Sample records for molecular plant-microbe interactions

  1. Program and abstracts: IS-MPMI sixth International Symposium on Molecular Plant-Microbe Interactions

    SciTech Connect (OSTI)

    Not Available

    1992-12-31T23:59:59.000Z

    This volume provides abstracts of oral and poster presentations made for the Sixth International Symposium on Molecular Plant-Microbe Interactions.

  2. PMI: Plant-Microbe Interfaces (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Schadt, Christopher [ORNL

    2013-03-01T23:59:59.000Z

    Christopher Schadt of Oak Ridge National Laboratory on "Plant-Microbe Interactions" in the context of poplar trees at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 held in Walnut Creek, Calif.

  3. Plant Microbe Interactions | Department of Energy

    Energy Savers [EERE]

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page onYou are now leaving Energy.gov You are now leaving Energy.gov You are being directed offOCHCO2:Introduction toManagementOPAM5Parabolic TroughPhotoCell|

  4. 740 / Molecular Plant-Microbe Interactions MPMI Vol. 20, No. 7, 2007, pp. 740750. doi:10.1094/MPMI-20-7-0740. 2007 The American Phytopathological Society

    E-Print Network [OSTI]

    Citovsky, Vitaly

    -20-7-0740. © 2007 The American Phytopathological Society TECHNICAL ADVANCE pSITE Vectors for Stable Integration or Transient Expression of Autofluorescent Protein Fusions in Plants: Probing Nicotiana, University of Kentucky, Lexington 40546, U.S.A.; 2 Department of Life Science, Dongguk University, South

  5. 280 / Molecular Plant-Microbe Interactions MPMI Vol. 10, No. 2, 1997, pp. 280289. Publication no. M-1997-0127-03R. 1997 The American Phytopathological Society

    E-Print Network [OSTI]

    Cohen, Michael F.

    that the transposi- tion site in strain UCD 328 lies within a 1,251-bp open reading frame (ORF), designated hrmA´ from the start of hrmA and has the signature sequences belonging to a fam- ily of NAD(P)H-dependent oxidoreductases. Strains hav- ing insertional mutations in hrmU or hrmA reproduce the strain UCD 328 phenotype

  6. Molecular conformations, interactions, and properties associated...

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

    Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors Molecular conformations, interactions, and...

  7. Detection of molecular interactions

    DOE Patents [OSTI]

    Groves, John T. (Berkeley, CA); Baksh, Michael M. (Fremont, CA); Jaros, Michal (Brno, CH)

    2012-02-14T23:59:59.000Z

    A method and assay are described for measuring the interaction between a ligand and an analyte. The assay can include a suspension of colloidal particles that are associated with a ligand of interest. The colloidal particles are maintained in the suspension at or near a phase transition state from a condensed phase to a dispersed phase. An analyte to be tested is then added to the suspension. If the analyte binds to the ligand, a phase change occurs to indicate that the binding was successful.

  8. Theoretical studies of molecular interactions

    SciTech Connect (OSTI)

    Lester, W.A. Jr. [Univ. of California, Berkeley (United States)

    1993-12-01T23:59:59.000Z

    This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

  9. Hole interactions with molecular vibrations on DNA

    E-Print Network [OSTI]

    A. Omerzu; M. Licer; T. Mertelj; V. V. Kabanov; D. Mihailovic

    2004-05-13T23:59:59.000Z

    We report on a study of the interactions between holes and molecular vibrations on dry DNA using photoinduced infrared absorption spectroscopy. Laser photoexcited (PE) holes are found to have a room-temperature lifetime in excess of 1 ms, clearly indicating the presence of localization. However, from a quantitative model analysis of the frequency shifts of vibrational modes caused by the PE holes, we find the holevibrational coupling constant to be relatively small, 0.2. This interaction leads to a change in the conformational energy of 0.015 eV, which is too small to cause selftrapping at room temperature. We conclude that, at least in the dry (A) form, DNA is best understood in terms of a double chain of coupled quantum dots arising from the pseudo-random chain sequence of base pairs, in which Anderson localization prevents the formation of a metallic state.

  10. Understanding Molecular-scale Complexity and Interactions of...

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

    iron and aluminum oxides) and complexation with ions (involving P, Ca, Fe, K) with an eye to understanding how molecular scale interactions influence the emergent structures and...

  11. Molecular interactions with ice: Molecular embedding, adsorption, detection, and release

    SciTech Connect (OSTI)

    Gibson, K. D.; Langlois, Grant G.; Li, Wenxin; Sibener, S. J., E-mail: s-sibener@uchicago.edu [The James Franck Institute and Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637 (United States); Killelea, Daniel R. [Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Ave., Chicago, Illinois 60660 (United States)

    2014-11-14T23:59:59.000Z

    The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion. We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF{sub 4} molecules with high translational energies (?3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is strongly activated by translational energy, but the CF{sub 4} embedding probability is much less than for Xe. In addition, a larger molecule, SF{sub 6}, did not embed at the same translational energies that both CF{sub 4} and Xe embedded. The embedding rate for a given energy thus goes in the order Xe > CF{sub 4} > SF{sub 6}. We do not have as much data for Kr, but it appears to have a rate that is between that of Xe and CF{sub 4}. Tentatively, this order suggests that for Xe and CF{sub 4}, which have similar van der Waals radii, the momentum is the key factor in determining whether the incident atom or molecule can penetrate deeply enough below the surface to embed. The more massive SF{sub 6} molecule also has a larger van der Waals radius, which appears to prevent it from stably embedding in the selvedge. We also determined that the maximum depth of embedding is less than the equivalent of four layers of hexagonal ice, while some of the atoms just below the ice surface can escape before ice desorption begins. These results show that energetic ballistic embedding in ice is a general phenomenon, and represents a significant new channel by which incident species can be trapped under conditions where they would otherwise not be bound stably as surface adsorbates. These findings have implications for many fields including environmental science, trace gas collection and release, and the chemical composition of astrophysical icy bodies in space.

  12. DockingShop: A Tool for Interactive Molecular Docking

    SciTech Connect (OSTI)

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24T23:59:59.000Z

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  13. Three Dimensional Molecular Imaging for Lignocellulosic Materials

    SciTech Connect (OSTI)

    Bohn, Paul W.; Sweedler, Jonathan V.

    2011-06-09T23:59:59.000Z

    The development of high efficiency, inexpensive processing protocols to render biomass components into fermentable substrates for the sequential processing of cell wall components into fuels and important feedstocks for the biorefinery of the future is a key goal of the national roadmap for renewable energy. Furthermore, the development of such protocols depends critically on detailed knowledge of the spatial and temporal infiltration of reagents designed to remove and separate the phenylpropenoid heteropolymer (lignin) from the processable sugar components sequestered in the rigid cell walls of plants. A detailed chemical and structural understanding of this pre-enzymatic processing in space and time was the focus of this program. We worked to develop new imaging strategies that produce real-time molecular speciation information in situ; extract sub-surface information about the effects of processing; and follow the spatial and temporal characteristics of the molecular species in the matrix and correlate this complex profile with saccharification. Spatially correlated SIMS and Raman imaging were used to provide high quality, high resolution subcellular images of Miscanthus cross sections. Furthermore, the combination of information from the mass spectrometry and Raman scattering allows specific chemical assignments of observed structures, difficult to assign from either imaging approach alone and lays the foundation for subsequent heterocorrelated imaging experiments targeted at more challenging biological systems, such as the interacting plant-microbe systems relevant to the rhizosphere.

  14. Collective transport of weakly interacting molecular motors with Langmuir kinetics

    E-Print Network [OSTI]

    Sameep Chandel; Abhishek Chaudhuri; Sudipto Muhuri

    2015-01-09T23:59:59.000Z

    Filament based intracellular transport involves the collective action of molecular motor proteins. Experimental evidences suggest that microtubule (MT) filament bound motor proteins such as {\\it kinesins} weakly interact among themselves during transport and with the surrounding cellular environment. Motivated by these observations we study a driven lattice gas model for collective unidirectional transport of molecular motors on open filament, which incorporates the short-range interactions between the motors on filaments and couples the transport process on filament with surrounding cellular environment through adsorption-desorption Langmuir (LK) kinetics of the motors. We analyse this model within the framework of a Mean Field (MF) theory in the limit of {\\it weak} interactions between the motors. We point to the mapping of this model with the non-conserved version of Katz-Lebowitz-Spohn (KLS) model. The system exhibits rich phase behavior with variety of inhomogeneous phases including localized shocks in the bulk of the filament. We obtain the steady state density and current profiles and analyse their variation as function of the strength of interaction. We compare these MF results with Monte Carlo simulations and find that the MF analysis shows reasonably good agreement as long as the motors are weakly interacting. We also construct the non-equilibrium MF phase diagram.

  15. Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies

    SciTech Connect (OSTI)

    Gary J. Blanchard

    2009-06-30T23:59:59.000Z

    This work focuses on two broad issues. These are (1) the molecular origin of the chemical selectivity achieved with ultrathin polymer multilayers, and (2) how the viscoelastic properties of the polymer layers are affected by exposure to solvent and analytes. These issues are inter-related, and to understand them we need to design experiments that probe both the energetic and kinetic aspects of interfacial adsorption processes. This project focuses on controling the chemical structure, thickness, morphology and sequential ordering of polymer layers bound to interfaces using maleimide-vinyl ether and closely related alternating copolymerization chemistry and efficient covalent cross-linking reactions that allow for layer-by-layer polymer deposition. This chemistry has been developed during the funding cycle of this Grant. We have measure the equilibrium constants for interactions between specific layers within the polymer interfaces and size-controlled, surface-functionalized gold nanoparticles. The ability to control both size and functionality of gold nanoparticle model analytes allows us to evaluate the average “pore size” that characterizes our polymer films. We have measured the “bulk” viscosity and shear modulus of the ultrathin polymer films as a function of solvent overlayer identity using quartz crystal microbalance complex impedance measurements. We have measured microscopic viscosity at specific locations within the layered polymer interfaces with time-resolved fluorescence lifetime and depolarization techniques. We combine polymer, cross-linking and nanoparticle synthetic expertise with a host of characterization techniques, including QCM gravimetry and complex impedance analysis, steady state and time-resolved spectroscopies.

  16. assessing molecular interaction: Topics by E-print Network

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

    Szilagyi a is modeled with a spatially and temporally discretized version of the linear kinematic wave equation written-aquifer interactions; Baseflow separation; Flow routing;...

  17. Molecular Cell Interaction of a DNA Zip Code with the Nuclear

    E-Print Network [OSTI]

    Brickner, Jason

    Molecular Cell Article Interaction of a DNA Zip Code with the Nuclear Pore Complex Promotes H2A codes'' in the promoters of yeast genes confer interaction with the NPC and localization at the nuclear, they remain at the nuclear periphery for several generations, primed for reactivation. Tran- scriptional

  18. Effect of Intra-molecular Disorder and Inter-molecular Electronic Interactions on the Electronic Structure of Poly-p-Phenylene Vinylene (PPV)

    E-Print Network [OSTI]

    Ping Yang; Enrique R. Batista; Sergei Tretiak; Avadh Saxena; Richard L. Martin; D. L. Smith

    2007-07-13T23:59:59.000Z

    We investigate the role of intra-molecular conformational disorder and inter-molecular electronic interactions on the electronic structure of disorder clusters of poly-p-phenylene vinylene (PPV) oligomers. Classical molecular dynamics is used to determine probable molecular geometries, and first-principle density functional theory (DFT) calculations are used to determine electronic structure. Intra-molecular and inter-molecular effects are disentangled by contrasting results for densely packed oligomer clusters with those for ensembles of isolated oligomers with the same intra-molecular geometries. We find that electron trap states are induced primarily by intra-molecular configuration disorder, while the hole trap states are generated primarily from inter-molecular electronic interactions.

  19. Molecular force spectroscopy of homophilic nectin-1 interactions

    SciTech Connect (OSTI)

    Vedula, Sri Ram Krishna [Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576 (Singapore); Lim, T.S. [Bioinformatics Institute (Singapore); NUS Graduate School for Integrative Sciences and Engineering (Singapore); Hui Shi [Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576 (Singapore); Kausalya, P. Jaya [Institute of Molecular and Cell Biology (Singapore); Lane, E. Birgitte [Institute of Medical Biology (Singapore); Rajagopal, Gunaretnam [Bioinformatics Institute (Singapore); Hunziker, Walter [Institute of Molecular and Cell Biology (Singapore); Lim, C.T. [Division of Bioengineering and Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576 (Singapore)], E-mail: ctlim@nus.edu.sg

    2007-11-03T23:59:59.000Z

    Nectins are Ca{sup 2+} independent cell adhesion molecules localizing at the cadherin based adherens junctions. In this study, we have used atomic force microscopy to study interaction of a chimera of extra cellular fragment of nectin-1 and Fc of human IgG (nef-1) with wild type L-fibroblasts that express endogenous nectin-1 to elucidate the biophysical characteristics of homophilic nectin-1 trans-interactions at the level of single molecule. Bond strength distribution revealed three distinct bound states (or configurations) of trans-interactions between paired nectins, where each bound state has a unique unstressed off-rate and reactive compliance. Kinetic analysis of force-dependent off-rate of the bound state involving trans-interacting V-V domains between paired nectin-1 (unstressed off-rate {approx}1.465 {+-} 0.779 s{sup -1}, reactive compliance {approx}0.143 {+-} 0.072 nm) was found to be closest to E-cadherin, indicating that V-V domain trans-interactions are probably necessary to initiate and promote adhesions of E-cadherin at adherens junctions (AJs)

  20. Molecular Interaction between Botulinum Neurotoxin B and Its Protein

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)Integrated Codes |IsLove Your1 SECTION A.ModelAlyssaReceptor Revealed Molecular

  1. Molecular theory for the effects of solute attractive forces on hydrophobic interactions

    E-Print Network [OSTI]

    Chaudhari, M I; Asthagiri, D; Tan, L; Pratt, L R

    2015-01-01T23:59:59.000Z

    We consider the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions. The principal result of LMF theory is outlined, then tested by obtaining radial distribution functions (rdfs) for Ar atoms in water, with and without attractive interactions distinguished by the Weeks-Chandler-Andersen (WCA) separation. Change from purely repulsive atomic solute interactions to include realistic attractive interactions substantially \\emph{diminishes} the strength of hydrophobic bonds. Since attractions make a big contribution to hydrophobic interactions, Pratt-Chandler theory, which did not include attractions, should not be simply comparable to computer simulation results with general physical interactions, including attractions. The rdfs permit evaluation of osmotic second virial coefficients $B_2$. Those $B_2$ are consistent with the conclusion that incorporation of attractive interactions leads to more positive (repulsive) values. In all cases here, $B_2$ becomes mor...

  2. Optimum protein-excipient interactions using molecular docking simulations

    E-Print Network [OSTI]

    Tarar, Haider

    2014-04-01T23:59:59.000Z

    Engineering ACADEMIC LEVEL Senior RESEARCH MENTOR Kyle Camarda, Associate Professor of Chemical Engineering 70 | JOURNAL OF UNDERGRADUATE RESEARCH by removing water to decrease its mobility and make it less vulnerable to water-based reactions. Even... conformations total for each excipient. Each conformation was evaluated to determine residues which were repeatedly involved in strong interactions (Van der Waal or hydrogen bonding) with the excipients. The computational results from the above procedure...

  3. Molecular? recognition? from? atomic ?interactions:?? insights ?into ?drug ?discovery?

    E-Print Network [OSTI]

    Higueruelo, Alicia Perez

    2012-05-08T23:59:59.000Z

    and selectivity, whilst trying to confer an appropriate therapeutic profile. This thesis starts with the description of the creation of TIMBAL, a database that holds small molecules disrupting protein-protein interactions. The thesis then focuses on the analysis... -like Growth Factor I IL2 Interleukin 2 IL2Ra Interleukin 2 Receptor Alpha subunit Inh Inhibitor iNOS Nitric Oxide Synthase, inducible IRAK-4 Interleukin-1 Receptor Associated Kinase 4 ITC Isothermal Titration Calorimetry IUPAC International Union of Pure...

  4. Interaction potentials for alumina and molecular dynamics simulations of amorphous and liquid alumina

    E-Print Network [OSTI]

    Southern California, University of

    Interaction potentials for alumina and molecular dynamics simulations of amorphous and liquid for preventing crystalliza- tion and giving chemical stability and durability to a glaze, for instance. Due been identified.4 A review of these crystal structures and their pre- cursors can be found in the work

  5. Molecular formations in ultracold mixtures of interacting and noninteracting atomic gases

    E-Print Network [OSTI]

    T. Nishimura; A. Matsumoto; H. Yabu

    2008-08-06T23:59:59.000Z

    Atom-molecule equilibrium for molecular formation processes is discussed for boson-fermion, fermion-fermion, and boson-boson mixtures of ultracold atomic gases in the framework of quasichemical equilibrium theory. After presentation of the general formulation, zero-temperature phase diagrams of the atom-molecule equilibrium states are calculated analytically; molecular, mixed, and dissociated phases are shown to appear for the change of the binding energy of the molecules. The temperature dependences of the atom or molecule densities are calculated numerically, and finite-temperature phase structures are obtained of the atom-molecule equilibrium in the mixtures. The transition temperatures of the atom or molecule Bose-Einstein condensations are also evaluated from these results. Quantum-statistical deviations of the law of mass action in atom-molecule equilibrium, which should be satisfied in mixtures of classical Maxwell-Boltzmann gases, are calculated, and the difference in the different types of quantum-statistical effects is clarified. Mean-field calculations with interparticle interactions (atom-atom, atom-molecule, and molecule-molecule) are formulated, where interaction effects are found to give the linear density-dependent term in the effective molecular binding energies. This method is applied to calculations of zero-temperature phase diagrams, where new phases with coexisting local-equilibrium states are shown to appear in the case of strongly repulsive interactions.

  6. The Molecular Oxygen Tetramer: Intermolecular Interactions and Implications for the $\\epsilon$ Solid Phase

    E-Print Network [OSTI]

    Bartolomei, Massimiliano; Hernández, Marta I; Pérez-Ríos, Jesús; Campos-Martínez, José; Hernández-Lamoneda, Ramón

    2011-01-01T23:59:59.000Z

    Recent data have determined that the structure of the high pressure $\\epsilon$ phase of solid oxygen consists of clusters composed of four O$_2$ molecules. This finding has opened the question about the nature of the intermolecular interactions within the molecular oxygen tetramer. We use multiconfigurational ab initio calculations to obtain an adequate characterization of the ground singlet state of (O$_2$)$_4$ which is compatible with the non magnetic character of the $\\epsilon$ phase. In contrast to previous suggestions implying chemical bonding, we show that (O$_2$)$_4$ is a van der Waals like cluster where exchange interactions preferentially stabilize the singlet state. However, as the cluster shrinks, there is an extra stabilization due to many-body interactions that yields a significant softening of the repulsive wall. We show that this short range behavior is a key issue for the understanding of the structure of $\\epsilon$-oxygen.

  7. 2012 ATOMIC AND MOLECULAR INTERACTIONS GORDON RESEARCH CONFERENCE AND GORDON RESEARCH SEMINAR, JULY 15-20, 2012

    SciTech Connect (OSTI)

    Zwier, Timothy

    2012-07-20T23:59:59.000Z

    At the 2012 Atomic and Molecular Interactions Gordon Conference, there will be talks in several broadly defined and partially overlapping areas: ? Intramolecular and single-collision reaction dynamics; ? Photophysics and photochemistry of excited states; ? Clusters, aerosols and solvation; ? Interactions at interfaces; ? Conformations and folding of large molecules; ? Interactions under extreme conditions of temperature and pressure. The theme of the Gordon Research Seminar on Atomic & Molecular Interactions, in keeping with the tradition of the Atomic and Molecular Interactions Gordon Research Conference, is far-reaching and involves fundamental research in the gas and condensed phases along with application of these ideas to practical chemical fields. The oral presentations, which will contain a combination of both experiment and theory, will focus on four broad categories: ? Ultrafast Phenomena; ? Excited States, Photoelectrons, and Photoions; ? Chemical Reaction Dynamics; ? Biomolecules and Clusters.

  8. Interaction of Polar and Nonpolar Organic Pollutants with Soil Organic Matter: Sorption Experiments and Molecular Dynamics Simulation

    E-Print Network [OSTI]

    Ahmed, Ashour A; Aziz, Saadullah G; Hilal, Rifaat H; Elroby, Shaaban A; Al-Youbi, Abdulrahman O; Leinweber, Peter; Kühn, Oliver

    2014-01-01T23:59:59.000Z

    The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question How organic pollutants interact with SOM? is lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model followed by carrying out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), representing the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and the theoretical outcomes explored four major points regarding sorption of SAA and HCB on soil. 1. The interaction depends on the SOM chemical composition mo...

  9. Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities

    E-Print Network [OSTI]

    Bing-Sui Lu; Ali Naji; Rudolf Podgornik

    2015-03-18T23:59:59.000Z

    We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel $r^{-5}$ scaling behavior of the van der Waals interaction energy for small inter-polymer separation $r$, in contradistinction to the $r^{-4}$ scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.

  10. Molecular mechanisms, thermodynamics, and dissociation kinetics of knob-hole interactions in fibrin

    E-Print Network [OSTI]

    Kononova, Olga; Zhmurov, Artem; Alekseenko, Andrey; Cheng, Chai-Ho; Agarwal, Silvi; Marx, Kenneth A; Weisel, John W; Barsegov, Valeri

    2015-01-01T23:59:59.000Z

    Polymerization of fibrin, the primary structural protein of blood clots and thrombi, occurs through binding of knobs 'A' and 'B' in the central nodule of fibrin monomer to complementary holes 'a' and 'b' in the beta- and gamma-nodules, respectively, of another monomer. We characterized the A:a and B:b knob-hole interactions under varying solution conditions using Molecular Dynamics simulations of the structural models of fibrin(ogen) fragment D complexed with synthetic peptides GPRP (knob 'A' mimetic) and GHRP (knob 'B' mimetic). The strength of A:a and B:b knob-hole complexes was roughly equal, decreasing with pulling force; yet, the dissociation kinetics were sensitive to variations in acidity (pH=5-7) and temperature (T=25-37 C). There were similar structural changes in holes 'a' and 'b' during forced dissociation of the knob-hole complexes: elongation of loop I, stretching of interior region, and translocation of the moveable flap. The disruption of the knob-hole interactions was not an "all-or-none" tran...

  11. Hydrogen-Bonding Interaction in Molecular Complexes and Clusters of Aerosol Nucleation Alexei Khalizov, and Renyi Zhang*

    E-Print Network [OSTI]

    Hydrogen-Bonding Interaction in Molecular Complexes and Clusters of Aerosol Nucleation Precursors, water, and ammonia. A central feature of the complexes is the presence of two hydrogen bonds. Organic acid-sulfuric acid complexes show one strong and one medium-strength hydrogen bond whereas

  12. THE FUELING DIAGRAM: LINKING GALAXY MOLECULAR-TO-ATOMIC GAS RATIOS TO INTERACTIONS AND ACCRETION

    SciTech Connect (OSTI)

    Stark, David V.; Kannappan, Sheila J.; Eckert, Kathleen D. [Physics and Astronomy Department, University of North Carolina, Chapel Hill, NC 27516 (United States); Wei, Lisa H. [Atmospheric and Environmental Research, 131 Hartwell Avenue, Lexington, MA 02421 (United States); Baker, Andrew J. [Department of Physics and Astronomy, Rutgers, the State University of New Jersey, 136 Frelinghuysen Road, Piscataway, NJ 08854 (United States); Leroy, Adam K. [National Radio Astronomy Observatory, 520 Edgemont Road, Charlottesville, VA 22903 (United States); Vogel, Stuart N. [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States)

    2013-05-20T23:59:59.000Z

    To assess how external factors such as local interactions and fresh gas accretion influence the global interstellar medium of galaxies, we analyze the relationship between recent enhancements of central star formation and total molecular-to-atomic (H{sub 2}/H I) gas ratios, using a broad sample of field galaxies spanning early-to-late type morphologies, stellar masses of 10{sup 7.2}-10{sup 11.2} M{sub Sun }, and diverse stages of evolution. We find that galaxies occupy several loci in a ''fueling diagram'' that plots H{sub 2}/H I ratio versus mass-corrected blue-centeredness, a metric tracing the degree to which galaxies have bluer centers than the average galaxy at their stellar mass. Spiral galaxies of all stellar masses show a positive correlation between H{sub 2}/H I ratio and mass-corrected blue-centeredness. When combined with previous results linking mass-corrected blue-centeredness to external perturbations, this correlation suggests a systematic link between local galaxy interactions and molecular gas inflow/replenishment. Intriguingly, E/S0 galaxies show a more complex picture: some follow the same correlation, some are quenched, and a distinct population of blue-sequence E/S0 galaxies (with masses below key scales associated with transitions in gas richness) defines a separate loop in the fueling diagram. This population appears to be composed of low-mass merger remnants currently in late- or post-starburst states, in which the burst first consumes the H{sub 2} while the galaxy center keeps getting bluer, then exhausts the H{sub 2}, at which point the burst population reddens as it ages. Multiple lines of evidence suggest connected evolutionary sequences in the fueling diagram. In particular, tracking total gas-to-stellar mass ratios within the fueling diagram provides evidence of fresh gas accretion onto low-mass E/S0s emerging from their central starburst episodes. Drawing on a comprehensive literature search, we suggest that virtually all galaxies follow the same evolutionary patterns found in our broad sample.

  13. Coarse-Grained Molecular Dynamics Simulations of Depletion-Induced Interactions for Soft Matter Systems

    E-Print Network [OSTI]

    Tyler N. Shendruk; Martin Bertrand; James L. Harden; Gary W. Slater; Hendrick W. de Haan

    2014-08-01T23:59:59.000Z

    Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (WCA) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap of the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density.

  14. Multi-scale coarse-graining of non-conservative interactions in molecular liquids

    SciTech Connect (OSTI)

    Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M. [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)] [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)

    2014-03-14T23:59:59.000Z

    A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger numerical errors in mapping out the dissipative forces. The framework presented herein can be used to develop computational models of real liquids which are capable of bridging the atomistic and mesoscopic scales.

  15. Effects of molecular transport on turbulence-chemistry interactions in a hydrogen-argon-air jet diffusion flame

    SciTech Connect (OSTI)

    Menon, S.; Calhoon, W.H. Jr.; Goldin, G. [Georgia Inst. of Tech., Atlanta, GA (United States). School of Aerospace Engineering; Kerstein, A.R. [Sandia National Labs., Livermore, CA (United States)

    1994-01-01T23:59:59.000Z

    A numerical simulation of entrainment, turbulent advection, molecular import and chemical kinetics in a turbulent diffusion flame is used to investigate effects of molecular transport on turbulence-chemistry interactions. A fun finite-rate chemical mechanism is used to represent the combustion of a hydrogen-argon mixture issuing into air. Results based on incorporation of differential diffusion and variable Lewis number are compared to cases with the former effect, or both-effects, suppressed. Significant impact on radical species production and on NO emission index (based on a reduced mechanism for thermal NO) is found. A reduced mechanism for hydrogen-air combustion, omitting both effects and incorporating other simplifications, performs comparably except that its NO predictions agree well with the case of full chemistry and molecular transport, possibly due to cancellation of errors.

  16. Genetics & Plant Biology Major Requirements Lower Division Requirements (all major requirements must be taken for a letter grade)

    E-Print Network [OSTI]

    and Bioinformatics Plant Microbe Interactions · PMB C134: Chromosome Biology and Cytogenetics [3 · PMB 142: Plant Microscopy [3] · BioE 131: Intro to Computational Molecular and Cell Biology [4] · BioE 143: Computational] · Math 127: Math. and Computational Methods in Molecular Biology [4] · Stat C143: Stat. Methods

  17. USE OF MOLECULAR MODELING TO DETERMINE THE INTERACTION AND COMPETITION OF GASES WITHIN COAL FOR CARBON DIOXIDE SEQUESTRATION

    SciTech Connect (OSTI)

    Jeffrey D. Evanseck; Jeffry D. Madura; Jonathan P. Mathews

    2005-05-27T23:59:59.000Z

    We have made progress in carrying out large scale molecular dynamics simulations using the CHARMM force field in order to refine our coal/guest interactions. There have been two issues facing us over the last year. First, we have had to create a completely new topology and parameter definition for coal. Since we are using a classical force field, we have adopted the strategy of treating coal composed of individual common fragments based upon a distribution of mass, composition, and bonding. Our procedure is similar to treating a protein as being composed of the discrete set of amino acids. Second, we have had to incorporate the quality CO{sub 2} parameters that we have developed over the last two years. There are the geometric and arithmetic procedures, which we have successfully implemented. We have utilized computational molecular modeling to generate a state-of-the-art large scale structural representation of a bituminous coal of low volatile bituminous rank. This structure(s) has been used to investigate the molecular forces between the bituminous coal structure (or idealized pores) and the molecular species CH{sub 4} and CO{sub 2}. We are close to carrying out molecular dynamics simulations, which will allow us to explore and test the newly created model of coal.

  18. Delineating Molecular Interaction Mechanisms in an In Vitro Microbial-Plant Community (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    SciTech Connect (OSTI)

    Larsen, Peter [Argonne

    2013-03-01T23:59:59.000Z

    Peter Larsen of Argonne National Lab on "Delineating molecular interaction mechanisms in an in vitro microbial-plant community" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  19. Molecular fluorescent reporters for force and smart surfaces for sensing cell-surface interaction

    E-Print Network [OSTI]

    Barch, Mariya

    2009-01-01T23:59:59.000Z

    Molecular sensors are powerful because they make it possible to adapt the measurement to the sample instead of a sample to an instrument. Many reporter are available for measuring the chemical properties of a sample, but ...

  20. Molecular Modeling Study for Interaction between Bacillus subtilis Obg and Nucleotides

    E-Print Network [OSTI]

    Lee, Keun Woo

    * 1 Division of Applied Life Science, Environmental Biotechnology National Core Research Center, Plant (2009-0093813), and Environmental Biotechnology National Core Research Center program (20090091489 Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongsangnam

  1. An Analysis of the Interactions between the Sem-5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations,

    E-Print Network [OSTI]

    Wang, Wei

    to the construction of van der Waals interaction energy profiles for each ligand as well as for wild-type and mutant Dynamics, Free Energy Calculations, and Sequence Analysis Wei Wang, Wendell A. Lim,, Araz Jakalian,§,# Jian the interactions between Sem-5 and its ligands using molecular dynamics (MD), free energy calculations

  2. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor

    E-Print Network [OSTI]

    Smith, Douglas E.

    motor Amy D. Migliori1 , Douglas E. Smith1,* , and Gaurav Arya2,* 1 Department of Physics, University viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic

  3. Streptavidin-peptide interaction as a model system for molecular recognition

    E-Print Network [OSTI]

    Lam, Kit S.

    this technology, we have identified several peptides with HPQ and HPM motifs that interact specifically, similar to HPQ and HPM, many of these ligands interact with streptavidin but not with avidin. IO05 #12;KXxXx xxxxx HPQ WkWpH RWYpH wyqea (3) wfrya HPM YgWpH DWFpH wyhea wymel QtWpH wydya LqWpH YvlfP wyefa AfWpH Yp

  4. A combined experimental and computational study of the molecular interactions between anionic ibuprofen and water

    SciTech Connect (OSTI)

    Zapata-Escobar, Andy; Manrique-Moreno, Marcela; Guerra, Doris; Hadad, C. Z.; Restrepo, Albeiro, E-mail: albeiro@exactas.udea.edu.co [Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52–21, Medellín (Colombia)] [Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52–21, Medellín (Colombia)

    2014-05-14T23:59:59.000Z

    In this work, we report a detailed study of the microsolvation of anionic ibuprofen, Ibu{sup ?}. Stochastic explorations of the configurational spaces for the interactions of Ibu{sup ?} with up to three water molecules at the DFT level lead to very rich and complex potential energy surfaces. Our results suggest that instead of only one preponderant structure, a collection of isomers with very similar energies would have significant contributions to the properties of the solvated drug. One of these properties is the shift on the vibrational frequencies of the asymmetric stretching band of the carboxylate group in hydrated Ibu{sup ?} with respect to the anhydrous drug, whose experimental values are nicely reproduced using the weighted contribution of the structures. We found at least three types of stabilizing interactions, including conventional CO {sub 2}{sup ?}?H{sub 2}O, H{sub 2}O?H{sub 2}O charge assisted hydrogen bonds (HBs), and less common H{sub 2}O?H–C and H{sub 2}O?? interactions. Biological water molecules, those in direct contact with Ibu{sup ?}, prefer to cluster around the carboxylate oxygen atoms via cyclic or bridged charge assisted hydrogen bonds. Many of those interactions are strongly affected by the formal carboxylate charge, resulting in “enhanced” HBs with increased strengths and degree of covalency. We found striking similarities between this case and the microsolvation of dymethylphosphate, which lead us to hypothesize that since microsolvation of phosphatidylcholine depends mainly on the formal charge of its ionic PO {sub 2}{sup ?} group in the polar head, then microsolvation of anionic ibuprofen and interactions of water molecules with eukaryotic cell membranes are governed by the same types of physical interactions.

  5. Understanding and engineering molecular interactions and electronic transport at 2D materials interfaces

    E-Print Network [OSTI]

    Shih, Chih-Jen, Ph. D. Massachusetts Institute of Technology

    2014-01-01T23:59:59.000Z

    2D materials are defined as solids with strong in-plane chemical bonds but weak out-of-plane, van der Waals (vdW) interactions. In order to realize potential applications of 2D materials in the areas of optoelectronics, ...

  6. On the Interaction Between Cosmic Rays and Dark Matter Molecular Clouds - II. The Age Distribution of Cosmic Ray Electrons

    E-Print Network [OSTI]

    D. W. Sciama

    1999-09-14T23:59:59.000Z

    We explore further the proposal in paper I of this series that the confinement time of cosmic ray nuclei in the Milky Way is determined by their interaction with dark matter molecular clouds rather than by their escape from the halo, as is assumed in conventional models of cosmic ray propagation. The same proposal can be made for cosmic ray electrons. This proposal leads to a specific age distribution for the electrons which is in agreement with Tang's (1984) observations of the electron spectrum at high energies but not with Nishimura et al's (1980) earlier data, which lead to a flatter spectrum. However, the simplest leaky box and diffusion models disagree with both sets of data so that our trapping model is supported if Tang's data are correct.

  7. Interaction of toluene with two-color asymmetric laser fields: Controlling the directional emission of molecular hydrogen fragments

    SciTech Connect (OSTI)

    Kaziannis, S.; Kotsina, N.; Kosmidis, C. [Department of Physics, Atomic and Molecular Physics Laboratory, University of Ioannina, University Campus, Ioannina GR-45110 (Greece)

    2014-09-14T23:59:59.000Z

    The interaction of toluene with strong asymmetric two-color laser irradiation of 40 fs duration is studied by means of Time of flight mass spectrometry. Highly energetic H{sub 2}{sup +} and H{sub 3}{sup +} fragment ions are produced through an isomerization process taking place within transient multiply charged parent ions. Comparative study of deuterium labeled toluene isotopes enables the discrimination between molecular hydrogen fragments formed exclusively within the CH{sub 3}- part from those that require hydrogen atom exchange between the former and the phenyl moiety. It is demonstrated that by manipulating the relative phase of the ?/2? field components the selective ionization of oriented toluene molecules can be used as a tool to control the directional emission of the H{sub 2}{sup +}, H{sub 3}{sup +} species.

