weak-lensing magnification with a new, independent technique using the distribution of galaxy sizes and magnitudes. These data come for free in galaxy surveys designed for measuring shear. We present the magnification estimator and apply it to an X-ray-selected sample of galaxy groups in the COSMOS Hubble Space Telescope survey. The measurement of the projected surface density {Sigma}(r) is consistent with the shear measurements within the uncertainties and has roughly 40% of the signal to noise of the latter. We discuss systematic issues and challenges to realizing the potential of this new probe of weak lensing.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    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.

  13. 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.

  14. Improved Tests of the Weak Nuclear Force from Beta Decay | U.S. DOE Office

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

    of Science (SC) Improved Tests of the Weak Nuclear Force from Beta Decay 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 » 08.19.16 Improved Tests of the Weak Nuclear

  15. 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.

  16. 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].

  17. 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.

  18. 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

  19. 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

  20. BPA FINAL Binding Arbitration policy | Department of Energy

    Office of Environmental Management (EM)

    BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding

  1. 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

  2. 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.

  3. 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 amorefactor of two. The finite energy sum rule helps addressing the uncertainty in that calculation due to possible duality violations.less

  4. 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.

  5. High-frequency electromagnetic surface waves in a semi-bounded weakly ionized plasma

    SciTech Connect (OSTI)

    Moaied, M.; Tyshetskiy, Yu.; Vladimirov, S. V.

    2013-02-15

    High-frequency electromagnetic surface waves (SWs) in a weakly ionized plasma half-space with Maxwellian electrons are studied taking into account elastic electron-neutral collisions. The SWs spectrum and damping rate are obtained numerically for a wide range of wavelengths, and the asymptotes of damping rate are analytically calculated in some limits. It is shown that the high-frequency SWs become strongly damped at wavelengths {lambda}<{lambda}{sub Min}, where {lambda}{sub Min} significantly depends on plasma parameters (e.g., electron temperature and electron and neutral atom density). The relative importance of collisional and Cherenkov (collisionless) damping of SWs is investigated and is graphically shown for a range of plasma parameters and SW wavelengths. The behavior of weakly ionized plasma with respect to the SW propagation has been recovered for the collisional parameter {eta}.

  6. Determination of magneto-optical constant of Fe films with weak measurements

    SciTech Connect (OSTI)

    Qiu, Xiaodong; Hu, Dejiao; Du, Jinglei; Gao, Fuhua; Zhang, Zhiyou; Zhou, Xinxing; Luo, Hailu

    2014-09-29

    In this letter, a detecting method for the magneto-optical constant is presented by using weak measurements. The photonic spin Hall effect (PSHE), which manifests itself as spin-dependent splitting, is introduced to characterize the magneto-optical constant, and a propagation model to describe the quantitative relation between the magneto-optical constant and the PSHE is established. According to the amplified shift of the PSHE detected by weak measurements, we determinate the magneto-optical constant of the Fe film sample. The Kerr rotation is measured via the standard polarimetry method to verify the rationality and feasibility of our method. These findings may provide possible applications in magnetic physics research.

  7. 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.

  8. 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

  9. Coenzyme A Binding to the Aminoglycoside Acetyltransferase (3)-IIIb Increases Conformational Sampling of Antibiotic Binding Site

    SciTech Connect (OSTI)

    Hu, Xiaohu; Norris, Adrianne; Baudry, Jerome Y; Serpersu, Engin H

    2011-01-01

    NMR spectroscopy experiments and molecular dynamics simulations were performed to describe the dynamic properties of the aminoglycoside acetyltransferase (3)-IIIb (AAC) in its apo and coenzyme A (CoASH) bound forms. The {sup 15}N-{sup 1}H HSQC spectra indicate a partial structural change and coupling of the CoASH binding site with another region in the protein upon the CoASH titration into the apo enzyme. Molecular dynamics simulations indicate a significant structural and dynamic variation of the long loop in the antibiotic binding domain in the form of a relatively slow (250 ns), concerted opening motion in the CoASH enzyme complex and that binding of the CoASH increases the structural flexibility of the loop, leading to an interchange between several similar equally populated conformations.

  10. 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)

  11. 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.

  12. 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.

  13. A multi-functional coordination polymer coexisting spontaneous chirality resolution and weak ferromagnetism

    SciTech Connect (OSTI)

    Li, Xiu-Hua; Zhang, Qi; Hu, Ping

    2014-10-15

    A multifunctional homochiral coordination polymer, [Co(H{sub 2}O)(BDC)(4,4′-BPY)]∙3H{sub 2}O (1) (H{sub 2}BDC=1,2-benzenedicarboxylate and 4,4′-BPY=4,4′-bipyridine), has been successfully isolated from Co(II) ions and mixed ligands (1,2-benzenedicarboxylate and 4,4′-bipyridine). Complex 1, which exhibits spontaneous chirality resolution and weak ferromagnetism, is built by chiral helices interconnected via end-to-end 4,4′-BPY bridges into a two-dimensional (2D) layer structure. - Graphical abstract: A 2D cobalt coordination polymer compound showing spontaneous chirality resolution and weak ferromagnetism. - Highlights: • A new 2D cobalt mix-ligand coordination polymer complex has been synthesized. • The cobalt coordination polymer complex shows spontaneous chirality resolution in solid state. • The cobalt coordination polymer complex displays dominant and weak intrachain ferromagnetic interactions.

  14. 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.

  15. Influence of reservoir stress path on deformation and permeability of weakly cemented sandstone reservoirs

    SciTech Connect (OSTI)

    Ruistuen, H.; Teufel, L.W.; Rhett, D.

    1996-12-31

    The influence of production-induced changes in reservoir stress state on compressibility and permeability of weakly cemented sandstones has been analyzed. Laboratory experiments simulating reservoir depletion have been conducted for the full range of stress paths that a reservoir may follow. Samples were loaded by reducing the pore pressure and controlling the confining pressure according to the desired stress path from initial reservoir conditions. The results show that compressibility of weakly cemented sandstones are stress path dependent. Compressibilities measured under uniaxial strain conditions, or a stress path with a K value lower than the one associated with uniaxial strain, are more than twice the corresponding value found under hydrostatic loading conditions. In contrast, matrix permeability measured in the maximum stress direction show no significant stress path dependence. Independently of stress path, the observed permeability reductions fall within the general trend expected for a sedimentary rock of relatively high initial permeability. A significant permeability decrease was only observed as the shear stress exceeded the yield limit of the rock, probably due to both mobilization of fine arains and an increase in tortuosity due to collapse of pore space. Results of this study suggest that stress path dependent properties of weakly cemented sandstones is a consequence of the heterogeneous nature of the sedimentary rock. Material properties are affected by grain-scale inelastic deformation processes and the pattern of these deformation processes is primarily controlled by reservoir stress path.

  16. 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.

  17. 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.

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

    SciTech Connect (OSTI)

    MacEwan, Scott J.

    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 Q2 =0.025 (GeV/c)2 in order to provide the first direct measurement of the proton's weak charge, QWp. 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 Q2 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.

  19. 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 20,000deg{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 ?}.

  20. 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.

  1. Polynucleotides encoding TRF1 binding proteins

    DOE Patents [OSTI]

    Campisi, Judith; Kim, Sahn-Ho

    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.

  2. Specific albumin binding to microvascular endothelium in culture

    SciTech Connect (OSTI)

    Schnitzer, J.E.; Carley, W.W.; Palade, G.E. )

    1988-03-01

    The specific binding of rat serum albumin (RSA) to confluent microvascular endothelial cells in culture derived from the vasculature of the rat epididymal fat pad was studied at 4{degree}C by radioassay and immunocytochemistry. Radioiodinated RSA ({sup 125}I-RSA) binding to the cells reached equilibrium at {approximately} 20 min incubation. Albumin binding was a slowly saturating function over concentrations ranging from 0.01 to 50 mg/ml. Specific RSA binding with a moderate apparent affinity constant of 1.0 mg/ml and with a maximum binding concentration of 90 ng/cm{sup 2} was immunolocalized with anti-RSA antibody to the outer (free) side of the enothelium. Scatchard analysis of the binding yielded a nonlinear binding curve with a concave-upward shape. Dissociation rate analysis supports negative cooperativity of albumin binding, but multiple binding sites may also be present. Albumin binding fulfilled many requirements for ligand specificity including saturability, reversibility, competibility, and dependence on both cell type and cell number. The results are discussed in terms of past in situ investigations on the localization of albumin binding to vascular endothelium and its effect on transendothelial molecular transport.

  3. Reflection-Based Python-C++ Bindings

    SciTech Connect (OSTI)

    Generowicz, Jacek; Lavrijsen, Wim T.L.P.; Marino, Massimo; Mato, Pere

    2004-10-14

    Python is a flexible, powerful, high-level language with excellent interactive and introspective capabilities and a very clean syntax. As such, it can be a very effective tool for driving physics analysis. Python is designed to be extensible in low-level C-like languages, and its use as a scientific steering language has become quite widespread. To this end, existing and custom-written C or C++ libraries are bound to the Python environment as so-called extension modules. A number of tools for easing the process of creating such bindings exist, such as SWIG and Boost. Python. Yet, the process still requires a considerable amount of effort and expertise. The C++ language has few built-in introspective capabilities, but tools such as LCGDict and CINT add this by providing so-called dictionaries: libraries that contain information about the names, entry points, argument types, etc. of other libraries. The reflection information from these dictionaries can be used for the creation of bindings and so the process can be fully automated, as dictionaries are already provided for many end-user libraries for other purposes, such as object persistency. PyLCGDict is a Python extension module that uses LCG dictionaries, as PyROOT uses CINT reflection information, to allow /cwPython users to access C++ libraries with essentially no preparation on the users' behalf. In addition, and in a similar way, PyROOT gives ROOT users access to Python libraries.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Testing the Standard Model by precision measurement of the weak charges of quarks

    SciTech Connect (OSTI)

    Ross Young; Roger Carlini; Anthony Thomas; Julie Roche

    2007-05-01

    In a global analysis of the latest parity-violating electron scattering measurements on nuclear targets, we demonstrate a significant improvement in the experimental knowledge of the weak neutral-current lepton-quark interactions at low-energy. The precision of this new result, combined with earlier atomic parity-violation measurements, limits the magnitude of possible contributions from physics beyond the Standard Model - setting a model-independent, lower-bound on the scale of new physics at ~1 TeV.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

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

    DOE Patents [OSTI]

    Cremers, David A.; Keller, Richard A.

    1985-01-01

    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.-5 cm.sup.-1 has been demonstrated using this technique.

  18. 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.

  19. 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.

  20. 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.

  1. A weak zero-one law for sequences of random distance graphs

    SciTech Connect (OSTI)

    Zhukovskii, Maksim E

    2012-07-31

    We study zero-one laws for properties of random distance graphs. Properties written in a first-order language are considered. For p(N) such that pN{sup {alpha}}{yields}{infinity} as N{yields}{infinity}, and (1-p)N{sup {alpha}} {yields} {infinity} as N {yields} {infinity} for any {alpha}>0, we succeed in refuting the law. In this connection, we consider a weak zero-one j-law. For this law, we obtain results for random distance graphs which are similar to the assertions concerning the classical zero-one law for random graphs. Bibliography: 18 titles.

  2. 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.

  3. 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.

  4. Binding Behavior of Dopamine Transporter Key to Understanding...

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

    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 ...

  5. 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.

  6. 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...

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

    Office of Scientific and Technical Information (OSTI)

    X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified ... LIFE SCIENCES; ALDEHYDES; CARBOXYLIC ACIDS; CRYSTAL STRUCTURE; IN VIVO; INFLAMMATION; ...

  8. Hydrodynamic and Membrane Binding Properties of Purified Rous...

    Office of Scientific and Technical Information (OSTI)

    Purified Rous Sarcoma Virus Gag Protein Citation Details In-Document Search Title: Hydrodynamic and Membrane Binding Properties of Purified Rous Sarcoma Virus Gag Protein ...

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

    Office of Scientific and Technical Information (OSTI)

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

  10. Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding...

    Office of Scientific and Technical Information (OSTI)

    Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change Mechanism Resources with Additional Information Paul D. Boyer Courtesy of UCLA 'For Paul Boyer, the Nobel Prize ...

  11. 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 20300?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.

  12. Determination of the Proton's Weak Charge via Parity Violating Electron Scattering

    SciTech Connect (OSTI)

    Hoskins, Joshua Russell

    2015-08-01

    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 Q2=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 Q2 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.

  13. 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.

  14. 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 Ingards 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.

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

    SciTech Connect (OSTI)

    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. 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.

  17. 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 6cls 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.