  8. Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method

    SciTech Connect (OSTI)

    Yoshida, Norio, E-mail: noriwo@chem.kyushu-univ.jp [Department of Chemistry, Graduate School of Sciences, Kyushu University, 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581 (Japan)

    2014-06-07T23:59:59.000Z

    The three-dimensional reference interaction site model (3D-RISM) method was efficiently implemented in the fragment molecular orbital (FMO) method. The method is referred to as the FMO/3D-RISM method, and allows us to treat electronic structure of the whole of a macromolecule, such as a protein, as well as the solvent distribution around a solute macromolecule. The formalism of the FMO/3D-RISM method, for the computationally available form and variational expressions, are proposed in detail. A major concern leading to the implementation of the method was decreasing the computational costs involved in calculating the electrostatic potential, because the electrostatic potential is calculated on numerous grid points in three-dimensional real space in the 3D-RISM method. In this article, we propose a procedure for decreasing the computational costs involved in calculating the electrostatic potential in the FMO method framework. The strategy involved in this procedure is to evaluate the electrostatic potential and the solvated Fock matrix in different manners, depending on the distance between the solute and the solvent. The electrostatic potential is evaluated directly in the vicinity of the solute molecule by integrating the molecular orbitals of monomer fragments of the solute molecule, whereas the electrostatic potential is described as the sum of multipole interactions when an analog of the fast multipole method is used. The efficiency of our method was demonstrated by applying it to a water trimer system and three biomolecular systems. The FMO/3D-RISM calculation can be performed within a reasonable computational time, retaining the accuracy of some physical properties.

  9. Ab initio molecular dynamics study of manganese porphine hydration and interaction with nitric oxide

    E-Print Network [OSTI]

    Kevin Leung; Craig J. Medforth

    2007-01-23T23:59:59.000Z

    The authors use ab initio molecular dynamics and the density functional theory+U (DFT+U) method to compute the hydration environment of the manganese ion in manganese (II) and manganese (III) porphines (MnP) dispersed in liquid water. These are intended as simple models for more complex water soluble porphyrins, which have important physiological and electrochemical applications. The manganese ion in Mn(II)P exhibits significant out-of-porphine plane displacement and binds strongly to a single H2O molecule in liquid water. The Mn in Mn(III)P is on average coplanar with the porphine plane and forms a stable complex with two H2O molecules. The residence times of these water molecules exceed 15 ps. The DFT+U method correctly predicts that water displaces NO from Mn(III)P-NO, but yields an ambiguous spin state for the MnP(II)-NO complex.

  10. MicroCantilever (MC) based nanomechanical sensor for detection of molecular interactions

    SciTech Connect (OSTI)

    Kang, Kyung

    2011-05-11T23:59:59.000Z

    Specific aims of this study are to investigate the mechanism governing surface stress generation associated with chemical or molecular binding on functionalized microcantilevers. Formation of affinity complexes on cantilever surfaces leads to charge redistribution, configurational change and steric hindrance between neighboring molecules resulting in surface stress change and measureable cantilever deformation. A novel interferometry technique employing two adjacent micromachined cantilevers (a sensing/reference pair) was utilized to measure the cantilever deformation. The sensing principle is that binding/reaction of specific chemical or biological species on the sensing cantilever transduces to mechanical deformation. The differential bending of the sensing cantilever respect to the reference cantilever ensures that measured response is insensitive to environmental disturbances. As a proof of principle for the measurement technique, surface stress changes associated with: self-assembly of alkanethiol, hybridization of ssDNA, and the formation of cocaine-aptamer complexes were measured. Dissociation constant (K{sub d}) for each molecular reaction was utilized to estimate the surface coverage of affinity complexes. In the cases of DNA hybridization and cocaine-aptamer binding, measured surface stress was found to be dependent on the surface coverage of the affinity complexes. In order to achieve a better sensitivity for DNA hybridization, immobilization of receptor molecules was modified to enhance the deformation of underlying surface. Single-stranded DNA (ssDNA) strands with thiol-modification on both 3-foot and 5-foot ends were immobilized on the gold surface such that both ends are attached to the gold surface. Immobilization condition was controlled to obtain similar receptor density as single-thiolated DNA strands. Hybridization of double-thiolated DNA strands leads to an almost two orders of magnitude increase in cantilever deformation. In both DNA hybridization and the conventional mode for cocaine detection, the lowest detectable concentration was determined by binding activity between the ligand and receptor molecules. In order to overcome this limitation for cocaine detection, a novel competition sensing mode that relies on rate of aptamers unbinding from the cantilever due to either diffusion or reaction with cocaine as target ligands in solution was investigated. The rate of unbinding is found to be dependent on the concentration of cocaine molecules. A model based on diffusion-reaction equation was developed to explain the experimental observation. Experimental results indicate that the competition mode reduces the lowest detectable threshold to 200 nM which is comparable to that achieved analytical techniques such as mass spectrometry.

  11. Simultaneous photon absorption as a probe of molecular interaction and hydrogen-bond correlation in liquids

    E-Print Network [OSTI]

    Sander Woutersen

    2007-03-06T23:59:59.000Z

    We have investigated the simultaneous absorption of near-infrared photons by pairs of neighboring molecules in liquid methanol. Simultaneous absorption by two OH-stretching modes is found to occur at an energy higher than the sum of the two absorbing modes. This frequency shift arises from interaction between the modes, and its value has been used to determine the average coupling between neighboring methanol molecules. We find a rms coupling strength of 46+/-1 cm-1, much larger than can be explained from transition-dipole coupling, suggesting that hydrogen-bond mediated interactions between neighboring molecules play an important role in liquid methanol. The most important aspect of simultaneous vibrational absorption is that it allows for a quantitative investigation of hydrogen-bond cooperativity. We derive the extent to which the hydrogen-bond strengths of neighboring molecules are correlated by comparing the line shape of the absorption band caused by simultaneous absorption with that of the fundamental transition. Surprisingly, neighboring hydrogen bonds in methanol are found to be strongly correlated, and from the data we obtain a hydrogen-bond correlation coefficient of 0.69+/-0.12.

  12. The Molecular Interaction of CAR and JAML Recruits the Central Cell Signal Transducer PI3K

    SciTech Connect (OSTI)

    Verdino, Petra; Witherden, Deborah A.; Havran, Wendy L.; Wilson, Ian A. (Scripps)

    2010-11-15T23:59:59.000Z

    Coxsackie and adenovirus receptor (CAR) is the primary cellular receptor for group B coxsackieviruses and most adenovirus serotypes and plays a crucial role in adenoviral gene therapy. Recent discovery of the interaction between junctional adhesion molecule-like protein (JAML) and CAR uncovered important functional roles in immunity, inflammation, and tissue homeostasis. Crystal structures of JAML ectodomain (2.2 angstroms) and its complex with CAR (2.8 angstroms) reveal an unusual immunoglobulin-domain assembly for JAML and a charged interface that confers high specificity. Biochemical and mutagenesis studies illustrate how CAR-mediated clustering of JAML recruits phosphoinositide 3-kinase (P13K) to a JAML intracellular sequence motif as delineated for the {alpha}{beta} T cell costimulatory receptor CD28. Thus, CAR and JAML are cell signaling receptors of the immune system with implications for asthma, cancer, and chronic nonhealing wounds.

  13. Interaction Interaction

    E-Print Network [OSTI]

    Hehner, Eric C.R.

    Interaction 1/54 #12;Interaction shared variables 2/54 #12;Interaction shared variables can be read and written by any process (most interaction) 3/54 #12;Interaction shared variables can be read and written by any process (most interaction) difficult to implement 4/54 #12;Interaction shared variables can

  14. Use of molecular modeling to determine the interaction and competition of gases within coal for carbon dioxide sequestration

    SciTech Connect (OSTI)

    Jeffrey D. Evanseck; Jeffry D. Madura; Jonathan P. Mathews

    2006-04-21T23:59:59.000Z

    Molecular modeling was employed to both visualize and probe our understanding of carbon dioxide sequestration within a bituminous coal. A large-scale (>20,000 atoms) 3D molecular representation of Pocahontas No. 3 coal was generated. This model was constructed based on a the review data of Stock and Muntean, oxidation and decarboxylation data for aromatic clustersize frequency of Stock and Obeng, and the combination of Laser Desorption Mass Spectrometry data with HRTEM, enabled the inclusion of a molecular weight distribution. The model contains 21,931 atoms, with a molecular mass of 174,873 amu, and an average molecular weight of 714 amu, with 201 structural components. The structure was evaluated based on several characteristics to ensure a reasonable constitution (chemical and physical representation). The helium density of Pocahontas No. 3 coal is 1.34 g/cm{sup 3} (dmmf) and the model was 1.27 g/cm{sup 3}. The structure is microporous, with a pore volume comprising 34% of the volume as expected for a coal of this rank. The representation was used to visualize CO{sub 2}, and CH{sub 4} capacity, and the role of moisture in swelling and CO{sub 2}, and CH{sub 4} capacity reduction. Inclusion of 0.68% moisture by mass (ash-free) enabled the model to swell by 1.2% (volume). Inclusion of CO{sub 2} enabled volumetric swelling of 4%.

  15. Microbial Protein-Protein Interactions (MiPPI) Data from the Genomics: GTL Center for Molecular and Cellular Systems (CMCS)

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

    The Genomic Science Center for Molecular and Cellular Systems (CMCS), established in 2002, seeks to identify and characterize the complete set of protein complexes within a cell to provide a mechanistic basis for the understanding of biochemical functions. The CMCS is anchored at ORNL and PNNL. CMCS initially focused on the identification and characterization of protein complexes in two microbial systems,Rhodopseudomonas palustris (R. palustris) and Shewanella oneidensis (S. oneidensis). These two organisms have also been the focus of major DOE Genomic Science/Microbial Cell Program (MCP) projects. To develop an approach for identifying the diverse types of complexes present in microbial organisms, CMCS incorporates a number of molecular biology, microbiology, analytical and computational tools in an integrated pipeline.

  16. Intra-membrane molecular interactions of K%2B channel proteins : application to problems in biodefense and bioenergy.

    SciTech Connect (OSTI)

    Moczydlowski, Edward G.

    2013-07-01T23:59:59.000Z

    Ion channel proteins regulate complex patterns of cellular electrical activity and ionic signaling. Certain K+ channels play an important role in immunological biodefense mechanisms of adaptive and innate immunity. Most ion channel proteins are oligomeric complexes with the conductive pore located at the central subunit interface. The long-term activity of many K+ channel proteins is dependent on the concentration of extracellular K+; however, the mechanism is unclear. Thus, this project focused on mechanisms underlying structural stability of tetrameric K+ channels. Using KcsA of Streptomyces lividans as a model K+ channel of known structure, the molecular basis of tetramer stability was investigated by: 1. Bioinformatic analysis of the tetramer interface. 2. Effect of two local anesthetics (lidocaine, tetracaine) on tetramer stability. 3. Molecular simulation of drug docking to the ion conduction pore. The results provide new insights regarding the structural stability of K+ channels and its possible role in cell physiology.

  17. Interdisciplinary Research and Training Program in the Plant Sciences. Technical progress report, February 1, 1991--November 30, 1992

    SciTech Connect (OSTI)

    Wolk, C.P.

    1992-07-01T23:59:59.000Z

    Research on plants continued. Topics include: Molecular basis of symbiotic plant-microbe interations; enzymatic mechanisms and regulation of plant cell wall biosynthesis; molecular mechanisms that regulate the expression of genes in plants; resistance of plants to environmental stress; studies on hormone biosynthesis and action; plant cell wall proteins; interaction of nuclear and organelle genomes; sensor transduction in plants; molecular mechanisms of trafficking in the plant cell; regulation of lipid metabolism; molecular bases of plant disease resistance mechanisms; biochemical and molecular aspects of plant pathogenesis; developmental biology of nitrogen-fixing cyanobacteria; environmental control of plant development and its relation to plant hormones.

  18. Interdisciplinary Research and Training Program in the Plant Sciences

    SciTech Connect (OSTI)

    Wolk, C.P.

    1992-01-01T23:59:59.000Z

    Research on plants continued. Topics include: Molecular basis of symbiotic plant-microbe interations; enzymatic mechanisms and regulation of plant cell wall biosynthesis; molecular mechanisms that regulate the expression of genes in plants; resistance of plants to environmental stress; studies on hormone biosynthesis and action; plant cell wall proteins; interaction of nuclear and organelle genomes; sensor transduction in plants; molecular mechanisms of trafficking in the plant cell; regulation of lipid metabolism; molecular bases of plant disease resistance mechanisms; biochemical and molecular aspects of plant pathogenesis; developmental biology of nitrogen-fixing cyanobacteria; environmental control of plant development and its relation to plant hormones.

  19. Gas Bubbles and Gas Pancakes at Liquid/Solid Interface: A Continuum Theory Incorporated with Molecular Interactions

    E-Print Network [OSTI]

    Zhaoxia Li; Xuehua Zhang; Lijuan Zhang; Xiaocheng Zeng; Jun Hu; Haiping Fang

    2007-10-27T23:59:59.000Z

    The states of gas accumulated at the liquid-solid interface are analyzed based on the continuum theory where the Hamaker constant is used to describe the long-range interaction at the microscopic scale. The Hamaker constant is always negative, whereas the gas spreading coefficient can be either sign. Despite the complexity of gas, including that the density profile may not be uniform due to absorption on both solid and liquid surfaces, we predict three possible gas states at the liquid-solid interface, i.e. complete wetting, partial wetting and pseudopartial wetting. These possible gas states correspond respectively to a gas pancake (or film) surrounded by a wet solid, a gas bubble with a finite contact angle, and a gas bubble(s) coexisting with a gas pancake. Typical thickness of the gas pancakes is at the nanoscale within the force range of the long-range interaction, whereas the radius of the gas bubbles can be large. The state of gas bubble(s) coexisting with a gas film is predicted theoretically for the first time. Our theoretical results can contribute to the development of a unified picture of gas nucleation at the liquid-solid interface.

  20. Multilevel summation methods for efficient evaluation of long-range pairwise interactions in atomistic and coarse-grained molecular simulation.

    SciTech Connect (OSTI)

    Bond, Stephen D.

    2014-01-01T23:59:59.000Z

    The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods who's cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.

  1. Ab initio molecular dynamics simulations of ion-solid interactions in Gd2Zr2O7 and Gd2Ti2O7

    SciTech Connect (OSTI)

    Wang, X J [University of Electronic Science and Technology of China (UESTC); Xiao, Haiyan [University of Tennessee, Knoxville (UTK); Zu, X T [University of Electronic Science and Technology of China (UESTC); Zhang, Yanwen [ORNL; Weber, William J [ORNL

    2013-01-01T23:59:59.000Z

    The development of ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion-solid interactions in materials, with identification determination of threshold displacement energies with ab initio accuracy, and prediction of new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order-disorder are more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be ~0.15, ~0.11-0.27 and ~0.1-0.13 |e| for Gd, Zr (or Ti), and O, respectively. Negligence of the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.

  2. Sandia National Laboratories: Molecular Geochemistry

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

    of aqueous uranyl carbonate interacting with the basal surface of sodium montmorillonite. Free energy profiles for cation adsorption to gibbsite surface calculated from molecular...

  3. Deciphering the relative contributions of multiple functions within plant-microbe symbioses

    E-Print Network [OSTI]

    Sikes, Benjamin A.; Powell, Jeff R.; Rillig, Matthias C.

    2010-06-01T23:59:59.000Z

    that vary based on the microbial species or functional group, plant species, and environment. Here we quantified the relative contributions of multiple functions provided by arbuscular mycorrhizal (AM) fungi to symbiont-mediated changes in plant biomass. We...

  4. Homogeneous Cooling with Repulsive and Attractive Long-range Interactions

    E-Print Network [OSTI]

    Luding, Stefan

    and for not too strong interaction potential enrgy. Keywords: 1/r potentials, Molecular Dynamics, granular gases

  5. Investigation of the effect of intra-molecular interactions on the gas-phase conformation of peptides as probed by ion mobility-mass spectrometry, gas-phase hydrogen/deuterium exchange, and molecular mechanics 

    E-Print Network [OSTI]

    Sawyer, Holly Ann

    2006-04-12T23:59:59.000Z

    Ion mobility-mass spectrometry (IM-MS), gas-phase hydrogen/deuterium (H/D) exchange ion molecule reactions and molecular modeling provide complimentary information and are used here for the characterization of peptide ion structure, including fine...

  6. Investigation of the effect of intra-molecular interactions on the gas-phase conformation of peptides as probed by ion mobility-mass spectrometry, gas-phase hydrogen/deuterium exchange, and molecular mechanics

    E-Print Network [OSTI]

    Sawyer, Holly Ann

    2006-04-12T23:59:59.000Z

    Ion mobility-mass spectrometry (IM-MS), gas-phase hydrogen/deuterium (H/D) exchange ion molecule reactions and molecular modeling provide complimentary information and are used here for the characterization of peptide ion structure, including fine...

  7. Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions

    SciTech Connect (OSTI)

    Shimada, Rintaro; Hamaguchi, Hiro-o, E-mail: hhama@nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan (China)

    2014-05-28T23:59:59.000Z

    We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-?-carotene (?-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute ?-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of ?-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of ?-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of the observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of ?-carotene with the vibrations of a proximate solvent molecule through solute–solvent dipole–dipole and dipole–quadrupole interactions. It is shown that the infrared active modes arise from the dipole–dipole interaction, whereas Raman active modes from the dipole–quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å.

  8. Jet-ISM Interaction in the Radio Galaxy 3C293: Jet-driven Shocks Heat ISM to Power X-ray and Molecular H2 emission

    E-Print Network [OSTI]

    Lanz, Lauranne; Evans, Daniel; Appleton, Philip N; Guillard, Pierre; Emonts, Bjorn

    2015-01-01T23:59:59.000Z

    We present a 70ks Chandra observation of the radio galaxy 3C293. This galaxy belongs to the class of molecular hydrogen emission galaxies (MOHEGs) that have very luminous emission from warm molecular hydrogen. In radio galaxies, the molecular gas appears to be heated by jet-driven shocks, but exactly how this mechanism works is still poorly understood. With Chandra, we observe X-ray emission from the jets within the host galaxy and along the 100 kpc radio jets. We model the X-ray spectra of the nucleus, the inner jets, and the X-ray features along the extended radio jets. Both the nucleus and the inner jets show evidence of 10^7 K shock-heated gas. The kinetic power of the jets is more than sufficient to heat the X-ray emitting gas within the host galaxy. The thermal X-ray and warm H2 luminosities of 3C293 are similar, indicating similar masses of X-ray hot gas and warm molecular gas. This is consistent with a picture where both derive from a multiphase, shocked interstellar medium (ISM). We find that radio-l...

  9. Magnetismo Molecular (Molecular Magentism)

    SciTech Connect (OSTI)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-07-01T23:59:59.000Z

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  10. Light Element Nucleosynthesis in a Molecular Cloud Interacting with a Supernova Remnant and the Origin of Beryllium-10 in the Protosolar Nebula

    E-Print Network [OSTI]

    Tatischeff, Vincent; de Séréville, Nicolas

    2014-01-01T23:59:59.000Z

    The presence of short-lived radionuclides in the early solar system provides important information about the astrophysical environment in which the solar system formed. The discovery of now extinct $^{10}$Be in calcium-aluminum-rich inclusions (CAIs) with Fractionation and Unidentified Nuclear isotope anomalies (FUN-CAIs) suggests that a baseline concentration of $^{10}$Be in the early solar system was inherited from the protosolar molecular cloud. In this paper, we first show that the $^{10}$Be recorded in FUN-CAIs cannot have been produced in situ by cosmic-ray (CR) irradiation of the FUN-CAIs themselves. We then show that trapping of Galactic CRs (GCRs) in the collapsing presolar cloud core induced a negligible $^{10}$Be contamination of the protosolar nebula. Irradiation of the presolar molecular cloud by background GCRs produced a steady-state $^{10}$Be/$^9$Be ratio ~2.3 times lower than the ratio recorded in FUN-CAIs, which suggests that the presolar cloud was irradiated by an additional source of CRs. ...

  11. DOI: 10.1126/science.1134239 , 515 (2007);315Science

    E-Print Network [OSTI]

    Poldrack, Russ

    , Eds. (CRC Press, Boca Raton, FL, 2004), pp. 683­695. 4. A. L. Dawe, D. L. Nuss, Annu. Rev. Genet. 35, 1987 (2001). 14. R. S. Redman, J. C. Ranson, R. J. Rodriguez, Mol. Plant- Microbe Interact. 12, 969

  12. Multielectron effects in high harmonic generation in N_2 and benzene: simulation using a non-adiabatic quantum molecular dynamics approach for laser-molecule interactions

    E-Print Network [OSTI]

    Dundas, Daniel

    2012-01-01T23:59:59.000Z

    A mixed quantum-classical approach is introduced which allows the dynamically response of molecules driven far from equilibrium to be modeled. This method is applied here to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations can be performed. The approach is applied to the study of high harmonic generation in N_2 and benzene using linearly-polarized laser pulses and to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N_2 an enhancement ...

  13. Synthesis, Structure Elucidation, and Redox Properties of [superscript 99]Tc Complexes of Lacunary Wells-Dawson Polyoxometalates: Insights into Molecular [superscript 99]Tc-Metal Oxide Interactions

    SciTech Connect (OSTI)

    McGregor, Donna; Burton-Pye, Benjamin P.; Howell, Robertha C.; Mbomekalle, Israel M.; Lukens, Jr., Wayne W.; Bian, Fang; Mausolf, Edward; Poineau, Frederic; Czerwinski, Kenneth R.; Francesconi, Lynn C. (UNLV); (City U/NY)

    2011-11-17T23:59:59.000Z

    The isotope {sup 99}Tc ({beta}{sub max}, 293.7; half-life, 2.1 x 10{sup 5} years) is an abundant product of uranium-235 fission in nuclear reactors and is present throughout the radioactive waste stored in underground tanks at the Hanford and Savannah River sites. Understanding and controlling the extensive redox chemistry of {sup 99}Tc is important in identifying tunable strategies to separate {sup 99}Tc from spent fuel and from waste tanks and, once separated, to identify and develop an appropriately stable waste form for {sup 99}Tc. Polyoxometalates (POMs), nanometer-sized models for metal oxide solid-state materials, are used in this study to provide a molecular level understanding of the speciation and redox chemistry of incorporated {sup 99}Tc. In this study, {sup 99}Tc complexes of the ({alpha}{sub 2}-P{sub 2}W{sub 17}O{sub 61}){sup 10-} and ({alpha}{sub 1}-P{sub 2}W{sub 17}O{sub 61}){sup 10-} isomers were prepared. Ethylene glycol was used as a 'transfer ligand' to minimize the formation of TcO{sub 2} {center_dot} xH{sub 2}O. The solution structures, formulations, and purity of TcVO({alpha}{sub 1}/{alpha}{sub 2}-P{sub 2}W{sub 17}O{sub 61}){sup 7-} were determined by multinuclear NMR. X-ray absorption spectroscopy of the complexes is in agreement with the formulation and structures determined from {sup 31}P and {sup 183}W NMR. Preliminary electrochemistry results are consistent with the EXAFS results, showing a facile reduction of the TcVO({alpha}{sub 1}-P{sub 2}W{sub 17}O{sub 61}){sup 7-} species compared to the TcVO({alpha}{sub 2}-P{sub 2}W{sub 17}O{sub 61}){sup 7-} analog. The {alpha}{sub 1} defect is unique in that a basic oxygen atom is positioned toward the {alpha}{sub 1} site, and the Tc{sup V}O center appears to form a dative metal-metal bond with a framework W site. These attributes may lead to the assistance of protonation events that facilitate reduction. Electrochemistry comparison shows that the ReV analogs are about 200 mV more difficult to reduce in accordance with periodic trends.

  14. Synthesis, structure elucidation and redox properties of 99Tc complexes of lacunary Wells Dawson polyoxometalates: insights into molecular 99Tc - metal oxide interactions

    SciTech Connect (OSTI)

    McGregor, Donna; Burton-Pye, Benjamin P.; Howell, Robertha C.; Mbomekalle, Israel M.; Lukens Jr, Wayne W.; Bian, Fang; Mausolf, Edward; Poineau, Frederic; Czerwinski, Kenneth R; Francesconi, Lynn C.

    2011-01-10T23:59:59.000Z

    The isotope 99Tc (beta max: 250 keV, half-life: 2 x 105 year) is an abundant product of uranium-235 fission in nuclear reactors and is present throughout the radioactive waste stored in underground tanks at Hanford and Savannah River. Understanding and controlling the extensive redox chemistry of 99Tc is important to identify tunable strategies to separate 99Tc from spent fuel and from waste tanks and once separated, to identify and develop an appropriately stable waste-form for 99Tc. Polyoxometalates (POMs), nanometer sized models for metal oxide solid-state materials, are used in this study to provide a molecular level understanding of the speciation and redox chemistry of incorporated 99Tc. In this study, 99Tc complexes of the (alpha 2-P2W17O61)10- and (alpha 1-P2W17O61)10- isomers were prepared. Ethylene glycol was used as a"transfer ligand" to minimize the formation of TcO2 cdot xH2O. The solution structures, formulations, and purity of TcVO(alpha 1/alpha 2-P2W17O61)7- were determined by multinuclear NMR. X-ray Absorption Spectroscopy of the complexes are in agreement with the formulation and structures determined from 31P and 183W NMR. Preliminary electrochemistry results are consistent with the EXAFS results, showing a facile reduction of the TcVO(alpha 1-P2W17O61)7- species compared to the TcVO(alpha 2-P2W17O61)7- analog. The alpha1- defect is unique in that a basic oxygen atom is positioned toward the alpha1- site and the TcVO center appears to form a dative metal-metal bond with a framework W site. These attributes may lead to the assistance of protonation events that facilitate reduction. Electrochemistry comparison shows that the ReV analogs are about 200 mV more difficult to reduce in accordance with periodic trends.

  15. BE.462J Molecular Principles of Biomaterials, Spring 2003

    E-Print Network [OSTI]

    Irvine, Darrell J.

    Analysis and design at a molecular scale of materials used in contact with biological systems, including biotechnology and biomedical engineering. Topics include molecular interactions between bio- and synthetic molecules ...

  16. Nanostructured gene and drug delivery systems based on molecular self-assembly

    E-Print Network [OSTI]

    Wood, Kris Cameron

    2007-01-01T23:59:59.000Z

    Molecular self-assembly describes the assembly of molecular components into complex, supramolecular structures governed by weak, non-covalent interactions. In recent years, molecular self-assembly has been used extensively ...

  17. New Observations of Extra-Disk Molecular Gas in Interacting Galaxy Systems, Including a Two-Component System in Stephan's Quintet

    E-Print Network [OSTI]

    B. J. Smith; C. Struck

    2000-11-03T23:59:59.000Z

    We present new CO (1 - 0) observations of eleven extragalactic tails and bridges in nine interacting galaxy systems, almost doubling the number of such features with sensitive CO measurements. Eight of these eleven features were undetected in CO to very low CO/HI limits, with the most extreme case being the NGC 7714/5 bridge. This bridge contains luminous H II regions and has a very high HI column density (1.6 X 10^21 cm^-2 in the 55" CO beam), yet was undetected in CO to rms T(R)* = 2.4 mK. The HI column density is higher than standard H2 and CO self-shielding limits for solar-metallicity gas, suggesting that the gas in this bridge is metal-poor and has an enhanced N(H2)/I(CO) ratio compared to the Galactic value. Only one of the eleven features in our sample was unambiguously detected in CO, a luminous HI-rich star formation region near an optical tail in the compact group Stephan's Quintet. We detect CO at two widely separated velocities in this feature, at ~6000 km/s and ~6700 km/s. Both of these components have HI and H-alpha counterparts. These velocities correspond to those of galaxies in the group, suggesting that this gas is material that has been removed from two galaxies in the group. The CO/HI/H-alpha ratios for both components are similar to global values for spiral galaxies.

  18. Photoassociative molecular spectroscopy for atomic radiative lifetimes.

    E-Print Network [OSTI]

    Boyer, Edmond

    very far apart, in so-called long- range molecular states, their mutual interaction is ruled by plain atomic properties. The high- resolution spectroscopic study of some molecular excited states populated by photoassociation of cold atoms (photoassociative spectroscopy) gives a good illustration of this property

  19. Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films

    E-Print Network [OSTI]

    Kim, Bo Hung

    2010-07-14T23:59:59.000Z

    Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the wall-fluid interface...

  20. Syntrophic interactions and mechanisms underpinning anaerobic methane oxidation: targeted metaproteogenomics, single-cell protein detection and quantitative isotope imaging of microbial consortia

    SciTech Connect (OSTI)

    Orphan, Victoria Jeanne [California Institute of Technology

    2014-11-26T23:59:59.000Z

    Syntrophy and mutualism play a central role in carbon and nutrient cycling by microorganisms. Yet, our ability to effectively study symbionts in culture has been hindered by the inherent interdependence of syntrophic associations, their dynamic behavior, and their frequent existence at thermodynamic limits. Now solutions to these challenges are emerging in the form of new methodologies. Developing strategies that establish links between the identity of microorganisms and their metabolic potential, as well as techniques that can probe metabolic networks on a scale that captures individual molecule exchange and processing, is at the forefront of microbial ecology. Understanding the interactions between microorganisms on this level, at a resolution previously intractable, will lead to our greater understanding of carbon turnover and microbial community resilience to environmental perturbations. In this project, we studied an enigmatic syntrophic association between uncultured methane-oxidizing archaea and sulfate-reducing bacteria. This environmental archaeal-bacterial partnership represents a globally important sink for methane in anoxic environments. The specific goals of this project were organized into 3 major tasks designed to address questions relating to the ecophysiology of these syntrophic organisms under changing environmental conditions (e.g. different electron acceptors and nutrients), primarily through the development of microanalytical imaging methods which enable the visualization of the spatial distribution of the partners within aggregates, consumption and exchange of isotopically labeled substrates, and expression of targeted proteins identified via metaproteomics. The advanced tool set developed here to collect, correlate, and analyze these high resolution image and isotope-based datasets from methane-oxidizing consortia has the potential to be widely applicable for studying and modeling patterns of activity and interactions across a broad range of spatially structured microbial partnerships, including other syntrophic associations, microbial mats, biofilms, and plant-microbe or animal-microbe symbioses in nature.

  1. Sandia Energy - Molecular Geochemistry

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

    molecular spectroscopy, and molecular simulation to complex multicomponent and multiphase systems; particular emphasis on the use of molecular simulation and various...

  2. Molecular Science Computing | EMSL

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

    Scientific Capabilities Molecular Science Computing Overview Cell Isolation and Systems Analysis Deposition and Microfabrication Mass Spectrometry Microscopy Molecular Science...

  3. Quantitative molecular graphics what is it? -use of molecular graphics at quantitative level employing high-quality pictures of molecules in various views (orthographic

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    Quantitative molecular graphics ­ what is it? -use of molecular graphics at quantitative level by using quantitative molecular graphics (34) and a priori QSAR (54- 60).2 A STUDY OF HIV-1 PROTEASE-INHIBITOR INTERMOLECULAR INTERACTIONS BY USING QUANTITATIVE MOLECULAR GRAPHICS AND A PRIORI QSAR Rudolf Kiralj and Márcia M

  4. Molecular Foundry

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItemResearch > The EnergyCenterDioxide Capture inFacility AMFInnovationMolecularOne of

  5. Molecular Foundry

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItemResearch > The EnergyCenterDioxide Capture inFacility AMFInnovationMolecularOne

  6. Molecular Foundry

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItemResearch > The EnergyCenterDioxide Capture inFacility AMFInnovationMolecularOneThe

  7. Computational approaches for identifying inhibitors of protein interactions 

    E-Print Network [OSTI]

    Mehio, Wissam

    2011-06-27T23:59:59.000Z

    Inter-molecular interaction is at the heart of biological function. Proteins can interact with ligands, peptides, small molecules, and other proteins to serve their structural or functional purpose. With advances in ...

  8. Molecular Gas in Galaxies

    E-Print Network [OSTI]

    F. Combes

    2000-07-21T23:59:59.000Z

    Knowledge of the molecular component of the ISM is fundamental to understand star formation. The H2 component appears to dominate the gas mass in the inner parts of galaxies, while the HI component dominates in the outer parts. Observation of the CO and other lines in normal and starburst galaxies have questioned the CO-to-H2 conversion factor, and detection of CO in dwarfs have shown how sensitive the conversion f actor is to metallicity. Our knowledge has made great progress in recent years, because of sensitivity and spatial resolution improvements. Large-scale CO maps of nearby galaxies are now available, which extend our knowledge on global properties, radial gradients, and spiral structure of the molecular ISM. Millimetric interferometers reveal high velocity gradients in galaxy nuclei, and formation of embedded structures, like bars within bars. Galaxy interactions are very effective to enhance gas concentrations and trigger starbursts. Nuclear disks or rings are frequently observed, that concentrate the star formation activity. Since the density of starbursting galaxies is strongly increasing with redshift, the CO lines and the mm dust emission are a privileged tool to follow evolution of galaxies and observe the ISM dynamics at high redshift: they could give an answer about the debated question of the star-formation history, since many massive remote starbursts could be dust-enshrouded.

  9. Molecular Science Computing | EMSL

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

    Molecular Science Computing Overview Cell Isolation and Systems Analysis Deposition and Microfabrication Mass Spectrometry Microscopy Molecular Science Computing NMR and EPR...

  10. Physics with fast molecular-ion beams

    SciTech Connect (OSTI)

    Kanter, E.P.

    1980-01-01T23:59:59.000Z

    Fast (MeV) molecular-ion beams provide a unique source of energetic projectile nuclei which are correlated in space and time. The recognition of this property has prompted several recent investigations of various aspects of the interactions of these ions with matter. High-resolution measurements on the fragments resulting from these interactions have already yielded a wealth of new information on such diverse topics as plasma oscillations in solids and stereochemical structures of molecular ions as well as a variety of atomic collision phenomena. The general features of several such experiments will be discussed and recent results will be presented.

  11. Balancing Intermolecular and MoleculeSubstrate Interactions in Supramolecular Assemblies

    E-Print Network [OSTI]

    Ortega, Enrique

    Balancing Intermolecular and Molecule­Substrate Interactions in Supramolecular Assemblies By Dimas of the relevant molecular interactions by the appropriate choice of molecular species in mixed supramolecular for Materials Science 1-1 Namiki, Tsukuba 305-0044 (Japan) Dr. E. Barrena, Prof. H. Dosch ITAP, Universita

  12. Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

    SciTech Connect (OSTI)

    Clabo, D.A. Jr.

    1987-04-01T23:59:59.000Z

    Inclusion of the anharmonicity normal mode vibrations (i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface) is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules.

  13. Molecular Cell Negative Regulation of Vps34

    E-Print Network [OSTI]

    Molecular Cell Article Negative Regulation of Vps34 by Cdk Mediated Phosphorylation Tsuyoshi Furuya Hughes Medical Institute Massachusetts Institute of Technology, Cambridge, MA 02139, USA 5Haldeman interacts with Beclin 1, an ortholog of Atg6 in yeast, to regulate the production of PtdIns3P and autophagy

  14. Molecular information ratchets 

    E-Print Network [OSTI]

    Wilson, Adam Christopher

    2012-11-28T23:59:59.000Z

    In the emerging aield of molecular machines, a molecular ratchet is a chemical system that allows the positional displacement of a submolecular component of be captured and directionally relea ...

  15. 20.462J / 3.962J Molecular Principles of Biomaterials (BE.462J), Spring 2003

    E-Print Network [OSTI]

    Irvine, Darrell J.

    Analysis and design at a molecular scale of materials used in contact with biological systems, including biotechnology and biomedical engineering. Topics include molecular interactions between bio- and synthetic molecules ...

  16. Equilibration of experimentally determined protein structures for molecular dynamics simulation Emily B. Walton and Krystyn J. VanVliet*

    E-Print Network [OSTI]

    Van Vliet, Krystyn J.

    Equilibration of experimentally determined protein structures for molecular dynamics simulation well studied, ranging from refinements of static x-ray crystallog- raphy structures to dynamic Preceding molecular dynamics simulations of biomolecular interactions, the molecule of interest is often

  17. EMSL - Molecular Science Computing

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

    computing Resources and Techniques Molecular Science Computing - Sophisticated and integrated computational capabilities, including scientific consultants, software, Cascade...

  18. QSAR and Molecular Graphics and Modeling Study on Some Novel Artemisinins as Potent Antimalarials

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    QSAR and Molecular Graphics and Modeling Study on Some Novel Artemisinins as Potent Antimalarials artemisinins was performed by means of quantum chemical, chemometric and molecular graphics and modeling-heme complex properties and heme-artemisinin interaction -> QSAR study, molecular graphics and modeling, other

  19. Calculation of molecular free energies in classical potentials

    E-Print Network [OSTI]

    Farhi, Asaf

    2015-01-01T23:59:59.000Z

    Free energy calculations in molecular simulations are used to predict the strength of molecular processes such as binding and solvation. We present an accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms that depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non interacting systems, the free energy associated with these atoms is analytically or numerically calculated. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.

  20. Dynamics of molecular superrotors in external magnetic field

    E-Print Network [OSTI]

    Korobenko, Aleksey

    2015-01-01T23:59:59.000Z

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to the qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane in three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

  1. Molecular electrostatic potentials by systematic molecular fragmentation

    SciTech Connect (OSTI)

    Reid, David M.; Collins, Michael A. [Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia)] [Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia)

    2013-11-14T23:59:59.000Z

    A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.

  2. Interactive Environments

    E-Print Network [OSTI]

    project assignment of an interactive social space, built up from autonomously operating smart building, interactive spaces in which people and buildings engage in a mutual relationship with one other. By connecting the data and experiences that develop though this relationship between buildings and their inhabitants

  3. Closed-orbit recurrences in molecular hydrogen

    SciTech Connect (OSTI)

    Wright, J. D.; DiSciacca, J. M.; Lambert, J. M.; Morgan, T. J. [Department of Physics, Wesleyan University, Middletown, Connecticut 06459 (United States)

    2010-06-15T23:59:59.000Z

    Using scaled-energy Stark spectroscopy, we report the observation of recurrences due to closed orbits, both geometric and diffractive, in the {nu}=0, R=1, nd Rydberg series of H{sub 2} (16interacting with the {nu}=0, R=3 series (13molecular closed-orbit theory prediction of diffractive trajectories due to inelastic scattering of the excited electron on the molecular core. We have made similar measurements in He, and a comparison between the recurrence properties of H{sub 2} and its united atom equivalent is given.

  4. Computational modeling of protein-biomolecule interactions with application to mechanotransduction and antibody maturation

    E-Print Network [OSTI]

    Zyto, Aurore

    2008-01-01T23:59:59.000Z

    Cell survival, growth, differentiation, migration, and communication all depend on the appropriate combination of specific interactions between proteins and biomolecules. Therefore, understanding the molecular mechanisms ...

  5. Atomic and molecular supernovae

    SciTech Connect (OSTI)

    Liu, W.

    1997-12-01T23:59:59.000Z

    Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

  6. developments. interactive

    E-Print Network [OSTI]

    Jaun, André

    interactive course: ffl web­pages for hyper­linked lecture notes, student exercises and projects, ffl java teachers: ffl public on the web y : lecture notes including the JBONE applet, ffl on demand: source Java

  7. Graduate Programs in Plant Biology and

    E-Print Network [OSTI]

    Wildermuth, Mary C

    not re- biochemistry, cell and molecular biology (B22). pmb.berkeley.edu Plant&Microbial Biology #12;The to the environment will continue to fuel the expansion of plant research well into the future. The plant biology program focuses on contemporary ba- sic plant research, design of biotechnologies, and plant-microbe

  8. Molecular Cluster Perturbation Theory. I. Formalism

    E-Print Network [OSTI]

    Jason N. Byrd; Nakul Jindal; Robert W. Molt, Jr.; Rodney J. Bartlett; Beverly A. Sanders; Victor F. Lotrich

    2015-03-23T23:59:59.000Z

    We present second-order molecular cluster perturbation theory (MCPT(2)), a linear scaling methodology to calculate arbitrarily large systems with explicit calculation of individual wavefunctions in a coupled-cluster framework. This new MCPT(2) framework uses coupled-cluster perturbation theory and an expansion in terms of molecular dimer interactions to obtain molecular wavefunctions that are infinite-order in both the electronic fluctuation operator and all possible dimer (and products of dimers) interactions. The MCPT(2) framework has been implemented in the new SIA/Aces4 parallel architecture, making use of the advanced dynamic memory control and fine grained parallelism to perform very large explicit molecular cluster calculations. To illustrate the power of this method, we have computed energy shifts, lattice site dipole moments, and harmonic vibrational frequencies via explicit calculation of the bulk system for the polar and non-polar polymorphs of solid hydrogen fluoride. The explicit lattice size (without using any periodic boundary conditions) was expanded up to 1,000 HF molecules, with 32,000 basis functions and 10,000 electrons. Our obtained HF lattice site dipole moments and harmonic vibrational frequencies agree well with the existing literature.

  9. Molecular Cluster Perturbation Theory. I. Formalism

    E-Print Network [OSTI]

    Jason N. Byrd; Nakul Jindal; Robert W. Molt, Jr.; Rodney J. Bartlett; Beverly A. Sanders; Victor F. Lotrich

    2015-01-14T23:59:59.000Z

    We present second-order molecular cluster perturbation theory (MCPT(2)), a linear scaling methodology to calculate arbitrarily large systems with explicit calculation of individual wavefunctions in a coupled-cluster framework. This new MCPT(2) framework uses coupled-cluster perturbation theory and an expansion in terms of molecular dimer interactions to obtain molecular wavefunctions that are infinite-order in both the electronic fluctuation operator and all possible dimer (and products of dimers) interactions. The MCPT(2) framework has been implemented in the new SIA/ACES parallel architecture, making use of the advanced dynamic memory control and fine grained parallelism to perform very large explicit molecular cluster calculations. To illustrate the power of this method, we have computed energy shifts and lattice site dipole moments via explicit calculation of the bulk system for the polar and non-polar polymorphs of solid hydrogen fluoride. The explicit lattice size without periodic boundary conditions was expanded up to 1,000 HF molecules, with 32,000 basis functions and 10,000 electrons. Our obtained HF lattice site dipole moments and harmonic vibrational frequencies agree well with the existing literature.

  10. DEPARTAMENTO DE BIOMEDICINA MOLECULAR

    E-Print Network [OSTI]

    . Estudio celular y mo- lecular de malaria maternal. rohernan@mail.cinvestav.mx ÍndiceÍndiceÍndice #12 (1994) Cinvestav. Temas de investigación: Estudio molecular y celular de las proteínas involucradas en el patogénesis de la amibiasis y caracterización molecular de la motilidad celular en Entamoeba

  11. Complex Interplay and Hierarchy of Interactions in Two-Dimensional

    E-Print Network [OSTI]

    Brune, Harald

    Complex Interplay and Hierarchy of Interactions in Two-Dimensional Supramolecular Assemblies Marta, Freiestrasse 3, 3012 Bern, Switzerland, and Empa, Swiss Federal Laboratories for Materials Science potential implementation of self- assembled supramolecular struc- tures in molecular electronic devices asks

  12. Computational methods for molecular docking

    SciTech Connect (OSTI)

    Klebe, G. [BASF AG, Ludwigshafen (Germany); Lengauer, T.

    1995-12-31T23:59:59.000Z

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Recently, it has been demonstrated that the knowledge of the three-dimensional structure of the protein can be used to derive new protein ligands with improved binding properties. This tutorial focuses on the following questions: What is its binding affinity toward a particular receptor? What are putative conformations of a ligand at the binding site? What are the similarities of different ligands in terms of their recognition capabilities? Where and in which orientation will a ligand bind to the active site? How is a new putative protein ligand selected? An overview is presented of the algorithms which are presently used to handle and predict protein-ligand interactions and to dock small molecule ligands into proteins.

  13. Radiation in molecular dynamic simulations

    SciTech Connect (OSTI)

    Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M

    2008-10-13T23:59:59.000Z

    Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.

  14. Title of Document: INTERACTION OF INTENSE SHORT LASER PULSES WITH GASES OF NANOSCALE

    E-Print Network [OSTI]

    Anlage, Steven

    ABSTRACT Title of Document: INTERACTION OF INTENSE SHORT LASER PULSES WITH GASES OF NANOSCALE-cluster interaction. #12;INTERACTION OF INTENSE SHORT LASER PULSES WITH GASES OF NANOSCALE ATOMIC AND MOLECULAR., Department of Electrical and Computer Engineering We study the interaction of intense laser pulses with gases

  15. Molecular heat pump

    E-Print Network [OSTI]

    Dvira Segal; Abraham Nitzan

    2005-10-11T23:59:59.000Z

    We propose a novel molecular device that pumps heat against a thermal gradient. The system consists of a molecular element connecting two thermal reservoirs that are characterized by different spectral properties. The pumping action is achieved by applying an external force that periodically modulates molecular levels. This modulation affects periodic oscillations of the internal temperature of the molecule and the strength of its coupling to each reservoir resulting in a net heat flow in the desired direction. The heat flow is examined in the slow and fast modulation limits and for different modulation waveforms, thus making it possible to optimize the device performance.

  16. Asymptotic Analysis of Cooperative Molecular Motor System

    E-Print Network [OSTI]

    Durrett, Richard

    Mesoscale Model for Collections of Molecular Motors Stochastic Asymptotic Techniques #12;Molecular Motors

  17. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

    SciTech Connect (OSTI)

    Nakata, Hiroya [Tokyo Institute of Technology; Schmidt, Michael W [Ames Laboratory; Fedorov, Dmitri G [National Institute of Advanced Industrial Science and Technology (AIST); Kitaura, Kazuo [Kobe University; Nakamura, Shinichiro [Nakamura Lab; Gordon, Mark S [Ames Laboratory

    2014-10-16T23:59:59.000Z

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  18. Outflow Driven Turbulence in Molecular Clouds

    E-Print Network [OSTI]

    Jonathan J. Carroll; Adam Frank; Eric G. Blackman; Andrew J. Cunningham; Alice C. Quillen

    2008-05-30T23:59:59.000Z

    In this paper we explore the relationship between protostellar outflows and turbulence in molecular clouds. Using 3-D numerical simulations we focus on the hydrodynamics of multiple outflows interacting within a parsec scale volume. We explore the extent to which transient outflows injecting directed energy and momentum into a sub-volume of a molecular cloud can be converted into random turbulent motions. We show that turbulence can readily be sustained by these interactions and show that it is possible to broadly characterize an effective driving scale of the outflows. We compare the velocity spectrum obtained in our studies to that of isotropically forced hydrodynamic turbulence finding that in outflow driven turbulence a power law is indeed achieved. However we find a steeper spectrum (beta ~ 3) is obtained in outflow driven turbulence models than in isotropically forced simulations (beta ~ 2). We discuss possible physical mechanisms responsible for these results as well and their implications for turbulence in molecular clouds where outflows will act in concert with other processes such as gravitational collapse.

  19. Interactive Jobs

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)Integrated Codes | National Nuclear SecurityIntellectual PropertyIntensityInteractive

  20. Molecular gas and the dynamics of galaxies

    E-Print Network [OSTI]

    F. Combes

    1999-02-01T23:59:59.000Z

    In this review, I discuss some highlights of recent research on molecular gas in galaxies; large-scale CO maps of nearby galaxies are being made, which extend our knowledge on global properties, radial gradients, and spiral structure of the molecular ISM. Very high resolution are provided by the interferometers, that reveal high velocity gradients in galaxy nuclei, and formation of embedded structures, like bars within bars. Observation of the CO and other lines in starburst galaxies have questioned the H2-to-CO conversion factor. Surveys of dwarfs have shown how the conversion factor depends on metallicity. The molecular content is not deficient in galaxy clusters, as is the atomic gas. Galaxy interactions are very effective to enhance gas concentrations and trigger starbursts. Nuclear disks or rings are frequently observed, that concentrate the star formation activity. Since the density of starbursting galaxies is strongly increasing with redshift, the CO lines are a privileged tool to follow evolution of galaxies and observe the ISM dynamics at high redshift: due to the high excitation of the molecular gas, the stronger high-$J$ CO lines are redshifted into the observable band, which facilitates the detection.

  1. The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Pan, Jianjun [University of South Florida, Tampa (USF)] [University of South Florida, Tampa (USF); Cheng, Xiaolin [ORNL] [ORNL; Monticelli, Luca [Institut National de la Santé et de la Recherche Médicale (INSERM) and INTS, France] [Institut National de la Santé et de la Recherche Médicale (INSERM) and INTS, France; Heberle, Frederick A [ORNL] [ORNL; Kucerka, Norbert [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,] [Atomic Energy of Canada Limited (AECL), Canadian Neutron Beam Centre (CNBC) and Comenius University,; Tieleman, D. Peter [University of Calgary, ALberta, Canada] [University of Calgary, ALberta, Canada; Katsaras, John [ORNL] [ORNL

    2014-01-01T23:59:59.000Z

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  2. Molecular Interactions of Plutonium(VI) with SyntheticManganese...

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

    on the surface of well-characterized synthetic manganese-substituted goethite minerals (Fe1-xMnxOOH) was studied using X-ray absorption spectroscopy. We chose to study the...

  3. Twelfth Annual Report Interactive Graphics for Molecular Studies

    E-Print Network [OSTI]

    North Carolina at Chapel Hill, University of

    of individual researchers through better tools. Facilities used by the project include: o VAX-11/780 · the UNIX operating system (Berkeley 4.2 bsd version for the VAX) · 4MB memory · 600 MB disk storage 7 #12;RR 02170 sensor · Ethernet link to department VAX, which has hard copy plotters, printer, and a dial-up con

  4. Molecular conformations, interactions, and properties associated with drug

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)Integrated Codes |IsLove Your1 SECTION A.ModelAlyssaReceptorinCenter

  5. MOLECULARPHYSICS, 1981, VOL. 43, No. 5, 1035-1041 Surface tension of a molecular fluid

    E-Print Network [OSTI]

    Grant, Martin

    MOLECULARPHYSICS, 1981, VOL. 43, No. 5, 1035-1041 Surface tension of a molecular fluid Many body for surface tension in a dense molecular fluid with an arbitrary many body interaction. This formula reduces. These last two expressions are analogous to the simple fluid surface tension for- mulas of Jhon, Desai

  6. Interactive Topic Modeling

    E-Print Network [OSTI]

    Pleple, Quentin

    26 Interactive LDA . . . . . . . . . . . . . . . .and B. Satinoff (2011). Interactive topic modeling. InOF CALIFORNIA, SAN DIEGO Interactive Topic Modeling A thesis

  7. Substructured multibody molecular dynamics.

    SciTech Connect (OSTI)

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01T23:59:59.000Z

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  8. Molecular Combinatory Computing for Nanostructure Synthesis and Control

    E-Print Network [OSTI]

    Wang, Xiaorui "Ray"

    sufficient for controlling the nanoscale synthesis and behavior of materials. To accomplish this we have made suggestive of supramolecular interactions. This theory shows that two simple substitution operations (known. OVERVIEW Molecular combinatory programs are supramolecular struc­ tures in the form of binary trees

  9. Molecular dynamics simulation of Li surface erosion and bubble formation

    E-Print Network [OSTI]

    Harilal, S. S.

    .49.Sf Keywords: Liquid metal; Lithium; Ion-surface interactions 1. Introduction Bombardment Structure and dynamical properties of liquid Li containing He atoms were studied by the Molecular Dynamics characteristics of light low-energy ions on a liquid Li surface and their diffusion properties have attracted much

  10. Molecular Cell Apollo Contributes to G Overhang Maintenance

    E-Print Network [OSTI]

    de Lange, Titia

    Molecular Cell Article Apollo Contributes to G Overhang Maintenance and Protects Leading to mediate telomere protec- tion. Here we identify the TRF2-interacting factor Apollo as a nuclease that contributes to the genera- tion/maintenance of this overhang. The function of mouse Apollo was determined

  11. (Quantum Molecular Dynamics Method) (Classical Molecular Dynamics Method)

    E-Print Network [OSTI]

    Maruyama, Shigeo

    1-1 (Quantum Molecular Dynamics Method) (Classical Molecular Dynamics Method) 2) Verlet(Verlet's leap frog) (17)(18) ( ) i i ii m t t t t t t F vv + -= + 22 (17

  12. Molecular Gas in Early-type Galaxies

    E-Print Network [OSTI]

    Alatalo, Katherine Anne

    2012-01-01T23:59:59.000Z

    toward the center (first seen in the molecular gas in A+3.4 Molecular Gas Mass . . . . . . .of the molecular gas . . . . . . . . . . 2.4.3 Mass of

  13. B13+: Photodriven Molecular Wankel Engine. | EMSL

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

    B13+: Photodriven Molecular Wankel Engine. B13+: Photodriven Molecular Wankel Engine. Abstract: Synthetic molecular motors that are capable of delivering controlled movement upon...

  14. Molecular Biology DEGREE PROGRAMME

    E-Print Network [OSTI]

    Levi, Ran

    to the course co-ordinator for that module (See University Catalogue of Courses or SMS World Wide Web Pages in molecular biology have a wide range of career options, including virtually all areas of biology, medicine with mastering statistics, graphics and word processing software packages. General Enquiries The Degree Programme

  15. 2007 Archaea: Ecology, Metabolism and Molecular Biology

    SciTech Connect (OSTI)

    Imke Schroeder

    2008-09-18T23:59:59.000Z

    The Archaea are a fascinating and diverse group of prokaryotic organisms with deep roots overlapping those of eukaryotes. The focus of this GRC conference, 'Archaea: Ecology Metabolism & Molecular Biology', expands on a number of emerging topics highlighting the evolution and composition of microbial communities and novel archaeal species, their impact on the environment, archaeal metabolism, and research that stems from sequence analysis of archaeal genomes. The strength of this conference lies in its ability to couple reputable areas with new scientific topics in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  16. FPGA Acceleration of Discrete Molecular Dynamics Simulation

    E-Print Network [OSTI]

    Herbordt, Martin

    ' & $ % FPGA Acceleration of Discrete Molecular Dynamics Simulation Joshua Model Thesis submitted UNIVERSITY COLLEGE OF ENGINEERING Thesis FPGA Acceleration of Discrete Molecular Dynamics Simulation Acceleration of Discrete Molecular Dynamics Simulation Joshua Model ABSTRACT Molecular dynamics simulation

  17. A simple theory of molecular organization in fullerene containing liquid crystals

    E-Print Network [OSTI]

    S. D. Peroukidis; A. G. Vanakaras; D. J. Photinos

    2005-01-10T23:59:59.000Z

    Systematic efforts to synthesise fullerene containing LCs have produced a variety of successful model compounds. We present a simple molecular theory relating the self-organisation observed in these systems to their molecular structure. The interactions are modelled by dividing each molecule into a number of sub-molecular blocks to which specific interactions are assigned. Three types of blocks are introduced, corresponding to fullerene units, mesogenic units, and non-mesogenic linkage units. The blocks are constrained to move on a rectangular 3-dimensional lattice and molecular flexibility is allowed by retaining a number of representative conformations within the block representation of the molecule. Calculations are presented for a variety of molecular architectures including twin mesogenic branch mono-adducts of C60, twin dendro-mesogenic branch mono-adducts and conical (badminton shuttlecock) multi-adducts of C60. In spite of its many simplifications, the theory accounts remarkably well for the phase behaviour of these systems.

  18. Photoelectron Angular Distribution and Molecular Structure in...

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

    Angular Distribution and Molecular Structure in Multiply Charged Anions. Photoelectron Angular Distribution and Molecular Structure in Multiply Charged Anions. Abstract:...

  19. Noble gas temperature control of metal clusters: A molecular dynamics study

    E-Print Network [OSTI]

    Noble gas temperature control of metal clusters: A molecular dynamics study Jan Westergren a noble gas atmosphere. The simulations are performed using a many-body interaction scheme for the intra-cluster potential, while a pairwise Lennard-Jones potential is used to model the interaction between the noble gas

  20. Atomistic modeling of dislocation-interface interactions

    SciTech Connect (OSTI)

    Wang, Jian [Los Alamos National Laboratory; Valone, Steven M [Los Alamos National Laboratory; Beyerlein, Irene J [Los Alamos National Laboratory; Misra, Amit [Los Alamos National Laboratory; Germann, T. C. [Los Alamos National Laboratory

    2011-01-31T23:59:59.000Z

    Using atomic scale models and interface defect theory, we first classify interface structures into a few types with respect to geometrical factors, then study the interfacial shear response and further simulate the dislocation-interface interactions using molecular dynamics. The results show that the atomic scale structural characteristics of both heterophases and homophases interfaces play a crucial role in (i) their mechanical responses and (ii) the ability of incoming lattice dislocations to transmit across them.

  1. Interactive portraiture : designing intimate interactive experiences

    E-Print Network [OSTI]

    Zuckerman, Orit

    2006-01-01T23:59:59.000Z

    In this thesis I present a set of interactive portrait experiences that strive to create an intimate connection between the viewer and the portrayed subject; an emotional experience, one of personal reflection. My interactive ...

  2. PDSF Interactive Nodes

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

    Interactive (login) Nodes Interactive (login) Nodes There are 3 interactive nodes at PDSF, pdsf6-8.nersc.gov, that should be accessed via ssh to pdsf.nersc.gov. These are the...

  3. Interactivity and Emotion Cinematography

    E-Print Network [OSTI]

    Tomlinson, Bill

    Interactivity and Emotion through Cinematography by William Michael Tomlinson, Jr. M #12;Interactivity and Emotion through Cinematography by William Michael Tomlinson, Jr. Submitted cinematography system for an interactive virtual environment. This system controls a virtual camera and several

  4. PDSF Interactive Batch Jobs

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

    Interactive Batch Jobs Running Interactive Batch Jobs You cannot login to the PDSF batch nodes directly but you can run an interactive session on a batch node using either qlogin...

  5. Sandia Energy - Molecular Geochemistry

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del Sol Home Distribution Grid Integration Permalink Gallery Mesa delMissionMolecular

  6. Assessment of Molecular Modeling & Simulation

    SciTech Connect (OSTI)

    None

    2002-01-03T23:59:59.000Z

    This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.

  7. QSAR of Progestogens: Use of a Priori and Computed Molecular Descriptors and Molecular Graphics

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    QSAR of Progestogens: Use of a Priori and Computed Molecular Descriptors and Molecular Graphics) and molecular graphics and modeling descriptors were employed. Mo- lecular graphics and modeling studies

  8. Self assembled molecular monolayers on high surface area materials as molecular getters

    DOE Patents [OSTI]

    King, D.E.; Herdt, G.C.; Czanderna, A.W.

    1997-01-07T23:59:59.000Z

    The present invention relates to a gettering material that may be used as a filtration medium to remove pollutants from the environment. The gettering material comprises a high surface area material having a metal surface that chemically bonds n-alkanethiols in an organized manner thereby forming a molecular monolayer over the metal surface. The n-alkanethiols have a free functional group that interacts with the environment thereby binding specific pollutants that may be present. The gettering material may be exposed to streams of air in heating, ventilation, and air conditioning systems or streams of water to remove specific pollutants from either medium. 9 figs.

  9. Self assembled molecular monolayers on high surface area materials as molecular getters

    DOE Patents [OSTI]

    King, David E. (Lakewood, CO); Herdt, Gregory C. (Denver, CO); Czanderna, Alvin W. (Denver, CO)

    1997-01-01T23:59:59.000Z

    The present invention relates to a gettering material that may be used as a filtration medium to remove pollutants from the environment. The gettering material comprises a high surface area material having a metal surface that chemically bonds n-alkanethiols in an organized manner thereby forming a molecular monolayer over the metal surface. The n-alkanethiols have a free functional group that interacts with the environment thereby binding specific pollutants that may be present. The gettering material may be exposed to streams of air in heating, ventilation, and air conditioning systems or streams of water to remove specific pollutants from either medium.

  10. Exploring the Environmental Preference of Weak Interactions in ( / )8 Barrel Proteins

    E-Print Network [OSTI]

    Babu, M. Madan

    Exploring the Environmental Preference of Weak Interactions in ( / )8 Barrel Proteins S of Biotechnology and Chemical Engineering, Vellore Institute of Technology, Vellore, India 2 MRC Laboratory of Molecular Biology, Cambridge, United Kingdom 3 National Center for Biotechnology Information, National

  11. Quantum information analysis of electronic states at different molecular structures

    E-Print Network [OSTI]

    G. Barcza; Ö. Legeza; K. H. Marti; M. Reiher

    2010-08-26T23:59:59.000Z

    We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization. We also discuss the application of the configuration interaction based dynamically extended active space procedure which significantly reduces the effective system size and accelerates the speed of convergence for complicated molecular electronic structures to a great extent. Our results indicate the importance of taking entanglement among molecular orbitals into account in order to devise an optimal orbital ordering and carry out efficient calculations on transition metal clusters. We propose a recipe to perform DMRG calculations in a black-box fashion and we point out the connections of our work to other tensor network state approaches.

  12. Large-Scale Molecular Dynamics Simulations for Highly Parallel Infrastructures

    E-Print Network [OSTI]

    Pazúriková, Jana

    2014-01-01T23:59:59.000Z

    Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body problem of atoms$-$it computes movements of atoms according to Newtonian physics and empirical descriptions of atomic electrostatic interactions. These simulations require high performance computing resources, as evaluations within each step are computationally demanding and billions of steps are needed to reach interesting timescales. Current methods decompose the spatial domain of the problem and calculate on parallel/distributed infrastructures. Even the methods with the highest strong scaling hit the limit at half a million cores: they are not able to cut the time to result if provided with more processors. At the dawn of exascale computing with massively parallel computational resources, we want to increase the level of parallelism by incorporating parallel-in-time comput...

  13. Collective dynamics of molecular motors pulling on fluid membranes

    E-Print Network [OSTI]

    O. Campas; Y. Kafri; K. B. Zeldovich; J. Casademunt; J. -F. Joanny

    2005-12-08T23:59:59.000Z

    The collective dynamics of $N$ weakly coupled processive molecular motors are considered theoretically. We show, using a discrete lattice model, that the velocity-force curves strongly depend on the effective dynamic interactions between motors and differ significantly from a simple mean field prediction. They become essentially independent of $N$ if it is large enough. For strongly biased motors such as kinesin this occurs if $N\\gtrsim 5$. The study of a two-state model shows that the existence of internal states can induce effective interactions.

  14. Molecular dynamics of gas phase hydrogen-bonded complexes

    E-Print Network [OSTI]

    Wofford, Billy Alan

    1987-01-01T23:59:59.000Z

    . These analyses have permitted the calculation of an approximate stretching harmonic force field for the hydrogen-bound heterodimer HCN---HF. In addition, a new technique is developed to determine both the ground state and equilibrium dissociation energies... OF FIGURES. CHAPTER I. INTRODUCTION. CHAPTER II. MOLECULAR DYNAMICS IN HYDROGEN-BONDED INTERACTIONS: A PRELIMINARY EXPERIMENTALLY DETERMINED HARMONIC STRETCHING FORCE FIELD FOR HCN---HF. Introduction. Experimental Calculations. 10 Discussion. 19...

  15. Fluorescence of molecular excimers

    SciTech Connect (OSTI)

    Nurmukhametov, R.N.; Sakhno, T.V.; Saukov, G.G.; Khakhel, O.A. [L. Ya. Karpov Research Physiochemical Institute, Moscow (Russian Federation)

    1995-11-01T23:59:59.000Z

    The phenomena of excimer fluorescence are most thoroughly studied in solutions of polycyclic aromatic hydrocarbons (PAHs). Therefore, excimer formation is usually treated with reference to molecules of this class of compounds. In the literature, only a qualitative picture of the energetics of excimer formation is given. It is assumed that dimerization of electron-excited and unexcited molecules is followed by the splitting of molecular electron-excited levels. PAH molecules are characterized by two lower excited levels: {sup 1}L{sub a} and {sup 1}L{sub b} (according to Platt`s classification). The S{sub 1}* state of some PAH compounds (e.g., naphthalene, phenanthrene, pyrene) is {sup 1}L{sub b}, while in other PAH (anthracene, naphthacene, perylene, etc.) it is the {sup 1}L{sub a} state. It is assumed that the {sup 1}L{sub a}-level is split more significantly than the {sup 1}L{sub b} level. Therefore, for all PAH investigated the excimer state is described as a lower-lying component of the split {sup 1}L{sub a} level. Quantum-chemical consideration of the splitting of electron levels of PAH molecules in excimers is undertaken. Unfortunately, in this case the description is also of a qualitative character. In the cited work, a correlation is noted between the energy of the {sup 1}L{sub a} state of the molecule and the wave number corresponding to the maximum of the emission band of the excimer. However, it does not give the wavelength of the maximum of the excimer band for some PAH, in other words, a definite dependence of the position of this band on molecular structure. The present work is devoted to a search for an answer to this question.

  16. Interactive Software Technology 1/24 Interactive Software Technology

    E-Print Network [OSTI]

    Wegner, Peter

    Interactive Software Technology 1/24 Interactive Software Technology Peter Wegner, Brown University Paradigms 2. Models of Interaction 3. Software Engineering, Artificial Intelligence, and Open Systems 4. Object­oriented Design: Sequential Interaction 5. Multiple Interface Models: Concurrent Interaction 6

  17. Molecular Weight & Energy Transport 7 September 2011

    E-Print Network [OSTI]

    Militzer, Burkhard

    't transport the bulk of the energy in the sun. #12;Molecular Weight & Energy Transport 7 September 2011 Goals · Review mean molecular weight this intuitively before looking back at your quantitative results. #12;molecular weight & energy transport 2 Energy

  18. Transition metal complex-based molecular machines 

    E-Print Network [OSTI]

    Sooksawat, Dhassida

    2015-06-30T23:59:59.000Z

    Inspired by the performance and evolutionarily-optimised natural molecular machines that carry out all the essential tasks contributing to the molecular basis of life, chemists aim towards fabricating synthetic molecular ...

  19. A search for molecular gas in restarting radio galaxies

    E-Print Network [OSTI]

    Lakshmi Saripalli; Karl-Heinz Mack

    2007-02-14T23:59:59.000Z

    Several radio galaxies are known that show radio morphological signatures that are best interpreted as restarting of nuclear activity after a period of quiescence. The conditions surrounding the phenomenon of nuclear recurrence are not understood. In this paper we have attempted to address this question by examining the nuclear fuelling characteristics in a sample of restarting radio galaxies. We have examined the detection rate for molecular gas in a representative sample of nine restarting radio galaxies, for seven of which we present new upper limits to the molecular gas mass derived from CO line observations we made with the IRAM 30-m telescope. We derive a low CO detection rate for the relatively young restarted radio galaxies suggesting that the cessation of the nuclear activity and its subsequent restarting may be a result of instabilities in the fuelling process rather than a case of depletion of fuel followed by a recent fuel acquisition. It appears that abundant molecular gas content at the level of few 10^8 to 10^9 solar masses does not necessarily accompany the nuclear restarting phenomenon. For comparison we also discuss the molecular gas properties of five normal giant radio galaxies, three of which we observed using SEST. Despite obvious signs of interactions and nuclear dust disks none of them has been found to host significant quantities of molecular gas.

  20. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    SciTech Connect (OSTI)

    Dr. Julie Maupin- Furlow

    2009-07-26T23:59:59.000Z

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  1. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    SciTech Connect (OSTI)

    Keneth Stedman

    2011-08-05T23:59:59.000Z

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  2. Coordinated Research Projects of the IAEA Atomic and Molecular Data Unit

    SciTech Connect (OSTI)

    Braams, B. J.; Chung, H.-K. [Nuclear Data Section, NAPC Division, International Atomic Energy Agency, P. O. Box 100, Vienna International Centre, A-1400 Vienna (Austria)

    2011-05-11T23:59:59.000Z

    The IAEA Atomic and Molecular Data Unit is dedicated to the provision of databases for atomic, molecular and plasma-material interaction (AM/PMI) data that are relevant for nuclear fusion research. IAEA Coordinated Research Projects (CRPs) are the principal mechanism by which the Unit encourages data evaluation and the production of new data. Ongoing and planned CRPs on AM/PMI data are briefly described here.

  3. Junction Plasmon-Induced Molecular Reorientation. | EMSL

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

    Junction Plasmon-Induced Molecular Reorientation. Junction Plasmon-Induced Molecular Reorientation. Abstract: Time and frequency dependent intensity variations in sequences of...

  4. Protein Structure Suggests Role as Molecular Adapter

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

    Protein Structure Suggests Role as Molecular Adapter Print To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the...

  5. Conformational Transitions in Molecular Systems

    E-Print Network [OSTI]

    Michael Bachmann; Wolfhard Janke

    2009-02-17T23:59:59.000Z

    Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

  6. Spring 2014 SWS6932 SPRING 2014

    E-Print Network [OSTI]

    Ma, Lena

    ) Biodiversity ­ functional diversity versus species or genetic diversity Plant-microbe feedbacks Carbon storage/sequestration

  7. Interaction, protection and epidemics

    E-Print Network [OSTI]

    Goyal, Sanjeev; Vigier, Adrien

    2015-03-06T23:59:59.000Z

    unique equilibrium: individuals who invest in protection choose to interact more relative to those who do not invest in protection. Changes in the contagiousness of the disease have non-monotonic effects: as a result interaction initially falls...

  8. 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

    2015-03-04T23:59:59.000Z

    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

  9. 1 SCIENTIFIC HIGHLIGHT OF THE MONTH Many-Body van der Waals Interactions

    E-Print Network [OSTI]

    W interactions play a central role in the fields of supramolecular chemistry and nano-materials, in which non" supramolecular host­guest complex, and cohesion in oligoacene molecular crystals. We find that the beyond) methods for treating many-body vdW interactions in complex materials. 1 Introduction The relevance of van

  10. 2004 Electron Donor Acceptor Interactions Gordon Conference - August 8-13, 2004

    SciTech Connect (OSTI)

    GUILFORD JONES

    2005-09-14T23:59:59.000Z

    The 2004 Gordon Conference on Donor/Acceptor Interactions will take place at Salve Regina University in Newport, Rhode Island on August 8-13, 2004. The conference will be devoted to the consequences of charge interaction and charge motion in molecular and materials systems.