  18. Babel Fortran 2003 Binding for Structured Data Types

    SciTech Connect (OSTI)

    Muszala, S; Epperly, T; Wang, N

    2008-05-02

    Babel is a tool aimed at the high-performance computing community that addresses the need for mixing programming languages (Java, Python, C, C++, Fortran 90, FORTRAN 77) in order to leverage the specific benefits of those languages. Scientific codes often rely on structured data types (structs, derived data types) to encapsulate data, and Babel has been lacking in this type of support until recently. We present a new language binding that focuses on their interoperability of C/C++ with Fortran 2003. The new binding builds on the existing Fortran 90 infrastructure by using the iso-c-binding module defined in the Fortran 2003 standard as the basis for C/C++ interoperability. We present the technical approach for the new binding and discuss our initial experiences in applying the binding in FACETS (Framework Application for Core-Edge Transport Simulations) to integrate C++ with legacy Fortran codes.

  19. 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.

  20. Electron-electron interaction, weak localization and spin valve effect in vertical-transport graphene devices

    SciTech Connect (OSTI)

    Long, Mingsheng; Gong, Youpin; Wei, Xiangfei; Zhu, Chao; Xu, Jianbao; Liu, Ping; Guo, Yufen; Li, Weiwei; Liu, Liwei; Liu, Guangtong

    2014-04-14

    We fabricated a vertical structure device, in which graphene is sandwiched between two asymmetric ferromagnetic electrodes. The measurements of electron and spin transport were performed across the combined channels containing the vertical and horizontal components. The presence of electron-electron interaction (EEI) was found not only at low temperatures but also at moderate temperatures up to ∼120 K, and EEI dominates over weak localization (WL) with and without applying magnetic fields perpendicular to the sample plane. Moreover, spin valve effect was observed when magnetic filed is swept at the direction parallel to the sample surface. We attribute the EEI and WL surviving at a relatively high temperature to the effective suppress of phonon scattering in the vertical device structure. The findings open a way for studying quantum correlation at relatively high temperature.

  1. 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.

  2. 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 4501000?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 280450?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.

  3. 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

  4. GALAXIES IN X-RAY GROUPS. II. A WEAK LENSING STUDY OF HALO CENTERING

    SciTech Connect (OSTI)

    George, Matthew R.; Ma, Chung-Pei; Leauthaud, Alexie; Bundy, Kevin; Finoguenov, Alexis; Rykoff, Eli S.; Tinker, Jeremy L.; Wechsler, Risa H.; Massey, Richard; Mei, Simona

    2012-09-20

    Locating the centers of dark matter halos is critical for understanding the mass profiles of halos, as well as the formation and evolution of the massive galaxies that they host. The task is observationally challenging because we cannot observe halos directly, and tracers such as bright galaxies or X-ray emission from hot plasma are imperfect. In this paper, we quantify the consequences of miscentering on the weak lensing signal from a sample of 129 X-ray-selected galaxy groups in the COSMOS field with redshifts 0 < z < 1 and halo masses in the range 10{sup 13}-10{sup 14} M{sub Sun }. By measuring the stacked lensing signal around eight different candidate centers (such as the brightest member galaxy, the mean position of all member galaxies, or the X-ray centroid), we determine which candidates best trace the center of mass in halos. In this sample of groups, we find that massive galaxies near the X-ray centroids trace the center of mass to {approx}< 75 kpc, while the X-ray position and centroids based on the mean position of member galaxies have larger offsets primarily due to the statistical uncertainties in their positions (typically {approx}50-150 kpc). Approximately 30% of groups in our sample have ambiguous centers with multiple bright or massive galaxies, and some of these groups show disturbed mass profiles that are not well fit by standard models, suggesting that they are merging systems. We find that halo mass estimates from stacked weak lensing can be biased low by 5%-30% if inaccurate centers are used and the issue of miscentering is not addressed.

  5. 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.

  6. Increased serum cortisol binding in chronic active hepatitis

    SciTech Connect (OSTI)

    Orbach, O.; Schussler, G.C.

    1989-01-01

    A high serum cortisol concentration, apparently due to increased cortisol-binding globulin (CBG), was found in a patient (index case) with chronic active hepatitis (CAH). We therefore performed further studies to determine whether increased cortisol binding is generally associated with CAH. Serum samples were obtained from 15 hospitalized patients with long-term liver function test elevations but no evidence of cirrhosis, 15 normal subjects without a history of hepatitis, four healthy pregnant women, and 10 alcoholic patients with stigmata of cirrhosis. Serum cortisol binding was measured by an adaptation of a previously described charcoal uptake method. Thyroxine-binding globulin (TBG) and sex hormone-binding globulin were determined by radioimmunoassays. Charcoal uptake of 125I cortisol from sera of normal subjects and additional patients with CAH revealed that increased serum cortisol binding by a saturable site, presumably CBG, was associated with CAH. Cortisol binding was significantly correlated with immunoassayable TBG, suggesting that in CAH, similar mechanisms may be responsible for increasing the serum concentrations of CBG and TBG.

  7. Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes

    SciTech Connect (OSTI)

    Bu, L.; Nimlos, M. R.; Shirts, M. R.; Stahlberg, J.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

    2012-07-13

    Cellulases hydrolyze {beta}-1,4 glycosidic linkages in cellulose, which are among the most prevalent and stable bonds in Nature. Cellulases comprise many glycoside hydrolase families and exist as processive or nonprocessive enzymes. Product inhibition negatively impacts cellulase action, but experimental measurements of product-binding constants vary significantly, and there is little consensus on the importance of this phenomenon. To provide molecular level insights into cellulase product inhibition, we examine the impact of product binding on processive and nonprocessive cellulases by calculating the binding free energy of cellobiose to the product sites of catalytic domains of processive and nonprocessive enzymes from glycoside hydrolase families 6 and 7. The results suggest that cellobiose binds to processive cellulases much more strongly than nonprocessive cellulases. We also predict that the presence of a cellodextrin bound in the reactant site of the catalytic domain, which is present during enzymatic catalysis, has no effect on product binding in nonprocessive cellulases, whereas it significantly increases product binding to processive cellulases. This difference in product binding correlates with hydrogen bonding between the substrate-side ligand and the cellobiose product in processive cellulase tunnels and the additional stabilization from the longer tunnel-forming loops. The hydrogen bonds between the substrate- and product-side ligands are disrupted by water in nonprocessive cellulase clefts, and the lack of long tunnel-forming loops results in lower affinity of the product ligand. These findings provide new insights into the large discrepancies reported for binding constants for cellulases and suggest that product inhibition will vary significantly based on the amount of productive binding for processive cellulases on cellulose.

  8. Distinct effects of anthropogenic aerosols on the East Asian summer monsoon between multidecadal strong and weak monsoon stages

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

    Xie, Xiaoning; Wang, Hongli; Liu, Xiaodong; Li, Jiandong; Wang, Zhaosheng; Liu, Yangang

    2016-06-18

    Industrial emissions of anthropogenic aerosols over East Asia have greatly increased in recent decades, and so the interactions between atmospheric aerosols and the East Asian summer monsoon (EASM) have attracted enormous attention. In order to further understand the aerosol-EASM interaction, we investigate the impacts of anthropogenic aerosols on the EASM during the multidecadal strong (1950–1977) and weak (1978–2000) EASM stages using the Community Atmospheric Model 5.1. Numerical experiments are conducted for the whole period, including the two different EASM stages, with present day (PD, year 2000) and preindustrial (PI, year 1850) aerosol emissions, as well as the observed time-varying aerosolmore » emissions. A comparison of the results from PD and PI shows that, with the increase in anthropogenic aerosols, the large-scale EASM intensity is weakened to a greater degree (-9.8%) during the weak EASM stage compared with the strong EASM stage (-4.4%). The increased anthropogenic aerosols also result in a significant reduction in precipitation over North China during the weak EASM stage, as opposed to a statistically insignificant change during the strong EASM stage. Because of greater aerosol loading and the larger sensitivity of the climate system during weak EASM stages, the aerosol effects are more significant during these EASM stages. Moreover, these results suggest that anthropogenic aerosols from the same aerosol emissions have distinct effects on the EASM and the associated precipitation between the multidecadal weak and strong EASM stages.« less

  9. Modeling of Carbohydrate Binding Modules Complexed to Cellulose

    SciTech Connect (OSTI)

    Nimlos, M. R.; Beckham, G. T.; Bu, L.; Himmel, M. E.; Crowley, M. F.; Bomble, Y. J.

    2012-01-01

    Modeling results are presented for the interaction of two carbohydrate binding modules (CBMs) with cellulose. The family 1 CBM from Trichoderma reesei's Cel7A cellulase was modeled using molecular dynamics to confirm that this protein selectively binds to the hydrophobic (100) surface of cellulose fibrils and to determine the energetics and mechanisms for locating this surface. Modeling was also conducted of binding of the family 4 CBM from the CbhA complex from Clostridium thermocellum. There is a cleft in this protein, which may accommodate a cellulose chain that is detached from crystalline cellulose. This possibility is explored using molecular dynamics.

  10. 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

  11. 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.

  12. Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-Binding Module on Cellulose

    SciTech Connect (OSTI)

    Nimlos, M. R.; Beckham, G. T.; Matthews, J. F.; Bu, L.; Himmel, M. E.; Crowley, M. F.

    2012-06-08

    Cellulase enzymes often contain carbohydrate-binding modules (CBMs) for binding to cellulose. The mechanisms by which CBMs recognize specific surfaces of cellulose and aid in deconstruction are essential to understand cellulase action. The Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase, Cel7A, is known to selectively bind to hydrophobic surfaces of native cellulose. It is most commonly suggested that three aromatic residues identify the planar binding face of this CBM, but several recent studies have challenged this hypothesis. Here, we use molecular simulation to study the CBM binding orientation and affinity on hydrophilic and hydrophobic cellulose surfaces. Roughly 43 {mu}s of molecular dynamics simulations were conducted, which enables statistically significant observations. We quantify the fractions of the CBMs that detach from crystal surfaces or diffuse to other surfaces, the diffusivity along the hydrophobic surface, and the overall orientation of the CBM on both hydrophobic and hydrophilic faces. The simulations demonstrate that there is a thermodynamic driving force for the Cel7A CBM to bind preferentially to the hydrophobic surface of cellulose relative to hydrophilic surfaces. In addition, the simulations demonstrate that the CBM can diffuse from hydrophilic surfaces to the hydrophobic surface, whereas the reverse transition is not observed. Lastly, our simulations suggest that the flat faces of Family 1 CBMs are the preferred binding surfaces. These results enhance our understanding of how Family 1 CBMs interact with and recognize specific cellulose surfaces and provide insights into the initial events of cellulase adsorption and diffusion on cellulose.

  13. 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

  14. 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

  15. 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.

  16. 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:...

  17. Visually Relating Gene Expression and in vivo DNA Binding Data

    SciTech Connect (OSTI)

    Huang, Min-Yu; Mackey, Lester; Ker?; nen, Soile V. E.; Weber, Gunther H.; Jordan, Michael I.; Knowles, David W.; Biggin, Mark D.; Hamann, Bernd

    2011-09-20

    Gene expression and in vivo DNA binding data provide important information for understanding gene regulatory networks: in vivo DNA binding data indicate genomic regions where transcription factors are bound, and expression data show the output resulting from this binding. Thus, there must be functional relationships between these two types of data. While visualization and data analysis tools exist for each data type alone, there is a lack of tools that can easily explore the relationship between them. We propose an approach that uses the average expression driven by multiple of ciscontrol regions to visually relate gene expression and in vivo DNA binding data. We demonstrate the utility of this tool with examples from the network controlling early Drosophila development. The results obtained support the idea that the level of occupancy of a transcription factor on DNA strongly determines the degree to which the factor regulates a target gene, and in some cases also controls whether the regulation is positive or negative.

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

    SciTech Connect (OSTI)

    Thürmer, 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.

  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. 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.

  1. Spin polarized photons from an axially charged plasma at weak coupling: Complete leading order

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

    Mamo, Kiminad A.; Yee, Ho-Ung

    2016-03-24

    In the presence of (approximately conserved) axial charge in the QCD plasma at finite temperature, the emitted photons are spin aligned, which is a unique P- and CP-odd signature of axial charge in the photon emission observables. We compute this “P-odd photon emission rate” in a weak coupling regime at a high temperature limit to complete leading order in the QCD coupling constant: the leading log as well as the constant under the log. As in the P-even total emission rate in the literature, the computation of the P-odd emission rate at leading order consists of three parts: (1) Comptonmore » and pair annihilation processes with hard momentum exchange, (2) soft t- and u-channel contributions with hard thermal loop resummation, (3) Landau-Pomeranchuk-Migdal resummation of collinear bremsstrahlung and pair annihilation. In conclusion, we present analytical and numerical evaluations of these contributions to our P-odd photon emission rate observable.« less

  2. 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.

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

    SciTech Connect (OSTI)

    Hagen, Gaute; Forssen, Christian; Nazarewicz, Witold; Papenbrock, Thomas F.; Bacca, S.; Barnea, Nir; Carlsson, Boris; Drischler, Christian; Hebeler, Kai; Hjorth-Jensen, M.; Miorelli, Mirko; Orlandini, Giuseppina; Schwenk, Achim; Simonis, Johannes; Jansen, Gustav R.; Ekstrom, A.; Wendt, K. A.

    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) 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.

  4. 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

  5. Improved limits on scattering of weakly interacting massive particles from reanalysis of 2013 LUX data

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

    Akerib, D. S.

    2016-04-20

    Here, we present constraints on weakly interacting massive particles (WIMP)-nucleus scattering from the 2013 data of the Large Underground Xenon dark matter experiment, including 1.4 × 104 kg day of search exposure. This new analysis incorporates several advances: single-photon calibration at the scintillation wavelength, improved event-reconstruction algorithms, a revised background model including events originating on the detector walls in an enlarged fiducial volume, and new calibrations from decays of an injected tritium β source and from kinematically constrained nuclear recoils down to 1.1 keV. Sensitivity, especially to low-mass WIMPs, is enhanced compared to our previous results which modeled the signalmore » only above a 3 keV minimum energy. Under standard dark matter halo assumptions and in the mass range above 4 GeV c–2, these new results give the most stringent direct limits on the spin-independent WIMP-nucleon cross section. The 90% C.L. upper limit has a minimum of 0.6 zb at 33 GeV c–2 WIMP mass.« less

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

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

    Thürmer, 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

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

    SciTech Connect (OSTI)

    Thurmer, Konrad; Yuan, Chunqing; Kimmel, Gregory A.; Kay, Bruce D.; Smith, R. Scott

    2015-11-01

    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. Similar desorption temperatures were observed for desorption from amorphous solid water.

  8. 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.

  9. Extraction of weakly reductive and reductive coals with sub- and supercritical water

    SciTech Connect (OSTI)

    Bo Wu; Haoquan Hu; Shiping Huang; Yunming Fang; Xian Li; Meng Meng

    2008-11-15

    On a semi-continuous apparatus, a weakly reductive Shenfu-Dongsheng (SD) coal and a reductive Pingshuo (PS) coal were non-isothermally extracted with sub- and supercritical water to explore the differences between the two coals. The effect of the temperature on the extract formation rate, conversion, and product composition under different pressures was investigated. The extraction results of two coal samples indicate that the extract formation rate has a maximum in the studied temperature range between room temperature and 500{degree}C. The temperature corresponding to the maximum extract formation rate, changing with the pressure, is between 390 and 410{degree}C. The gas yield, extract yield, and conversion of two coals increase with the increasing pressure. In comparison to PS coal, SD coal has a low temperature corresponding to the maximum extract formation rate under the same pressure. Both coals have a main fraction of asphaltene, but SD coal has a higher fraction of oil than PS coal. The main gas components are CO{sub 2}, CH{sub 4}, and H{sub 2}. The gas from PS coal has a higher CH{sub 4} content and lower CO{sub 2} content than that from SD coal. The analysis results of the extraction residue indicated that SD coal has a low residue yield and the residue shows a large surface area and small average pore diameter compared to PS coal. 17 refs., 4 figs., 8 tabs.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Nonlinear Langmuir structures: Soliton and shock in a rotating weakly relativistic electron-positron magnetoplasma with stationary positive ions

    SciTech Connect (OSTI)

    El-Labany, S. K.; Moslem, W. M.; El-Awady, E. I.

    2010-06-15

    Theoretical and numerical studies are performed for nonlinear Langmuir structures (soliton and shock) in a rotating weakly relativistic electron-positron magnetoplasma with background stationary positive ions. For this purpose, the reductive perturbation technique is employed to the weakly relativistic hydrodynamical electrons/positrons fluid equations and Poisson equation, obtaining extended Zakharov-Kuznetsov equation. The latter has been solved analytically. The features of the nonlinear excitations and their propagation conditions are investigated numerically. Our finding could elucidate the nonlinear electrostatic structures that propagate in astrophysical plasma situations where rotating, magnetized plasma can exist; such as polar cups region of pulsars, around active galactic nuclei, neutron stars, and white dwarfs.

  15. SIMULATIONS OF TURBULENCE INDUCED ELLIPTICITY OVER LARGE FIELDS-OF-VIEW: THE FIRST STEP TOWARDS ENABLING LSST WEAK LENSING SCIENCE

    SciTech Connect (OSTI)

    Schlaufman, K

    2004-10-11

    Atmospheric turbulence can mimic the effects of weak lensing in astronomical images, so it is necessary to understand to what degree turbulence affects weak lensing measurements. In particular, we studied the ellipticity induced upon the point-spread functions (PSFs) of a grid of simulated stars separated by distances (d {approx} 1{prime}) that will be characteristic of Large Synoptic Survey Telescope (LSST) images. We observe that atmospherically induced ellipticity changes on small scales (d < 0.5{prime}) and use linear interpolation between stars separated by d = 0.5{prime} to determine the induced ellipticity everywhere in the field-of-view.

  16. 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

  17. 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

  18. 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

  19. 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:

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

    SciTech Connect (OSTI)

    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 the 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.

  1. 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

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

    Office of Scientific and Technical Information (OSTI)

    Menin binds the JUN family transcription factor JUND and inhibits its transcriptional ... A recent report on the tethering of MLL1 to chromatin binding factor lens ...

  3. 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...

  4. 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

  5. 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.

  6. 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

  7. 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 Schrdinger 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.

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

    SciTech Connect (OSTI)

    Petri, Andrea; May, Morgan; Haiman, Zoltn; 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.

  9. 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.

  10. Cosmology and astrophysics from relaxed galaxy clusters - IV: Robustly calibrating hydrostatic masses with weak lensing

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

    Applegate, D. E; Mantz, A.; Allen, S. W.; von der Linden, A.; Morris, R. G.; Hilbert, S.; Kelly, P. L.; Burke, D. L.; Ebeling, H.; Rapetti, D. A.; et al

    2016-02-04

    This is the fourth in a series of papers studying the astrophysics and cosmology of massive, dynamically relaxed galaxy clusters. Here, we use measurements of weak gravitational lensing from the Weighing the Giants project to calibrate Chandra X-ray measurements of total mass that rely on the assumption of hydrostatic equilibrium. This comparison of X-ray and lensing masses measures the combined bias of X-ray hydrostatic masses from both astrophysical and instrumental sources. While we cannot disentangle the two sources of bias, only the combined bias is relevant for calibrating cosmological measurements using relaxed clusters. Assuming a fixed cosmology, and within amore » characteristic radius (r2500) determined from the X-ray data, we measure a lensing to X-ray mass ratio of 0.96 ± 9% (stat) ± 9% (sys). We find no significant trends of this ratio with mass, redshift or the morphological indicators used to select the sample. Our results imply that any departures from hydrostatic equilibrium at these radii are offset by calibration errors of comparable magnitude, with large departures of tens-of-percent unlikely. In addition, we find a mean concentration of the sample measured from lensing data of c200 = 3.0+4.4–1.8. In conclusion, anticipated short-term improvements in lensing systematics, and a modest expansion of the relaxed lensing sample, can easily increase the measurement precision by 30–50%, leading to similar improvements in cosmological constraints that employ X-ray hydrostatic mass estimates, such as on Ωm from the cluster gas mass fraction.« less

  11. 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

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

    SciTech Connect (OSTI)

    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.; Reeves, G. D.; Funsten, H. O.; Blake, J. B.

    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 to 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.

  13. 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 σ8m/0.27)0.63 = 0.85+0.03-0.03.

  14. 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

  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. Phonons and magnetic excitation correlations in weak ferromagnetic YCrO{sub 3}

    SciTech Connect (OSTI)

    Sharma, Yogesh; Sahoo, Satyaprakash E-mail: guptaraj@iitk.ac.in Perez, William; Katiyar, Ram S. E-mail: guptaraj@iitk.ac.in; Mukherjee, Somdutta; Gupta, Rajeev E-mail: guptaraj@iitk.ac.in; Garg, Ashish; Chatterjee, Ratnamala

    2014-05-14

    Here, we report the temperature dependent Raman spectroscopic studies on orthorhombically distorted perovskite YCrO{sub 3} over a temperature range of 20–300 K. Temperature dependence of DC-magnetization measurements under field cooled and zero field cooled protocols confirmed a Néel transition at T{sub N} ∼ 142 K. Magnetization isotherms recorded at 125 K show a clear loop opening without any magnetization saturation up to 20 kOe, indicating a coexistence of antiferromagnetic (AFM) and weak ferromagnetic (WFM) phases. Estimation of exchange constants using mean-field approximation further confirm the presence of a complex magnetic phase below T{sub N}. Temperature evolution of Raman line-shape parameters of the selected modes (associated with the octahedral rotation and A(Y)-shift in the unit-cell) reveal an anomalous phonon shift near T{sub N}. An additional phonon anomaly was identified at T{sup *} ∼ 60 K, which could possibly be attributed to the change in the spin dynamics. Moreover, the positive and negative shifts in Raman frequencies between T{sub N} and T{sup *} suggest competing WFM and AFM interactions. A close match between the phonon frequency of B{sub 3g} (3)-octahedral rotation mode with the square of sublattice magnetization between T{sub N} and T{sup *} is indicative of the presence of spin-phonon coupling in multiferroic YCrO{sub 3}.

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

    SciTech Connect (OSTI)

    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, energetically 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.

  18. 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

  19. 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, sin2(theta_W). The final Qweak measurement will provide the most precise measurement of the weak mixing angle below the Z0 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 sin2(theta_W) = 0.23429 ± 0.00211.

  20. 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; Bentez, Narciso [Instituto de Astrofsica de Andaluca (CSIC), E-18008 Granada (Spain); Seitz, Stella; Gruen, Daniel [Universitts-Sternwarte, Mnchen, 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

  1. 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

  2. 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.

  3. 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

  4. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

    SciTech Connect (OSTI)

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

    2015-02-25

    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. Moreover, 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, furthermore, we 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. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  5. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

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

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

    2015-02-25

    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. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of themore » 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, furthermore, we 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. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    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.

  13. Inhibition Of Call-Cell Binding By Kipid Assemblies

    DOE Patents [OSTI]

    Nagy, Jon O. , Bargatze, Robert F.

    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.

  14. Inhibition of cell-cell binding by lipid assemblies

    DOE Patents [OSTI]

    Nagy, Jon O.; Bargatze, Robert F.

    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.

  15. Structural basis for DNA binding by replication initiator Mcm10

    SciTech Connect (OSTI)

    Warren, Eric M.; Vaithiyalingam, Sivaraja; Haworth, Justin; Greer, Briana; Bielinsky, Anja-Katrin; Chazin, Walter J.; Eichman, Brandt F.

    2009-06-30

    Mcm10 is an essential eukaryotic DNA replication protein required for assembly and progression of the replication fork. The highly conserved internal domain (Mcm10-ID) has been shown to physically interact with single-stranded (ss) DNA, DNA polymerase alpha, and proliferating cell nuclear antigen (PCNA). The crystal structure of Xenopus laevis Mcm10-ID presented here reveals a DNA binding architecture composed of an oligonucleotide/oligosaccharide-fold followed in tandem by a variant and highly basic zinc finger. NMR chemical shift perturbation and mutational studies of DNA binding activity in vitro reveal how Mcm10 uses this unique surface to engage ssDNA. Corresponding mutations in Saccharomyces cerevisiae result in increased sensitivity to replication stress, demonstrating the functional importance of DNA binding by this region of Mcm10 to replication. In addition, mapping Mcm10 mutations known to disrupt PCNA, polymerase alpha, and DNA interactions onto the crystal structure provides insight into how Mcm10 might coordinate protein and DNA binding within the replisome.

  16. 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.

  17. 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.

  18. 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.

  19. Modeling silver binding to gills of rainbow trout (Oncorhynchus mykiss)

    SciTech Connect (OSTI)

    Janes, N.; Playle, R.C.

    1995-11-01

    Rainbow trout (Oncorhynchus mykiss, 1--3 g) were exposed to {approximately} 1.0 {micro}M silver (Ag) ({approximately} 11 {micro}g {center_dot} L{sup {minus}1} Ag) for 2 to 3 h in synthetic soft water (Ca, Na {approximately} 300 {micro}M, pH 6.5--7.5) to which was added Ca, Na, H{sup +}, dissolved organic carbon (DOC), Cl, or thiosulfate (S{sub 2}O{sub 3}). Gills were extracted and gill Ag concentrations were measured using graphite-furnace atomic absorption spectrophotometry. The concentration of cations (Ca, Na, H{sup +}) and complexing agents (DOC, Cl, S{sub 2}O{sub 3}) needed to keep Ag off the gills were used to calculate conditional equilibrium binding constants (K) at the gills. Log K for Ag-gill binding was 10.0, with approximately 1.3 nmol Ag binding sites per fish. All experimentally determined log K values were entered into an aquatic chemistry equilibrium model, MINEQL{sup +}, to predict Ag binding at trout gills. For a series of natural waters, model-predicted gill Ag concentrations correlated well with observed gill Ag concentrations, with one exception, very hard city of Waterloo tapwater. This exception may indicate a kinetic constraint on the thermodynamic basis of the model.