  11. Atomic hydrogen interactions with amorphous carbon thin films Bhavin N. Jariwala,1

    E-Print Network [OSTI]

    Ciobanu, Cristian

    Atomic hydrogen interactions with amorphous carbon thin films Bhavin N. Jariwala,1 Cristian V-scale interactions of H atoms with hydrogenated amorphous carbon a-C:H films were identified using molecular dynamics through a detailed analysis of the MD trajectories. The MD simulations showed that hydrogenation occurs

  12. Molecular biomechanics of collagen molecules

    E-Print Network [OSTI]

    Chang, Shu-Wei

    Collagenous tissues, made of collagen molecules, such as tendon and bone, are intriguing materials that have the ability to respond to mechanical forces by altering their structures from the molecular level up, and convert ...

  13. Molecular Gas in Quasar Hosts

    E-Print Network [OSTI]

    Richard Barvainis

    1997-01-29T23:59:59.000Z

    The study of molecular gas in quasar host galaxies addresses a number of interesting questions pertaining to the hosts' ISM, to unified schemes relating quasars and IR galaxies, and to the processes fueling nuclear activity. In this contribution I review observations of molecular gas in quasar hosts from z=0.06 to z=4.7. The Cloverleaf quasar at z=2.5 is featured as a case where there are now enough detected transitions (four in CO, and one each in CI and HCN) to allow detailed modeling of physical conditions in the molecular ISM. We find that the CO-emitting gas is warmer, denser, and less optically thick than that found in typical Galactic molecular clouds. These differences are probably due to the presence of the luminous quasar in the nucleus of the Cloverleaf's host galaxy.

  14. Interaction of Polycrystalline CVD

    E-Print Network [OSTI]

    Adler, Joan

    Interaction of Polycrystalline CVD Diamond Thin Films with Atomic Oxygen Ze'ev Shpilman #12;#12;Interaction of Polycrystalline CVD Diamond Thin Films with Atomic Oxygen Research thesis In Partial.................................................................... 6 1.2.1 Polycrystalline CVD diamond films: growth and structure 7 1.3. Interaction of carbon

  15. Understanding nanofluid stability through molecular simulation

    SciTech Connect (OSTI)

    Dang, Liem X.; Annapureddy, Harsha V.; Sun, Xiuquan; Thallapally, Praveen K.; McGrail, B. Peter

    2012-11-01T23:59:59.000Z

    We performed molecular dynamics simulations to study solvation of a nanoparticle and nanoparticle-nanoparticle interactions in an n-hexane solution. Structural signatures are barely observed between the nanoparticle and n-hexane molecules because of weak binding and steric effects. The dynamic properties of the n-hexane molecule, on the other hand, are significantly influenced by the solvated nanoparticle. The diffusion of n-hexane molecules inside the nanoparticle is significantly decreased mainly because of the loss of dimensions of translation. Because one translational degree of freedom is lost by colliding with the wall of nanoparticle, the n-hexane molecules outside the nanoparticle diffuse 30% slower than the molecules in pure solution. The computed free energy profiles illustrate that the arrangement of the nanoparticles in bulk n-hexane solution are dependent on the orientation and functional group. We found that the n-hexane solvent exerts some effects on the interactions between the solvated nanoparticles. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences and by the Office of Energy Efficiency and Renewable Energy, Geothermal Technologies Program. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.

  16. INTERACTIVE DISPLAY OF POLYGONAL DATA

    E-Print Network [OSTI]

    Wood, Peter M.

    2011-01-01T23:59:59.000Z

    P. SEEDIS Workbook III, Interactive Polygon Mapping. LBL-August, 1974. Wood, P.M. Interactive Thematic ~mpping -- Aprivatelyownedrights. LBL-6490 INTERACTIVE DISPLAY OF

  17. AN INTERACTIVE SPIRES PLOT PROTOCOL

    E-Print Network [OSTI]

    Cerny, Barbara

    2013-01-01T23:59:59.000Z

    LBL-11068 AN INTERACTIVE SPIRES PLOT PROTOCOL Barbara Cerny,11068 PLOT PROTOCOL AN INTERACTIVE by Barbara Cerny, Geraldit gives immediate interactive plots that can be displayed

  18. Tuning Structural and Mechanical Properties of Two-Dimensional Molecular Crystals: The Roles of Carbon Side Chains

    SciTech Connect (OSTI)

    Cun, Huanyao (HY) [Institute of Physics, Chinese Academy of Science; Wang, Yeliang (YL) [Institute of Physics, Chinese Academy of Science; Du, S X [Chinese Academy of Sciences; Zhang, Lei [Institute of Physics, Chinese Academy of Science; Zhang, Lizhi [Institute of Physics, Chinese Academy of Science; Yang, Bing [Institute of Physics, Chinese Academy of Science; He, Xiaobo [Institute of Physics, Chinese Academy of Science; Wang, Yue [Jilin University, Changchun; Zhu, Xueyan [Chinese Academy of Sciences; Yuan, Quanzi [Chinese Academy of Sciences; Zhao, Ya-Pu [Chinese Academy of Sciences; Ouyang, Min [University of Maryland; Hofer, Werner A. [University of Liverpool; Pennycook, Stephen J [ORNL; Gao, Hong-jun [Institute of Physics, Chinese Academy of Science

    2012-01-01T23:59:59.000Z

    A key requirement for the future applicability of molecular electronics devices is a resilience of their properties to mechanical deformation. At present, however, there is no fundamental understanding of the origins of mechanical properties of molecular films. Here we use quinacridone, which possesses flexible carbon side chains, as a model molecular system to address this issue. Eight molecular configurations with different molecular coverage are identified by scanning tunneling microscopy. Theoretical calculations reveal quantitatively the roles of different molecule-molecule and molecule-substrate interactions and predict the observed sequence of configurations. Remarkably, we find that a single Young's modulus applies for all configurations, the magnitude of which is controlled by side chain length, suggesting a versatile avenue for tuning not only the physical and chemical properties of molecular films but also their elastic properties.

  19. Ab-Initio Molecular Dynamics

    E-Print Network [OSTI]

    Thomas D. Kühne

    2013-03-26T23:59:59.000Z

    Computer simulation methods, such as Monte Carlo or Molecular Dynamics, are very powerful computational techniques that provide detailed and essentially exact information on classical many-body problems. With the advent of ab-initio molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method and the recently devised efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics, which unifies best of both schemes are discussed. The predictive power of this novel second-generation Car-Parrinello approach is demonstrated by a series of applications ranging from liquid metals, to semiconductors and water. This development allows for ab-initio molecular dynamics simulations on much larger length and time scales than previously thought feasible.

  20. Ab-Initio Molecular Dynamics

    E-Print Network [OSTI]

    Kühne, Thomas D

    2012-01-01T23:59:59.000Z

    Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.

  1. Interactive dynamic aircraft scheduling

    E-Print Network [OSTI]

    Deckwitz, Thomas Anthony

    1984-01-01T23:59:59.000Z

    Introducing recent advances in computer technology to improve aircraft scheduling is investigated. Incorporating interactive graphics, modern database manipulation techniques, and decision support algorithms, the computer ...

  2. Nerve-pulse interactions

    SciTech Connect (OSTI)

    Scott, A.C.

    1982-01-01T23:59:59.000Z

    Some recent experimental and theoretical results on mechanisms through which individual nerve pulses can interact are reviewed. Three modes of interactions are considered: (1) interaction of pulses as they travel along a single fiber which leads to velocity dispersion; (2) propagation of pairs of pulses through a branching region leading to quantum pulse code transformations; and (3) interaction of pulses on parallel fibers through which they may form a pulse assembly. This notion is analogous to Hebb's concept of a cell assembly, but on a lower level of the neural hierarchy.

  3. Interaction and Intelligent Behavior

    E-Print Network [OSTI]

    Mataric, Maja J.

    1994-08-01T23:59:59.000Z

    We introduce basic behaviors as primitives for control and learning in situated, embodied agents interacting in complex domains. We propose methods for selecting, formally specifying, algorithmically implementing, ...

  4. Can Protostellar Jets Drive Supersonic Turbulence in Molecular Clouds?

    E-Print Network [OSTI]

    Robi Banerjee; Ralf S. Klessen; Christian Fendt

    2007-06-25T23:59:59.000Z

    Jets and outflows from young stellar objects are proposed candidates to drive supersonic turbulence in molecular clouds. Here, we present the results from multi-dimensional jet simulations where we investigate in detail the energy and momentum deposition from jets into their surrounding environment and quantify the character of the excited turbulence with velocity probability density functions. Our study include jet--clump interaction, transient jets, and magnetised jets. We find that collimated supersonic jets do not excite supersonic motions far from the vicinity of the jet. Supersonic fluctuations are damped quickly and do not spread into the parent cloud. Instead subsonic, non-compressional modes occupy most of the excited volume. This is a generic feature which can not be fully circumvented by overdense jets or magnetic fields. Nevertheless, jets are able to leave strong imprints in their cloud structure and can disrupt dense clumps. Our results question the ability of collimated jets to sustain supersonic turbulence in molecular clouds.

  5. Charge exchange molecular ion source

    DOE Patents [OSTI]

    Vella, Michael C.

    2003-06-03T23:59:59.000Z

    Ions, particularly molecular ions with multiple dopant nucleons per ion, are produced by charge exchange. An ion source contains a minimum of two regions separated by a physical barrier and utilizes charge exchange to enhance production of a desired ion species. The essential elements are a plasma chamber for production of ions of a first species, a physical separator, and a charge transfer chamber where ions of the first species from the plasma chamber undergo charge exchange or transfer with the reactant atom or molecules to produce ions of a second species. Molecular ions may be produced which are useful for ion implantation.

  6. Radiative transfer in molecular lines

    E-Print Network [OSTI]

    A. Asensio Ramos; J. Trujillo Bueno; J. Cernicharo

    2001-02-15T23:59:59.000Z

    The highly convergent iterative methods developed by Trujillo Bueno and Fabiani Bendicho (1995) for radiative transfer (RT) applications are generalized to spherical symmetry with velocity fields. These RT methods are based on Jacobi, Gauss-Seidel (GS), and SOR iteration and they form the basis of a new NLTE multilevel transfer code for atomic and molecular lines. The benchmark tests carried out so far are presented and discussed. The main aim is to develop a number of powerful RT tools for the theoretical interpretation of molecular spectra.

  7. Molecular weight and molecular weight distribution of kraft lignins

    SciTech Connect (OSTI)

    Schmidl, W.; Dong, D.; Fricke, A.L. (Univ. of Florida, Gainesville, FL (United States))

    1990-01-01T23:59:59.000Z

    Kraft lignins are the lignin degradation products from kraft pulping. They are complex, heterogeneous polymers with some polar character. The molecular weight of kraft lignins greatly affect the physical properties of black liquors, and are of primary importance in separation from black liquor and in evaluating potential uses. Several purified kraft lignins from slash pine were analyzed for number average molecular weight by vapor pressure osmometry (VPO), for weight average molecular weight by low angle laser light scattering (LALLS), and for the molecular weight distribution by high temperature size exclusion chromatography (SEC). The lignins were run in tetrahydrofuran (THF), N,N-dimethyl formamide (DMF), DMF with 0.1M LiBr, and pyridine at conditions above the Theta temperature. Experimental methods are discussed. The results show that VPO may be used to determine M[sub n] for kraft lignins if the purity of the lignins and the identity of the impurities are known. LALLS can be used to determine M[sub w] for kraft lignins if measurements are made at or above the Theta temperature of the lignin-solvent pair. SEC should be used at temperatures at, or above, the Theta temperature of the lignin-solvent pair. Size separation is highly dependent on the solvent used, and DMF is a much better solvent than THF for high temperature SEC. Future work using moment resolution procedures to derive an accurate calibration curve are also discussed.

  8. Molecular Dynamics Simulation of Damage Cascade Formation in Ion Bombarded Solids

    E-Print Network [OSTI]

    Chen, Di

    2012-10-19T23:59:59.000Z

    .......................................................................................................... 10 CHAPTER III MOLECULAR DYNAMICS SIMULATION OF DEFECT……………... CREATION DUE TO INTERACTIONS OF DAMAGE CASCADE IN SELF ION…… IRRADIATED SI………….…….………........................................................................12 3... ....................................................................................... 14 CHAPTER IV USING CLUSTER ION BOMBARDMENT TO DETERMINE………… AMORPHIZATION MODE..…………………………………………...........................26 4.1 Introduction of Irradiated Amorphization ........................................................... 26 4...

  9. Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation Pengyu Ren and Jay W. Ponder*

    E-Print Network [OSTI]

    Ponder, Jay

    Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation Pengyu Ren and Jay W empirical potential is proposed for water. The model uses a polarizable atomic multipole description of electrostatic interactions. Multipoles through the quadrupole are assigned to each atomic center based

  10. Ab Initio Description of High-Temperature Superconductivity in Dense Molecular Hydrogen P. Cudazzo,1

    E-Print Network [OSTI]

    Gross, E.K.U.

    Ab Initio Description of High-Temperature Superconductivity in Dense Molecular Hydrogen P. Cudazzo-principles study of the electron-phonon interaction and the prediction of the superconducting critical temperature superconductivity: mainly, a rich and complex Fermi surface and strongly coupled phonon modes driving the intra

  11. Stopping supersonic oxygen with a series of pulsed electromagnetic coils: A molecular coilgun Edvardas Narevicius,1

    E-Print Network [OSTI]

    Texas at Austin. University of

    Stopping supersonic oxygen with a series of pulsed electromagnetic coils: A molecular coilgun, using a series of pulsed electromagnetic coils. A series of coils is fired in a timed sequence to bring in some experiments by interactions with pulsed electric fields Stark decelerator 4­6 , by inter- actions

  12. Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

    E-Print Network [OSTI]

    Fayer, Michael D.

    Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level

  13. Eighth international congress on nitrogen fixation

    SciTech Connect (OSTI)

    Not Available

    1990-01-01T23:59:59.000Z

    This volume contains the proceedings of the Eighth International Congress on Nitrogen Fixation held May 20--26, 1990 in Knoxville, Tennessee. The volume contains abstracts of individual presentations. Sessions were entitled Recent Advances in the Chemistry of Nitrogen Fixation, Plant-microbe Interactions, Limiting Factors of Nitrogen Fixation, Nitrogen Fixation and the Environment, Bacterial Systems, Nitrogen Fixation in Agriculture and Industry, Plant Function, and Nitrogen Fixation and Evolution.

  14. Eighth international congress on nitrogen fixation. Final program

    SciTech Connect (OSTI)

    Not Available

    1990-12-31T23:59:59.000Z

    This volume contains the proceedings of the Eighth International Congress on Nitrogen Fixation held May 20--26, 1990 in Knoxville, Tennessee. The volume contains abstracts of individual presentations. Sessions were entitled Recent Advances in the Chemistry of Nitrogen Fixation, Plant-microbe Interactions, Limiting Factors of Nitrogen Fixation, Nitrogen Fixation and the Environment, Bacterial Systems, Nitrogen Fixation in Agriculture and Industry, Plant Function, and Nitrogen Fixation and Evolution.

  15. Interactive Multimedia Presentation Capabilities

    E-Print Network [OSTI]

    Boll, Susanne

    Interactive Multimedia Presentation Capabilities for an Object-Oriented DBMS Susanne Boll, Michael and Mathematics (ERCIM) Workshop Reports, 9th ERCIM Database Research Group Workshop on Multimedia Database Sys, FRANCE, 1996. #12;Interactive Multimedia Presentation Capabilities for an Object-Oriented DBMS Susanne

  16. Interactive Virtual Environments Introduction

    E-Print Network [OSTI]

    Petriu, Emil M.

    sensor data or by animation scripts. Human users can interact and directly manipulate objects within Reality Interactive Virtual Reality Virtualized Reality Augmented Reality #12;HUMAN PERCEPTION OF REALITY REAL WORLD / ENVIRONMENT HUMAN (sentient living animal able of sensible reasoning) #12;Real

  17. Resonant coupling between localized plasmons and anisotropic molecular coatings in ellipsoidal metal nanoparticles

    E-Print Network [OSTI]

    Ambjornsson, T; Kall, M; Mukhopadhyay, G; Ambjornsson, Tobias; Kall, Mikael; Mukhopadhyay, Gautam

    2006-01-01T23:59:59.000Z

    We present an analytic theory for the optical properties of ellipsoidal plasmonic particles covered by anisotropic molecular layers. The theory is applied to the case of a prolate spheroid covered by chromophores oriented parallel and perpendicular to the metal surface. For the case that the molecular layer resonance frequency is close to being degenerate with one of the particle plasmon resonances strong hybridization between the two resonances occur. Approximate analytic expressions for the hybridized resonance frequencies, their extinction cross section peak heights and widths are derived. The strength of the molecular - plasmon interaction is found to be strongly dependent on molecular orientation and suggest that this sensitivity could be the basis for novel nanoparticle based bio/chemo-sensing applications.

  18. Cavity-enhanced field-free molecular alignment at high repetition rate

    E-Print Network [OSTI]

    Benko, Craig; Allison, Thomas K; Labaye, François; Ye, Jun

    2015-01-01T23:59:59.000Z

    Extreme ultraviolet frequency combs are a versatile tool with applications including precision measurement, strong-field physics, and solid-state physics. Here we report on an application of extreme ultraviolet frequency combs and their driving lasers to studying strong-field effects in molecular systems. We perform field-free molecular alignment and high-order hamonic generation with aligned molecules in a gas jet at 154 MHz repetition rate using a high-powered optical frequency comb inside a femtosecond enhancement cavity. The cavity-enhanced system provides means to reach suitable intensities to study field-free molecular alignment and enhance the observable effects of the molecule-field interaction. We observe modulations of the driving field, arising from the nature of impulsive stimulated Raman scattering responsible for coherent molecular rotations. We foresee impact of this work on the study of molecule-based strong-field physics, with improved precision and a more fundamental understanding of the int...

  19. Molecular dynamics simulation and ab intio studies of electrolytes...

    Broader source: Energy.gov (indexed) [DOE]

    DFT calculations on molecular clusters and electrode surfaces, reactive molecular dynamics simulations allowing modeling of SEI formation, and classical molecular dynamics...

  20. Amorphous Molecular Organic Solids for Gas Adsorption. | EMSL

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

    Molecular Organic Solids for Gas Adsorption. Amorphous Molecular Organic Solids for Gas Adsorption. Abstract: We show that molecular organic compounds with large accessible...

  1. aluminophosphate molecular sieves: Topics by E-print Network

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

    performing ethyleneethane (C?H?C?H?) separation carbon molecular sieve (CMS) dense film membranes. (more) Rungta, Meha 2012-01-01 15 Molecular Squares as Molecular Sieves:...

  2. aluminophosphate molecular sieve: Topics by E-print Network

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

    performing ethyleneethane (C?H?C?H?) separation carbon molecular sieve (CMS) dense film membranes. (more) Rungta, Meha 2012-01-01 15 Molecular Squares as Molecular Sieves:...

  3. aluminosilicate molecular sieve: Topics by E-print Network

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

    performing ethyleneethane (C?H?C?H?) separation carbon molecular sieve (CMS) dense film membranes. (more) Rungta, Meha 2012-01-01 14 Molecular Squares as Molecular Sieves:...

  4. alpo4 molecular sieves: Topics by E-print Network

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

    performing ethyleneethane (C?H?C?H?) separation carbon molecular sieve (CMS) dense film membranes. (more) Rungta, Meha 2012-01-01 15 Molecular Squares as Molecular Sieves:...

  5. BE.442 Molecular Structure of Biological Materials, Fall 2005

    E-Print Network [OSTI]

    Zhang, Shuguang, Dr.

    Basic molecular structural principles of biological materials. Molecular structures of various materials of biological origin, including collagen, silk, bone, protein adhesives, GFP, self-assembling peptides. Molecular ...

  6. RMP Colloquia Modeling molecular motors

    E-Print Network [OSTI]

    Jülicher, Frank

    The authors present general considerations and simple models for the operation of isothermal motors at small structural differences from the usual Carnot engines. Turning to more explicit models for a single motorRMP Colloquia Modeling molecular motors Frank Ju¨licher,* Armand Ajdari, and Jacques Prost

  7. Gnzburg, Germany Molecular Diabetology and

    E-Print Network [OSTI]

    Pfeifer, Holger

    April 12th ­ 14th 2010 Günzburg, Germany Molecular Diabetology and Endocrinology in Medicine GRK-Einstein-Allee 23 89081 Ulm, Germany Contact Person: Erika Thanner Speaker GRK 1208 Prof. Dr. J. Köhrle Institut für Experimentelle Endokrinologie, Charité Berlin Augustenburger Platz 1 13353 Berlin, Germany Contact Person: Elke

  8. Molecular Foundry, Berkeley, California (Revised)

    SciTech Connect (OSTI)

    Carlisle, N.

    2008-03-01T23:59:59.000Z

    This case study provides information on the Molecular Foundry, which incorporates Labs21 principles in its design and construction. The design includes many of the strategies researched at Lawrence Berkeley Laboratory for energy efficient cleanroom and data centers. The result is an energy efficient high-performing sustainable laboratory.

  9. Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite

    E-Print Network [OSTI]

    A. Ito; H. Nakamura

    2006-04-26T23:59:59.000Z

    Hydrogen adsorption by graphite is examined by classical molecular dynamics simulation using a modified Brenner REBO potential. Such interactions are typical in chemical sputtering experiments, and knowledge of the fundamental behavior of hydrogen and graphene in collisional conditions is essential for modeling the sputtering mechanism. The hydrogen adsorption rate is found to be dependent on the incident hydrogen energy and not on graphene temperature. Rather than destroying the graphene, hydrogen incidence at energies of less than 100 eV can be classified into three regimes of adsorption, reflection and penetration through one or more graphene layers. Incidence at the lowest energies is shown to distort the graphene structure.

  10. Nanoplasmonic molecular ruler for nuclease activity and DNA footprinting

    DOE Patents [OSTI]

    Chen, Fanqing Frank; Liu, Gang L; Lee, Luke P

    2013-10-29T23:59:59.000Z

    This invention provides a nanoplasmonic molecular ruler, which can perform label-free and real-time monitoring of nucleic acid (e.g., DNA) length changes and perform nucleic acid footprinting. In various embodiments the ruler comprises a nucleic acid attached to a nanoparticle, such that changes in the nucleic acid length are detectable using surface plasmon resonance. The nanoplasmonic ruler provides a fast and convenient platform for mapping nucleic acid-protein interactions, for nuclease activity monitoring, and for other footprinting related methods.

  11. Molecular Theory of Dendritic Liquid Crystals: Self Organization and Phase Transitions

    E-Print Network [OSTI]

    Alexandros G. Vanakaras; Demetri J. Photinos

    2005-01-10T23:59:59.000Z

    We formulate the configurational partition function for dendrimers, taking explicit account of their conformations and segmental interactions. Two approximate schemes are presented, one based on the effective dendrimer-dendrimer interactions and the other based on the interactions among the mesogenic units comprising the dendrimers. In the latter scheme, the description of the dendromesogenic system reduces to that of an ensemble of mesogenic dimers. Results of lattice calculations for phase transitions are presented showing that the minimal inclusion of shape anisotropy and of sub-molecular partitioning into chemically distinct parts reproduces the variety of phases and phase sequences observed experimentally and provides insights into the conformational aspect of these transitions.

  12. Challenges for molecular neuroimaging with MRI

    E-Print Network [OSTI]

    Lelyveld, Victor S.

    Magnetic resonance (MRI)-based molecular imaging methods are beginning to have impact in neuroscience. A growing number of molecular imaging agents have been synthesized and tested in vitro, but so far relatively few have ...

  13. FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS

    E-Print Network [OSTI]

    Herbordt, Martin

    ' & $ % FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS YONGFENG GU Dissertation submitted;BOSTON UNIVERSITY COLLEGE OF ENGINEERING Dissertation FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS DYNAMICS SIMULATIONS (Order No. ) YONGFENG GU Boston University, College of Engineering, 2008 Major

  14. Statistical Analysis of Molecular Signal Recording

    E-Print Network [OSTI]

    Glaser, Joshua I.

    A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a “molecular ticker tape”, in which an engineered DNA polymerase (DNAP) ...

  15. MIMESIS: Interactive Interface for Mass-Interaction Matthieu Evrard

    E-Print Network [OSTI]

    MIMESIS: Interactive Interface for Mass-Interaction Modeling Matthieu Evrard ICA Laboratory introduces MIMESIS, a end-user software based on mass-interaction modeling. In MIMESIS, the mass-interaction-based modeling, simulation, animation, mass-interaction network, user-friendly interface, animation language. 1

  16. Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps

    E-Print Network [OSTI]

    Roie Volkovich; Uri Peskin

    2010-12-01T23:59:59.000Z

    The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor molecular junction model yields currents which transfer charge (electron and holes) unevenly to the two leads in the absence of a bias potential. The utility of this mechanism for charge pumping in steady state conditions is proposed.

  17. Ab initio investigation of intermolecular interactions in solid benzene

    E-Print Network [OSTI]

    O. Bludsky; M. Rubes; P. Soldan

    2008-01-04T23:59:59.000Z

    A computational strategy for the evaluation of the crystal lattice constants and cohesive energy of the weakly bound molecular solids is proposed. The strategy is based on the high level ab initio coupled-cluster determination of the pairwise additive contribution to the interaction energy. The zero-point-energy correction and non-additive contributions to the interaction energy are treated using density functional methods. The experimental crystal lattice constants of the solid benzene are reproduced, and the value of 480 meV/molecule is calculated for its cohesive energy.

  18. Journal of Molecular Graphics and Modelling 21 (2003) 499515 A priori molecular descriptors in QSAR

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    Journal of Molecular Graphics and Modelling 21 (2003) 499­515 A priori molecular descriptors in QSAR: a case of HIV-1 protease inhibitors II. Molecular graphics and modeling Rudolf Kiralj, Márcia M; accepted 14 November 2002 Abstract Molecular graphics and modeling methods illustrated the chemical

  19. Molecular Ecology NCGR May 2003 Physiology and Molecular Ecology of Synechococcus WH8102

    E-Print Network [OSTI]

    Molecular Ecology NCGR May 2003 1 Physiology and Molecular Ecology of Synechococcus WH8102 DOE is to provide a summary of the literature on the physiology and molecular ecology of bacteria and in particular to be a comprehensive review. Excellent current detailed reviews are available on the physiology and molecular ecology

  20. Interactive Holographic Cinema

    E-Print Network [OSTI]

    Portales, Christopher

    2012-07-16T23:59:59.000Z

    computer program performs stereoscopic reconstruction in real-time during presentation. Artists and computer users could then use a hardware device, such as the Microsoft Kinect, to explore the holographic cinematic form interactively....

  1. BNL | ATF Interaction Chambers

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

    with translation actuators. Beam profile monitors at interaction region as well as chamber entrance and exit. Available port for 200 ls turbo pump. Operates in the 10-8 Torr range...

  2. Multiple jet interactions

    E-Print Network [OSTI]

    Hehr, Roger James

    1983-01-01T23:59:59.000Z

    MULTIPLE JET INTERACTIONS A Thesis by ROGER JAMES HEHR Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 1983 Major Subject: Aerospace Engineering... MULTIPLE JET INTERACTIONS A Thesis by ROGER JAMES HEHR Approved as to style and content by: David . Norton (Chairman of Committee) raid L. orrison (Mem er) Leland A. Carlson (Member) Er est . Cross, r. (Head of Department) August 1983 ABSTRACT...

  3. Human-machine interactions

    DOE Patents [OSTI]

    Forsythe, J. Chris (Sandia Park, NM); Xavier, Patrick G. (Albuquerque, NM); Abbott, Robert G. (Albuquerque, NM); Brannon, Nathan G. (Albuquerque, NM); Bernard, Michael L. (Tijeras, NM); Speed, Ann E. (Albuquerque, NM)

    2009-04-28T23:59:59.000Z

    Digital technology utilizing a cognitive model based on human naturalistic decision-making processes, including pattern recognition and episodic memory, can reduce the dependency of human-machine interactions on the abilities of a human user and can enable a machine to more closely emulate human-like responses. Such a cognitive model can enable digital technology to use cognitive capacities fundamental to human-like communication and cooperation to interact with humans.

  4. Hierarchical analysis of molecular spectra

    SciTech Connect (OSTI)

    Davis, M.J.

    1996-03-01T23:59:59.000Z

    A novel representation of molecular spectra in terms of hierarchical trees has proven to be an important aid for the study of many significant problems in gas-phase chemical dynamics. Trees are generated from molecular spectra by monitoring the changes that occur in a spectrum as resolution is changed in a continuous manner. A tree defines a genealogy among all lines of a spectrum. This allows for a detailed understanding of the assignment of features of a spectrum that may be difficult to obtain any other way as well as an understanding of intramolecular energy transfer time scales, mechanisms, and pathways. The methodology has been applied to several problems: transition state spectroscopy, intramolecular energy transfer in highly excited molecules, high-resolution overtone spectroscopy, and the nature of the classical-quantum correspondence when there is classical chaos (``quantum chaos``).

  5. Molecular engineering with bridged polysilsesquioxanes

    SciTech Connect (OSTI)

    LOY,DOUGLAS A.; SHEA,KENNETH J.

    2000-05-09T23:59:59.000Z

    Bridged polysilsesquioxanes are a class of hybrid organic-inorganic materials that permit molecular engineering of bulk properties including porosity. Prepared by sol-gel polymerization of monomers with two or more trialkoxysilyl groups, the materials are highly cross-linked amorphous polymers that are readily obtained as gels. The bridging configuration of the hydrocarbon group insures that network polymers are readily formed and that the organic functionality is homogeneously distributed throughout the polymeric scaffolding at the molecular level. This permits the bulk properties, including surface area, pore size, and dielectric constant to be engineered through the selection of the bridging organic group. Numerous bridging groups have been incorporated. This presentation will focus on the effects that the length, flexibility, and substitution geometry of the hydrocarbon bridging groups have on the properties of the resulting bridged polysilsesquioxanes. Details of the preparation, characterization, and some structure property relationships of these bridged polysilsesquioxanes will be given.

  6. Molecular gas and AGN fueling

    E-Print Network [OSTI]

    F. Combes

    2003-08-01T23:59:59.000Z

    CO emission, tracing the molecular content and distribution in galaxies, is a privileged tool to trace gas towards the nucleus, since the HI tracer is in general depleted there. A review is done of recent CO line observations, with sufficient spatial resolution to indicate the morphology and kinematics of the gas near the nucleus. The puzzling result that nuclei presently observed in an active phase have little sign of fueling, is discussed.

  7. Molecular Science Computing: 2010 Greenbook

    SciTech Connect (OSTI)

    De Jong, Wibe A.; Cowley, David E.; Dunning, Thom H.; Vorpagel, Erich R.

    2010-04-02T23:59:59.000Z

    This 2010 Greenbook outlines the science drivers for performing integrated computational environmental molecular research at EMSL and defines the next-generation HPC capabilities that must be developed at the MSC to address this critical research. The EMSL MSC Science Panel used EMSL’s vision and science focus and white papers from current and potential future EMSL scientific user communities to define the scientific direction and resulting HPC resource requirements presented in this 2010 Greenbook.

  8. Modeling and Control Interactive Networks

    E-Print Network [OSTI]

    Amin, S. Massoud

    Modeling and Control of Complex Interactive Networks By Massoud Amin E nergy, telecommunications complex networks, geographi- cally dispersed, nonlinear, and interacting both among themselves, distributed, highly interactive networks, nor does any such entity have the ability to evaluate, monitor

  9. The Interactive Process: Reasonable Accommodation

    E-Print Network [OSTI]

    Tsien, Roger Y.

    The Interactive Process: Reasonable Accommodation March 2009 Manager's Guide #12;Table of Contents .......................................................13 #12;3THE INTERACTIVE PROCESS: REASONABLE ACCOMMODATION MANAGER'S GUIDE--March 2009 Overview This Managers' Guide on the Interactive Process: Reasonable Accommodation provides supportive information

  10. Journal of Molecular Graphics and Modelling 21 (2003) 435448 A priori molecular descriptors in QSAR: a case of

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    Journal of Molecular Graphics and Modelling 21 (2003) 435­448 A priori molecular descriptors- panion paper, Part II, which interprets a priori molecular descriptors in terms of molecular graphics

  11. Surprising Quasiparticle Interactions in Graphene

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

    Surprising Quasiparticle Interactions in Graphene Surprising Quasiparticle Interactions in Graphene Print Wednesday, 31 October 2007 00:00 Until now, the world's electronics have...

  12. 2012 MOLECULAR AND IONIC CLUSTERS GORDON RESEARCH CONFERENCE, JANUARY 29 - FEBRUARY 3, 2012

    SciTech Connect (OSTI)

    Anne McCoy

    2012-02-03T23:59:59.000Z

    The Gordon Research Conference on 'Molecular and Ionic Clusters' focuses on clusters, which are the initial molecular species found in gases when condensation begins to occur. Condensation can take place solely from molecules interacting with each other, mostly at low temperatures, or when molecules condense around charged particles (electrons, protons, metal cations, molecular ions), producing ion molecule clusters. These clusters provide models for solvation, allow a pristine look at geometric as well as electronic structures of molecular complexes or matter in general, their interaction with radiation, their reactivity, their thermodynamic properties and, in particular, the related dynamics. This conference focuses on new ways to make clusters composed of different kinds of molecules, new experimental techniques to investigate the properties of the clusters and new theoretical methods with which to calculate the structures, dynamical motions and energetics of the clusters. Some of the main experimental methods employed include molecular beams, mass spectrometry, laser spectroscopy (from infrared to XUV; in the frequency as well as the time domain) and photoelectron spectroscopy. Techniques include laser absorption spectroscopy, laser induced fluorescence, resonance enhanced photoionization, mass-selected photodissociation, photofragment imaging, ZEKE photoelectron spectroscopy, etc. From the theoretical side, this conference highlights work on potential surfaces and measurable properties of the clusters. The close ties between experiment, theory and computation have been a hallmark of the Gordon Research Conference on Molecular and Ionic Clusters. In the 2012 meeting, we plan to have sessions that will focus on topics including: (1) The use of cluster studies to probe fundamental phenomena; (2) Finite size effects on structure and thermodynamics; (3) Intermolecular forces and cooperative effects; (4) Molecular clusters as models for solvation; and (5) Studies of clusters at XUV light sources.

  13. Lattice cluster theory for polymer melts with specific interactions

    E-Print Network [OSTI]

    Wen-Sheng Xu; Karl F. Freed

    2014-07-12T23:59:59.000Z

    Despite the long-recognized fact that chemical structure and specific interactions greatly influence the thermodynamic properties of polymer systems, a predictive molecular theory that enables systematically addressing the role of chemical structure and specific interactions has been slow to develop even for polymer melts. While the lattice cluster theory (LCT) provides a powerful vehicle for understanding the influence of various molecular factors, such as monomer structure, on the thermodynamic properties of polymer melts and blends, the application of the LCT has heretofore been limited to the use of the simplest polymer model in which all united atom groups within the monomers of a species interact with a common monomer averaged van der Waals energy. Thus, the description of a compressible polymer melt involves a single van der Waals energy. As a first step towards developing more realistic descriptions to aid in the analysis of experimental data and the design of new materials, the LCT is extended here to treat models of polymer melts in which the backbone and side groups have different interaction strengths, so three energy parameters are present, namely, backbone-backbone, side group-side group, and backbone-side group interaction energies. Because of the great algebraic complexity of this extension, we retain maximal simplicity within this class of models by further specializing this initial study to models of polymer melts comprising chains with poly($n$-$\\alpha$-olefin) structures where only the end segments on the side chains may have different, specific van der Waals interaction energies with the other united atom groups. An analytical expression for the LCT Helmholtz free energy is derived for the new model. Illustrative calculations are presented to demonstrate the degree to which the thermodynamic properties of polymer melts can be controlled by specific interactions.

  14. The Development of New User Research Capabilities in Environmental Molecular Science: Workshop Report

    SciTech Connect (OSTI)

    Felmy, Andrew R.; Baer, Donald R.; Fredrickson, Jim K.; Gephart, Roy E.; Rosso, Kevin M.

    2006-10-31T23:59:59.000Z

    On August 1, and 2, 2006, 104 scientists representing 40 institutions including 24 Universities and 5 National Laboratories gathered at the W.R. Wiley Environmental Molecular Sciences Laboratory, a National scientific user facility, to outline important science challenges for the next decade and identify major capabilities needed to pursue advanced research in the environmental molecular sciences. EMSL’s four science themes served as the framework for the workshop. The four science themes are 1) Biological Interactions and Interfaces, 2) Geochemistry/Biogeochemistry and Surface Science, 3) Atmospheric Aerosol Chemistry, and 4) Science of Interfacial Phenomena.

  15. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    E-Print Network [OSTI]

    Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01T23:59:59.000Z

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

  16. Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: Probing inter-molecular interactions using PFG NMR

    E-Print Network [OSTI]

    D'Agostino, Carmine; Gladden, Lynn F.; Mantle, Mick D.; Abbott, Andrew P.; Ahmed, Essa I.; Al-Murshedi, Azhar Y. m.; Harris, Robert C.

    2015-06-02T23:59:59.000Z

    but significantly improves the mass transport characteristics of the liquids. In the applications listed above water is often added to improve conductivity and aid filtration; the amount of water added often being chosen empirically It has been empirically noted... in determining the macroscopic behaviour. The HBD is known to form a complex with the anion of the salt, resulting in the formation of a bulky asymmetric anion, which decreases the lattice energy thus decreasing the freezing point of the system.12 The whole...

  17. Drug interactions evaluation: An integrated part of risk assessment of therapeutics

    SciTech Connect (OSTI)

    Zhang, Lei; Reynolds, Kellie S.; Zhao, Ping [Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Building 51, Room 3188, 10903 New Hampshire Avenue, Silver Spring, MD 20993 (United States); Huang, Shiew-Mei, E-mail: shiewmei.huang@fda.hhs.go [Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Building 51, Room 3188, 10903 New Hampshire Avenue, Silver Spring, MD 20993 (United States)

    2010-03-01T23:59:59.000Z

    Pharmacokinetic drug interactions can lead to serious adverse events or decreased drug efficacy. The evaluation of a new molecular entity's (NME's) drug-drug interaction potential is an integral part of risk assessment during drug development and regulatory review. Alteration of activities of enzymes or transporters involved in the absorption, distribution, metabolism, or excretion of a new molecular entity by concomitant drugs may alter drug exposure, which can impact response (safety or efficacy). The recent Food and Drug Administration (FDA) draft drug interaction guidance ( (http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm072101.pdf)) highlights the methodologies and criteria that may be used to guide drug interaction evaluation by industry and regulatory agencies and to construct informative labeling for health practitioner and patients. In addition, the Food and Drug Administration established a 'Drug Development and Drug Interactions' website to provide up-to-date information regarding evaluation of drug interactions ( (http://www.fda.gov/Drugs/DevelopmentApprovalProcess/DevelopmentResources/DrugInteractionsLabeling/ucm080499.htm)). This review summarizes key elements in the FDA drug interaction guidance and new scientific developments that can guide the evaluation of drug-drug interactions during the drug development process.

  18. Molecular Design of Branched and Binary Molecules at Ordered Interfaces

    SciTech Connect (OSTI)

    Kirsten Larson Genson

    2005-12-27T23:59:59.000Z

    This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformation which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.

  19. Dike/Drift Interactions

    SciTech Connect (OSTI)

    E. Gaffiney

    2004-11-23T23:59:59.000Z

    This report presents and documents the model components and analyses that represent potential processes associated with propagation of a magma-filled crack (dike) migrating upward toward the surface, intersection of the dike with repository drifts, flow of magma in the drifts, and post-magma emplacement effects on repository performance. The processes that describe upward migration of a dike and magma flow down the drift are referred to as the dike intrusion submodel. The post-magma emplacement processes are referred to as the post-intrusion submodel. Collectively, these submodels are referred to as a conceptual model for dike/drift interaction. The model components and analyses of the dike/drift interaction conceptual model provide the technical basis for assessing the potential impacts of an igneous intrusion on repository performance, including those features, events, and processes (FEPs) related to dike/drift interaction (Section 6.1).

  20. Generalized interaction in multigravity

    E-Print Network [OSTI]

    Duplij, Steven

    2013-01-01T23:59:59.000Z

    A general approach to description of multigravity models in D-dimensional space-time is presented. Different possibilities of generalization of the invariant volume are given. Then a most general form of the interaction potential is constructed, which for bigravity coincides with the Pauli-Fierz model. A thorough analysis of the model along the 3+1 expansion formalism is done. It is shown that the absence of ghosts the considered bigravity model is equivalent in the weak field limit to the massive gravity (the Pauli-Fierz model). Thus, on the concrete example it is shown, that the interaction between metrics leads to nonvanishing mass of graviton.

  1. Synchrotrons Explore Water's Molecular Mysteries

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengthening a solid ...SuccessSurprisingSynchrotrons Explore Water's Molecular

  2. Crystal structure and interaction dependence of the crystal-melt interfacial free energy

    E-Print Network [OSTI]

    Davidchack, Ruslan L.; Laird, Brian Bostian

    2005-03-01T23:59:59.000Z

    we examine, via molecular simulation, the interfacial free energies for a large number of systems interacting with inverse-power potentials of varying range, crystal orientation, and crystal structure (fcc or bcc). By focusing on a general class... of model interaction potentials 0031-9007= understanding of the dependence of .0013 on is largely empirical. In 1950, Turnbull values of .0013 for a variety of materials, ob- from nucleation rate experiments. ed a strong correlation between the en- per...

  3. Temperature inversion in long-range interacting systems

    E-Print Network [OSTI]

    Teles, Tarcisio N; Casetti, Lapo

    2015-01-01T23:59:59.000Z

    Temperature inversions occur in nature, e.g., in the solar corona and in interstellar molecular clouds: somewhat counterintuitively, denser parts of the system are colder than dilute ones. We propose a simple and appealing mechanism to spontaneously generate temperature inversions in systems with long-range interactions, by preparing them in inhomogeneous thermal equilibrium states and then applying an impulsive perturbation. In similar situations, short-range systems would typically relax to another thermal equilibrium, with uniform temperature profile. By contrast, in long-range systems, the interplay between wave-particle interaction and spatial inhomogeneity drives the system to nonequilibrium stationary states that generically exhibit temperature inversion. Our work underlines the crucial role the range of interparticle interaction plays in determining the nature of steady states attained when macroscopic systems are brought out of thermal equilibrium.

  4. Towards Using Molecular States as Qubits

    SciTech Connect (OSTI)

    Goswami, Debabrata; Goswami, Tapas; Kumar, S. K. Karthick; Das, Dipak K. [Department of Chemistry, Indian Institute of Technology Kanpur Kanpur-208016 (India)

    2011-09-23T23:59:59.000Z

    Molecular systems are presented as possible qubit systems by exploring non-resonant molecular fragmentation of n-propyl benzene with femtosecond laser pulses as a model case. We show that such laser fragmentation process is dependent on the phase and polarization characteristics of the laser. The effect of the chirp and polarization of the femtosecond pulse when applied simultaneously is mutually independent of each other, which makes chirp and polarization as useful 'logic' implementing parameters for such molecular qubits.

  5. Being Interactive Health Care

    E-Print Network [OSTI]

    Being Interactive Treating Health Care T he numbers are staggering. In a chilling report, the U care, training staff, and accrediting staff and health-care facilities, which involve determin- ing.ahrq.gov/clinic/ptsafety/summary.htm). Pressures on Health Care To come up with a credible approach for improv- ing patient safety, we need

  6. The Digital Interactive Video

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    The Digital Interactive Video Exploration and Reflection (Diver) system lets users create virtual pathways through existing video content using a virtual camera and an annotation window for commentary repurposing, and discussion. W ith the inexorable growth of low-cost consumer video elec- tronics

  7. Molecular Components of Catalytic Selectivity

    SciTech Connect (OSTI)

    Somorjai, Gabor A.; Park, Jeong Y.

    2008-07-02T23:59:59.000Z

    Selectivity, that is, to produce one molecule out of many other thermodynamically feasible product molecules, is the key concept to develop 'clean manufacturing' processes that do not produce byproducts (green chemistry). Small differences in potential energy barriers for elementary reaction steps control which reaction channel is more likely to yield the desired product molecule (selectivity), instead of the overall activation energy for the reaction that controls turnover rates (activity). Recent studies have demonstrated the atomic- or molecular-level tailoring of parameters such as the surface structures of active sites that give rise to nanoparticle size and shape dependence of turnover rates and reaction selectivities. Here, we highlight seven molecular components that influence reaction selectivities. These include: surface structure, adsorbate-induced restructuring, adsorbate mobility, reaction intermediates, surface composition, charge transport, and oxidation states for model metal single crystal and colloid nanoparticle catalysts. We show examples of their functioning and describe in-situ instruments that permit us to investigate their roles in surface reactions.

  8. Molecular Hydrogen in Infrared Cirrus

    E-Print Network [OSTI]

    Kristen Gillmon; J. Michael Shull

    2005-07-25T23:59:59.000Z

    We combine data from our recent FUSE survey of interstellar molecular hydrogen absorption toward 50 high-latitude AGN with COBE-corrected IRAS 100 micron emission maps to study the correlation of infrared cirrus with H2. A plot of the H2 column density vs. IR cirrus intensity shows the same transition in molecular fraction, f_H2, as seen with total hydrogen column density, N_H. This transition is usually attributed to H2 self-shielding, and it suggests that many diffuse cirrus clouds contain H2 in significant fractions, f_H2 = 1-30%. These clouds cover approximately 50% of the northern sky at latitudes b > 30 degrees, at temperature-corrected 100 micron intensities D_100 > 1.5 MJy/sr. The sheetlike cirrus clouds, with hydrogen densities n_H > 30 cm^-3, may be compressed by dynamical processes at the disk-halo interface, and they are conducive to H2 formation on grain surfaces. Exploiting the correlation between N(H2) and 100 micron intensity, we estimate that cirrus clouds at b > 30 contain approximately 3000 M_sun in H2. Extrapolated over the inner Milky Way, the cirrus may contain 10^7 M_sun of H2 and 10^8 M_sun in total gas mass. If elevated to 100 pc, their gravitational potential energy is ~10^53 erg.

  9. A Molecular Dynamics Investigation of Hydrolytic Polymerization...

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

    Hydrolytic Polymerization in a Metal-Hydroxide Gel. A Molecular Dynamics Investigation of Hydrolytic Polymerization in a Metal-Hydroxide Gel. Abstract: The early stages of the...

  10. Molecular dynamics simulation studies of electrolytes andelectrolyte...

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

    Merit Review and Peer Evaluation Meeting, May 18-22, 2009 -- Washington D.C. es40smith.pdf More Documents & Publications Molecular Dynamics Simulation Studies of...

  11. Molecular Characterization of Nitrogen Containing Organic Compounds...

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

    Nitrogen Containing Organic Compounds in Biomass Burning Aerosols Using High Resolution Mass Molecular Characterization of Nitrogen Containing Organic Compounds in Biomass Burning...

  12. Molecular Characterization of Biomass Burning Aerosols Using...

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

    Biomass Burning Aerosols Using High Resolution Mass Spectrometry. Molecular Characterization of Biomass Burning Aerosols Using High Resolution Mass Spectrometry. Abstract: Chemical...

  13. Molecular biology of signal transduction in plants

    SciTech Connect (OSTI)

    Not Available

    1991-01-01T23:59:59.000Z

    This volume contains abstracts of oral presentations and poster sessions of the 1991 Cold Springs Harbor Meeting entitled Molecular Biology of Signal Transduction in Plants.

  14. Molecular architecture and functionalization of graphene surface...

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

    Molecular architecture and functionalization of graphene surface; Synthesis and characterization Wednesday, November 12, 2014 - 3:00pm SLAC, Redtail Hawk Conference Room 108A...

  15. Molecular dynamics simulation of threshold displacement energies...

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

    experimental estimates in ceramics. Citation: Moreira PA, R Devanathan, J Yu, and WJ Weber.2009."Molecular dynamics simulation of threshold displacement energies in...

  16. Molecular Characterization of Organic Aerosols Using Nanospray...

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

    in OA, which is important for understanding chemical aging phenomena. Citation: Roach PJ, J Laskin, and A Laskin.2010."Molecular Characterization of Organic Aerosols Using...

  17. Institute for Molecular Engineering | Argonne National Laboratory

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

    at a molecular scale has the potential for societal impact in such areas as energy, health care, and the environment. The institute benefits from leading scientists and...

  18. Distribution Category: Atomic, Molecular, and Chemical Physics

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

    Atomic, Molecular, and Chemical Physics (UC-411) ARGONNE NATIONAL LABORATORY 9700 South Cass Avenue Argonne, TIlinois 60439 ANLI APSILS-151 RESULTS OF DESIGN CALCULATIONS FOR THE...

  19. Sandia National Laboratories: Molecular Simulations Guide Nanowire...

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

    Innovation Summit Experimental Smart Outlet Brings Flexibility, Resiliency to Grid Architecture Molecular Simulations Guide Nanowire Research On March 7, 2012, in Capabilities,...

  20. 2012 CELLULAR & MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 17 - 22, 2012

    SciTech Connect (OSTI)

    Judith Berman

    2012-06-22T23:59:59.000Z

    The Gordon Research Conference on CELLULAR & MOLECULAR FUNGAL BIOLOGY was held at Holderness School, Holderness New Hampshire, June 17 - 22, 2012. The 2012 Gordon Conference on Cellular and Molecular Fungal Biology (CMFB) will present the latest, cutting-edge research on the exciting and growing field of molecular and cellular aspects of fungal biology. Topics will range from yeast to filamentous fungi, from model systems to economically important organisms, and from saprophytes and commensals to pathogens of plants and animals. The CMFB conference will feature a wide range of topics including systems biology, cell biology and morphogenesis, organismal interactions, genome organisation and regulation, pathogenesis, energy metabolism, biomass production and population genomics. The Conference was well-attended with 136 participants. Gordon Research Conferences does not permit publication of meeting proceedings.

  1. Bias-dependent molecular-level structure of electrical double layer in ionic liquid on graphite

    SciTech Connect (OSTI)

    Black, Jennifer M [ORNL] [ORNL; Walters, Deron [Asylum Research, Santa Barbara, CA] [Asylum Research, Santa Barbara, CA; Labuda, Aleksander [Asylum Research, Santa Barbara, CA] [Asylum Research, Santa Barbara, CA; Feng, Guang [ORNL] [ORNL; Hillesheim, Patrick C [ORNL] [ORNL; Dai, Sheng [ORNL] [ORNL; Cummings, Peter T [ORNL] [ORNL; Kalinin, Sergei V [ORNL] [ORNL; Proksch, Roger [Asylum Research, Santa Barbara, CA] [Asylum Research, Santa Barbara, CA; Balke, Nina [ORNL] [ORNL

    2013-01-01T23:59:59.000Z

    Bias-dependent structure of electrochemical double layers at liquid-solid interfaces underpin a multitude of phenomena in virtually all areas of scientific enquiry ranging from energy storage and conversion systems, biology, to geophysics and geochemistry. Here we report the bias-evolution of the electric double layer structure of an ionic liquid on highly ordered pyrolytic graphite as a model system for carbon-based electrodes for electrochemical supercapacitors measured by atomic force microscopy. Matching the observed structures to molecular dynamics simulations allows us to resolve steric effects due to cation and anion layers. We observe reconfiguration under applied bias and the orientational transitions in the Stern layer. The synergy between molecular dynamics simulation and experiment provides a comprehensive picture of structural phenomena and long- and short range interactions. This insight will improve understanding of the mechanism of charge storage in electrochemical capacitors on a molecular level which can be used to enhance their electrochemical performance.

  2. Molecular to fluid dynamics: The consequences of stochastic molecular motion Stefan Heinz*

    E-Print Network [OSTI]

    Heinz, Stefan

    to derive a hierarchy of algebraic expressions for the molecular stress tensor and heat flux. A scaling of ordinary irreversible thermodynamics [3]) transport equations for the molecular stress tensor and heat flux equations. The stochastic model is used to derive fluid dynamic equations where the molecular stress tensor

  3. Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms

    E-Print Network [OSTI]

    Richardson, David

    Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit) for analyzing interaction patterns in the molecules themselves. # 1999 Academic Press Keywords: protein internal, 1711±1733 0022-2836/99/041711±23 $30.00/0 # 1999 Academic Press #12;Introduction Remarkably ordered

  4. A quantum simulator for molecules: Imaging molecular orbitals and electronic dynamics with ultracold atoms

    E-Print Network [OSTI]

    Lühmann, Dirk-Sören; Sengstock, Klaus

    2015-01-01T23:59:59.000Z

    In the recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly-correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully-adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated pi electron system with special regard to localization and spin order. The dynamical timescale of ultracold atom simulators are on the order milliseconds which allow for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated pi system of the artificial benzene molecule.

  5. Interactive design center.

    SciTech Connect (OSTI)

    Pomplun, Alan R. (Sandia National Laboratories, Livermore, CA)

    2005-07-01T23:59:59.000Z

    Sandia's advanced computing resources provide researchers, engineers and analysts with the ability to develop and render highly detailed large-scale models and simulations. To take full advantage of these multi-million data point visualizations, display systems with comparable pixel counts are needed. The Interactive Design Center (IDC) is a second generation visualization theater designed to meet this need. The main display integrates twenty-seven projectors in a 9-wide by 3-high array with a total display resolution of more than 35 million pixels. Six individual SmartBoard displays offer interactive capabilities that include on-screen annotation and touch panel control of the facility's display systems. This report details the design, implementation and operation of this innovative facility.

  6. Interactive optical panel

    DOE Patents [OSTI]

    Veligdan, J.T.

    1995-10-03T23:59:59.000Z

    An interactive optical panel assembly includes an optical panel having a plurality of ribbon optical waveguides stacked together with opposite ends thereof defining panel first and second faces. A light source provides an image beam to the panel first face for being channeled through the waveguides and emitted from the panel second face in the form of a viewable light image. A remote device produces a response beam over a discrete selection area of the panel second face for being channeled through at least one of the waveguides toward the panel first face. A light sensor is disposed across a plurality of the waveguides for detecting the response beam therein for providing interactive capability. 10 figs.

  7. Interactive optical panel

    DOE Patents [OSTI]

    Veligdan, James T. (Manorville, NY)

    1995-10-03T23:59:59.000Z

    An interactive optical panel assembly 34 includes an optical panel 10 having a plurality of ribbon optical waveguides 12 stacked together with opposite ends thereof defining panel first and second faces 16, 18. A light source 20 provides an image beam 22 to the panel first face 16 for being channeled through the waveguides 12 and emitted from the panel second face 18 in the form of a viewable light image 24a. A remote device 38 produces a response beam 40 over a discrete selection area 36 of the panel second face 18 for being channeled through at least one of the waveguides 12 toward the panel first face 16. A light sensor 42,50 is disposed across a plurality of the waveguides 12 for detecting the response beam 40 therein for providing interactive capability.

  8. ELEMENTARY PARTICLE INTERACTIONS

    SciTech Connect (OSTI)

    EFREMENKO, YURI; HANDLER, THOMAS; KAMYSHKOV, YURI; SIOPSIS, GEORGE; SPANIER, STEFAN

    2013-07-30T23:59:59.000Z

    The High-Energy Elementary Particle Interactions group at UT during the last three years worked on the following directions and projects: Collider-based Particle Physics; Neutrino Physics, particularly participation in “NO?A”, “Double Chooz”, and “KamLAND” neutrino experiments; and Theory, including Scattering amplitudes, Quark-gluon plasma; Holographic cosmology; Holographic superconductors; Charge density waves; Striped superconductors; and Holographic FFLO states.

  9. Interactive Transportable Architecture

    E-Print Network [OSTI]

    Oliver Irschitz; Priam Givord; Newyork Exit Newyork; Flavia Sparacino

    Transportable architecture which embeds the means to communicate with real or imaginary digital information spaces in a natural fashion offers unprecedented opportunities to make multimedia experiences available to the public almost everywhere. This installation demonstrates an example of interactive transportable architecture which incorporates unencumebered real-time body tracking and gesture recognition to explore a 3-D cityscape and a brain-like web-based information space.

  10. Neutrino Interactions with Nuclei

    SciTech Connect (OSTI)

    Leitner, T.; Buss, O.; Mosel, U. [Institut fuer Theoretische Physik, Universitaet Giessen (Germany); Alvarez-Ruso, L. [Departamento de Fisica Teorica and IFIC, Universidad de Valencia-CSIC (Spain)

    2007-12-21T23:59:59.000Z

    We investigate neutrino-nucleus collisions at intermediate energies incorporating quasielastic scattering and the excitation of 13 resonances as elementary processes, taking into account medium effects such as Fermi motion, Pauli blocking, mean-field potentials and in-medium spectral functions. A coupled-channel treatment of final state interactions is achieved with the GiBUU transport model. Results for inclusive reactions, neutrino- and electron-induced, as well as for pion production and nucleon knockout are presented.

  11. Thermoelectric effect in molecular electronics

    E-Print Network [OSTI]

    M. Paulsson; S. Datta

    2003-01-14T23:59:59.000Z

    We provide a theoretical estimate of the thermoelectric current and voltage over a Phenyldithiol molecule. We also show that the thermoelectric voltage is (1) easy to analyze, (2) insensitive to the detailed coupling to the contacts, (3) large enough to be measured and (4) give valuable information, which is not readily accessible through other experiments, on the location of the Fermi energy relative to the molecular levels. The location of the Fermi-energy is poorly understood and controversial even though it is a central factor in determining the nature of conduction (n- or p-type). We also note that the thermoelectric voltage measured over Guanine molecules with an STM by Poler et al., indicate conduction through the HOMO level, i.e., p-type conduction.

  12. Optimal prediction in molecular dynamics

    E-Print Network [OSTI]

    Benjamin Seibold

    2008-08-22T23:59:59.000Z

    Optimal prediction approximates the average solution of a large system of ordinary differential equations by a smaller system. We present how optimal prediction can be applied to a typical problem in the field of molecular dynamics, in order to reduce the number of particles to be tracked in the computations. We consider a model problem, which describes a surface coating process, and show how asymptotic methods can be employed to approximate the high dimensional conditional expectations, which arise in optimal prediction. The thus derived smaller system is compared to the original system in terms of statistical quantities, such as diffusion constants. The comparison is carried out by Monte-Carlo simulations, and it is shown under which conditions optimal prediction yields a valid approximation to the original system.

  13. Turbulence-chemistry interactions in reacting flows

    SciTech Connect (OSTI)

    Barlow, R.S.; Carter, C.D. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01T23:59:59.000Z

    Interactions between turbulence and chemistry in nonpremixed flames are investigated through multiscalar measurements. Simultaneous point measurements of major species, NO, OH, temperature, and mixture fraction are obtained by combining spontaneous Raman scattering, Rayleigh scattering, and laser-induced fluorescence (LIF). NO and OH fluorescence signals are converted to quantitative concentrations by applying shot-to-shot corrections for local variations of the Boltzmann fraction and collisional quenching rate. These measurements of instantaneous thermochemical states in turbulent flames provide insights into the fundamental nature of turbulence-chemistry interactions. The measurements also constitute a unique data base for evaluation and refinement of turbulent combustion models. Experimental work during the past year has focused on three areas: (1) investigation of the effects of differential molecular diffusion in turbulent combustion: (2) experiments on the effects of Halon CF{sub 3}Br, a fire retardant, on the structure of turbulent flames of CH{sub 4} and CO/H{sub 2}/N{sub 2}; and (3) experiments on NO formation in turbulent hydrogen jet flames.

  14. Electron localization following attosecond molecular photoionization

    E-Print Network [OSTI]

    Kling, Matthias

    - second pump­probe strategies as a powerful tool for investigating the complex molecular dynamics , their use in studying atomic photo- excitation and photoionization6,7 and electron dynamics in solids8 has and biomolecular complexes11,12 . Extremely fast molecular dynamics involving electron correlation can also

  15. Clinical Molecular Geneticist Two-Year Fellowship

    E-Print Network [OSTI]

    Finley Jr., Russell L.

    Clinical Molecular Geneticist Two-Year Fellowship YEAR 1 YEAR 2 MONDAY TUESDAY WEDNESDAY THURSDAY FRIDAY A.M. 11-12 DNA Sign- out conference Lab Research & Clinical Training Lab Research & Clinical Training (includes rotation in Molecular Microbiology lab) Lab Research & Clinical Training Lab Research

  16. Molecular Simulation of Nanofluids Mark J. Biggs

    E-Print Network [OSTI]

    Adler, Joan

    Molecular Simulation of Nanofluids Mark J. Biggs School of Chemical Engineering, The University of Adelaide, South Australia, Australia, 5005. mark.biggs@adelaide.edu.au Models of nanofluid systems ­ which suited in many cases to those of nanofluid systems. It is for this reason that molecular simulation has

  17. SLAC All Access: Atomic, Molecular and Optical Science Instrument

    SciTech Connect (OSTI)

    Bozek, John

    2013-11-05T23:59:59.000Z

    John Bozek, a staff scientist at SLAC's Linac Coherent Light Source (LCLS) X-ray laser who manages the LCLS Soft X-ray Department, takes us behind the scenes at the Atomic, Molecular and Optical Science (AMO) instrument, the first of six experimental stations now operating at LCLS. Samples used in AMO experiments include atoms, molecules, clusters, and nanoscale objects such as protein crystals or viruses. Science performed at AMO includes fundamental studies of light-matter interactions in the extreme X-ray intensity of the LCLS pules, time-resolved studies of increasingly charged states of atoms and molecules, X-ray diffraction imaging of nanocrystals, and single-shot imaging of a variety of objects.

  18. SLAC All Access: Atomic, Molecular and Optical Science Instrument

    ScienceCinema (OSTI)

    Bozek, John

    2014-06-03T23:59:59.000Z

    John Bozek, a staff scientist at SLAC's Linac Coherent Light Source (LCLS) X-ray laser who manages the LCLS Soft X-ray Department, takes us behind the scenes at the Atomic, Molecular and Optical Science (AMO) instrument, the first of six experimental stations now operating at LCLS. Samples used in AMO experiments include atoms, molecules, clusters, and nanoscale objects such as protein crystals or viruses. Science performed at AMO includes fundamental studies of light-matter interactions in the extreme X-ray intensity of the LCLS pules, time-resolved studies of increasingly charged states of atoms and molecules, X-ray diffraction imaging of nanocrystals, and single-shot imaging of a variety of objects.

  19. MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS

    SciTech Connect (OSTI)

    Athanassios Z. Panagiotopoulos

    2009-09-09T23:59:59.000Z

    The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.

  20. PII S0016-7037(01)00595-6 Spectroscopic studies of Pb(II)-sulfate interactions at the goethite-water interface

    E-Print Network [OSTI]

    Sparks, Donald L.

    PII S0016-7037(01)00595-6 Spectroscopic studies of Pb(II)-sulfate interactions at the goethite molecular scale studies on Pb(II)-sulfate interactions at the solid-water interface of goethite at pH 4.5, 5 the formation Pb-SO4 ternary complexes at the goethite surface. Based on the combined information from the IR

  1. Excitation and Disruption of a Giant Molecular Cloud by the Supernova Remnant 3C391

    E-Print Network [OSTI]

    William T. Reach; Jeonghee Rho

    1998-07-28T23:59:59.000Z

    Using the IRAM 30-m telescope, we observed the supernova remnant 3C 391 (G31.9+0.0) and its surroundings in the CO(2-1), HCO+(1-0), CS(2-1), CS(3-2), and CS(5-4) lines. The ambient molecular gas at the distance (9 kpc) of the remnant comprises a giant molecular cloud whose edge is closely parallel to a ridge of bright non-thermal radio continuum, which evidently delineates the blast-wave into the cloud. We found that in a small (0.6 pc) portion of the radio shell, the molecular line profiles consist of a narrow (2 km/s) component, plus a very wide (> 20 km/s) component. Both spectral components peak within 20" of a previously-detected OH 1720 MHz maser. We name this source 3C 391:BML (broad molecular line); it provides a new laboratory, similar to IC 443 but on a larger scale, to study shock interactions with dense molecular gas. The wide spectral component is relatively brighter in the higher-excitation lines. We interpret the wide spectral component as post-shock gas, either smoothly accelerated or partially dissociated and reformed behind the shock. The narrow component is either the pre-shock gas or cold gas reformed behind a fully dissociative shock. Using the 3 observed CS lines, we measured the temperature, CS column density, and H2 volume density in a dense clump in the parent molecular cloud as well as the wide-line and narrow-line portions of the shocked clump. The physical conditions of the narrow-line gas are comparable to the highest-density clumps in the giant molecular cloud, while the wide-line gas is both warmer and denser. The mass of compressed gas in 3C 391:BML is high enough that its self-gravity is significant, and eventually it could form one or several stars.

  2. On statistics of molecular chaos

    E-Print Network [OSTI]

    Yuriy Kuzovlev

    2009-11-03T23:59:59.000Z

    It is shown that the BBGKY equations for a particle interacting with ideal gas imply exact relations between probability distribution of path of the particle, its derivatives in respect to the gas density and irreducible many-particle correlations of gas atoms with the path. These relations visualize that the correlations of any order always significantly contribute to evolution of the path distribution, so that the exact statistical mechanics theory does not reduce to the classical kinetics even in the low-density (or Boltzmann-Grad) limit.

  3. Mass Spectral Molecular Networking of Living Microbial Colonies

    SciTech Connect (OSTI)

    Watrous, Jeramie D.; Roach, Patrick J.; Alexandrov, Theodore; Heath, Brandi S.; Yang, Jane Y.; Kersten, Roland; vander Voort, Menno; Pogliano, Kit; Gross, Harald; Raaijmakers, Jos M.; Moore, Bradley S.; Laskin, Julia; Bandeira, Nuno; Dorrestein, Pieter C.

    2012-06-26T23:59:59.000Z

    Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a "holy grail" in microbiology. This work describes a highly sensitive, broadly applicable, and costeffective approach that allows metabolic profiling of live microbial colonies directly from a Petri dish without any sample preparation. Nanospray desorption electrospray ionization mass spectrometry (MS), combined with alignment of MS data and molecular networking, enabled monitoring of metabolite production from live microbial colonies from diverse bacterial genera, including Bacillus subtilis, Streptomyces coelicolor, Mycobacterium smegmatis, and Pseudomonas aeruginosa. This work demonstrates that, by using these tools to visualize small molecular changes within bacterial interactions, insights can be gained into bacterial developmental processes as a result of the improved organization of MS/MS data. To validate this experimental platform, metabolic profiling was performed on Pseudomonas sp. SH-C52, which protects sugar beet plants from infections by specific soil-borne fungi [R. Mendes et al. (2011) Science 332:1097–1100]. The antifungal effect of strain SHC52 was attributed to thanamycin, a predicted lipopeptide encoded by a nonribosomal peptide synthetase gene cluster. Our technology, in combination with our recently developed peptidogenomics strategy, enabled the detection and partial characterization of thanamycin and showed that it is amonochlorinated lipopeptide that belongs to the syringomycin family of antifungal agents. In conclusion, the platform presented here provides a significant advancement in our ability to understand the spatiotemporal dynamics of metabolite production in live microbial colonies and communities.

  4. Cold Water Vapor in the Barnard 5 Molecular Cloud

    E-Print Network [OSTI]

    Wirström, E S; Persson, C M; Buckle, J V; Cordiner, M A; Takakuwa, S

    2014-01-01T23:59:59.000Z

    After more than 30 years of investigations, the nature of gas-grain interactions at low temperatures remains an unresolved issue in astrochemistry. Water ice is the dominant ice found in cold molecular clouds, however, there is only one region where cold (~10 K) water vapor has been detected - L1544. This study aims to shed light on ice desorption mechanisms under cold cloud conditions by expanding the sample. The clumpy distribution of methanol in dark clouds testifies to transient desorption processes at work -- likely to also disrupt water ice mantles. Therefore, the Herschel HIFI instrument was used to search for cold water in a small sample of prominent methanol emission peaks. We report detections of the ground-state transition of o-H2O (J = 1_10 - 1_01) at 556.9360 GHz toward two positions in the cold molecular cloud Barnard 5. The relative abundances of methanol and water gas support a desorption mechanism which disrupts the outer ice mantle layers, rather than causing complete mantle removal.

  5. On the Computational Power of Molecular Heat Engines

    E-Print Network [OSTI]

    Dominik Janzing

    2005-02-02T23:59:59.000Z

    A heat engine is a machine which uses the temperature difference between a hot and a cold reservoir to extract work. Here both reservoirs are quantum systems and a heat engine is described by a unitary transformation which decreases the average energy of the bipartite system. On the molecular scale, the ability of implementing such a unitary heat engine is closely connected to the ability of performing logical operations and classical computing. This is shown by several examples: (1) The most elementary heat engine is a SWAP-gate acting on 1 hot and 1 cold two-level systems with different energy gaps. (2) An optimal unitary heat engine on a pair of 3-level systems can directly implement OR and NOT gates, as well as copy operations. The ability to implement this heat engine on each pair of 3-level systems taken from the hot and the cold ensemble therefore allows universal classical computation. (3) Optimal heat engines operating on one hot and one cold oscillator mode with different frequencies are able to calculate polynomials and roots approximately. (4) An optimal heat engine acting on 1 hot and n cold 2-level systems with different level spacings can even solve the NP-complete problem KNAPSACK. Whereas it is already known that the determination of ground states of interacting many-particle systems is NP-hard, the optimal heat engine is a thermodynamic problem which is NP-hard even for n non-interacting spin systems. This result suggest that there may be complexity-theoretic limitations on the efficiency of molecular heat engines.