  20. Methods of use of cellulose binding domain proteins

    DOE Patents [OSTI]

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    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.

  1. Accurate nuclear radii and binding energies from a chiral interaction

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

    Ekstrom, Jan A.; Jansen, G. R.; Wendt, Kyle A.; Hagen, Gaute; Papenbrock, Thomas F.; Carlsson, Boris; Forssen, Christian; Hjorth-Jensen, M.; Navratil, Petr; Nazarewicz, Witold

    2015-05-01

    With the goal of developing predictive ab initio capability for light and medium-mass nuclei, two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective Jπ=3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shellmore » nuclei are in reasonable agreement with experiment.« less

  2. Accurate nuclear radii and binding energies from a chiral interaction

    SciTech Connect (OSTI)

    Ekstrom, Jan A.; Jansen, G. R.; Wendt, Kyle A.; Hagen, Gaute; Papenbrock, Thomas F.; Carlsson, Boris; Forssen, Christian; Hjorth-Jensen, M.; Navratil, Petr; Nazarewicz, Witold

    2015-05-01

    With the goal of developing predictive ab initio capability for light and medium-mass nuclei, two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective Jπ=3− states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

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

    SciTech Connect (OSTI)

    ., Nuruzzaman

    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

  4. Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change

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

    Mechanism Paul D. Boyer, Adenosine Triphosphate (ATP), and the Binding Change Mechanism Resources with Additional Information Paul D. Boyer Courtesy of UCLA 'For Paul Boyer, the Nobel Prize was "an unexpected pleasure." It had been 20 years since he formulated a hypothesis to describe what he calls "the most prominent chemical reaction in the whole world." It is the process by which molecules produce ATP (adenosine triphosphate), thereby transmuting light, air, water and

  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. 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

  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 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

  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. 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.

  12. 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.

  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. 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

  16. Thermodynamics of Binding Biomass to Cellulases for Renewable Fuel |

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

    Argonne Leadership Computing Facility Thermodynamics of Binding Biomass to Cellulases for Renewable Fuel PI Name: Michael Crowley PI Email: michael.crowley@nrel.gov Institution: National Renewable Energy Laboratory Allocation Program: INCITE Allocation Hours at ALCF: 70 Million Year: 2013 Research Domain: Energy Technologies The U.S. Department of Energy (DOE) has stipulated that 30% of the gasoline demand be displaced by renewable transportation fuels from non-food feedstock by 2030. The

  17. 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

  18. 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

  19. 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...

  20. 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...

  1. 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 ...

  2. 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.

  3. 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.

  4. On nonlinear evolution of low-frequency Alfvén waves in weakly-expanding solar wind plasmas

    SciTech Connect (OSTI)

    Nariyuki, Y.

    2015-02-15

    A multi-dimensional nonlinear evolution equation for Alfvén waves in weakly-expanding solar wind plasmas is derived by using the reductive perturbation method. The expansion of solar wind plasma parcels is modeled by an expanding box model, which includes the accelerating expansion. It is shown that the resultant equation agrees with the Wentzel-Kramers-Brillouin prediction of the low-frequency Alfvén waves in the linear limit. In the cold and one-dimensional limit, a modified derivative nonlinear Schrodinger equation is obtained. Direct numerical simulations are carried out to discuss the effect of the expansion on the modulational instability of monochromatic Alfvén waves and the propagation of Alfvén solitons. By using the instantaneous frequency, it is quantitatively shown that as far as the expansion rate is much smaller than wave frequencies, effects of the expansion are almost adiabatic. It is also confirmed that while shapes of Alfvén solitons temporally change due to the expansion, some of them can stably propagate after their collision in weakly-expanding plasmas.

  5. 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.

  6. 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 .

  7. 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.

  8. Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-Binding Module

    SciTech Connect (OSTI)

    Taylor, C. B.; Talib, M. F.; McCabe, C.; Bu, L.; Adney, W. S.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

    2012-01-27

    Carbohydrate-binding modules (CBMs) are ubiquitous components of glycoside hydrolases, which degrade polysaccharides in nature. CBMs target specific polysaccharides, and CBM binding affinity to cellulose is known to be proportional to cellulase activity, such that increasing binding affinity is an important component of performance improvement. To ascertain the impact of protein and glycan engineering on CBM binding, we use molecular simulation to quantify cellulose binding of a natively glycosylated Family 1 CBM. To validate our approach, we first examine aromatic-carbohydrate interactions on binding, and our predictions are consistent with previous experiments, showing that a tyrosine to tryptophan mutation yields a 2-fold improvement in binding affinity. We then demonstrate that enhanced binding of 3-6-fold over a nonglycosylated CBM is achieved by the addition of a single, native mannose or a mannose dimer, respectively, which has not been considered previously. Furthermore, we show that the addition of a single, artificial glycan on the anterior of the CBM, with the native, posterior glycans also present, can have a dramatic impact on binding affinity in our model, increasing it up to 140-fold relative to the nonglycosylated CBM. These results suggest new directions in protein engineering, in that modifying glycosylation patterns via heterologous expression, manipulation of culture conditions, or introduction of artificial glycosylation sites, can alter CBM binding affinity to carbohydrates and may thus be a general strategy to enhance cellulase performance. Our results also suggest that CBM binding studies should consider the effects of glycosylation on binding and function.

  9. 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.

  10. Hydroxyapatite-binding peptides for bone growth and inhibition

    DOE Patents [OSTI]

    Bertozzi, Carolyn R.; Song, Jie; Lee, Seung-Wuk

    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.

  11. 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

  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. 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

  14. 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.

  15. 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.

  16. 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.

  17. The analog of Blanc`s law for drift velocities of electrons in gas mixtures in weakly ionized plasma

    SciTech Connect (OSTI)

    Chiflikian, R.V.

    1995-10-01

    The analog of Blanc`s law for drift velocities of electrons in multicomponent gas mixtures in weakly ionized spatially homogeneous low-temperature plasma is derived. The obtained approximate-analytical expressions are valid for average electron energy in the 1--5 eV range typical for plasma conditions of low-pressure direct current (DC) discharges. The accuracy of these formulas is {plus_minus}5%. The analytical criterion of the negative differential conductivity (NDC) of electrons in binary mixtures of gases is obtained. NDC of electrons is predicted in He:Kr and He:Xe rare gas mixtures. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  18. Cross-talk dynamics of optical solitons in a broadband Kerr nonlinear system with weak cubic loss

    SciTech Connect (OSTI)

    Peleg, Avner; Nguyen, Quan M.; Chung, Yeojin

    2010-11-15

    We study the dynamics of fast soliton collisions in a Kerr nonlinear optical waveguide with weak cubic loss. We obtain analytic expressions for the amplitude and frequency shifts in a single two-soliton collision and show that the impact of a fast three-soliton collision is given by the sum of the two-soliton interactions. Our analytic predictions are confirmed by numerical simulations with the perturbed nonlinear Schroedinger (NLS) equation. Furthermore, we show that the deterministic collision-induced dynamics of soliton amplitudes in a broadband waveguide system with N frequency channels is described by a Lotka-Volterra model for N competing species. For a two-channel system we find that stable transmission with equal prescribed amplitudes can be achieved by a proper choice of linear amplifier gain. The predictions of the Lotka-Volterra model are confirmed by numerical solution of a perturbed coupled-NLS model.

  19. Measuring the Weak Charge of the Proton and the Hadronic Parity Violation of the N → Δ Transition

    SciTech Connect (OSTI)

    Leacock, John D.

    2012-10-16

    Qweak will determine the weak charge of the proton, Qp{sub W}, via an asymmetry measurement of parity-violating elastic electron-proton scattering at low four momentum transfer to a precision of 4%. QpW has a firm Standard Model prediction and is related to the weak mixing angle, sin2 ΦW, a well-defined Standard Model parameter. Qweak will probe a subset of new physics to the TeV mass scale and test the Standard Model. The details of how this measurement was performed and the analysis of the 25% elastic dataset will be presented in this thesis. Also, an analysis of an auxiliary measurement of the parity-violating asymmetry in the N → Δ transition is presented. It is used as a systematic inelastic background correction in the elastic analysis and to extract information about the hadronic parity violation through the low energy constant, dΔ. The elastic asymmetry at Q2 = 0.0252 ± 0.0007 GeV2 was measured to be Aep = -265 ± 40 ± 22 ± 68 ppb (stat., sys., and blinding). Extrapolated to Q2 = 0, the value of the proton's weak charge was measured to be QpW = 0.077 ± 0.019 (stat. and sys.) ± 0.026 (blinding). This is within 1 σ of the Standard Model prediction of QpW = 0.0705 ± 0.0008. The N → Δ inelastic asymmetry at Q2 = 0.02078 ± 0.0005 GeV2 and W = 1205 MeV was measured to be Ainel = -3.03 ± 0.65 ± 0.73 ± 0.07 ppm (stat., sys., and blinding). This result constrains the low energy constant to be dΔ = 5.8 ± 22gπ, and, if the result of the G0 experiment is included, dΔ = 5.8 ± 17gπ. This result rules out suggested large values of dΔ motivated by radiative hyperon decays. The elastic measurement is the first direct measurement of the weak charge of the proton while the inelastic measurement is only the second

  20. Van der Waals metal-semiconductor junction: Weak Fermi level pinning enables effective tuning of Schottky barrier

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

    Liu, Yuanyue; Stradins, Paul; Wei, Su -Huai

    2016-04-22

    Two-dimensional (2D) semiconductors have shown great potential for electronic and optoelectronic applications. However, their development is limited by a large Schottky barrier (SB) at the metal-semiconductor junction (MSJ), which is difficult to tune by using conventional metals because of the effect of strong Fermi level pinning (FLP). We show that this problem can be overcome by using 2D metals, which are bounded with 2D semiconductors through van der Waals (vdW) interactions. This success relies on a weak FLP at the vdW MSJ, which is attributed to the suppression of metal-induced gap states. Consequently, the SB becomes tunable and can vanishmore » with proper 2D metals (for example, H-NbS2). This work not only offers new insights into the fundamental properties of heterojunctions but also uncovers the great potential of 2D metals for device applications.« less

  1. 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.

  2. MEASURING THE GEOMETRY OF THE UNIVERSE FROM WEAK GRAVITATIONAL LENSING BEHIND GALAXY GROUPS IN THE HST COSMOS SURVEY

    SciTech Connect (OSTI)

    Taylor, James E.; Massey, Richard J.; Leauthaud, Alexie; Tanaka, Masayuki; George, Matthew R.; Rhodes, Jason; Ellis, Richard; Scoville, Nick; Kitching, Thomas D.; Capak, Peter; Finoguenov, Alexis; Ilbert, Olivier; Kneib, Jean-Paul; Jullo, Eric; Koekemoer, Anton M.

    2012-04-20

    Gravitational lensing can provide pure geometric tests of the structure of spacetime, for instance by determining empirically the angular diameter distance-redshift relation. This geometric test has been demonstrated several times using massive clusters which produce a large lensing signal. In this case, matter at a single redshift dominates the lensing signal, so the analysis is straightforward. It is less clear how weaker signals from multiple sources at different redshifts can be stacked to demonstrate the geometric dependence. We introduce a simple measure of relative shear which for flat cosmologies separates the effect of lens and source positions into multiplicative terms, allowing signals from many different source-lens pairs to be combined. Applying this technique to a sample of groups and low-mass clusters in the COSMOS survey, we detect a clear variation of shear with distance behind the lens. This represents the first detection of the geometric effect using weak lensing by multiple, low-mass groups. The variation of distance with redshift is measured with sufficient precision to constrain the equation of state of the universe under the assumption of flatness, equivalent to a detection of a dark energy component {Omega}{sub X} at greater than 99% confidence for an equation-of-state parameter -2.5 {<=} w {<=} -0.1. For the case w = -1, we find a value for the cosmological constant density parameter {Omega}{sub {Lambda}} = 0.85{sup +0.044}{sub -}0{sub .19} (68% CL) and detect cosmic acceleration (q{sub 0} < 0) at the 98% CL. We consider the systematic uncertainties associated with this technique and discuss the prospects for applying it in forthcoming weak-lensing surveys.

  3. 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.

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

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

    Dorf, Mikhail A.; Davidson, Ronald C.; Kaganovich, Igor D.; Startsev, Edward A.

    2012-05-31

    In this study, 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 ionmore » 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~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 plasmaelectrons, 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 electrondynamics strongly affected by a weak applied magnetic field.« less

  5. 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)

  6. Weak-link capacitor

    DOE Patents [OSTI]

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

    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.

  7. 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.