  6. Molecular mechanisms of hydrogen loaded B-hydroquinone clathrate

    SciTech Connect (OSTI)

    Daschbach, John L.; Chang, Tsun-Mei; Corrales, Louis R.; Dang, Liem X.; McGrail, B. Peter

    2006-09-07T23:59:59.000Z

    Molecular dynamics simulations are used to investigate the molecular interactions of hydrogen loaded beta-hydroquinone clathrate. It is found that at lower temperatures, higher loadings are more stable, whereas, at higher temperatures, lower loadings are more stable. This trend can be understood based on the interactions in the system. For loadings greater than one, the repulsive forces between the guest molecules shove each other towards the attractive forces between the guest and host molecules leading to a stabilized minimum energy configuration at low temperatures. At higher temperatures greater displacements take the system away from the shallow energy minimum and the trend reverses. The asymmetries of the clathrate cage structure are due to the presence of the attractive forces at loadings greater than one that lead to confined states. The nature of the cavity structure is nearly spherical for a loading of one, leads to preferential occupation near the hydroxyl ring crowns of the cavity with a loading of two, and at higher loadings, leads to occupation of the interstitial sites (the hydroxyl rings) between cages by a single H2 molecule with the remaining molecules occupying the equatorial plane of the cavity. At higher temperatures, the cavity is more uniformly occupied for all loadings, where the occupation of the interstitial positions of the cavities leads to facile diffusion. ACKNOWLEDGEMENT This work was partially supported by NIDO (Japan), LDRD (PNNL), EERE U.S. Department of Energy, and by OBES, U.S. DOE. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy

  7. PDSF Interactive Batch Jobs

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of Science (SC)IntegratedSpeeding access toTest andOptimize832 2.860 2.864 2.867039 JEmailInteractive

  8. Signature molecular descriptor : advanced applications.

    SciTech Connect (OSTI)

    Visco, Donald Patrick, Jr. (Tennessee Technological University, Cookeville, TN)

    2010-04-01T23:59:59.000Z

    In this work we report on the development of the Signature Molecular Descriptor (or Signature) for use in the solution of inverse design problems as well as in highthroughput screening applications. The ultimate goal of using Signature is to identify novel and non-intuitive chemical structures with optimal predicted properties for a given application. We demonstrate this in three studies: green solvent design, glucocorticoid receptor ligand design and the design of inhibitors for Factor XIa. In many areas of engineering, compounds are designed and/or modified in incremental ways which rely upon heuristics or institutional knowledge. Often multiple experiments are performed and the optimal compound is identified in this brute-force fashion. Perhaps a traditional chemical scaffold is identified and movement of a substituent group around a ring constitutes the whole of the design process. Also notably, a chemical being evaluated in one area might demonstrate properties very attractive in another area and serendipity was the mechanism for solution. In contrast to such approaches, computer-aided molecular design (CAMD) looks to encompass both experimental and heuristic-based knowledge into a strategy that will design a molecule on a computer to meet a given target. Depending on the algorithm employed, the molecule which is designed might be quite novel (re: no CAS registration number) and/or non-intuitive relative to what is known about the problem at hand. While CAMD is a fairly recent strategy (dating to the early 1980s), it contains a variety of bottlenecks and limitations which have prevented the technique from garnering more attention in the academic, governmental and industrial institutions. A main reason for this is how the molecules are described in the computer. This step can control how models are developed for the properties of interest on a given problem as well as how to go from an output of the algorithm to an actual chemical structure. This report provides details on a technique to describe molecules on a computer, called Signature, as well as the computer-aided molecule design algorithm built around Signature. Two applications are provided of the CAMD algorithm with Signature. The first describes the design of green solvents based on data in the GlaxoSmithKline (GSK) Solvent Selection Guide. The second provides novel non-steroidal glucocorticoid receptor ligands with some optimally predicted properties. In addition to using the CAMD algorithm with Signature, it is demonstrated how to employ Signature in a high-throughput screening study. Here, after classifying both active and inactive inhibitors for the protein Factor XIa using Signature, the model developed is used to screen a large, publicly-available database called PubChem for the most active compounds.

  9. Control of hydrogen release and uptake in amine borane molecular...

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

    uptake in amine borane molecular complexes: Thermodynamics of ammonia borane, ammonium Control of hydrogen release and uptake in amine borane molecular complexes: Thermodynamics of...

  10. Molecular dynamics simulation and ab intio studies of electrolytes...

    Broader source: Energy.gov (indexed) [DOE]

    Molecular dynamics simulation and ab intio studies of electrolytes and electrolyteelectrode interfaces Molecular dynamics simulation and ab intio studies of electrolytes and...

  11. Molecular Dynamics Simulation of the AgCl/Electrolyte Interfacial...

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

    Simulation of the AgClElectrolyte Interfacial Capacity. Molecular Dynamics Simulation of the AgClElectrolyte Interfacial Capacity. Abstract: Molecular dynamics simulation of the...

  12. Comparative molecular dynamics analysis of tapasin-dependent...

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

    molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles. Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I...

  13. Atomic and Molecular Adsorption on Re(0001). | EMSL

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

    Molecular Adsorption on Re(0001). Atomic and Molecular Adsorption on Re(0001). Abstract: Using periodic, self-consistent density functional theory calculations, the adsorption of...

  14. Combined Quantum Mechanical and Molecular Mechanics Studies of...

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

    Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Combined Quantum Mechanical and Molecular Mechanics Studies of the...

  15. Electron-Stimulated Production of Molecular Oxygen in Amorphous...

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

    Water. Electron-Stimulated Production of Molecular Oxygen in Amorphous Solid Water. Abstract: The low-energy, electron-stimulated production of molecular oxygen from pure amorphous...

  16. Functionalized Graphene Sheets as Molecular Templates for Controlled...

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

    as Molecular Templates for Controlled Nucleation and Self-Assembly of Metal Oxide-Graphene Functionalized Graphene Sheets as Molecular Templates for Controlled Nucleation and...

  17. MESTRADO EM MICROBIOLOGIA MICROBIOLOGIA MOLECULAR E CELULAR Instituto Superior Tcnico

    E-Print Network [OSTI]

    Instituto de Sistemas e Robotica

    MESTRADO EM MICROBIOLOGIA MICROBIOLOGIA MOLECULAR E CELULAR ­ Instituto Superior Técnico Objectivos. * Biologia Celular e Molecular, C. Azevedo, C.E. Sunkel, 2012, LIDEL ­ Edições Técnicas, Lisboa. #12;

  18. The influence of molecular orientation on organic bulk heterojunction...

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

    The influence of molecular orientation on organic bulk heterojunction solar cells The influence of molecular orientation on organic bulk heterojunction solar cells Print Monday, 28...

  19. Chitosan Molecular Structure as a Function of N-Acetylation....

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

    Chitosan Molecular Structure as a Function of N-Acetylation. Abstract: Molecular dynamics simulations have been carried out to characterize the structure and solubility of...

  20. Neutron Powder Diffraction and Molecular Simulation Study of...

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

    Powder Diffraction and Molecular Simulation Study of the Structural Evolution of Ammonia Borane from 15 to 340 K. Neutron Powder Diffraction and Molecular Simulation Study of the...

  1. An efficient parallelization scheme for molecular dynamics simulations...

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

    efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical An efficient parallelization scheme for molecular dynamics...

  2. B13+: Photodriven Molecular Wankel Engine

    SciTech Connect (OSTI)

    Zhang, Jin; Sergeeva, Alina P.; Sparta, Manuel; Alexandrova, Anastassia N.

    2012-07-09T23:59:59.000Z

    Synthetic molecular motors that are capable of delivering controlled movement upon energy input are one of the key building blocks in nanomachinery. The major energy sources of molecular motors are from chemical reactions, photon beams, or electric current, which are converted into mechanical forces through the excitation of the electronic states of the molecule. The energy scale of the electronic excitation is normally two orders of magnitude larger than the molecular vibrational frequencies. To reduce the heat dissipation and increase the energy utilization efficiency, a motor running purely on the electronic ground-state (GS) potential energy surfaces is highly desirable.

  3. The efficiency of the molecular motors

    E-Print Network [OSTI]

    Yunxin Zhang

    2009-02-12T23:59:59.000Z

    Molecular motors convert chemical energy into mechanical work while operating in an environment dominated by Brownian motion. The aim of this paper is to explore the flow of energy between the molecular motors and its surroundings, in particular, its efficiency. Based on the Fokker-Planck equation with either $N$ or infinite chemical states, we find that the energy efficiency of the molecular motors, whether the Stokes efficiency or the usual thermodynamic efficiency, is strictly bounded by 1, because of the dissipation of the energy in both the overdamped surroundings and in the process of the chemical reaction.

  4. Niobate-based octahedral molecular sieves

    DOE Patents [OSTI]

    Nenoff, Tina M.; Nyman, May D.

    2003-07-22T23:59:59.000Z

    Niobate-based octahedral molecular sieves having significant activity for multivalent cations and a method for synthesizing such sieves are disclosed. The sieves have a net negatively charged octahedral framework, comprising niobium, oxygen, and octahedrally coordinated lower valence transition metals. The framework can be charge balanced by the occluded alkali cation from the synthesis method. The alkali cation can be exchanged for other contaminant metal ions. The ion-exchanged niobate-based octahedral molecular sieve can be backexchanged in acidic solutions to yield a solution concentrated in the contaminant metal. Alternatively, the ion-exchanged niobate-based octahedral molecular sieve can be thermally converted to a durable perovskite phase waste form.

  5. Niobate-based octahedral molecular sieves

    DOE Patents [OSTI]

    Nenoff, Tina M.; Nyman, May D.

    2006-10-17T23:59:59.000Z

    Niobate-based octahedral molecular sieves having significant activity for multivalent cations and a method for synthesizing such sieves are disclosed. The sieves have a net negatively charged octahedral framework, comprising niobium, oxygen, and octahedrally coordinated lower valence transition metals. The framework can be charge balanced by the occluded alkali cation from the synthesis method. The alkali cation can be exchanged for other contaminant metal ions. The ion-exchanged niobate-based octahedral molecular sieve can be backexchanged in acidic solutions to yield a solution concentrated in the contaminant metal. Alternatively, the ion-exchanged niobate-based octahedral molecular sieve can be thermally converted to a durable perovskite phase waste form.

  6. Reactions of small molecular systems

    SciTech Connect (OSTI)

    Wittig, C. [Univ. of Southern California, Los Angeles, CA (United States)

    1993-12-01T23:59:59.000Z

    This DOE program remains focused on small molecular systems relevant to combustion. Though a number of experimental approaches and machines are available for this research, the authors` activities are centered around the high-n Rydberg time-of-flight (HRTOF) apparatus in this laboratory. One student and one postdoc carry out experiments with this machine and also engage in small intra-group collaborations involving shared equipment. This past year was more productive than the previous two, due to the uninterrupted operation of the HRTOF apparatus. Results were obtained with CH{sub 3}OH, CH{sub 3}SH, Rg-HX complexes, HCOOH, and their deuterated analogs where appropriate. One paper is in print, three have been accepted for publication, and one is under review. Many preliminary results that augur well for the future were obtained with other systems such as HNO{sub 3}, HBr-HI complexes, toluene, etc. Highlights from the past year are presented below that display some of the features of this program.

  7. LATTICE: AN INTERACTIVE LATTICE COMPUTER CODE

    E-Print Network [OSTI]

    Staples, John

    2010-01-01T23:59:59.000Z

    4500-R65 I LATTICE AN INTERACTIVE LATTICE COMPUTER CODE Johnr LBL-4843 LATTICE An interactive lattice computer code Johncode which enables an interactive user to calculate the

  8. Interactive visual supports for children with autism

    E-Print Network [OSTI]

    Hayes, Gillian R.; Hirano, Sen; Marcu, Gabriela; Monibi, Mohamad; Nguyen, David H.; Yeganyan, Michael

    2010-01-01T23:59:59.000Z

    010-0294-8 ORIGINAL ARTICLE Interactive visual supports fordesign guidelines for interactive visual supports that wouldvSked, a multi-device interactive visual schedule system.

  9. Symbiogenic Experiences in the Interactive Arts

    E-Print Network [OSTI]

    Castellanos, Carlos; Gromala, Diane

    2009-01-01T23:59:59.000Z

    Symbiogenic Experiences in the Interactive Arts CarlosCastellanos School of Interactive Arts and Technology SimonDiane Gromala School of Interactive Arts and Technology

  10. Torchestra : reducing interactive trac delays over Tor

    E-Print Network [OSTI]

    Gopal, Deepika

    2012-01-01T23:59:59.000Z

    Torchestra : Reducing interactive traffic delays over Tor ATorchestra : Reducing interactive traffic delays over Tor byon the internet including interactive traffic as well as for

  11. Non-Local Correlations and Interactive Games

    E-Print Network [OSTI]

    Preda, Daniel Ciprian

    2011-01-01T23:59:59.000Z

    and multi-prover interactive proof systems . . . . . . . .correspondence to multi-prover interactive proof systems. AWigderson. Multi-prover interactive proofs: How to remove

  12. Interactive motion planning with motion capture data

    E-Print Network [OSTI]

    Lo, Wan-Yen

    2012-01-01T23:59:59.000Z

    Abe, and Jovan Popovi´c. Interactive simulation of stylizedc. Motion fields for interactive character locomotion. ACMon Computer graphics and interactive techniques, SIGGRAPH ’

  13. Biological Interactions and Dynamics Workshop | EMSL

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

    Biological Interactions and Dynamics Workshop Biological Interactions and Dynamics Workshop Wiley HS, Kaplan S. 2011. "Biological Interactions and Dynamics Science Theme Advisory...

  14. TYCHO SN 1572: A NAKED Ia SUPERNOVA REMNANT WITHOUT AN ASSOCIATED AMBIENT MOLECULAR CLOUD

    SciTech Connect (OSTI)

    Tian, W. W. [National Astronomical Observatories, CAS, Beijing 100012 (China); Leahy, D. A., E-mail: tww@bao.ac.cn [Department of Physics and Astronomy, University of Calgary, Calgary, Alberta T2N 1N4 (Canada)

    2011-03-10T23:59:59.000Z

    The historical supernova remnant (SNR) Tycho SN 1572 originates from the explosion of a normal Type Ia supernova that is believed to have originated from a carbon-oxygen white dwarf in a binary system. We analyze the 21 cm continuum, H I, and {sup 12}CO-line data from the Canadian Galactic Plane Survey in the direction of SN 1572 and the surrounding region. We construct H I absorption spectra to SN 1572 and three nearby compact sources. We conclude that SN 1572 has no molecular cloud interaction, which argues against previous claims that a molecular cloud is interacting with the SNR. This new result does not support a recent claim that dust, newly detected by AKARI, originates from such an SNR-cloud interaction. We suggest that the SNR has a kinematic distance of 2.5-3.0 kpc based on a nonlinear rotational curve model. Very high energy {gamma}-ray emission from the remnant has been detected by the VERITAS telescope, so our result shows that its origin should not be an SNR-cloud interaction. Both radio and X-ray observations support that SN 1572 is an isolated Type Ia SNR.

  15. Electronic structure of the dioxygen to transition metal bond: generalized molecular orbital calculations on models of manganese, iron, and cobalt porphyrins 

    E-Print Network [OSTI]

    Newton, James Edward

    1982-01-01T23:59:59.000Z

    calculat1on y1elded a I ground. state conf1gurat1on in which the bonding orbital has an occu- pation number of 1. 97 and the antibond1ng orbital has an occupat1on number of 0. 03 electrons. Both Pauling and Griffith geometr1es of Nn(0 )(H C H ) y1... Geometries. Basis sets. . Results Fenske-Hall molecular orbi tal calculations. Restricted Hartree-Fock-Roothaan-Configuration Interaction calculations. 56 58 59 ~ ~ 59 ~ ~ 61 62 62 65 Generalized Molecular Orbi tal-Conf i gurati on Interaction...

  16. WANTED: Undergraduate Research Assistant Betelgeuse's Molecular Inventory

    E-Print Network [OSTI]

    Harper, Graham

    WANTED: Undergraduate Research Assistant Betelgeuse's Molecular Inventory GHRS Pre-COSTAR LSA G140L Assistant Opportunity We are seeking an undergraduate research assistant to help make an inventory

  17. Novel molecular architectures from iptycene polymers

    E-Print Network [OSTI]

    Tsui, Nicholas T. (Nicholas Tang)

    2007-01-01T23:59:59.000Z

    This thesis explored the incorporation of iptycenes into polymers as a means to enhance the mechanical properties. Iptycene structures were targeted because they possess a unique structural property called internal molecular ...

  18. Intra-molecular refrigeration in enzymes

    E-Print Network [OSTI]

    Hans J. Briegel; Sandu Popescu

    2009-12-14T23:59:59.000Z

    We present a simple mechanism for intra-molecular refrigeration, where parts of a molecule are actively cooled below the environmental temperature. We discuss the potential role and applications of such a mechanism in biology, in particular in enzymatic reactions.

  19. Molecular Selectivity of Brown Carbon Chromophores. | EMSL

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

    of strong brown carbon chromophores. Citation: Laskin J, A Laskin, S Nizkorodov, PJ Roach, PA Eckert, MK Gilles, B Wang, HJ Lee, and Q Hu.2014."Molecular Selectivity of Brown...

  20. Analysis of programmable molecular electronic systems

    E-Print Network [OSTI]

    Ma, Yuefei

    2007-09-17T23:59:59.000Z

    of the programmable molecular array is performed. First, theoretical calculations for single molecules are carried out. The effect of bias voltage on the electron transmission through the molecule is reported. Next, electrical measurements are conducted...

  1. Molecular Nanomagnets of Fe(III) 

    E-Print Network [OSTI]

    Gass, Ian Andrew

    2008-01-01T23:59:59.000Z

    Two routes for preparing polymetallic clusters of iron have been investigated: the first strategy is to make molecular analogues of naturally occurring magnetic oxides using controlled hydrolysis and the second involves ...

  2. Genetics and molecular biology of breast cancer

    SciTech Connect (OSTI)

    King, M.C. [California Univ., Berkeley, CA (United States); Lippman, M. [Georgetown Univ. Medical Center, Washington, DC (United States)] [comps.

    1992-12-31T23:59:59.000Z

    This volume contains the abstracts of oral presentations and poster sessions presented at the Cold Springs Harbor Meeting on Cancer Cells, this meeting entitled Genetics and Molecular Biology of Breast Cancer.

  3. Environmental Molecular Sciences Laboratory 2007 Annual Report

    SciTech Connect (OSTI)

    Showalter, Mary Ann; Foster, Nancy S.

    2008-03-19T23:59:59.000Z

    This annual report provides details on the research conducted at the Environmental Molecular Sciences Laboratory in Fiscal Year 2007 and path forward for capability upgrades in Fiscal Year 2008.

  4. Combinatorial molecular optimization of cement hydrates

    E-Print Network [OSTI]

    Abdolhosseini Qomi, Mohammad

    Despite its ubiquitous presence in the built environment, concrete’s molecular-level properties are only recently being explored using experimental and simulation studies. Increasing societal concerns about concrete’s ...

  5. Comprehensive molecular profiling of lung adenocarcinoma

    E-Print Network [OSTI]

    Lander, Eric S.

    Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, ...

  6. 12.458 Molecular Biogeochemistry, Fall 2006

    E-Print Network [OSTI]

    Summons, Roger

    This course covers all aspects of molecular biosignatures from their pathways of lipid biosynthesis, the distribution patterns of lipid biosynthetic pathways with regard to phylogeny and physiology, isotopic contents, ...

  7. Non standard neutrino interactions

    E-Print Network [OSTI]

    Miranda, O G

    2015-01-01T23:59:59.000Z

    Neutrino oscillations have become well-known phenomenon; the measurements of neutrino mixing angles and mass squared differences are continuously improving. Future oscillation experiments will eventually determine the remaining unknown neutrino parameters, namely, the mass ordering, normal or inverted, and the CP-violating phase. On the other hand, the absolute mass scale of neutrinos could be probed by cosmological observations, single beta decay as well as by neutrinoless double beta decay experiments. Furthermore, the last one may shed light on the nature of neutrinos, Dirac or Majorana, by measuring the effective Majorana mass of neutrinos. However, the neutrino mass generation mechanism remains unknown. A well-motivated phenomenological approach to search for new physics, in the neutrino sector, is that of non-standard interactions. In this short review, the current constraints in this picture, as well as the perspectives from future experiments, are discussed.

  8. Weak Interaction and Cosmology

    E-Print Network [OSTI]

    P. R. Silva

    2008-04-16T23:59:59.000Z

    In this paper we examine the connection among the themes: the cosmological constant, the weak interaction and the neutrino mass. Our main propose is to review and modify the ideas first proposed by Hayakawa [ Prog. Theor. Phys.Suppl.,532(1965).], in the light of the new-fashioned features of contemporary physics. Assuming the pressure of a Fermi gas of neutrinos should be balanced by its gravitational attraction, we evaluate the mass of the background neutrino and its number.The neutrino mass here evaluated is compatible with the known value for the cosmological constant (or dark energy).Taking in account the role played by the weak forces experimented by the neutrinos, we also determined a value for the electroweak mixing angle. For sake of comparison, an alternative evaluation of the neutrino mass is also done.

  9. Loose mechanochemical coupling of molecular motors

    E-Print Network [OSTI]

    Yunxin Zhang

    2011-05-05T23:59:59.000Z

    In living cells, molecular motors convert chemical energy into mechanical work. Its thermodynamic energy efficiency, i.e. the ratio of output mechanical work to input chemical energy, is usually high. However, using two-state models, we found the motion of molecular motors is loosely coupled to the chemical cycle. Only part of the input energy can be converted into mechanical work. Others is dissipated into environment during substeps without contributions to the macro scale unidirectional movement.

  10. New silicotitanate molecular sieve and condensed phases

    SciTech Connect (OSTI)

    Nenoff, Tina M.; Nyman, May D.

    2000-11-01T23:59:59.000Z

    This patent application relates to an invention for a new silicotitanate molecular sieve ion exchange material for the capture and immobilization of divalent cations from aqueous and/or hydrocarbon solutions, including elements such as radioactive strontium or industrial RCRA metal cations. The invention also relates to the ability to either recycle the captured metal for future use or to encapsulate the cation through thermal treatment of the molecular sieve to a condensed phase.

  11. SANS studies of interacting hemoglobin in intact erythrocytes

    SciTech Connect (OSTI)

    Krueger, S.; Nossal, R.

    1988-01-01T23:59:59.000Z

    Small angle neutron scattering (SANS) was used to investigate interaction forces between hemoglobin (Hb) molecules contained within human red cells. The scattering separately attributable to cell membranes and intracellular Hb was identified. A series of D/sub 2/O-H/sub 2/O contrast variation measurements were made in order to establish conditions for which scattering from the cell membrane is minimized (approximately 15% D/sub 2/O). Measurements then were performed to examine changes in intermolecular Hb interactions occurring when the cells are contracted or swollen by varying the ionic strength of the suspension buffer. The scattering cross-sections were fitted to structure factors computed by a mean spherical approximation, and molecular parameters thereby extracted. Oxygenation studies on normal cells were performed, and results contrasted with those of similar studies of erythrocytes obtained from sickle cell disease patients.

  12. ENERGETIC PHOTON AND ELECTRON INTERACTIONS WITH POSITIVE IONS

    SciTech Connect (OSTI)

    Phaneuf, Ronald A. [UNR

    2013-07-01T23:59:59.000Z

    The objective of this research is a deeper understanding of the complex multi-electron interactions that govern inelastic processes involving positive ions in plasma environments, such as those occurring in stellar cares and atmospheres, x-ray lasers, thermonuclear fusion reactors and materials-processing discharges. In addition to precision data on ionic structure and transition probabilities, high resolution quantitative measurements of ionization test the theoretical methods that provide critical input to computer codes used for plasma modeling and photon opacity calculations. Steadily increasing computational power and a corresponding emphasis on simulations gives heightened relevance to precise and accurate benchmark data. Photons provide a highly selective probe of the internal electronic structure of atomic and molecular systems, and a powerful means to better understand more complex electron-ion interactions.

  13. Final Report - Molecular Mechanisms of Bacterial Mercury Transformation - UCSF

    SciTech Connect (OSTI)

    Miller, Susan M. [UCSF

    2014-04-24T23:59:59.000Z

    The bacterial mercury resistance (mer) operon functions in Hg biogeochemistry and bioremediation by converting reactive inorganic Hg(II) and organic [RHg(II)]1+ mercurials to relatively inert monoatomic mercury vapor, Hg(0). Its genes regulate operon expression (MerR, MerD, MerOP), import Hg(II) (MerT, MerP, and MerC), and demethylate (MerB) and reduce (MerA) mercurials. We focus on how these components interact with each other and with the host cell to allow cells to survive and detoxify Hg compounds. Understanding how this ubiquitous detoxification system fits into the biology and ecology of its bacterial host is essential to guide interventions that support and enhance Hg remediation. In the current overall project we focused on two aspects of this system: (1) investigations of the energetics of Hg(II)-ligand binding interactions, and (2) both experimental and computational approaches to investigating the molecular mechanisms of Hg(II) acquisition by MerA and intramolecular transfer of Hg(II) prior to reduction within the MerA enzyme active site. Computational work was led by Prof. Jeremy Smith and took place at the University of Tennessee, while experimental work on MerA was led by Prof. Susan Miller and took place at the University of California San Francisco.

  14. The dynamics of cargo driven by molecular motors in the context of asymmetric simple exclusion processes

    E-Print Network [OSTI]

    Carla Goldman; Elisa T. Sena

    2008-10-07T23:59:59.000Z

    We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of an asymmetric simple exclusion processes (ASEP). The model is formulated to account for i) excluded volume interactions, ii) the observed asymmetry of the stochastic movement of individual motors and iii) interactions between motors and cargo. Items (i) and (ii) form the basis of ASEP models and have already been considered in the literature to study the behavior of motor density profile [Parmeggiani 03]. Item (iii) is new. It is introduced here as an attempt to describe explicitly the dependence of cargo movement on the dynamics of motors. The steady-state solutions of the model indicate that the system undergoes a phase transition of condensation type as the motor density varies. We study the consequences of this transition to the properties of cargo velocity.

  15. Shifting of infrared radiation using rotational raman resonances in diatomic molecular gases

    DOE Patents [OSTI]

    Kurnit, Norman A. (Santa Fe, NM)

    1980-01-01T23:59:59.000Z

    A device for shifting the frequency of infrared radiation from a CO.sub.2 laser by stimulated Raman scattering in either H.sub.2 or D.sub.2. The device of the preferred embodiment comprises an H.sub.2 Raman laser having dichroic mirrors which are reflective for 16 .mu.m radiation and transmittive for 10 .mu.m, disposed at opposite ends of an interaction cell. The interaction cell contains a diatomic molecular gas, e.g., H.sub.2, D.sub.2, T.sub.2, HD, HT, DT and a capillary waveguide disposed within the cell. A liquid nitrogen jacket is provided around the capillary waveguide for the purpose of cooling. In another embodiment the input CO.sub.2 radiation is circularly polarized using a Fresnel rhomb .lambda./4 plate and applied to an interaction cell of much longer length for single pass operation.

  16. Dynamics in the presence of attractive patchy interactions

    E-Print Network [OSTI]

    Cristiano De Michele; Simone Gabrielli; Francesco Sciortino; Piero Tartaglia

    2005-11-04T23:59:59.000Z

    We report extensive monte-carlo and event-driven molecular dynamics simulations of a liquid composed by particles interacting via hard-sphere interactions complemented by four tetrahedrally coordinated short-range attractive ("sticky") spots, a model introduced several years ago by Kolafa and Nezbeda [J. Kolafa and I. Nezbeda, Mol. Phys. 161, 87 (1987)]. To access the dynamic properties of the model we introduce and implement a new event-driven molecular dynamics algorithm suited to study the evolution of hard bodies interacting, beside the repulsive hard-core, with a short-ranged inter-patch square well potential. We evaluate the thermodynamic properties of the model in deep supercooled states, where the bond network is fully developed, providing evidence of density anomalies. We show that, differing from models of spherically symmetric interacting particles, in a wide region of packing fractions the liquid can be super-cooled without encountering the gas-liquid spinodal. In particular, we suggest that there is one optimal packing fraction (not very different from the hexagonal ice packing fraction) at which the bond tetrahedral network fully develops. We find evidence of the dynamic anomalies characterizing network forming liquids. Indeed, around the optimal network packing, dynamics fasten both on increasing and decreasing the packing fraction. Finally we locate the shape of the isodiffusivity lines in the packing fraction-temperature plane and establish the shape of the dynamic arrest line in the phase diagram of the model. Results are discussed in connection to colloidal dispersions of sticky particles and gel forming proteins and their ability to form dynamically arrested states.

  17. The Application of XML Languages for Integrating Molecular Resources

    E-Print Network [OSTI]

    Rzepa, Henry S.

    The Application of XML Languages for Integrating Molecular Resources Content 1) The Application of XML Languages for Integrating Molecular Resources 2) Georgios V. Gkoutos,a Peter Murray-Rust,b Henry S of Molecular Resources 7) Molecular Integration based on XML 8) The ChemDig Project 9) Chemical Markup Language

  18. atom-scale molecular interactions: Topics by E-print Network

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

    with both trans and gauche conformations bound to the gold clusters at top, bridge and hollow bonding sites. Comparing our results with the experimental data of Hihath et al....

  19. Chemistry 685 (CHE 685) Advanced Organic Chemistry: Organic Reaction Mechanisms and Molecular Interactions

    E-Print Network [OSTI]

    Mather, Patrick T.

    which presents material and concepts complementary to those covered in CHE675 in the fall semester, macromolecular, and supramolecular systems. CHE675 covered topics relating to chemical bonding, energetics materials may be provided by handout or online through the Blackboard site. Office hours Please make

  20. Polarization Interactions and Boroxol Ring Formation in Boron Oxide: A Molecular Dynamics Study

    E-Print Network [OSTI]

    Stillinger, Frank

    is favored. I. Introduction Boron oxide [chemical formula B 2 O 3 ] is a network glass­former. The short scattering (1,2), nuclear magnetic resonance (3­6), nuclear quadrupole resonance (7­9), Raman scattering (10 such structures (25­33). A reverse Monte Carlo study (34) has shown that a high percentage of boroxol rings cannot

  1. Molecular Interactions in Poly(methacrylic acid)/Poly(N-isopropyl acrylamide) Interpenetrating Polymer Networks

    E-Print Network [OSTI]

    Peppas, Nicholas A.

    /PNIPAAm) interpenetrating polymer networks (IPNs) were investigated using attenuated total reflectance (ATR)- Fourier­14 Interpenetrating polymer networks (IPNs) composed of pH-sensitive poly(methacrylic acid) (PMAA) and temperature Polymer Networks JING ZHANG, NICHOLAS A. PEPPAS Polymer Science and Engineering Laboratories, School

  2. Molecular Interactions of Plutonium(VI) with Synthetic Manganese-Substituted Goethite

    E-Print Network [OSTI]

    Hu, Yung-Jin

    2011-01-01T23:59:59.000Z

    WA 99352 Savannah River National Laboratory, Aiken, SCWork at the Savannah River National Laboratory (SRNL) was

  3. Molecular mechanics of cartilage : quantification of GAG electrostatic interactions via high-resolution force spectroscopy

    E-Print Network [OSTI]

    Seog, Joonil, 1969-

    2003-01-01T23:59:59.000Z

    Intermolecular repulsion forces between negatively charged glycosaminoglycan (CS-GAG) macromolecules are a major determinant of cartilage biomechanical properties. It is thought that the electrostatic component of the total ...

  4. Dynamic Interactions and Molecular Rearrangements Occurring when RNA Polymerase II Meets the Nucleosome

    E-Print Network [OSTI]

    Bintu, Lacramioara

    2010-01-01T23:59:59.000Z

    Larson, K.C. Neuman, J. Gelles, R. Landick, and S.M. Block.E.A. Abbondanzieri, R. Landick, J. Gelles, and S.M. Block.

  5. Design and fabrication of a microfluidies gradient generator system for high-throughput molecular interaction studies

    E-Print Network [OSTI]

    Chen, Guan-Jong, 1981-

    2004-01-01T23:59:59.000Z

    Design and fabrication of a microfluidics system capable of generating reproducible and controlled micro-biochemical environments that can be used as a diagnostic assay and microreactor is important. Here, a simple technique ...

  6. Protein Oligomerization Through Domain Swapping: Role of Inter-molecular Interactions and

    E-Print Network [OSTI]

    Yang, Sichun

    show that prevention of domain swapping inhibits amyloid fibrils by 80%,11 and strongly support the idea that domain swapping has an important role in fibril formation. Domain swapping is a term used found to form domain-swapped configurations, such as the human prion,12,13 the SH3 domain,14,15 p13suc1

  7. Chemotherapy efficiency increase via shock wave interaction with biological membranes: a molecular dynamics study

    E-Print Network [OSTI]

    Espinosa, Silvia

    Application of ultrasound to biological tissues has been identified as a promising cancer treatment technique relying on temporal enhancement of biological membrane permeability via shock wave impact. In the present study, ...

  8. Molecular Interactions of Plutonium(VI) with Synthetic Manganese-Substituted Goethite

    E-Print Network [OSTI]

    Hu, Yung-Jin

    2011-01-01T23:59:59.000Z

    Mn-Substituted Goethite Synthesis Manganese substituted (Mn-The laboratory synthesis of Mn-substituted goethite requiresgoethite existed as Mn(III), even though Mn was added during mineral synthesis

  9. Molecular Interactions of Plutonium(VI) with Synthetic Manganese-Substituted Goethite

    E-Print Network [OSTI]

    Hu, Yung-Jin

    2011-01-01T23:59:59.000Z

    VI) with the Iron Oxide Goethite, University of California,Values for Synthetic Goethite and Pyrolusite" submitted tothe two Mn-substituted goethite minerals used in this study.

  10. An interactive teaching device simulating intussusception reduction

    E-Print Network [OSTI]

    2010-01-01T23:59:59.000Z

    1764-x TECHNICAL INNOVATION An interactive teaching deviceIRB. We developed an interactive teaching device to simulate

  11. Interacting Multiple Model Kalman Filters (IMMKF) Interacting Multiple Model Kalman Filters

    E-Print Network [OSTI]

    Williams, Brian C.

    Interacting Multiple Model Kalman Filters (IMMKF) Interacting Multiple Model Kalman Filters (IMMKF R.Q.A. Santana Interacting Multiple Model Kalman Filters (IMMKF) #12;Interacting Multiple Model Kalman Filters (IMMKF) Sumário 1 Introdução Abordagens de múltiplos modelos Introdução ao Interacting

  12. Final Report: Molecular Basis for Microbial Adhesion and Geochemical Surface Reactions: A Study Across Scales

    SciTech Connect (OSTI)

    Dixon, David Adams [The University of Alabama

    2013-06-27T23:59:59.000Z

    Computational chemistry was used to help provide a molecular level description of the interactions of Gram-negative microbial membranes with subsurface materials. The goal is to develop a better understanding of the molecular processes involved in microbial metal binding, microbial attachment to mineral surfaces, and, eventually, oxidation/reduction reactions (electron transfer) that can occur at these surfaces and are mediated by the bacterial exterior surface. The project focused on the interaction of the outer microbial membrane, which is dominated by an exterior lipopolysaccharide (LPS) portion, of Pseudomonas aeruginosa with the mineral goethite and with solvated ions in the environment. This was originally a collaborative project with T.P. Straatsma and B. Lowery of the Pacific Northwest National Laboratory. The University of Alabama effort used electronic structure calculations to predict the molecular behavior of ions in solution and the behavior of the sugars which form a critical part of the LPS. The interactions of the sugars with metal ions are expected to dominate much of the microscopic structure and transport phenomena in the LPS. This work, in combination with the molecular dynamics simulations of Straatsma and the experimental electrochemistry and microscopy measurements of Lowry, both at PNNL, is providing new insights into the detailed molecular behavior of these membranes in geochemical environments. The effort at The University of Alabama has three components: solvation energies and structures of ions in solution, prediction of the acidity of the critical groups in the sugars in the LPS, and binding of metal ions to the sugar anions. An important aspect of the structure of the LPS membrane as well as ion transport in the LPS is the ability of the sugar side groups such as the carboxylic acids and the phosphates to bind positively charged ions. We are studying the acidity of the acidic side groups in order to better understand the ability of these groups to bind metal ions. We need to understand the solvation properties of the metal ions in solution and their ability to bind not only to the sugars but to proteins and to other anions. Our goal is then to be able to predict the ability of the side groups to bind metal ions. One result from the earlier molecular dynamics simulations is the exclusion of water from the inner hydrophobic part of the membrane. We thus need to investigate the binding of the cations in media with different dielectric constants.

  13. Surprising Quasiparticle Interactions in Graphene

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

    Surprising Quasiparticle Interactions in Graphene Print Until now, the world's electronics have been dominated by silicon, whose properties, while excellent, significantly limit...

  14. Truck Pavement Interactions: Requisite Research

    E-Print Network [OSTI]

    Monismith, C.L.; Lysmer, J.; Sousa, J.; Hedrick, J.K.

    1988-01-01T23:59:59.000Z

    Dynamic Loads on Highway Pavements - Part I Vehicle Re-of Asphalt Concrete Pavements," Paper presented at 67thregulation. or Truck Pavement Interactions: Requisite

  15. ANTswers: an interactive library FAQ

    E-Print Network [OSTI]

    Kane, Danielle A.

    2105-01-01T23:59:59.000Z

    ANTswers: an interactive library FAQ Danielle Kane, Researchand Service Innovation, UCI Libraries ALA Annual 2015 – Sanquestions about the UCI Libraries but to also respond to

  16. Interaction of acetonitrile with thin films of solid water

    SciTech Connect (OSTI)

    Bahr, S.; Kempter, V. [Institut fuer Physik und Physikalische Technologien, Technische Universitaet Clausthal, Leibnizstr. 4, D-38678 Clausthal-Zellerfeld (Germany)

    2009-06-07T23:59:59.000Z

    Thin films of water were prepared on Ag at 124 K. Their properties were studied with metastable impact electron spectroscopy, reflection absorption infrared spectroscopy, and temperature programmed desorption. The interaction of acetonitrile (ACN) with these films was studied with the abovementioned techniques. From the absence of any infrared activity in the initial adsorption stage, it is concluded that ACN adsorbs linearly and that the C{identical_to}N axis is aligned parallel to the water surface (as also found on neat Ag). Initially, the interaction with water surface species involves their dangling OD groups. During the completion of the first adlayer the ACN-ACN lateral interaction becomes of importance as well, and the ACN molecules become tilted with respect to the water surface. ACN shows propensity to stay at the surface after surface adsorption even during annealing up to the onset of desorption. The present results for the ACN-water interaction are compared with available classical molecular dynamics calculations providing the orientation profile for ACN on water as well as the ACN bonding properties.

  17. Molecular Surgery with Pulsed Electric Fields: Molecular Dynamics Simulations of Nanopore Formation and

    E-Print Network [OSTI]

    Southern California, University of

    Molecular Surgery with Pulsed Electric Fields: Molecular Dynamics Simulations of Nanopore Formation Family Department of Chemical Engineering and Materials Science, §Department of Electrical Engineering of water molecules spanning the membrane, decay within a few nanoseconds when the electric field is removed

  18. Determining the Overpotential for a Molecular Electrocatalyst

    SciTech Connect (OSTI)

    Appel, Aaron M.; Helm, Monte L.

    2014-02-07T23:59:59.000Z

    “The additional potential (beyond the thermodynamic requirement) needed to drive a reaction at a certain rate is called the overpotential.”1 Over the last decade there has been considerable interest in the design and testing of molecular electrocatalysis for the interconversion of renewable energy and chemical fuels.2-5 One of the primary motivations for such research is the replacement of expensive and rare precious metal catalysts, such as platinum, with cheaper, more abundant metals.2,6-8 To become competitive with current electrocatalytic energy conversion technologies, new catalysts must be robust, fast, and energy-efficient. This last feature, the energy-efficiency, is dependent upon the overpotential. For molecular catalysts, the determination and reporting of overpotentials can be complicated by the frequent dependence on assumptions, especially when working in nonaqueous solvents. As overpotentials become lower, the meaningful comparison of molecular catalysts will require improved accuracy and precision. The intended purpose of this viewpoint is to provide a clear and concise description of overpotential and recommendation for its determination in molecular electrocatalysis. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

  19. HIERARCHICAL STORAGE SYSTEMS FOR INTERACTIVE

    E-Print Network [OSTI]

    Tobagi, Fouad

    HIERARCHICAL STORAGE SYSTEMS FOR INTERACTIVE VIDEO­ON­DEMAND Shueng­Han Gary Chan and Fouad A; Hierarchical Storage Systems for Interactive Video­On­Demand Shueng­Han Gary Chan and Fouad A. Tobagi Technical­9040 pubs@shasta.stanford.edu Abstract On­demand video servers based on hierarchical storage systems

  20. Interactive Video Cubism Sidney Fels

    E-Print Network [OSTI]

    Fels, Sidney S.

    Interactive Video Cubism Sidney Fels Dept. of Electrical and Computer Engineering University@mic.atr.co.jp ABSTRACT This paper presents an interactive video visualization system. In this visualization video data is considered to be a block of three dimensional data where frames of video data comprise the third dimension

  1. Examination of the change in returning molecular weight obtained during inhibitor squeeze treatments using polyacrylate based inhibitors

    SciTech Connect (OSTI)

    Graham, G.M.; Sorbie, K.S. [Heriot-Watt Univ., Edinburgh (United Kingdom)

    1995-11-01T23:59:59.000Z

    Scale inhibitors based on small polyelectrolytes are often employed in oilfield scale prevention treatments. These materials are injected into the near-well formation of producers in a scale inhibitor squeeze treatment. When the well is brought back on production, the objective is for the return concentration level of the inhibitor in the produced brine to be at or above a certain threshold level, C{sub t}. This threshold level is the minimum inhibitor concentration required to prevent the formation of mineral carbonate or sulfate scales in that well. The squeeze lifetime depends strongly on the nature of the interaction between the inhibitor and the formation either through an adsorption or precipitation mechanism. Both adsorption and precipitation processes depend on the molecular weight of the scale inhibitor, as well as on a range of other factors. However, polymeric inhibitor species always display some degree of polydispersity (spread of molecular weight). In this paper, the authors examine the effects of molecular weight on adsorption/desorption phenomena for polyacrylate based inhibitor species. This work shows that, in the inhibitor effluent after a squeeze treatment, the molecular weight of the returning inhibitor may be different from that which was injected. For commercially available polymeric inhibitor species, they demonstrate using core floods that preferential retention of higher molecular weight components occurs and preferential desorption of lower molecular weight components is observed. This leads to a gradation in molecular weight in the return profile, which can lead to increased molecular weight components returning as the inhibitor concentration approaches the threshold level. The significance of this observation to field application of polymeric inhibitor species is discussed.

  2. Molecular Dynamic Approach of Enhanced Self-Propelled Nano-Droplet Motion on Wettability Gradient Surfaces

    E-Print Network [OSTI]

    Chakraborty, Monojit; Bhusan, Richa; DasGupta, Sunando

    2015-01-01T23:59:59.000Z

    Droplet motion over a surface with wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics. GROMACS and Visual Molecular Dynamics (VMD) were used for simulation and intermittent visualization of the droplet configuration respectively. The simulations mimic experiments in a comprehensive manner wherein micro-sized droplets are propelled by surface wettability gradient against a number of retarding forces. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature were varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction was observed to be a strong function of temperature at atomistic scales, confirming the experimentally observed inverse functionality between the coefficient of contact line friction and increase in temperatures. These MD simulation results were successfully compared with the results from a model for self-propelled droplet motion on gradient surfaces.

  3. Hydration of Clays at the Molecular Scale: The Promising Perspective of Classical Density Functional Theory

    E-Print Network [OSTI]

    Jeanmairet, Guillaume; Levesque, Maximilien; Rotenberg, Benjamin; Borgis, Daniel

    2014-01-01T23:59:59.000Z

    We report here how the hydration of complex surfaces can be efficiently studied thanks to recent advances in classical molecular density functional theory. This is illustrated on the example of the pyrophylite clay. After presenting the most recent advances, we show that the strength of this implicit method is that (i) it is in quantitative or semi-quantitative agreement with reference all-atoms simulations (molecular dynamics here) for both the solvation structure and energetics, and that (ii) the computational cost is two to three orders of magnitude less than in explicit methods. The method remains imperfect, in that it locally overestimates the polarization of water close to hydrophylic sites of the clay. The high numerical efficiency of the method is illustrated and exploited to carry a systematic study of the electrostatic and van der Waals components of the surface-solvant interactions within the most popular force field for clays, CLAYFF. Hydration structure and energetics are found to weakly depend u...

  4. Theory and Modeling of the Zeeman and Paschen-Back effects in Molecular Lines

    E-Print Network [OSTI]

    A. Asensio Ramos; J. Trujillo Bueno

    2005-10-10T23:59:59.000Z

    This paper describes a very general approach to the calculation of the Zeeman splitting effect produced by an external magnetic field on the rotational levels of diatomic molecules. The method is valid for arbitrary values of the total electronic spin and of the magnetic field strength -that is, it holds for molecular electronic states of any multiplicity and for both the Zeeman and incomplete Paschen-Back regimes. It is based on an efficient numerical diagonalization of the effective Zeeman Hamiltonian, which can incorporate easily all the contributions one may eventually be interested in, such as the hyperfine interaction of the external magnetic field with the spin motions of the nuclei. The reliability of the method is demonstrated by comparing our results with previous ones obtained via formulae valid only for doublet states. We also present results for molecular transitions arising between non-doublet electronic states, illustrating that their Zeeman patterns show signatures produced by the Paschen-Back effect.

  5. Towards Microsecond Biological Molecular Dynamics Simulations on Hybrid Processors

    SciTech Connect (OSTI)

    Hampton, Scott S [ORNL; Agarwal, Pratul K [ORNL

    2010-01-01T23:59:59.000Z

    Biomolecular simulations continue to become an increasingly important component of molecular biochemistry and biophysics investigations. Performance improvements in the simulations based on molecular dynamics (MD) codes are widely desired. This is particularly driven by the rapid growth of biological data due to improvements in experimental techniques. Unfortunately, the factors, which allowed past performance improvements of MD simulations, particularly the increase in microprocessor clock frequencies, are no longer improving. Hence, novel software and hardware solutions are being explored for accelerating the performance of popular MD codes. In this paper, we describe our efforts to port and optimize LAMMPS, a popular MD framework, on hybrid processors: graphical processing units (GPUs) accelerated multi-core processors. Our implementation is based on porting the computationally expensive, non-bonded interaction terms on the GPUs, and overlapping the computation on the CPU and GPUs. This functionality is built on top of message passing interface (MPI) that allows multi-level parallelism to be extracted even at the workstation level with the multi-core CPUs as well as extend the implementation on GPU clusters. The results from a number of typically sized biomolecular systems are provided and analysis is performed on 3 generations of GPUs from NVIDIA. Our implementation allows up to 30-40 ns/day throughput on a single workstation as well as significant speedup over Cray XT5, a high-end supercomputing platform. Moreover, detailed analysis of the implementation indicates that further code optimization and improvements in GPUs will allow {approx}100 ns/day throughput on workstations and inexpensive GPU clusters, putting the widely-desired microsecond simulation time-scale within reach to a large user community.

  6. 1984 Bibliography of atomic and molecular processes

    SciTech Connect (OSTI)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howard, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1985-04-01T23:59:59.000Z

    This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  7. 1985 bibliography of atomic and molecular processes

    SciTech Connect (OSTI)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howald, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1986-06-01T23:59:59.000Z

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  8. 1982 bibliography of atomic and molecular processes

    SciTech Connect (OSTI)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-05-01T23:59:59.000Z

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  9. Molecular diffusion in plasma-polymerized tetrafluoroethylene

    SciTech Connect (OSTI)

    Butler, M.A.; Buss, R.J. (Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States))

    1992-11-01T23:59:59.000Z

    Diffusion of an array of molecules in micrometer-thick films of plasma-polymerized tetrafluoroethylene has been measured using an optical interferometric technique. The diffusivity is approximately independent of molecular size up to a molar volume of about 100 cm{sup 3} and drops rapidly for larger molecules. For much larger molecules no penetration of the films is observed. These results suggest that plasma-polymerized tetrafluoroethylene films are heavily cross linked and that this limits the size of the molecules that can penetrate the polymer. The temperature dependence and the molecular size dependence of the diffusivities are discussed in the context of free-volume theory.

  10. Molecular Hydrogen Emission from Protoplanetary Disks

    E-Print Network [OSTI]

    H. Nomura; T. J. Millar

    2005-05-06T23:59:59.000Z

    We have modeled self-consistently the density and temperature profiles of gas and dust in protoplanetary disks, taking into account irradiation from a central star. Making use of this physical structure, we have calculated the level populations of molecular hydrogen and the line emission from the disks. As a result, we can reproduce the observed strong line spectra of molecular hydrogen from protoplanetary disks, both in the ultraviolet (UV) and the near-infrared, but only if the central star has a strong UV excess radiation.

  11. Final Technical Report for "Feature Extraction, Characterization, and Visualization for Protein Interaction via Geometric and Topological Methods"

    SciTech Connect (OSTI)

    Wang, Yusu

    2013-03-25T23:59:59.000Z

    Shape analysis plays an important role in many applications. In particular, in molecular biology, analyzing molecular shapes is essential to the fundamental problem of understanding how molecules interact. This project aims at developing efficient and effective algorithms to characterize and analyze molecular structures using geometric and topological methods. Two main components of this project are (1) developing novel molecular shape descriptors; and (2) identifying and representing meaningful features based on those descriptors. The project also produces accompanying (visualization) software. Results from this project (09/2006â??10/2009) include the following publications. We have also set up web-servers for the software developed in this period, so that our new methods are accessible to a broader scientific community. The web sites are given below as well. In this final technical report, we first list publications and software resulted from this project. We then briefly explain the research conducted and main accomplishments during the period of this project.

  12. Synergistic Gelation of Silica Nanoparticles and a Sorbitol-Based Molecular Gelator to Yield Highly-Conductive Free-Standing Gel

    E-Print Network [OSTI]

    Rubloff, Gary W.

    combination of properties. The gels are prepared by utilizing the synergistic interactions between a molecular, Maryland 20742-2111, United States ABSTRACT: Lithium-ion batteries have emerged as the preferred type lithium perchlorate salt, the liquid electrolyte is converted into a free-standing gel due

  13. Perturbative gadgets without strong interactions

    E-Print Network [OSTI]

    Yudong Cao; Daniel Nagaj

    2014-08-25T23:59:59.000Z

    Perturbative gadgets are used to construct a quantum Hamiltonian whose low-energy subspace approximates a given quantum $k$-body Hamiltonian up to an absolute error $\\epsilon$. Typically, gadget constructions involve terms with large interaction strengths of order $\\text{poly}(\\epsilon^{-1})$. Here we present a 2-body gadget construction and prove that it approximates a target many-body Hamiltonian of interaction strength $\\gamma = O(1)$ up to absolute error $\\epsilon\\ll\\gamma$ using interactions of strength $O(\\epsilon)$ instead of the usual inverse polynomial in $\\epsilon$. A key component in our proof is a new condition for the convergence of the perturbation series, allowing our gadget construction to be applied in parallel on multiple many-body terms. We also show how to apply this gadget construction for approximating 3- and $k$-body Hamiltonians. The price we pay for using much weaker interactions is a large overhead in the number of ancillary qubits, and the number of interaction terms per particle, both of which scale as $O(\\text{poly}(\\epsilon^{-1}))$. Our strong-from-weak gadgets have their primary application in complexity theory (QMA hardness of restricted Hamiltonians, a generalized area law counterexample, gap amplification), but could also motivate practical implementations with many weak interactions simulating a much stronger quantum many-body interaction.

  14. Molecular Mechanisms for Microtubule Length Regulation by Kinesin-8 and XMAP215 Proteins

    E-Print Network [OSTI]

    Louis Reese; Anna Melbinger; Erwin Frey

    2014-05-22T23:59:59.000Z

    The cytoskeleton is regulated by a plethora of enzymes that influence the stability and dynamics of cytoskeletal filaments. Molecular motors of the kinesin-8 protein family depolymerise microtubules in a length-dependent manner, and experimental and theoretical evidence suggest a role for kinesin-8 in the dynamic regulation of microtubules. However, so far the detailed molecular mechanisms how these molecular motors interact with the growing microtubule tip remain elusive. Here we investigate two interaction scenarios for kinesin-8 and the microtubule tip. We give a comprehensive analysis of regimes where length-regulation is possible and characterise how the stationary length depends on the biochemical rates and the bulk concentrations of the various proteins. For a neutral scenario, where microtubules grow irrespective of whether the microtubule tip is occupied by a molecular motor, length regulation is possible only for a narrow range of biochemical rates and limited to small polymerisation rates. In contrast, for an inhibition scenario, where the presence of a motor at the microtubule tip inhibits microtubule growth, the regime of length regulation is extremely broad and includes high growth rates. These results also apply to situations where polymerising enzymes, like XMAP215, and kinesin-8 mutually exclude each other from the microtubule tip. We also investigate the stochastic dynamics of the two scenarios. While for the neutral scenario length is tightly controlled, length dynamics is intermittent for the inhibition scenario and exhibits extended periods of microtubule growth and shrinkage, reminiscent of microtubule dynamic instability. On a broader perspective, the set of models established in this work quite generally suggests that mutual exclusion of molecules at the ends of cytoskeletal filaments is an important factor for filament dynamics and regulation.

  15. Structure and dynamics of microbe-exuded polymers and their interactions with calcite surfaces.

    SciTech Connect (OSTI)

    Cygan, Randall Timothy; Mitchell, Ralph (Harvard University, Cambridge, MA); Perry, Thomas D. (Harvard University, Cambridge, MA)

    2005-12-01T23:59:59.000Z

    Cation binding by polysaccharides is observed in many environments and is important for predictive environmental modeling, and numerous industrial and food technology applications. The complexities of these organo-cation interactions are well suited to predictive molecular modeling studies for investigating the roles of conformation and configuration of polysaccharides on cation binding. In this study, alginic acid was chosen as a model polymer and representative disaccharide and polysaccharide subunits were modeled. The ability of disaccharide subunits to bind calcium and to associate with the surface of calcite was investigated. The findings were extended to modeling polymer interactions with calcium ions.

  16. Laser studies of the interaction of SiO with the surface of a thin film

    SciTech Connect (OSTI)

    Ho, P.; Buss, R.J. (Sandia National Labs., Albuquerque, NM (USA)); Weber, M.E. (Texas Instruments, Inc., Dallas, TX (USA))

    1990-01-01T23:59:59.000Z

    The interaction of SiO radicals from a SiCl{sub 4}/O{sub 2} plasma with the surface of a depositing thin film is studied with the IRIS (Imaging of Radicals Interacting with Surfaces) technique, which combines spatially-resolved laser-induced fluorescence with molecular beam methods. In contrast to previous results for SiH, SiO appears not to react at the surface of the depositing film, but desorbs with a cosine spatial distribution for a wide range of substrate temperatures. No evidence is observed for specular scattering of the molecules. 6 refs., 5 figs.

  17. Incoherence and multiple parton interactions

    SciTech Connect (OSTI)

    Calucci, G.; Treleani, D. [Dipartimento di Fisica Teorica dell'Universita di Trieste and INFN, Sezione di Trieste, Strada Costiera 11, Miramare-Grignano, I-34151 Trieste (Italy)

    2009-09-01T23:59:59.000Z

    At the LHC multiple parton interactions will represent an important feature of the minimum bias and of the underlying event, and will give important contributions in many channels of interest in the search for new physics. Different numbers of multiple collisions may contribute to the production of a given final state, and one should expect important interference effects in the regime where different contributions have similar rates. We show, on the contrary, that, once multiple parton interactions are identified by their different topologies, terms with different numbers of multiple parton interactions do not interfere in the final cross section.

  18. Hydrophobic force field as molecular alternative to surface-area models

    SciTech Connect (OSTI)

    Hummer, G.

    1999-07-07T23:59:59.000Z

    An effective force field for hydrophobic interactions is developed based on a modified potential-of-mean-force (PMF) expansion of the effective many-body interactions between nonpolar molecules in water. For the simplest nonpolar solutes in water, hard particles, the modified PMF expansion is exact in both limiting cases of infinite separation and perfect overlap. The hydrophobic interactions are parametrized by using the information-theory model of hydrophobic hydration. The interactions between nonpolar solutes are short-ranged and can be evaluated efficiently on a computer. The force field is compared with simulation data for alkane conformational equilibria in water as well as a model for the formation of a hydrophobic core of a protein. The modified PMF expansion can be extended to solutes with attractive interactions. The observed accuracy, computational efficiency, and atomic detail of the model suggest that this simple hydrophobic force field can lead to a molecular alternative for phenomenological surface-area models with applications in ligand-binding and protein-folding studies.

  19. Role of Water States on Water Uptake and Proton Transport in Nafion using Molecular Simulations and Bimodal Network

    SciTech Connect (OSTI)

    U. Michigan; Hwang, Gi Suk; Kaviany, Massoud; Gostick, Jeffrey T.; Kientiz, Brian; Weber, Adam Z.; Kim, Moo Hwan

    2010-11-19T23:59:59.000Z

    Using molecular simulations and a bimodal domain network, the role of water state on Nafion water uptake and water and proton transport is investigated. Although the smaller domains provide moderate transport pathways, their effectiveness remains low due to strong, resistive water molecules/domain surface interactions. The water occupancy of the larger domains yields bulk-like water, and causes the observed transition in the water uptake and significant increases in transport properties.

  20. Generalized Entropy Theory of Glass Formation in Polymer Melts with Specific Interactions

    E-Print Network [OSTI]

    Wen-Sheng Xu; Karl F. Freed

    2015-03-21T23:59:59.000Z

    Chemical structure has been long recognized to greatly influence polymer glass formation, but a general molecular theory that predicts how chemical structure determines the properties of glass-forming polymers has been slow to develop. While the generalized entropy theory (GET) explains the influence of various molecular details on polymer glass formation, the application of the GET has heretofore been limited to the use of the simplest polymer model in which all united atom groups within the monomers of a species interact with a common monomer averaged van der Waals energy. However, energetic heterogeneities are ubiquitous within the monomers of real polymers, and their implications for polymer glass formation remain to be investigated theoretically. This paper uses an extension of the GET to explore the influence of energetic heterogeneities within monomers upon the nature of polymer glass formation. The present paper focuses on establishing general trends for the variation of characteristic properties of glass formation, such as the isobaric fragility parameter $m_P$ and the glass transition temperature $T_g$, with molecular details, such as the specific interactions and chain stiffness. Our computations confirm that the previously used model with monomer averaged interactions correctly captures general trends in the variation of $m_P$ and $T_g$ with various molecular parameters. More importantly, adjustment of the energetic heterogeneities within monomers alone are shown to provide an efficient mechanism for tailoring the properties of glass-forming polymers. The variations of polymer properties along iso-fragility and iso-$T_g$ lines are illustrated as important design tools for exhibiting the combined influence of specific interactions and chain stiffness.

  1. Control-volume representation of molecular dynamics

    E-Print Network [OSTI]

    E. R. Smith; D. M. Heyes; D. Dini; T. A. Zaki

    2012-05-24T23:59:59.000Z

    A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' Transport Theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-Control-Volume (\\CV) conversion function $\\vartheta_{i}$, for each molecule $i$. The \\CV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the Volume Average (VA, Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, Todd et al, Phys. Rev. E 52, 1627 (1995)) emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and non-equilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative, and is therefore ideally suited to obtain macroscopic properties from a discrete system.

  2. Huntington's disease: underlying molecular mechanisms and emerging

    E-Print Network [OSTI]

    Morimoto, Richard

    transcriptional mechanism also dictates the expression of polygluta- mine proteins. Here, we summarize the key with no disease modifying treatments available [1]. At the molecular level, HD is caused by a CAG trinu- cleotide is composed of proteins involved in transcription, DNA maintenance, cell cycle regulation, cellular orga

  3. ORIGINAL ARTICLE Phylogeny, molecular ecology and taxonomy

    E-Print Network [OSTI]

    Green, Andy J.

    ORIGINAL ARTICLE Phylogeny, molecular ecology and taxonomy of southern Iberian lineages of Triops that in total, the species is divided into six distinct clades, comprising T. m. mauritanicus, T. m. simplex supplementary material The online version of this article (doi:10.1007/s13127-010-0026-y) contains supplementary

  4. Molecular Biology Basics Planning Restriction Enzyme Digests

    E-Print Network [OSTI]

    Aris, John P.

    Molecular Biology Basics Planning Restriction Enzyme Digests A. Checklist: Buffer type Addition of BSA Optimum temperature Number of units of enzyme B. Plan to digest DNA with an "excess" of enzyme activity. Plan for the "excess" to be divided between time of digestion and number of units of enzyme

  5. Molecular Cell Signaling Motifs and Weber's Law

    E-Print Network [OSTI]

    Molecular Cell Previews Signaling Motifs and Weber's Law James E. Ferrell, Jr.1,* 1Department that Weber's law of sensory perception may apply to a number of cell signaling processes. Most of us can shouting in our ear. This is the essence of Weber's law, put forward by the German physiologist Ernst Weber

  6. THERMODYNAMICS Molecular Simulation of Multicomponent Reaction

    E-Print Network [OSTI]

    Lisal, Martin

    THERMODYNAMICS Molecular Simulation of Multicomponent Reaction and Phase Equilibria in MTBE Ternary System Martin Lisal´ E. Hala Laboratory of Thermodynamics, Institute of Chemical Process Fundamentals N1G 2W1, Canada Ivo Nezbeda E. Hala Laboratory of Thermodynamics, Institute of Chemical Process

  7. CeBiTec Symposium Molecular Biotechnology

    E-Print Network [OSTI]

    Moeller, Ralf

    : Bacterial and Environmental Biotechnology Chair: Volker F. Wendisch 12:30 Jörn Kalinowski (Technology for biotechnological applications 14:30 Coffee and Cake / Poster Presentation Session II: Biopolymers Chair: Dirk9th CeBiTec Symposium Molecular Biotechnology Center for Interdisciplinary Research (Zi

  8. Brownian Ratchets: Molecular Separations in Lipid Bilayers

    E-Print Network [OSTI]

    Boxer, Steven G.

    Brownian Ratchets: Molecular Separations in Lipid Bilayers Supported on Patterned Arrays Alexander van Oudenaarden and Steven G. Boxer* Brownian ratchets use a time-varying asymmetric potential that can be applied to separate diffusing particles or molecules. A new type of Brownian ratchet

  9. The mean molecular mass of Titan's atmosphere

    E-Print Network [OSTI]

    Withers, Paul

    , Mars, Mars #12;Science Questions · Mean molecular mass (µ) -> Chemical composition · How did Titan form? · Current reservoirs of volatiles · Ethane/methane puddles/ocean · Thermal structure of atmosphere #12, delicate, etc ­ T/p sensors are simple, cheap, reliable · Is it possible to know µ based on simple

  10. Molecular sieving silica membrane fabrication process

    DOE Patents [OSTI]

    Raman, N.K.; Brinker, C.J.

    1999-08-10T23:59:59.000Z

    A process is described for producing a molecular sieve silica membrane comprising depositing a hybrid organic-inorganic polymer comprising at least one organic constituent and at least one inorganic constituent on a porous substrate material and removing at least a portion of the at least one organic constituent of the hybrid organic-inorganic polymer, forming a porous film. 11 figs.

  11. ScheduleDay 1: Molecular Evolution Introduction

    E-Print Network [OSTI]

    Goldschmidt, Christina

    -Cantor Model Do Exercise Read Ponting, study slides from day 3 and find questions. Day 3: Comparative Genomics Lecture: Comparative Genomics Prepare Projects Practical: Models of Sequence Evolution Read HSW1, study questions. Day 10: Projects Project 1 ­ Population Genomics: Selective Sweeps Project 2 ­ Molecular

  12. EVOLUTION AT MOLECULAR RESOLUTIONa P. SCHUSTER

    E-Print Network [OSTI]

    Schuster, Peter

    EVOLUTION AT MOLECULAR RESOLUTIONa P. SCHUSTER Institute for Theoretical Chemistry, University. In the simplest conceivable case, in vitro evolution of RNA molecules, both phenomena can be incorporated led to the no- tion of quasispecies which has been applied successfully to evolution of molecules

  13. Reaction dynamics in polyatomic molecular systems

    SciTech Connect (OSTI)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01T23:59:59.000Z

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  14. A Quadratic Assignment Formulation of the Molecular

    E-Print Network [OSTI]

    Neumaier, Arnold

    in molecular bio­ physics and biochemistry is the protein folding problem (Gierasch and King 1990). The protein­ tion concern. The value of computation of protein folding patterns is that although it is now quite conformation problem'' does not in itself solve the protein folding problem; however, this general approach

  15. Applications to Computational Molecular Biology Giuseppe Lancia

    E-Print Network [OSTI]

    Lancia, Giuseppe

    of the first type Bioinformatics problems, and reserve the term Computational Biology for the study of problemsApplications to Computational Molecular Biology Giuseppe Lancia 1 Introduction Computational decade. The seeds for the birth of Computational Biology were sowed in the end of the Seventies, when

  16. Groundwater Report Goes Online, Interactive

    Broader source: Energy.gov [DOE]

    RICHLAND, Wash. – EM’s Richland Operations Office (RL) has moved its 1,200-page annual report on groundwater monitoring to a fully online and interactive web application.

  17. Interactive crayon rendering for animation

    E-Print Network [OSTI]

    Halstead, Howard John IV

    2006-04-12T23:59:59.000Z

    This thesis describes the design and implementation of an interactive, nonphotorealistic rendering system for three-dimensional computer animation. The system provides a two-dimensional interface for coloring successive frames of animation using a...

  18. Succinct non-Interactive arguments

    E-Print Network [OSTI]

    Chiesa, Alessandro

    2014-01-01T23:59:59.000Z

    Succinct non-interactive arguments (SNARGs), also known as "CS proofs" [Micali, FOCS 1994], enable verifying NP statements with much lower complexity than required for classical NP verification (in fact, with complexity ...

  19. Variation after Angular Momentum Projection for the Study of Excited States Based on Antisymmetrized Molecular Dynamics

    E-Print Network [OSTI]

    Y. Kanada-En'yo

    2002-04-15T23:59:59.000Z

    In order to study the structure of excited states we perform a variational calculation after spin parity projection (VAP) within the framework of Antisymmetrized Molecular Dynamics (AMD). The framework is proven to be a new powerful approach for the study of the various structures of excited states because it is free from model assumptions such as inert cores, existence of clusters, and the axial symmetry. By using finite range interactions with a density dependent term we reproduce well all the energy levels below 15 MeV in $^{12}$C. This is the first theoretical model that reproduces many $E2$ transition rates and $\\beta$ decays to $^{12}$C successfully.

  20. Antisymmetrized Molecular Dynamics with Coherent State Pion and Its Application to Excited Spectrum of 12C

    E-Print Network [OSTI]

    Akinori Isshiki; Kenichi Naito; Akira Ohnishi

    2005-07-13T23:59:59.000Z

    We have introduced coherent state neutral pion into Antisymmetrized Molecular Dynamics. With the aid of coherent state technique, it becomes possible to calculate transition matrix elements of the pion field operator and to study excited states containing pions. For large pion-nucleon coupling fpiN > 1.6, pions have a finite expectation value and bring large energy gain in 12C. We discuss two aspects of pionic effects in spectroscopy; the LS interaction like effect and the mixing of different nucleon parity states, which would modify low energy nuclear levels.

  1. Peeling back the layers: a molecular dynamics investigation into heterogeneous ice nucleation

    E-Print Network [OSTI]

    Cox, Stephen J; Slater, Ben; Michaelides, Angelos

    2015-01-01T23:59:59.000Z

    Coarse grained molecular dynamics simulations are presented in which the sensitivity of the ice nucleation rate to the hydrophilicity of a graphene nanoflake is investigated. We find that an optimal interaction strength for promoting ice nucleation exists, which coincides with that found previously for an FCC (111) surface. We further investigate the role that the layering of interfacial water plays in heterogeneous ice nucleation, and demonstrate that the extent of layering is not a good indicator of ice nucleating ability for all surfaces. Our results suggest that to be an efficient ice nucleating agent, a surface should not bind water too strongly if it is able to accommodate high coverages of water.

  2. Wetting kinetics of water nano-droplet containing non-surfactant nanoparticles: A molecular dynamics study

    SciTech Connect (OSTI)

    Lu, Gui [Key Laboratory for Thermal Science and Power Engineering of MOE, Beijing Key Laboratory for CO2 Utilization and Reduction Technology, Tsinghua University, Beijing 100084 (China) [Key Laboratory for Thermal Science and Power Engineering of MOE, Beijing Key Laboratory for CO2 Utilization and Reduction Technology, Tsinghua University, Beijing 100084 (China); Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104 (United States); Hu, Han; Sun, Ying, E-mail: yyduan@tsinghua.edu.cn, E-mail: ysun@coe.drexel.edu [Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104 (United States)] [Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104 (United States); Duan, Yuanyuan, E-mail: yyduan@tsinghua.edu.cn, E-mail: ysun@coe.drexel.edu [Key Laboratory for Thermal Science and Power Engineering of MOE, Beijing Key Laboratory for CO2 Utilization and Reduction Technology, Tsinghua University, Beijing 100084 (China)] [Key Laboratory for Thermal Science and Power Engineering of MOE, Beijing Key Laboratory for CO2 Utilization and Reduction Technology, Tsinghua University, Beijing 100084 (China)

    2013-12-16T23:59:59.000Z

    In this Letter, dynamic wetting of water nano-droplets containing non-surfactant gold nanoparticles on a gold substrate is examined via molecular dynamics simulations. The results show that the addition of non-surfactant nanoparticles hinders the nano-second droplet wetting process, attributed to the increases in both surface tension of the nanofluid and friction between nanofluid and substrate. The droplet wetting kinetics decreases with increasing nanoparticle loading and water-particle interaction energy. The observed wetting suppression and the absence of nanoparticle ordering near the contact line of nano-sized droplets differ from the wetting behaviors reported from nanofluid droplets of micron size or larger.

  3. Covalent features in the hydrogen bond of a water dimer: molecular orbital analysis

    E-Print Network [OSTI]

    Wang, Bo; Dai, Xing; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2015-01-01T23:59:59.000Z

    The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs) crossing the O and H atoms of the hydrogen-bond in water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. These results illustrate the covalent-like character of the hydrogen bond between water molecules, which contributes to the essential understanding of ice, liquid water, related materials, and life sciences.

  4. All-Optical Production of quantum degeneracy and molecular BEC of $^6$Li

    E-Print Network [OSTI]

    Deng, Shujing; Yu, Qianli; Wu, Haibin

    2015-01-01T23:59:59.000Z

    We achieve a highly degenerate and strongly interacting Fermi gas in a mixture of the two lowest hyperfine states of $^6$Li by direct evaporative cooling in a high power crossed optical dipole trap. The trap is loaded from a large atom number magneto-optical trap (MOT) which is realized by a laser system of 2.5-watts intracavity-frequency-doubled light output at 671 nm. With this system, we also demonstrate the production of a molecular Bose-Einstein condensates (mBEC), and observe the anisotropic expansion of Fermi gases in the so-called BEC-BCS crossover regime.