  8. Distinct effects of anthropogenic aerosols on the East Asian summer monsoon between multi-decadal strong and weak monsoon stages: Effects of aerosols on EASM

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

    Xie, Xiaoning; Wang, Hongli; Liu, Xiaodong; Li, Jiandong; Wang, Zhaosheng; Liu, Yangang

    2016-06-18

    Industrial emissions of anthropogenic aerosols over East Asia have greatly increased in recent decades, and so the interactions between atmospheric aerosols and the East Asian summer monsoon (EASM) have attracted enormous attention. In order to further understand the aerosol-EASM interaction, we investigate the impacts of anthropogenic aerosols on the EASM during the multidecadal strong (1950–1977) and weak (1978–2000) EASM stages using the Community Atmospheric Model 5.1. Numerical experiments are conducted for the whole period, including the two different EASM stages, with present day (PD, year 2000) and preindustrial (PI, year 1850) aerosol emissions, as well as the observed time-varying aerosolmore » emissions. A comparison of the results from PD and PI shows that, with the increase in anthropogenic aerosols, the large-scale EASM intensity is weakened to a greater degree (-9.8%) during the weak EASM stage compared with the strong EASM stage (-4.4%). The increased anthropogenic aerosols also result in a significant reduction in precipitation over North China during the weak EASM stage, as opposed to a statistically insignificant change during the strong EASM stage. Because of greater aerosol loading and the larger sensitivity of the climate system during weak EASM stages, the aerosol effects are more significant during these EASM stages. Moreover, these results suggest that anthropogenic aerosols from the same aerosol emissions have distinct effects on the EASM and the associated precipitation between the multidecadal weak and strong EASM stages.« less

  9. 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.

  10. 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.

  11. Fabrication of superconducting metal-oxide textiles by heating impregnated polymeric material in a weakly oxidizing atmosphere

    SciTech Connect (OSTI)

    Van den Sype, J.S.

    1993-07-13

    A process is described for producing crystalline fibers, textiles or shapes comprised of YBa[sub 2]Cu[sub 3]O[sub 7[minus]x] where x varies from about 0 to about 0.4, said process comprising: (a) impregnating a preformed organic polymeric material with three metal compounds to provide metal elements in said material in substantially the atomic ratio occurring in said YBa[sub 2]Cu[sub 3]O[sub 7[minus]x]; (b) heating said impregnated material in a weakly oxidizing atmosphere containing from about 0.05% to about 2% oxygen by volume to a temperature sufficiently high to at least partially pyrolize and oxidize said organic material and at least partially oxidize said metal compounds substantially without ignition of said organic material and without formation of a molten phase or reaching a decomposition temperature of said YBa[sub 2]Cu[sub 3]O[sub 7[minus]x]; and (c) cooling the resulting material in at least a moderately oxidizing atmosphere to room temperature so as to obtain said fibers, textiles or shapes.

  12. 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.

  13. Weak hybridization and isolated localized magnetic moments in the compounds CeT2Cd20 (T = Ni, Pd)

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

    White, B. D.; Yazici, D.; Ho, P. -C.; Kanchanavatee, N.; Pouse, N.; Fang, Y.; Breindel, A. J.; Friedman, A. J.; Maple, M. B.

    2015-07-20

    Here, we report the physical properties of single crystals of the compounds CeT2Cd20 (T = Ni, Pd) that were grown in a molten Cd flux. Large separations of ~6.7- 6.8 Å between Ce ions favor the localized magnetic moments that are observed in measurements of the magnetization. The strength of the Ruderman-Kittel-Kasuya- Yosida magnetic exchange interaction between the localized moments is severely limited by the large Ce-Ce separations and by weak hybridization between localized Ce 4f and itinerant electron states. Measurements of electrical resistivity performed down to 0.138 K were unable to observe evidence for the emergence of magnetic order;more » however, magnetically-ordered ground states with very low transition temperatures are still expected in these compounds despite the isolated nature of the localized magnetic moments. Such a fragile magnetic order could be highly susceptible to tuning via applied pressure, but evidence for the emergence of magnetic order has not been observed so far in our measurements up to 2.5 GPa.« less

  14. Tunable inverse topological heterostructure utilizing (Bi1−xInx)2Se3 and multichannel weak-antilocalization effect

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

    Brahlek, Matthew J.; Koirala, Nikesh; Liu, Jianpeng; Yusufaly, Tahir I.; Salehi, Maryam; Han, Myung-Geun; Zhu, Yimei; Vanderbilt, David; Oh, Seongshik

    2016-03-10

    In typical topological insulator (TI) systems the TI is bordered by a non-TI insulator, and the surrounding conventional insulators, including vacuum, are not generally treated as part of the TI system. Here, we implement a material system where the roles are reversed, and the topological surface states form around the non-TI (instead of the TI) layers. This is realized by growing a layer of the tunable non-TI (Bi1-xInx)2Se3 in between two layers of the TI Bi2Se3 using the atomically precise molecular beam epitaxy technique. On this tunable inverse topological platform, we systematically vary the thickness and the composition of themore » (Bi1-xInx)2Se3 layer and show that this tunes the coupling between the TI layers from strongly coupled metallic to weakly coupled, and finally to a fully decoupled insulating regime. This system can be used to probe the fundamental nature of coupling in TI materials and provides a tunable insulating layer for TI devices.« less

  15. Strong and Reversible Binding of Carbon Dioxide in a Green Metal...

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

    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. ...

  16. 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.

  17. 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

  18. 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).

  19. 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.

  20. 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.

  1. Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding

    SciTech Connect (OSTI)

    Gomes, Diego Eb; Lins, Roberto D.; Pascutti, Pedro G.; Lei, Chenghong; Soares, Thereza A.

    2011-12-31

    The bacterial enzyme organophosphorus hydrolase (OPH) exhibits both catalytic and substrate promiscuity. It hydrolyzes bonds in a variety of phosphotriester (P-O), phosphonothioate (P-S), phosphofluoridate (P-F) and phosphonocyanate (F-CN) compounds. However, its catalytic efficiency varies markedly for different substrates, limiting the broad-range application of OPH as catalyst in the bioremediation of pesticides and chemical war agents. In the present study, pK{sub a} calculations and multiple explicit-solvent molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of OPH bound to two substrates hydrolyzed with very distinct catalytic efficiencies: the nerve agent soman (O-pinacolyl-methyl-phosphonofluoridate) and the pesticide paraoxon (diethyl p-nitrophenyl phosphate). pK{sub a} calculations for the substrate-bound and unbound enzyme showed a significant pK{sub a} shift from standard values ({Delta}pK{sub a} = {+-} 3 units) for residues 254His and 275Arg. MD simulations of the doubly protonated 254His revealed a dynamic hydrogen bond network connecting the catalytic residue 301Asp via 254His to 232Asp, 233Asp, 275Arg and 235Asp, and is consistent with a previously postulated proton relay mechanism to ferry protons away from the active site with substrates that do not require activation of the leaving group. Hydrogen bonds between 301Asp and 254His were persistent in the OPH-paraoxon complex but not in the OPH-soman one, suggesting a potential role for such interaction in the more efficient hydrolysis of paraoxon over soman by OPH. These results are in line with previous mutational studies of residue 254His, which led to an increase of the catalytic efficiency of OPH over soman yet decreased its efficiency for paraoxon. In addition, comparative analysis of the molecular trajectories for OPH bound to soman and paraoxon suggests that binding of the latter facilitates the conformational transition of OPH from the

  2. Consequences of CCD imperfections for cosmology determined by weak lensing surveys: from laboratory measurements to cosmological parameter bias

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

    Okura, Yuki; Petri, Andrea; May, Morgan; Plazas, Andrés A.; Tamagawa, Toru

    2016-06-27

    Weak gravitational lensing causes subtle changes in the apparent shapes of galaxies due to the bending of light by the gravity of foreground masses. By measuring the shapes of large numbers of galaxies (millions in recent surveys, up to tens of billions in future surveys) we can infer the parameters that determine cosmology. Imperfections in the detectors used to record images of the sky can introduce changes in the apparent shape of galaxies, which in turn can bias the inferred cosmological parameters. Here in this paper we consider the effect of two widely discussed sensor imperfections: tree-rings, due to impuritymore » gradients which cause transverse electric fields in the Charge-Coupled Devices (CCD), and pixel-size variation, due to periodic CCD fabrication errors. These imperfections can be observed when the detectors are subject to uniform illumination (flat field images). We develop methods to determine the spurious shear and convergence (due to the imperfections) from the flat-field images. We calculate how the spurious shear when added to the lensing shear will bias the determination of cosmological parameters. We apply our methods to candidate sensors of the Large Synoptic Survey Telescope (LSST) as a timely and important example, analyzing flat field images recorded with LSST prototype CCDs in the laboratory. In conclusion, we find that tree-rings and periodic pixel-size variation present in the LSST CCDs will introduce negligible bias to cosmological parameters determined from the lensing power spectrum, specifically w,Ωm and σ8.« less

  3. 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.

  4. 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.

  5. 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.

  6. Single Molecule Kinetics of ENTH Binding to Lipid Membranes

    SciTech Connect (OSTI)

    Rozovsky, Sharon; Forstner, Martin B.; Sondermann, Holger; Groves, Jay T.

    2012-04-03

    Transient recruitment of proteins to membranes is a fundamental mechanism by which the cell exerts spatial and temporal control over proteins’ localization and interactions. Thus, the specificity and the kinetics of peripheral proteins’ membrane residence are an attribute of their function. In this article, we describe the membrane interactions of the interfacial epsin N-terminal homology (ENTH) domain with its target lipid phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P2). The direct visualization and quantification of interactions of single ENTH molecules with supported lipid bilayers is achieved using total internal reflection fluorescence microscopy (TIRFM) with a time resolution of 13 ms. This enables the recording of the kinetic behavior of ENTH interacting with membranes with physiologically relevant concentrations of PtdIns(4,5)P2 despite the low effective binding affinity. Subsequent single fluorophore tracking permits us to build up distributions of residence times and to measure ENTH dissociation rates as a function of membrane composition. In addition, due to the high time resolution, we are able to resolve details of the motion of ENTH associated with a simple, homogeneous membrane. In this case ENTH’s diffusive transport appears to be the result of at least three different diffusion processes.

  7. Superlattices assembled through shape-induced directional binding

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

    Lu, Fang; Yager, Kevin G.; Zhang, Yugang; Xin, Huolin; Gang, Oleg

    2015-04-23

    Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks—cubes and octahedrons—when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined bymore » the spatial symmetry of the block’s facets, while structural order depends on DNA-tuned interactions and particle size ratio. Lastly, the presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.« less

  8. 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.

  9. 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 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 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.

  10. rVISTA for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites

    SciTech Connect (OSTI)

    Loots, Gabriela G.; Ovcharenko, Ivan; Pachter, Lior; Dubchak, Inna; Rubin, Edward M.

    2002-03-08

    Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVISTA, for high-throughput discovery of cis-regulatory elements that combines transcription factor binding site prediction and the analysis of inter-species sequence conservation. Here, we illustrate the ability of rVISTA to identify true transcription factor binding sites through the analysis of AP-1 and NFAT binding sites in the 1 Mb well-annotated cytokine gene cluster1 (Hs5q31; Mm11). The exploitation of orthologous human-mouse data set resulted in the elimination of 95 percent of the 38,000 binding sites predicted upon analysis of the human sequence alone, while it identified 87 percent of the experimentally verified binding sites in this region.

  11. Position specific variation in the rate of evolution intranscription factor binding sites

    SciTech Connect (OSTI)

    Moses, Alan M.; Chiang, Derek Y.; Kellis, Manolis; Lander, EricS.; Eisen, Michael B.

    2003-08-28

    The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Here we analyze the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikataeto study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artifacts of computational motif finding algorithms. As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative

  12. Solution structure of telomere binding domain of AtTRB2 derived from Arabidopsis thaliana

    SciTech Connect (OSTI)

    Yun, Ji-Hye; Lee, Won Kyung; Kim, Heeyoun; Kim, Eunhee; Cheong, Chaejoon; Cho, Myeon Haeng; Lee, Weontae

    2014-09-26

    Highlights: • We have determined solution structure of Myb domain of AtTRB2. • The Myb domain of AtTRB2 is located in the N-terminal region. • The Myb domain of AtTRB2 binds to plant telomeric DNA without fourth helix. • Helix 2 and 3 of the Myb domain of AtTRB2 are involved in DNA recognition. • AtTRB2 is a novel protein distinguished from other known plant TBP. - Abstract: Telomere homeostasis is regulated by telomere-associated proteins, and the Myb domain is well conserved for telomere binding. AtTRB2 is a member of the SMH (Single-Myb-Histone)-like family in Arabidopsis thaliana, having an N-terminal Myb domain, which is responsible for DNA binding. The Myb domain of AtTRB2 contains three α-helices and loops for DNA binding, which is unusual given that other plant telomere-binding proteins have an additional fourth helix that is essential for DNA binding. To understand the structural role for telomeric DNA binding of AtTRB2, we determined the solution structure of the Myb domain of AtTRB2 (AtTRB2{sub 1–64}) using nuclear magnetic resonance (NMR) spectroscopy. In addition, the inter-molecular interaction between AtTRB2{sub 1–64} and telomeric DNA has been characterized by the electrophoretic mobility shift assay (EMSA) and NMR titration analyses for both plant (TTTAGGG)n and human (TTAGGG)n telomere sequences. Data revealed that Trp28, Arg29, and Val47 residues located in Helix 2 and Helix 3 are crucial for DNA binding, which are well conserved among other plant telomere binding proteins. We concluded that although AtTRB2 is devoid of the additional fourth helix in the Myb-extension domain, it is able to bind to plant telomeric repeat sequences as well as human telomeric repeat sequences.

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

    DOE Data Explorer [Office of Scientific and Technical Information (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 1σ and 2σ above the mean, as opposed to the greater than 2σ 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 1σ and 2σ 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

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

    DOE Data Explorer [Office of Scientific and Technical Information (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 1σ and 2σ above the mean, as opposed to the greater than 2σ 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 1σ and 2σ 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

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

    DOE Data Explorer [Office of Scientific and Technical Information (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 1σ and 2σ above the mean, as opposed to the greater than 2σ 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 1σ and 2σ 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

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

    DOE Data Explorer [Office of Scientific and Technical Information (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 1σ and 2σ above the mean, as opposed to the greater than 2σ 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 2σ 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

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

    DOE Data Explorer [Office of Scientific and Technical Information (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 1σ and 2σ above the mean, as opposed to the greater than 2σ 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 2σ 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

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

    DOE Data Explorer [Office of Scientific and Technical Information (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 1σ and 2σ above the mean, as opposed to the greater than 2σ 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 2σ 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

  19. 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

  20. 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.

  1. 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.

  2. Cell Context Dependent p53 Genome-Wide Binding Patterns and Enrichment at Repeats

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

    Botcheva, Krassimira; McCorkle, Sean R.

    2014-11-21

    The p53 ability to elicit stress specific and cell type specific responses is well recognized, but how that specificity is established remains to be defined. Whether upon activation p53 binds to its genomic targets in a cell type and stress type dependent manner is still an open question. Here we show that the p53 binding to the human genome is selective and cell context-dependent. We mapped the genomic binding sites for the endogenous wild type p53 protein in the human cancer cell line HCT116 and compared them to those we previously determined in the normal cell line IMR90. We reportmore » distinct p53 genome-wide binding landscapes in two different cell lines, analyzed under the same treatment and experimental conditions, using the same ChIP-seq approach. This is evidence for cell context dependent p53 genomic binding. The observed differences affect the p53 binding sites distribution with respect to major genomic and epigenomic elements (promoter regions, CpG islands and repeats). We correlated the high-confidence p53 ChIP-seq peaks positions with the annotated human repeats (UCSC Human Genome Browser) and observed both common and cell line specific trends. In HCT116, the p53 binding was specifically enriched at LINE repeats, compared to IMR90 cells. The p53 genome-wide binding patterns in HCT116 and IMR90 likely reflect the different epigenetic landscapes in these two cell lines, resulting from cancer-associated changes (accumulated in HCT116) superimposed on tissue specific differences (HCT116 has epithelial, while IMR90 has mesenchymal origin). In conclusion, our data support the model for p53 binding to the human genome in a highly selective manner, mobilizing distinct sets of genes, contributing to distinct pathways.« less

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

    DOE Patents [OSTI]

    Warner, Benjamin P.; Havrilla, George J.; Mann, Grace

    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.

  4. Weak radiative decay [Lambda][r arrow][ital n][gamma] and the radiative capture reaction [ital K][sup [minus

    SciTech Connect (OSTI)

    Larson, K.D.; Noble, A.J.; Bassalleck, B.; Burkhardt, H.; Fickinger, W.J.; Hall, J.R.; Hallin, A.L.; Hasinoff, M.D.; Horvath, D.; Jones, P.G.; Lowe, J.; McIntyre, E.K.; Measday, D.F.; Miller, J.P.; Roberts, B.L.; Robinson, D.K.; Sakitt, M.; Salomon, M.; Stanislaus, S.; Waltham, C.E.; Warner, T.M.; Whitehouse, D.A.; Wolfe, D.M. Boston University, Boston, Massachusetts 02215 University of British Columbia, Vancouver, British Columbia, V6T 1Z1 Brookhaven National Laboratory, Upton, New York 11973 Case Western Reserve University, Cleveland, Ohio 44106 Central Research Institute for Physics, H-1525 Budapest Los Alamos Meson Physics Facility, Los Alamos, New Mexico 87545 University of New Mexico, Albuquerque, New Mexico 87131 University of Nottingham, Nottingham, NG7 2RD Princeton University, Princeton, New Jersey

    1993-02-01

    The branching ratio for the [Lambda] weak radiative decay [Lambda][r arrow][ital n][gamma] has been measured. Three statistically independent results from the same experiment (Brookhaven E811) are reported here. They are combined with a previously published measurement, also from Brookhaven E811, to yield a result of ([Lambda][r arrow][ital n][gamma])/([Lambda][r arrow]anything)=(1.75[plus minus]0.15)[times]10[sup [minus]3], based on 1800 events after background subtraction. This represents a factor of 75 increase in statistics over the previous world total. A comparison with recent theoretical papers shows that no existing model provides a completely satisfactory description of all data on weak radiative decays. A search is also reported for the radiative capture process [ital K][sup [minus

  5. 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.

  6. Gap solitons and Bloch waves of interacting bosons in one-dimensional optical lattices: From the weak- to the strong-interaction limits

    SciTech Connect (OSTI)

    Xu, T.F.; Guo, X.M.; Jing, X.L.; Wu, W.C.; Liu, C.S.

    2011-04-15

    We study the gap solitons and nonlinear Bloch waves of interacting bosons in one-dimensional optical lattices, taking into account the interaction from the weak to the strong limits. It is shown that composition relation between the gap solitons and nonlinear Bloch waves exists for the whole span of the interaction strength. The linear stability analysis indicates that the gap solitons are stable when their energies are near the bottom of the linear Bloch band gap. By increasing the interaction strength, the stable gap solitons can become unstable. It is argued that the stable gap solitons can easily be formed in a weakly interacting system with energies near the bottom of the lower-level linear Bloch band gaps.

  7. 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.

  8. 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.

  9. 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 surveythe 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.

  10. Selective Binding of O2 over N2 in a Redox-Active Metal-Organic...

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

    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. ...

  11. 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 ...

  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. Secondary PDZ domain-binding site on class B plexins enhances...

    Office of Scientific and Technical Information (OSTI)

    Title: Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ-RhoGEF Authors: Pascoe, Heath G. ; Gutowski, Stephen ; Chen, Hua ; Brautigam, Chad A. ; ...

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

    Office of Scientific and Technical Information (OSTI)

    Title: New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins Authors: Zhang, Qi ; Fan, Lixin ; Hou, Feng ; Dong, Aiping ; Wang, Yun-Xing ; Tong, Yufeng ...

  15. 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, ... Figure 1. Overall structure of human TLR3 ECD. The N-terminal region is colored blue, the ...

  16. 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.

  17. 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.

  18. Applying Kβ Valence-to-Core X-ray Emission Spectroscopy to Cu(I) Binding

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

    Proteins with Relevance to Peptidylglycine Monooxygenase Reactivity | Stanford Synchrotron Radiation Lightsource Applying Kβ Valence-to-Core X-ray Emission Spectroscopy to Cu(I) Binding Proteins with Relevance to Peptidylglycine Monooxygenase Reactivity Thursday, June 30, 2016 Copper serves as a redox center in metalloproteins, often cycling between the +1 and +2 oxidation states. Oxidases, such as petidylglycine monooxygenase (PHM), bind oxygen at Cu(I) sites giving rise to "oxo"

  19. 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

  20. 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.

  1. 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.

  2. Quantum Monte Carlo calculation of the binding energy of the beryllium dimer

    SciTech Connect (OSTI)

    Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.

    2015-08-28

    The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be{sub 2} is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be{sub 2} from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be{sub 2}, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm{sup −1}, only slightly below the 935 cm{sup −1} value derived from experiment.

  3. 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.

  4. 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

  5. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules

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

    Walker, Johnnie A.; Takasuka, Taichi E.; Deng, Kai; Bianchetti, Christopher M.; Udell, Hannah S.; Prom, Ben M.; Kim, Hyunkee; Adams, Paul D.; Northen, Trent R.; Fox, Brian G.

    2015-12-21

    Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolyticmore » activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. In conclusion, we have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.« less

  6. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules

    SciTech Connect (OSTI)

    Walker, Johnnie A.; Takasuka, Taichi E.; Deng, Kai; Bianchetti, Christopher M.; Udell, Hannah S.; Prom, Ben M.; Kim, Hyunkee; Adams, Paul D.; Northen, Trent R.; Fox, Brian G.

    2015-12-21

    Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. In conclusion, we have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.

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

    SciTech Connect (OSTI)

    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 also 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.

  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. Gate-modulated weak anti-localization and carrier trapping in individual Bi{sub 2}Se{sub 3} nanoribbons

    SciTech Connect (OSTI)

    Wang, Li-Xian; Yan, Yuan; Liao, Zhi-Min Yu, Da-Peng

    2015-02-09

    We report a gate-voltage modulation on the weak anti-localization of individual topological insulator Bi{sub 2}Se{sub 3} nanoribbons. The phase coherence length decreases with decreasing the carrier density of the surface states on the bottom surface of the Bi{sub 2}Se{sub 3} nanoribbon as tuning the gate voltage from 0 to −100 V, indicating that the electron-electron interaction dominates the decoherence at low carrier density. Furthermore, we observe an abnormal conductance decline at positive gate voltage regime, which is ascribed to the capture of surface carriers by the trapping centers in the surface oxidation layer.

  10. 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.

  11. High resolution rotational spectroscopy of weakly bound ionic clusters: ArH/sub 3//sup +/, ArD/sub 3//sup +/

    SciTech Connect (OSTI)

    Bogey, M.; Bolvin, H.; Demuynck, C.; Destombes, J.L.

    1987-03-09

    The first high-resolution study of weakly bound cluster ions is reported. The millimeter- and submillimeter-wave rotational spectra of ArH/sub 3/ /sup +/ and ArD/sub 3/ /sup +/ have been observed in a magnetically confined, liquid-nitrogen--cooled glow discharge and a partial molecular structure has been derived from their analysis. ArH/sub 3/ /sup +/ appears to be planar, with the Ar atom lying on a symmetry axis of the H/sub 3/ /sup +/ equilateral triangle, 2.38 A from the H/sub 3/ /sup +/ centroid. SPlitting of some of the lines is strong evidence for tunneling motion.

  12. Teaching a cell new tricks

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

    Teaching a cell new tricks Teaching a cell new tricks At Los Alamos National Laboratory, one group has been investigating the cellular mechanism that controls fatty acid synthesis. May 20, 2016 In panel A, a precursor of the fatty acid (the colored figure) is shown in the binding pocket of the transcription regulator. In the upper figure, the dashed red line indicates a strong interaction at a region of the two molecules. Note that in the lower figure, the dashed line is missing, indicating that

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

    SciTech Connect (OSTI)

    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 that 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.

  14. 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

  15. 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 apoferritinSDS complex was determined at a resolution of 1.9 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 M 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 proteinSDS interactions that give rise to binding and may prove useful in the design of novel SDS-like ligands for some proteins.

  16. 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 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.

  17. 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.

  18. 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.

  19. Effects of oxygen stoichiometry on the scaling behaviors of YBa{sub 2}Cu{sub 3}O{sub x} grain boundary weak-links

    SciTech Connect (OSTI)

    Wu, K.H.; Fu, C.M.; Jeng, W.J.

    1994-12-31

    The effects of oxygen stoichiometry on the transport properties of the pulsed laser deposited YBa{sub 2}Cu{sub 3}O{sub x} bicrystalline grain boundary weak-link junctions were studied. It is found that not only the cross boundary resistive transition foot structure can be manipulated repeatedly with oxygen annealling processes but the junction behaviors are also altered in accordance. In the fully oxygenated state i.e. with x=7.0 in YBa{sub 2}Cu{sub 3}O{sub x} stoichiometry, the junction critical current exhibits a power of 2 scaling behavior with temperature. In contrast, when annealed in the conditions of oxygen-deficient state (e.g. with x=6.9 in YBa{sub 2}Cu{sub 3}O{sub x} stoichiometry) the junction critical current switches to a linear temperature dependence behavior. The results are tentatively attributed to the modification of the structure in the boundary area upon oxygen annealing, which, in turn, will affect the effective dimension of the geometrically constrained weak-link bridges. The detailed discussion on the responsible physical mechanisms as well as the implications of the present results on device applications will be given.

  20. 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 03136708 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.

  1. Arabidopsis dynamin-related protein 1A polymers bind, but do not tubulate, liposomes

    SciTech Connect (OSTI)

    Backues, Steven K.; Bednarek, Sebastian Y.

    2010-03-19

    The Arabidopsis dynamin-related protein 1A (AtDRP1A) is involved in endocytosis and cell plate maturation in Arabidopsis. Unlike dynamin, AtDRP1A does not have any recognized membrane binding or protein-protein interaction domains. We report that GTPase active AtDRP1A purified from Escherichia coli as a fusion to maltose binding protein forms homopolymers visible by negative staining electron microscopy. These polymers interact with protein-free liposomes whose lipid composition mimics that of the inner leaflet of the Arabidopsis plasma membrane, suggesting that lipid-binding may play a role in AtDRP1A function. However, AtDRP1A polymers do not appear to assemble and disassemble in a dynamic fashion and do not have the ability to tubulate liposomes in vitro, suggesting that additional factors or modifications are necessary for AtDRP1A's in vivo function.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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??). The binding energies of the resultant gaseous 1:1 complexes (1Cl?,1Br?, 1I?, 1SCN?, 1NO??, 1IO?? and 1SO??) 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??. 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

  10. 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; Hoekstra, Henk; Babul, Arif; Bildfell, Chris; Jeltema, Tesla; Henry, J. Patrick

    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.

  11. 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

  12. Mass calibration of galaxy clusters at redshift 0.11.0 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 massrichness 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 massrichness 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 massrichness relations using richness measure NVT with each of these effects considered separately as well as considered altogether. We also examine redshift evolution of the massrichness 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 h1 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.

  13. 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.

  14. 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.

  15. Thermodynamics imprinting reveals differential binding of metals to {alpha}-synuclein: Relevance to parkinson's disease

    SciTech Connect (OSTI)

    Bharathi; Rao, K.S.J. . E-mail: kjr5n@yahoo.co.in

    2007-07-20

    The aggregation of {alpha}-synuclein is a hallmark feature of Parkinson's disease (PD) and other synucleinopathies. Metals are the significant etiological factors in PD, and their interaction with {alpha}-synuclein affect dramatically the kinetics of fibrillation in vitro and are proposed to play an important and potential neurodegenerative role in vivo. In the present study, we investigated the stoichiometry of binding of copper [Cu (II)] and iron [Fe (III)] with {alpha}-synuclein (wild recombinant type and A30P, A53T, E46K mutant forms) using isothermal titration calorimetry (ITC). {alpha}-Synuclein monomer (wild and mutant forms) titrated by Cu (II), showed two binding sites, with an apparent K {sub B} of 10{sup 5} M and 10{sup 4} M, respectively. But, {alpha}-synuclein (wild type and mutant forms) titrated with Fe (III) revealed a K {sub B} of 10{sup 5} M with single binding site. The present investigation uncovers the detailed binding propensities between metals and {alpha}-synuclein and has biological implications in PD.

  16. Selection of staphylococcal enterotoxin B (SEB)-binding peptide using phage display technology

    SciTech Connect (OSTI)

    Soykut, Esra Acar; Dudak, Fahriye Ceyda; Boyaci, Ismail Hakki

    2008-05-23

    In this study, peptides were selected to recognize staphylococcal enterotoxin B (SEB) which cause food intoxication and can be used as a biological war agent. By using commercial M13 phage library, single plaque isolation of 38 phages was done and binding affinities were investigated with phage-ELISA. The specificities of the selected phage clones showing high affinity to SEB were checked by using different protein molecules which can be found in food samples. Furthermore, the affinities of three selected phage clones were determined by using surface plasmon resonance (SPR) sensors. Sequence analysis was realized for three peptides showing high binding affinity to SEB and WWRPLTPESPPA, MNLHDYHRLFWY, and QHPQINQTLYRM amino acid sequences were obtained. The peptide sequence with highest affinity to SEB was synthesized with solid phase peptide synthesis technique and thermodynamic constants of the peptide-SEB interaction were determined by using isothermal titration calorimetry (ITC) and compared with those of antibody-SEB interaction. The binding constant of the peptide was determined as 4.2 {+-} 0.7 x 10{sup 5} M{sup -1} which indicates a strong binding close to that of antibody.

  17. Kits and methods of detection using cellulose binding domain fusion proteins

    DOE Patents [OSTI]

    Shoseyov, Oded

    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.

  18. Methanobactin: a copper binding compound having antibiotic and antioxidant activity isolated from methanotrophic bacteria

    DOE Patents [OSTI]

    DiSpirito, Alan A.; Zahn, James A.; Graham, David W.; Kim, Hyung J.; Alterman, Michail; Larive, Cynthia

    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.

  19. 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.

  20. MeRNA: a Database of Metal Ion Binding Sites in RNAStructures

    SciTech Connect (OSTI)

    Stefan, Liliana R.; Zhang, Rui; Levitan, Aaron G.; Hendrix, DonnaF.; Brenner, Steven E.; Holbrook, Stephen R.

    2005-10-05

    Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA three-dimensional structures available from the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements; in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using original literature references. MeRNA includes eight manually identified metal-ion binding motifs, which are described in the literature. MeRNA is searchable by PDB identifier, metal ion, method of structure determination, resolution and R-values for X-ray structure, and distance from metal to any RNA atom or to water. New structures with their respective binding motifs will be added to the database as they become available. The MeRNA database will further our understanding of the roles of metal ions in RNA folding and catalysis and have applications in structural and functional analysis, RNA design and engineering.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Results on the spin-dependent scattering of weakly interacting massive particles on nucleons from the Run 3 Data of the LUX Experiment

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

    Akerib, D. S.

    2016-04-20

    Here, we present experimental constraints on the spin-dependent WIMP (weakly interacting massive particle)-nucleon elastic cross sections from LUX data acquired in 2013. LUX is a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility (Lead, South Dakota), which is designed to observe the recoil signature of galactic WIMPs scattering from xenon nuclei. A profile likelihood ratio analysis of 1.4 × 104 kg day of fiducial exposure allows 90% C.L. upper limits to be set on the WIMP-neutron (WIMP-proton) cross section of σn = 9.4 × 10–41 cm2 (σp = 2.9 × 10–39 cm2) at 33 GeV/c2. Themore » spin-dependent WIMP-neutron limit is the most sensitive constraint to date.« less

  6. Two-dimensional nonlinear finite element analysis of well damage due to reservoir compaction, well-to-well interactions, and localization on weak layers

    SciTech Connect (OSTI)

    Hilbert, L.B. Jr.; Fredrich, J.T.; Bruno, M.S.; Deitrick, G.L.; Rouffignac, E.P. de

    1996-05-01

    In this paper the authors present the results of a coupled nonlinear finite element geomechanics model for reservoir compaction and well-to-well interactions for the high-porosity, low strength diatomite reservoirs of the Belridge field near Bakersfield, California. They show that well damage and failures can occur under the action of two distinct mechanisms: shear deformations induced by pore compaction, and subsidence, and shear deformations due to well-to-well interactions during production or water injection. They show such casting damage or failure can be localized to weak layers that slide or slip under shear due to subsidence. The magnitude of shear displacements and surface subsidence agree with field observations.

  7. 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

    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.

  8. 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.

  9. Calculation of positron binding energies using the generalized any particle propagator theory

    SciTech Connect (OSTI)

    Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Mrcio T. do N.; Reyes, Andrs

    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. Daz-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.

  10. Glycosylation Helps Cellulase Enzymes Bind to Plant Cell Walls (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-06-01

    Computer simulations suggest a new strategy to design enhanced enzymes for biofuels production. Large-scale computer simulations predict that the addition of glycosylation on carbohydrate-binding modules can dramatically improve the binding affinity of these protein domains over amino acid mutations alone. These simulations suggest that glycosylation can be used as a protein engineering tool to enhance the activity of cellulase enzymes, which are a key component in the conversion of cellulose to soluble sugars in the production of biofuels. Glycosylation is the covalent attachment of carbohydrate molecules to protein side chains, and is present in many proteins across all kingdoms of life. Moreover, glycosylation is known to serve a wide variety of functions in biological recognition, cell signaling, and metabolism. Cellulase enzymes, which are responsible for deconstructing cellulose found in plant cell walls to glucose, contain glycosylation that when modified can affect enzymatic activity-often in an unpredictable manner. To gain insight into the role of glycosylation on cellulase activity, scientists at the National Renewable Energy Laboratory (NREL) used computer simulation to predict that adding glycosylation on the carbohydrate-binding module of a cellulase enzyme dramatically boosts the binding affinity to cellulose-more than standard protein engineering approaches in which amino acids are mutated. Because it is known that higher binding affinity in cellulases leads to higher activity, this work suggests a new route to designing enhanced enzymes for biofuels production. More generally, this work suggests that tuning glycosylation in cellulase enzymes is a key factor to consider when engineering biochemical conversion processes, and that more work is needed to understand how glycosylation affects cellulase activity at the molecular level.

  11. Specific Fluorine Labeling of the HyHEL10 Antibody Affects Antigen Binding and Dynamics

    SciTech Connect (OSTI)

    Acchione, Mauro; Lee, Yi-Chien; DeSantis, Morgan E.; Lipschultz, Claudia A.; Wlodawer, Alexander; Li, Mi; Shanmuganathan, Aranganathan; Walter, Richard L.; Smith-Gill, Sandra; Barchi, Jr., Joseph J.

    2012-10-16

    To more fully understand the molecular mechanisms responsible for variations in binding affinity with antibody maturation, we explored the use of site specific fluorine labeling and {sup 19}F nuclear magnetic resonance (NMR). Several single-chain (scFv) antibodies, derived from an affinity-matured series of anti-hen egg white lysozyme (HEL) mouse IgG1, were constructed with either complete or individual replacement of tryptophan residues with 5-fluorotryptophan ({sup 5F}W). An array of biophysical techniques was used to gain insight into the impact of fluorine substitution on the overall protein structure and antigen binding. SPR measurements indicated that {sup 5F}W incorporation lowered binding affinity for the HEL antigen. The degree of analogue impact was residue-dependent, and the greatest decrease in affinity was observed when {sup 5F}W was substituted for residues near the binding interface. In contrast, corresponding crystal structures in complex with HEL were essentially indistinguishable from the unsubstituted antibody. {sup 19}F NMR analysis showed severe overlap of signals in the free fluorinated protein that was resolved upon binding to antigen, suggesting very distinct chemical environments for each {sup 5F}W in the complex. Preliminary relaxation analysis suggested the presence of chemical exchange in the antibody-antigen complex that could not be observed by X-ray crystallography. These data demonstrate that fluorine NMR can be an extremely useful tool for discerning structural changes in scFv antibody-antigen complexes with altered function that may not be discernible by other biophysical techniques.

  12. 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.

  13. 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.

  14. 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.)

  15. 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.)

  16. 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 Msr

  17. Quenching methods for background reduction in luminescence-based probe-target binding assays

    DOE Patents [OSTI]

    Cai, Hong; Goodwin, Peter M; Keller, Richard A.; Nolan, Rhiannon L.

    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.

  18. 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.

  19. 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).

  20. 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.

  1. Tight-binding calculation studies of vacancy and adatom defects in graphene

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

    Zhang, Wei; Lu, Wen-Cai; Zhang, Hong-Xing; Ho, K. M.; Wang, C. Z.

    2016-02-19

    Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

  2. 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

  3. 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

  4. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

    SciTech Connect (OSTI)

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang

    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 hydrophobic 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.

  5. 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

  6. 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

  7. Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding

    SciTech Connect (OSTI)

    Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka

    2015-07-31

    Classical nuclear localization signal (NLS) sequences have been used for artificial localization of green fluorescent protein (GFP) in the nucleus as a positioning marker or for measurement of the nuclear-cytoplasmic shuttling rate in living cells. However, the detailed mechanism of nuclear retention of GFP-NLS remains unclear. Here, we show that a candidate mechanism for the strong nuclear retention of GFP-NLS is via the RNA-binding ability of the NLS sequence. GFP tagged with a classical NLS derived from Simian virus 40 (GFP-NLS{sup SV40}) localized not only in the nucleoplasm, but also to the nucleolus, the nuclear subdomain in which ribosome biogenesis takes place. GFP-NLS{sup SV40} in the nucleolus was mobile, and intriguingly, the diffusion coefficient, which indicates the speed of diffusing molecules, was 1.5-fold slower than in the nucleoplasm. Fluorescence correlation spectroscopy (FCS) analysis showed that GFP-NLS{sup SV40} formed oligomers via RNA binding, the estimated molecular weight of which was larger than the limit for passive nuclear export into the cytoplasm. These findings suggest that the nuclear localization of GFP-NLS{sup SV40} likely results from oligomerization mediated via RNA binding. The analytical technique used here can be applied for elucidating the details of other nuclear localization mechanisms, including those of several types of nuclear proteins. In addition, GFP-NLS{sup SV40} can be used as an excellent marker for studying both the nucleoplasm and nucleolus in living cells. - Highlights: • Nuclear localization signal-tagged GFP (GFP-NLS) showed clear nuclear localization. • The GFP-NLS dynamically localized not only in the nucleoplasm, but also to the nucleolus. • The nuclear localization of GFP-NLS results from transient oligomerization mediated via RNA binding. • Our NLS-tagging procedure is ideal for use in artificial sequestration of proteins in the nucleus.

  8. 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.

  9. Presence of specific growth hormone binding sites in rainbow trout (Oncorhynchus mykiss) tissues: characterization of the hepatic receptor

    SciTech Connect (OSTI)

    Yao, K.; Niu, P.D.; Le Gac, F.; Le Bail, P.Y. )

    1991-01-01

    The present work outlines the presence of specific binding for chinook salmon growth hormone (sGH) in different tissue preparations of rainbow trout. Optimal incubation conditions (pH, Tris, MgCl{sub 2}) were determined. Specific binding was very sensitive to salt concentration during incubation. The specific binding reached a plateau after 15 and 25 hr of incubation at 12 and 4 {degree}. At 20 {degree}, specific and nonspecific binding were not stable. Specific binding dissociation was slower than association and was only partial. The binding was saturable (Bmax = 187 +/- 167 pmol), of high affinity (Ka = 2.4 +/- 0.8 10(9) M-1), and very specific for GH, properties which are in agreement with the characteristics of hormonal receptors. Sea bream and mammalian GH appeared 2- and 30-fold, respectively, less potent than cold sGH2 for displacing {sup 125}I-sGH2. Tissue preparations from ovary, testis, fat, skin, cartilage, gill, blood pellet, brain, spleen, kidney, and muscle showed significant saturable binding.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. Protein arginine deiminase 2 binds calcium in an ordered fashion: Implications for inhibitor design

    SciTech Connect (OSTI)

    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; Gross, Michael L.; Thompson, Paul R.

    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 ions 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.

  16. Pathway Analysis Revealed Potential Diverse Health Impacts of Flavonoids that Bind Estrogen Receptors

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

    Ye, Hao; Ng, Hui; Sakkiah, Sugunadevi; Ge, Weigong; Perkins, Roger; Tong, Weida; Hong, Huixiao

    2016-03-26

    Flavonoids are frequently used as dietary supplements in the absence of research evidence regarding health benefits or toxicity. Furthermore, ingested doses could far exceed those received from diet in the course of normal living. Some flavonoids exhibit binding to estrogen receptors (ERs) with consequential vigilance by regulatory authorities at the U.S. EPA and FDA. Regulatory authorities must consider both beneficial claims and potential adverse effects, warranting the increases in research that has spanned almost two decades. Here, we report pathway enrichment of 14 targets from the Comparative Toxicogenomics Database (CTD) and the Herbal Ingredients’ Targets (HIT) database for 22 flavonoidsmore » that bind ERs. The selected flavonoids are confirmed ER binders from our earlier studies, and were here found in mainly involved in three types of biological processes, ER regulation, estrogen metabolism and synthesis, and apoptosis. Besides cancers, we conjecture that the flavonoids may affect several diseases via apoptosis pathways. We find diseases such as amyotrophic lateral sclerosis, viral myocarditis and non-alcoholic fatty liver disease could be implicated. More generally, apoptosis processes may be importantly evolved biological functions of flavonoids that bind ERs and high dose ingestion of those flavonoids could adversely disrupt the cellular apoptosis process.« less

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Weak hybridization and isolated localized magnetic moments in the compounds CeT2Cd20 (T = Ni, Pd)

    SciTech Connect (OSTI)

    White, B. D.; Yazici, D.; Ho, P. -C.; Kanchanavatee, N.; Pouse, N.; Fang, Y.; Breindel, A. J.; Friedman, A. J.; Maple, M. B.

    2015-07-20

    Here, we report the physical properties of single crystals of the compounds CeT2Cd20 (T = Ni, Pd) that were grown in a molten Cd flux. Large separations of ~6.7- 6.8 Å between Ce ions favor the localized magnetic moments that are observed in measurements of the magnetization. The strength of the Ruderman-Kittel-Kasuya- Yosida magnetic exchange interaction between the localized moments is severely limited by the large Ce-Ce separations and by weak hybridization between localized Ce 4f and itinerant electron states. Measurements of electrical resistivity performed down to 0.138 K were unable to observe evidence for the emergence of magnetic order; however, magnetically-ordered ground states with very low transition temperatures are still expected in these compounds despite the isolated nature of the localized magnetic moments. Such a fragile magnetic order could be highly susceptible to tuning via applied pressure, but evidence for the emergence of magnetic order has not been observed so far in our measurements up to 2.5 GPa.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Suppression of unimolecular decay of laser desorbed peptide and protein ions by entrainment in rarefied supersonic gas jets under weak electric fields

    SciTech Connect (OSTI)

    Hieke, Andreas

    2014-01-21

    Unimolecular decay of sample ions imposes a limit on the usable laser fluence in matrix-assisted laser desorption/ionization (MALDI) ion sources. Traditionally, some modest degree of collisional sample ion cooling has been achieved by connecting MALDI ion sources directly to gas-filled radio frequency (RF) multipoles. It was also discovered in the early 1990s that gas-filled RF multipoles exhibit increased ion transmission efficiency due to collisional ion focusing effects. This unexpected experimental finding was later supported by elementary Monte Carlo simulations. Both experiments and simulations assumed a resting background gas with typical pressures of the order of 1 Pa. However, considerable additional improvements can be achieved if laser desorbed sample ions are introduced immediately after desorption, still within the ion source, in an axisymmetric rarefied supersonic gas jet with peak pressure of the order of 100 Pa and flow velocities >300 m/s, and under weak electric fields. We describe here the design principle and report performance data of an ion source coined “MALDI-2,” which incorporates elements of both rarefied aerodynamics and particle optics. Such a design allows superb suppression of metastable fragmentation due to rapid collisional cooling in <10 μs and nearly perfect injection efficiency into the attached RF ion guide, as numerous experiments have confirmed.

  9. 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.

  10. 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.

  11. 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

    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.

  12. Particle trap to sheath non-binding contact for a gas-insulated transmission line having a corrugated outer conductor

    DOE Patents [OSTI]

    Fischer, William H.

    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.

  13. More light on the 2ν{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 [η{sub s} = 0.05, W. Holzer and R. Ouillon, Chem. Phys. Lett. 24, 589 (1974)], the 2ν{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|Δα|000000〉| was derived and this value was found to be comparable to that of the mean-polarizability ((000020), α{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}.

  14. Characterization and reactivity of the weakly bound complexes of the [H, N, S]{sup −} anionic system with astrophysical and biological implications

    SciTech Connect (OSTI)

    Trabelsi, T.; Ajili, Y.; Ben Yaghlane, S.; Jaidane, N.-E.; Mogren Al-Mogren, M.; Francisco, J. S.; Hochlaf, M.

    2015-07-21

    We investigate the lowest electronic states of doublet and quartet spin multiplicity states of HNS{sup −} and HSN{sup −} together with their parent neutral triatomic molecules. Computations were performed using highly accurate ab initio methods with a large basis set. One-dimensional cuts of the full-dimensional potential energy surfaces (PESs) along the interatomic distances and bending angle are presented for each isomer. Results show that the ground anionic states are stable with respect to the electron detachment process and that the long range parts of the PESs correlating to the SH{sup −} + N, SN{sup −} + H, SN + H{sup −}, NH + S{sup −}, and NH{sup −} + S are bound. In addition, we predict the existence of long-lived weakly bound anionic complexes that can be formed after cold collisions between SN{sup −} and H or SH{sup −} and N. The implications for the reactivity of these species are discussed; specifically, it is shown that the reactions involving SH{sup −}, SN{sup −}, and NH{sup −} lead either to the formation of HNS{sup −} or HSN{sup −} in their electronic ground states or to autodetachment processes. Thus, providing an explanation for why the anions, SH{sup −}, SN{sup −}, and NH{sup −}, have limiting detectability in astrophysical media despite the observation of their corresponding neutral species. In a biological context, we suggest that HSN{sup −} and HNS{sup −} should be incorporated into H{sub 2}S-assisted heme-catalyzed reduction mechanism of nitrites in vivo.

  15. Precision Measurement of the proton neutral weak form factors at Q{sup 2} ~ 0.1 GeV{sup 2}

    SciTech Connect (OSTI)

    Lisa Kaufman

    2007-02-01

    This thesis reports the HAPPEX measurement of the parity-violating asymmetry for longitudinally polarized electrons elastically scattered from protons in a liquid hydrogen target. The measurement was carried out in Hall A at Thomas Jefferson National Accelerator Facility using a beam energy E = 3 GeV and scattering angle <θ{sub lab}> = 6◦. The asymmetry is sensitive to the weak neutral form factors from which we extract the strange quark electric and magnetic form factors (G{sup s}{sub E} and G{sup s}{sub M}) of the proton. The measurement was conducted during two data-taking periods in 2004 and 2005. This thesis describes the methods for controlling the helicity-correlated beam asymmetries and the analysis of the raw asymmetry. The parity-violating asymmetry has been measured to be A{sub PV} = −1.14± 0.24 (stat)±0.06 (syst) ppm at = 0.099 GeV{sup 2} (2004), and A{sub PV} = −1.58±0.12 (stat)±0.04 (syst) ppm at = 0.109 GeV{sup 2} (2005). The strange quark form factors extracted from the asymmetry are G{sup s}{sub E} + 0.080G{sup s}{sub M} = 0.030 ± 0.025 (stat) ± 0.006 (syst) ± 0.012 (FF) (2004) and G{sup s}{sub E} +0.088G{sup s}{sub M} = 0.007±0.011 (stat)±0.004 (syst)±0.005 (FF) (2005). These results place the most precise constraints on the strange quark form factors and indicate little strange dynamics in the proton.

  16. Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

    SciTech Connect (OSTI)

    Wang, Zhongshan; Xiang, Quanju; Zhu, Xiaofeng; Dong, Haohao; He, Chuan; Wang, Haiyan; Zhang, Yizheng; Wang, Wenjian; Dong, Changjiang

    2014-09-26

    Highlights: • Determination of the structure of the wild-type LptB in complex with ATP and Mg{sup 2+}. • Demonstrated that ATP binding residues are essential for LptB’s ATPase activity and LPS transport. • Dimerization is required for the LptB’s function and LPS transport. • Revealed relationship between activity of the LptB and the vitality of E. coli cells. - Abstract: Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria, which plays an essential role in protecting the bacteria from harsh conditions and antibiotics. LPS molecules are transported from the inner membrane to the outer membrane by seven LPS transport proteins. LptB is vital in hydrolyzing ATP to provide energy for LPS transport, however this mechanism is not very clear. Here we report wild-type LptB crystal structure in complex with ATP and Mg{sup 2+}, which reveals that its structure is conserved with other nucleotide-binding proteins (NBD). Structural, functional and electron microscopic studies demonstrated that the ATP binding residues, including K42 and T43, are crucial for LptB’s ATPase activity, LPS transport and the vitality of Escherichia coli cells with the exceptions of H195A and Q85A; the H195A mutation does not lower its ATPase activity but impairs LPS transport, and Q85A does not alter ATPase activity but causes cell death. Our data also suggest that two protomers of LptB have to work together for ATP hydrolysis and LPS transport. These results have significant impacts in understanding the LPS transport mechanism and developing new antibiotics.

  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 (UO₂²⁺) 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. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. It is anticipated that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials. The focus of this study is to synthesize uranyl complexes incorporating amidinate and guanidinate ligands. Both synthetic and computational methods are used to investigate novel equatorial ligand coordination and how this affects the basicity of the oxo ligands. Such an understanding will later apply to designing ligands incorporating functionalities that can bind uranyl both equatorially and axially for highly selective sequestration. Efficient and durable chromatography supports for lanthanide separation will be generated by (1) identifying robust peptoid-based ligands capable of binding different lanthanides with variable affinities, and (2) developing practical synthetic methods for the attachment of these ligands to Dowex ion exchange resins.

  18. 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.

  19. Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein

    SciTech Connect (OSTI)

    Kuffel, Anna; Czapiewski, Dariusz; Zielkiewicz, Jan

    2015-10-07

    The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularly far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that—from the three analyzed solvation shells of CfAFP—the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice.

  20. Ammonium Additives to Dissolve Li2S through Hydrogen Binding for High

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

    Energy Li-S Batteries - Joint Center for Energy Storage Research July 1, 2016, Research Highlights Ammonium Additives to Dissolve Li2S through Hydrogen Binding for High Energy Li-S Batteries (a) Solubility of Li2S in DMSO solvent with different amounts of NH4NO3 as additive. (b) 1H chemical shifts as a function of Li2S concentration in DMSO-d6 with NH4NO3 additive. (c) DFT-derived structure of Li2S-NH4-NO3-8DMSO system shows the dissolution process of Li2S is enhanced through hydrogen