  5. Orderly Spectra from Random Interactions

    SciTech Connect (OSTI)

    Johnson, C.W. [Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803-4001 (United States)] [Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803-4001 (United States); Bertsch, G.F. [Department of Physics, FM-15, University of Washington, Seattle, Washington 98195 (United States)] [Department of Physics, FM-15, University of Washington, Seattle, Washington 98195 (United States); Dean, D.J.; Dean, D.J. [Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996 (United States) [Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996 (United States); Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803-4001 (United States)

    1998-03-01T23:59:59.000Z

    We investigate the low-lying spectra of many-body systems with random two-body interactions, specifying that the ensemble be invariant under particle-hole conjugation. Surprisingly we find patterns reminiscent of more orderly interactions, such as a predominance of J=0 ground states separated by a gap from the excited states, and evidence of phonon vibrations in the low-lying spectra. {copyright} {ital 1998} {ital The American Physical Society}

  6. Height fluctuations in interacting dimers

    E-Print Network [OSTI]

    Alessandro Giuliani; Vieri Mastropietro; Fabio Lucio Toninelli

    2015-05-05T23:59:59.000Z

    We consider a non-integrable model for interacting dimers on the two-dimensional square lattice. Configurations are perfect matchings of $\\mathbb Z^2$, i.e. subsets of edges such that each vertex is covered exactly once ("close-packing" condition). Dimer configurations are in bijection with discrete height functions, defined on faces $\\boldsymbol{\\xi}$ of $\\mathbb Z^2$. The non-interacting model is "integrable" and solvable via Kasteleyn theory; it is known that all the moments of the height difference $h_{\\boldsymbol{\\xi}}-h_{\\boldsymbol{\\eta}}$ converge to those of the massless Gaussian Free Field (GFF), asymptotically as $|{\\boldsymbol{\\xi}}-{\\boldsymbol{\\eta}}|\\to \\infty$. We prove that the same holds for small non-zero interactions, as was conjectured in the theoretical physics literature. Remarkably, dimer-dimer correlation functions are instead not universal and decay with a critical exponent that depends on the interaction strength. Our proof is based on an exact representation of the model in terms of lattice interacting fermions, which are studied by constructive field theory methods. In the fermionic language, the height difference $h_{\\boldsymbol{\\xi}}-h_{\\boldsymbol{\\eta}}$ takes the form of a non-local operator, consisting of a sum of monomials along an {\\it arbitrary} path connecting $\\boldsymbol{\\xi}$ and $\\boldsymbol{\\eta}$. As in the non-interacting case, this path-independence plays a crucial role in the proof.

  7. Computer simulations of adsorption and molecular recognition phenomena in molecularly imprinted polymers 

    E-Print Network [OSTI]

    Dourado, Eduardo Manuel de Azevedo

    2011-11-22T23:59:59.000Z

    Molecularly imprinted polymers (MIPs) are a novel, promising family of porous materials with potential applications ranging from separations, chemical sensing and catalysis to drug delivery and artificial immunoassays. The ...

  8. auf molecular imaging: Topics by E-print Network

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

    in molecular such as the use of 18 F-deox- yglucose in positron-emission tomography (PET) ima- ging. Molecular imaging McKenzie, Rick 3 Sparse image reconstruction for...

  9. advance molecular imaging: Topics by E-print Network

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

    in molecular such as the use of 18 F-deox- yglucose in positron-emission tomography (PET) ima- ging. Molecular imaging McKenzie, Rick 6 New Thermal Imaging Camera Advances UNL...

  10. atherosclerosis molecular imaging: Topics by E-print Network

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

    in molecular such as the use of 18 F-deox- yglucose in positron-emission tomography (PET) ima- ging. Molecular imaging McKenzie, Rick 4 Sparse image reconstruction for...

  11. OpenAtom -- Ab initio molecular dynamics package

    SciTech Connect (OSTI)

    Roberto Car

    2008-01-01T23:59:59.000Z

    OpenAtom is a highly scalable and portable parallel application for molecular dynamics simulations at the quantum level. It implements the Car-Parrinello ab-initio Molecular Dynamics (CPAIMD) method.

  12. animal studies molecular: Topics by E-print Network

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

    12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Molecular dynamics of B DNA Supplementary Animations Chemistry Websites Summary: Molecular dynamics of B...

  13. FPGA-BASED MULTIGRID COMPUTATION FOR MOLECULAR DYNAMICS SIMULATIONS

    E-Print Network [OSTI]

    Herbordt, Martin

    FPGA-BASED MULTIGRID COMPUTATION FOR MOLECULAR DYNAMICS SIMULATIONS Yongfeng Gu Martin C. Herbordt serial code. 1. INTRODUCTION Molecular Dynamics simulations (MD) are a fundamental tool for gaining Computer Architecture and Automated Design Laboratory Department of Electrical and Computer Engineering

  14. Optical activity of electronically delocalized molecular aggregates: Nonlocal response formulation

    E-Print Network [OSTI]

    Mukamel, Shaul

    Optical activity of electronically delocalized molecular aggregates: Nonlocal response formulation and optical rotation in small optically active molecules, larger conjugated molecules, and molecular aggregates is developed using spatially nonlocal electric and magnetic optical response tensors (r

  15. Top 10 plant pathogenic bacteria in molecular plant pathology.

    E-Print Network [OSTI]

    2012-01-01T23:59:59.000Z

    Foster, G.D. (2012) The top 10 fungal pathogens in molecularBLACKWELL PUBLISHING LTD Top 10 plant pathogenic bacteriaC. and Foster, G.D. (2011) Top 10 plant viruses in molecular

  16. Experimental Tools to Study Molecular Recognition within the Nanoparticle Corona

    E-Print Network [OSTI]

    Kruss, Sebastian

    Advancements in optical nanosensor development have enabled the design of sensors using synthetic molecular recognition elements through a recently developed method called Corona Phase Molecular Recognition (CoPhMoRe). The ...

  17. QSAR, Molecular Graphics and Modeling Study on -Lactam Antibiotics as

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    QSAR, Molecular Graphics and Modeling Study on -Lactam Antibiotics as Substrates of the Multidrug of them in non-linear form. Molecular graphics and docking studies: 2D and 3D docking of some drugs

  18. Processing and thermal properties of molecularly oriented polymers

    E-Print Network [OSTI]

    Skow, Erik (Erik Dean)

    2007-01-01T23:59:59.000Z

    High molecular weight polymers that are linear in molecular construction can be oriented such that some of their physical properties in the oriented direction are enhanced. For over 50 years polymer orientation and processing ...

  19. INTERACTIVE ANALYSIS AND DISPLAY OF TABULAR DATA

    E-Print Network [OSTI]

    Benson, W.H.

    2010-01-01T23:59:59.000Z

    July 1976. Kitous,B. Interactive matrix displays andSS98{~ tA(!. -3.2 . I INTERACTIVE ANALYSIS AND DISPLAY OF ·owned rights. ~j • 6 U I INTERACTIVE ANALYSIS AND DISPLAY OF

  20. Interactive Volume Rendering of Diffusion Tensor Data

    E-Print Network [OSTI]

    Hlawitschka, Mario

    2010-01-01T23:59:59.000Z

    ller. Volumeshop: o Interactive direct volume illustration.Kin04] [KKW05] [KTW06] Interactive Volume Rendering of Di?magic volume lens: An interactive focus+context technique

  1. Single-strips for fast interactive rendering

    E-Print Network [OSTI]

    Diaz-Gutierrez, Pablo; Bhushan, Anusheel; Gopi, M; Pajarola, Renato

    2006-01-01T23:59:59.000Z

    of the 2001 symposium on Interactive 3D graphics, pp. 49–58.of the 1997 symposium on Interactive 3D graphics, pp. 75–ff.Computer graphics and interactive techniques, pp. 199–208.

  2. Technology Enhanced Interaction Framework Kewalin Angkananon

    E-Print Network [OSTI]

    Technology Enhanced Interaction Framework Kewalin Angkananon ECS University of Southampton interaction framework to help design technology to support communication between people and improve interactions between people, technology and objects, particularly in complex situations. A review of existing

  3. Hydrodynamical simulations of the decay of high-speed molecular turbulence. I. Dense molecular regions

    E-Print Network [OSTI]

    Georgi Pavlovski; Michael D. Smith; Mordecai-Mark Mac Low; Alexander Rosen

    2002-08-15T23:59:59.000Z

    We present the results from three dimensional hydrodynamical simulations of decaying high-speed turbulence in dense molecular clouds. We compare our results, which include a detailed cooling function, molecular hydrogen chemistry and a limited C and O chemistry, to those previously obtained for decaying isothermal turbulence. After an initial phase of shock formation, power-law decay regimes are uncovered, as in the isothermal case. We find that the turbulence decays faster than in the isothermal case because the average Mach number remains higher, due to the radiative cooling. The total thermal energy, initially raised by the introduction of turbulence, decays only a little slower than the kinetic energy. We discover that molecule reformation, as the fast turbulence decays, is several times faster than that predicted for a non-turbulent medium. This is caused by moderate speed shocks which sweep through a large fraction of the volume, compressing the gas and dust. Through reformation, the molecular density and molecular column appear as complex patterns of filaments, clumps and some diffuse structure. In contrast, the molecular fraction has a wider distribution of highly distorted clumps and copious diffuse structure, so that density and molecular density are almost identically distributed during the reformation phase. We conclude that molecules form in swept-up clumps but effectively mix throughout via subsequent expansions and compressions.

  4. Verification of the vibronic origin of long-lived coherence in an artificial molecular light harvester

    E-Print Network [OSTI]

    Lim, James; Caycedo-Soler, Felipe; Lincoln, Craig N; Prior, Javier; von Berlepsch, Hans; Huelga, Susana F; Plenio, Martin B; Zigmantas, Donatas; Hauer, Jürgen

    2015-01-01T23:59:59.000Z

    Is quantum coherence responsible for the surprisingly high efficiency of natural light harvesters? If so, how do such systems avoid the loss of coherence due to interaction with their warm, wet and noisy environments? The answer to these important questions rests in the beneficial interplay between electronic and vibrational degrees of freedom. Here we report experimental and theoretical verification of coherent exciton-vibrational (vibronic) coupling as the origin of long-lasting coherence in an artificial light harvester, a molecular J-aggregate. In this macroscopically aligned tubular system, polarization controlled 2D spectroscopy delivers an uncongested and specific optical response. This clarity of signal provided the opportunity to unambiguously assign the origin of the observed long-lived coherences to vibronic coupling and rule out other explanations based upon correlated fluctuations. The discussed vibronic coupling is functionally relevant, as it describes interaction between vibrations and electro...

  5. Benchmark values for molecular three-center integrals arising in Dirac equation

    E-Print Network [OSTI]

    Bagci, A

    2015-01-01T23:59:59.000Z

    The authors in their previous papers obtained compact, arbitrarily accurate expressions for two center one and two electron Dirac integrals expressed over Slater orbitals with noninteger principal quantum numbers. In this present study, the accuracy limits of given expressions is examined for three-center nuclear attraction integrals, which are the first integral set do not have analytically closed form relations. They are expressed through new molecular auxiliary functions obtained via Neumann expansion of Coulomb interaction. The numerical global adaptive method is used to evaluate these integrals for arbitrarily values of orbital parameters, principal quantum numbers in Slater orbitals. Several methods, such as Laplace expansion of Coulomb interaction, single center expansions, Fourier transformation methods, have been developed for evaluation of three-center integrals when integer principal quantum number is used. This is the first attempts to study the three-center integrals with noninteger Slater orbita...

  6. Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics

    E-Print Network [OSTI]

    Zhao, Hongkai

    1 Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision University, Raleigh, NC 27695 Abstract Violation of energy conservation in Poisson-Boltzmann molecular is the observed violation of energy conservation in Poisson-Boltzmann molecular dynamics, in part due to its

  7. Molecular Dynamics Simulations on High-Performance Reconfigurable

    E-Print Network [OSTI]

    Herbordt, Martin

    23 Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems MATT CHIU. 2010. Molecular dynamics simulations on high performance recon- figurable computing systems. ACM Trans://doi.acm.org/10.1145/1862648.1862653. 1. INTRODUCTION Molecular dynamics simulation (MD) is a

  8. Material Transfer Agreement Molecular Libraries Screening Centers Network (MLSCN)

    E-Print Network [OSTI]

    Baker, Chris I.

    Institutes of Health (NIH) Roadmap Molecular Libraries and Imaging Initiative Background Information The NIH Roadmap Molecular Libraries and Imaging Initiative is a research program designed to develop small organic activities funded under the NIH Roadmap Molecular Libraries and Imaging Initiative and carried out

  9. Classical density functional theory to tackle solvation in molecular liquids

    E-Print Network [OSTI]

    Jeanmairet, Guillaume; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-01-01T23:59:59.000Z

    We present a brief review of the classical density functional theory of atomic and molecular fluids. We focus on the application of the theory to the determination of the solvation properties of arbitrary molecular solutes in arbitrary molecular solvent. This includes the prediction of the solvation free energies, as well as the characterization of the microscopic, three-dimensional solvent structure.

  10. Africa Infrastructure Country Diagnostic Documents: Interactive...

    Open Energy Info (EERE)

    Interactive MAP in PDF, all Countries Jump to: navigation, search Tool Summary LAUNCH TOOL Name: Africa Infrastructure Country Diagnostic Documents: Interactive MAP in PDF, all...

  11. Constant pressure and temperature discrete-time Langevin molecular dynamics

    E-Print Network [OSTI]

    Niels Grønbech-Jensen; Oded Farago

    2014-11-13T23:59:59.000Z

    We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems - a one dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb & Dunweg, show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.

  12. Gravitational Collapse in Turbulent Molecular Clouds. II. Magnetohydrodynamical Turbulence

    E-Print Network [OSTI]

    F. Heitsch; M. -M. Mac Low; R. S. Klessen

    2000-09-14T23:59:59.000Z

    Hydrodynamic supersonic turbulence can only prevent local gravitational collapse if the turbulence is driven on scales smaller than the local Jeans lengths in the densest regions, a very severe requirement (Paper I). Magnetic fields have been suggested to support molecular clouds either magnetostatically or via magnetohydrodynamic (MHD) waves. Whereas the first mechanism would form sheet-like clouds, the second mechanism not only could exert a pressure onto the gas counteracting the gravitational forces, but could lead to a transfer of turbulent kinetic energy down to smaller spatial scales via MHD wave interactions. This turbulent magnetic cascade might provide sufficient energy at small scales to halt local collapse. We test this hypothesis with MHD simulations at resolutions up to 256^3 zones, done with ZEUS-3D. We first derive a resolution criterion for self-gravitating, magnetized gas: in order to prevent collapse of magnetostatically supported regions due to numerical diffusion, the minimum Jeans length must be resolved by four zones. Resolution of MHD waves increases this requirement to roughly six zones. We then find that magnetic fields cannot prevent local collapse unless they provide magnetostatic support. Weaker magnetic fields do somewhat delay collapse and cause it to occur more uniformly across the supported region in comparison to the hydrodynamical case. However, they still cannot prevent local collapse for much longer than a global free-fall time.

  13. The Molecular Bond April 2015 | EMSL

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

    With our users, we're working to understand the chemical reactions taking place in soil organic matter, the role of carbon in Arctic permafrost, and the interaction of carbon in...

  14. Molecular graphics approach to bacterial AcrB proteinb-lactam antibiotic molecular recognition in drug efflux mechanism

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    Molecular graphics approach to bacterial AcrB protein­b-lactam antibiotic molecular recognition graphics study of the pump components AcrB and TolC, 16 b-lactam antibiotics and 7 other substrates; Multidrug resistance; Molecular graphics; Vestibules; Pore 1. Introduction Transmembrane solute transporters

  15. QSAR de alguns inibidores peptdicos da enzima HIV-1 protease utilizando "a priori" descritores moleculares e molecular graphics

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    moleculares e molecular graphics Rudolf Kiralj (PQ), Márcia Miguel Castro Ferreira (PQ) rudolf-calculator count/calculation using only 1D and 2D chemical formula). A work on COMBINE (COMparative BINding Energy of molecular graphics, are discussed in terms both of the a priori approach and of the HIV-1 protease inhibitor

  16. Self-doped molecular composite battery electrolytes

    DOE Patents [OSTI]

    Harrup, Mason K.; Wertsching, Alan K.; Stewart, Frederick F.

    2003-04-08T23:59:59.000Z

    This invention is in solid polymer-based electrolytes for battery applications. It uses molecular composite technology, coupled with unique preparation techniques to render a self-doped, stabilized electrolyte material suitable for inclusion in both primary and secondary batteries. In particular, a salt is incorporated in a nano-composite material formed by the in situ catalyzed condensation of a ceramic precursor in the presence of a solvated polymer material, utilizing a condensation agent comprised of at least one cation amenable to SPE applications. As such, the counterion in the condensation agent used in the formation of the molecular composite is already present as the electrolyte matrix develops. This procedure effectively decouples the cation loading levels required for maximum ionic conductivity from electrolyte physical properties associated with condensation agent loading levels by utilizing the inverse relationship discovered between condensation agent loading and the time domain of the aging step.

  17. Traffic by small teams of molecular motors

    E-Print Network [OSTI]

    Melanie J. I. Müller; Janina Beeg; Rumiana Dimova; Stefan Klumpp; Reinhard Lipowsky

    2008-07-07T23:59:59.000Z

    Molecular motors transport various cargos along cytoskeletal filaments, analogous to trucks on roads. In contrast to vehicles, however, molecular motors do not work alone but in small teams. We describe a simple model for the transport of a cargo by one team of motors and by two teams of motors, which walk into opposite directions. The cooperation of one team of motors generates long-range transport, which we observed experimentally in vitro. Transport by two teams of motors leads to a variety of bidirectional motility behaviour and to dynamic instabilities reminiscent of spontaneous symmetry breaking. We also discuss how cargo transport by teams of motors allows the cell to generate robust long-range bidirectional transport.

  18. Molecular Science Research Center, 1991 annual report

    SciTech Connect (OSTI)

    Knotek, M.L.

    1992-03-01T23:59:59.000Z

    During 1991, the Molecular Science Research Center (MSRC) experienced solid growth and accomplishment and the Environmental, and Molecular Sciences Laboratory (EMSL) construction project moved forward. We began with strong programs in chemical structure and dynamics and theory, modeling, and simulation, and both these programs continued to thrive. We also made significant advances in the development of programs in materials and interfaces and macromolecular structure and dynamics, largely as a result of the key staff recruited to lead these efforts. If there was one pervasive activity for the past year, however, it was to strengthen the role of the EMSL in the overall environmental restoration and waste management (ER/WM) mission at Hanford. These extended activities involved not only MSRC and EMSL staff but all PNL scientific and technical staff engaged in ER/WM programs.

  19. Counting molecular-beam grown graphene layers

    SciTech Connect (OSTI)

    Plaut, Annette S. [School of Physics, University of Exeter, Exeter EX4 4QL (United Kingdom)] [School of Physics, University of Exeter, Exeter EX4 4QL (United Kingdom); Wurstbauer, Ulrich [Department of Physics, Columbia University, New York, New York 10027 (United States)] [Department of Physics, Columbia University, New York, New York 10027 (United States); Pinczuk, Aron [Department of Physics, Columbia University, New York, New York 10027 (United States) [Department of Physics, Columbia University, New York, New York 10027 (United States); Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027 (United States); Garcia, Jorge M. [MBE Lab, IMM-Instituto de Microelectronica de Madrid (CNM-CSIC), Madrid, E-28760 (Spain)] [MBE Lab, IMM-Instituto de Microelectronica de Madrid (CNM-CSIC), Madrid, E-28760 (Spain); Pfeiffer, Loren N. [Electrical Engineering Department, Princeton University, New Jersey 08544 (United States)] [Electrical Engineering Department, Princeton University, New Jersey 08544 (United States)

    2013-06-17T23:59:59.000Z

    We have used the ratio of the integrated intensity of graphene's Raman G peak to that of the silicon substrate's first-order optical phonon peak, accurately to determine the number of graphene layers across our molecular-beam (MB) grown graphene films. We find that these results agree well both, with those from our own exfoliated single and few-layer graphene flakes, and with the results of Koh et al.[ACS Nano 5, 269 (2011)]. We hence distinguish regions of single-, bi-, tri-, four-layer, etc., graphene, consecutively, as we scan coarsely across our MB-grown graphene. This is the first, but crucial, step to being able to grow, by such molecular-beam-techniques, a specified number of large-area graphene layers, to order.

  20. Dust Emission from the Perseus Molecular Cloud

    E-Print Network [OSTI]

    S. Schnee; J. Li; A. A. Goodman; A. I. Sargent

    2008-05-27T23:59:59.000Z

    Using far-infrared emission maps taken by IRAS and Spitzer and a near-infrared extinction map derived from 2MASS data, we have made dust temperature and column density maps of the Perseus molecular cloud. We show that the emission from transiently heated very small grains and the big grain dust emissivity vary as a function of extinction and dust temperature, with higher dust emissivities for colder grains. This variable emissivity can not be explained by temperature gradients along the line of sight or by noise in the emission maps, but is consistent with grain growth in the higher density and lower temperature regions. By accounting for the variations in the dust emissivity and VSG emission, we are able to map the temperature and column density of a nearby molecular cloud with better accuracy than has previously been possible.

  1. Simulated Quantum Computation of Molecular Energies

    E-Print Network [OSTI]

    Alán Aspuru-Guzik; Anthony D. Dutoi; Peter J. Love; Martin Head-Gordon

    2006-04-26T23:59:59.000Z

    The calculation time for the energy of atoms and molecules scales exponentially with system size on a classical computer but polynomially using quantum algorithms. We demonstrate that such algorithms can be applied to problems of chemical interest using modest numbers of quantum bits. Calculations of the water and lithium hydride molecular ground-state energies have been carried out on a quantum computer simulator using a recursive phase-estimation algorithm. The recursive algorithm reduces the number of quantum bits required for the readout register from about 20 to 4. Mappings of the molecular wave function to the quantum bits are described. An adiabatic method for the preparation of a good approximate ground-state wave function is described and demonstrated for a stretched hydrogen molecule. The number of quantum bits required scales linearly with the number of basis functions, and the number of gates required grows polynomially with the number of quantum bits.

  2. Institute for Molecular Medicine Research Program

    SciTech Connect (OSTI)

    Phelps, Michael E

    2012-12-14T23:59:59.000Z

    The objectives of the project are the development of new Positron Emission Tomography (PET) imaging instrumentation, chemistry technology platforms and new molecular imaging probes to examine the transformations from normal cellular and biological processes to those of disease in pre-clinical animal models. These technology platforms and imaging probes provide the means to: 1. Study the biology of disease using pre-clinical mouse models and cells. 2. Develop molecular imaging probes for imaging assays of proteins in pre-clinical models. 3. Develop imaging assays in pre-clinical models to provide to other scientists the means to guide and improve the processes for discovering new drugs. 4. Develop imaging assays in pre-clinical models for others to use in judging the impact of drugs on the biology of disease.

  3. Molecular Life Science | Daniel Loos | loos@mls.uni-luebeck.de IM FOCUS DAS LEBEN

    E-Print Network [OSTI]

    Lübeck, Universität zu

    Was ist Molecular Life Science? Hämoglobin. Protein Data Bank: 1HHO #12;Daniel Loos Molecular Life Science

  4. Molecular Mechanism of Biological Proton Transport

    SciTech Connect (OSTI)

    Pomes, R.

    1998-09-01T23:59:59.000Z

    Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

  5. Stochastic heating of a molecular nanomagnet

    E-Print Network [OSTI]

    L. Chotorlishvili; P. Schwab; Z. Toklikishvili; J. Berakdar

    2010-07-02T23:59:59.000Z

    We study the excitation dynamics of a single molecular nanomagnet by static and pulsed magnetic fields. Based on a stability analysis of the classical magnetization dynamics we identify analytically the fields parameters for which the energy is stochastically pumped into the system in which case the magnetization undergoes diffusively and irreversibly a large angle deflection. An approximate analytical expression for the diffusion constant in terms of the fields parameters is given and assessed by full numerical calculations.

  6. Molecular Science Research Center 1992 annual report

    SciTech Connect (OSTI)

    Knotek, M.L.

    1994-01-01T23:59:59.000Z

    The Molecular Science Research Center is a designated national user facility, available to scientists from universities, industry, and other national laboratories. After an opening section, which includes conferences hosted, appointments, and projects, this document presents progress in the following fields: chemical structure and dynamics; environmental dynamics and simulation; macromolecular structure and dynamics; materials and interfaces; theory, modeling, and simulation; and computing and information sciences. Appendices are included: MSRC staff and associates, 1992 publications and presentations, activities, and acronyms and abbreviations.

  7. Nanoscale molecularly imprinted polymers and method thereof

    DOE Patents [OSTI]

    Hart, Bradley R. (Brentwood, CA); Talley, Chad E. (Brentwood, CA)

    2008-06-10T23:59:59.000Z

    Nanoscale molecularly imprinted polymers (MIP) having polymer features wherein the size, shape and position are predetermined can be fabricated using an xy piezo stage mounted on an inverted microscope and a laser. Using an AMF controller, a solution containing polymer precursors and a photo initiator are positioned on the xy piezo and hit with a laser beam. The thickness of the polymeric features can be varied from a few nanometers to over a micron.

  8. Frontiers of NMR in Molecular Biology

    SciTech Connect (OSTI)

    NONE

    1999-08-25T23:59:59.000Z

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  9. 2004 Reversible Associations in Structure & Molecular Biology

    SciTech Connect (OSTI)

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23T23:59:59.000Z

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  10. An NMR (nuclear magnetic resonance) investigation of the chemical association and molecular dynamics in asphalt ridge tar sand ore and bitumen

    SciTech Connect (OSTI)

    Netzel, D.A.; Coover, P.T.

    1987-09-01T23:59:59.000Z

    Preliminary studies on tar sand bitumen given in this report have shown that the reassociation of tar sand bitumen to its original molecular configuration after thermal stressing is a first-order process requiring nearly a week to establish equilibrium. Studies were also conducted on the dissolution of tar sand bitumen in solvents of varying polarity. At a high-weight fraction of solute to solvent the apparent molecular weight of the bitumen molecules was greater than that of the original bitumen when dissolved in chloroform-d/sub 1/ and benzene-d/sub 6/. This increase in the apparent molecular weight may be due to micellar formation or a weak solute-solvent molecular complex. Upon further dilution with any of the solvents studied, the apparent molecular weight of the tar sand bitumen decreased because of reduced van der Waals forces of interaction and/or hydrogen bonding. To define the exact nature of the interactions, it will be necessary to have viscosity measurements of the solutions. 30 refs., 3 figs., 3 tabs.

  11. Molecular modeling gives insight into nonionic surfactants

    SciTech Connect (OSTI)

    Gdanski, R.

    1995-11-01T23:59:59.000Z

    This paper describes the study of a nonionic surfactant through the use of molecular modeling software. The surfactant was decyl alcohol capped with 8 moles of ethylene oxide. This nonionic surfactant is a strong water-wetting agent as well as a good aqueous foaming agent. Four molecular dynamics studies of a single surfactant molecule were conducted under the following conditions: at a water surface at 80 F; in bulk water at 260 F; in bulk hexane at 80 F; at a hexane/water interface at 80 F. The conformations of the surfactant were observed and compared to known solubility data. The results from molecular modeling dynamics calculations will provide new insights into the behavior of surfactant molecules at surfaces and interfaces. This methodology was also extended to aggregates of surfactants to promote understanding of wetting behavior and non-emulsification behavior. In this paper, two studies were performed involving aggregates: one in bulk water at 80 F and another in bulk water at 260 F.

  12. Molecular heat pump for rotational states

    E-Print Network [OSTI]

    C. Lazarou; M. Keller; B. M. Garraway

    2010-01-25T23:59:59.000Z

    In this work we investigate the theory for three different uni-directional population transfer schemes in trapped multilevel systems which can be utilized to cool molecular ions. The approach we use exploits the laser-induced coupling between the internal and motional degrees of freedom so that the internal state of a molecule can be mapped onto the motion of that molecule in an external trapping potential. By sympathetically cooling the translational motion back into its ground state the mapping process can be employed as part of a cooling scheme for molecular rotational levels. This step is achieved through a common mode involving a laser-cooled atom trapped alongside the molecule. For the coherent mapping we will focus on adiabatic passage techniques which may be expected to provide robust and efficient population transfers. By applying far-detuned chirped adiabatic rapid passage pulses we are able to achieve an efficiency of better than 98% for realistic parameters and including spontaneous emission. Even though our main focus is on cooling molecular states, the analysis of the different adiabatic methods has general features which can be applied to atomic systems.

  13. Molecular Selectivity of Brown Carbon Chromophores

    SciTech Connect (OSTI)

    Laskin, Julia; Laskin, Alexander; Nizkorodov, Sergey; Roach, Patrick J.; Eckert, Peter A.; Gilles, Mary K.; Wang, Bingbing; Lee, Hyun Ji; Hu, Qichi

    2014-09-18T23:59:59.000Z

    Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (SOA) generated from ozonolysis of two structural monoterpene isomers: D-limonene (LSOA) and a-pinene (PSOA). Laboratory simulated aging of LSOA and PSOA, through conversion of carbonyls into imines mediated by NH3 vapors in humid air, resulted in selective browning of the LSOA sample, while the PSOA sample remained white. Comparative analysis of the reaction products in the aged LSOA and PSOA samples provided insights into chemistry relevant to formation of brown carbon chromophores. A significant fraction of carbonyl-imine conversion products with identical molecular formulas were detected in both samples. This reflects the high level of similarity in the molecular composition of these two closely related SOA materials. Several highly conjugated products were detected exclusively in the brown LSOA sample and were identified as potential chromophores responsible for the observed color change. The majority of the unique products in the aged LSOA sample with the highest number of double bonds contain two nitrogen atoms. We conclude that chromophores characteristic of the carbonyl- imine chemistry in LSOA are highly conjugated oligomers of secondary imines (Schiff bases) present at relatively low concentrations. Formation of this type of conjugated compounds in PSOA is hindered by the structural rigidity of the a-pinene oxidation products. Our results suggest that the overall light-absorbing properties of SOA may be determined by trace amounts of strong brown carbon chromophores.

  14. Dynamical Study of Guest-Host Orientational Interaction in LiquidCrystalline Materials

    SciTech Connect (OSTI)

    Truong, Thai Viet

    2005-12-20T23:59:59.000Z

    Guest-host interaction has long been a subject of interest in many disciplines. Emphasis is often on how a small amount of guest substance could significantly affect the properties of a host material. This thesis describe our work in studying a guest-host effect where dye-doping of liquid crystalline materials greatly enhances the optical Kerr nonlinearity of the material. The dye molecules, upon excitation and via intermolecular interaction, provides an extra torque to reorient the host molecules, leading to the enhanced optical Kerr nonlinearity. We carried out a comprehensive study on the dynamics of the photoexcited dye-doped liquid crystalline medium. Using various experimental techniques, we separately characterized the dynamical responses of the relevant molecular species present in the medium following photo-excitation, and thus were able to follow the transient process in which photo-excitation of the dye molecules exert through guest-host interaction a net torque on the host LC material, leading to the observed enhanced molecular reorientation. We also observed for the first time the enhanced reorientation in a pure liquid crystal system, where the guest population is created through photoexcitation of the host molecules themselves. Experimental results agree quantitatively with the time-dependent theory based on a mean-field model of the guest-host interaction.

  15. Interactions of mobile helium clusters with surfaces and grain boundaries of plasma-exposed tungsten

    SciTech Connect (OSTI)

    Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu [Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003-9303 (United States); Hammond, Karl D.; Wirth, Brian D. [Department of Nuclear Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States)

    2014-05-07T23:59:59.000Z

    We report results of atomistic computations for the interactions of small mobile helium clusters (He{sub n}) with free surfaces and grain boundaries (GBs) in tungsten toward development of continuum drift-diffusion-reaction models for the dynamics of mobile helium clusters in plasma-exposed tungsten. Molecular-statics (MS) simulations based on reliable many-body interatomic potentials are carried out for He{sub n} (1???n???7) clusters near sinks to obtain the potential energy profiles of the He{sub n} clusters as a function of the clusters' center-of-mass distance from a sink. Sinks investigated include surfaces, GBs, and regions in the vicinity of junctions where GBs intersect free surfaces. Elastic interaction potentials based on elastic inclusion theory provide an excellent description of the MS results for the cluster-sink interactions. The key parameter in the elastic models is the sink segregation strength, which is found to increase with increasing cluster size. Such cluster-sink interactions are responsible for the migration of small helium clusters by drift and for helium segregation on surfaces and grain boundaries in tungsten. Such helium segregation on sinks is observed in large-scale molecular-dynamics simulations of helium aggregation in model polycrystalline tungsten at 933?K upon helium implantation.

  16. Cosmology and the weak interaction

    SciTech Connect (OSTI)

    Schramm, D.N. (Fermi National Accelerator Lab., Batavia, IL (USA)):(Chicago Univ., IL (USA))

    1989-12-01T23:59:59.000Z

    The weak interaction plays a critical role in modern Big Bang cosmology. This review will emphasize two of its most publicized cosmological connections: Big Bang nucleosynthesis and Dark Matter. The first of these is connected to the cosmological prediction of Neutrino Flavours, N{sub {nu}} {approximately} 3 which is now being confirmed at SLC and LEP. The second is interrelated to the whole problem of galaxy and structure formation in the universe. This review will demonstrate the role of the weak interaction both for dark matter candidates and for the problem of generating seeds to form structure. 87 refs., 3 figs., 5 tabs.

  17. Theoretical calculations of magnetic order and anisotropy energies in molecular magnets

    SciTech Connect (OSTI)

    Pederson, M. R. [Center for Computational Materials Science - 6392, Naval Research Laboratory, Washington, D.C. 20375-5000 (United States)] [Center for Computational Materials Science - 6392, Naval Research Laboratory, Washington, D.C. 20375-5000 (United States); Porezag, D. V. [Center for Computational Materials Science - 6392, Naval Research Laboratory, Washington, D.C. 20375-5000 (United States)] [Center for Computational Materials Science - 6392, Naval Research Laboratory, Washington, D.C. 20375-5000 (United States); Kortus, J. [Center for Computational Materials Science - 6392, Naval Research Laboratory, Washington, D.C. 20375-5000 (United States)] [Center for Computational Materials Science - 6392, Naval Research Laboratory, Washington, D.C. 20375-5000 (United States); Khanna, S. N. [Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284-2000 (United States)] [Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284-2000 (United States)

    2000-05-01T23:59:59.000Z

    We present theoretical electronic structure calculations on the nature of electronic states and the magnetic coupling in the Mn{sub 12}O{sub 12} free cluster and the Mn{sub 12}O{sub 12}(RCOO){sub 16}(H{sub 2}O){sub 4} molecular magnetic crystal. The calculations have been performed with the all-electron full-potential NRLMOL code. We find that the free Mn{sub 12}O{sub 12} cluster relaxes to an antiferromagnetic cluster with no net moment. However, when coordinated by sixteen HCOO ligands and four H{sub 2}O groups, as it is in the molecular crystal, we find that the ferrimagnetic ordering and geometrical and magnetic structure observed in the experiments is restored. Local Mn moments for the free and ligandated molecular magnets are presented and compared to experiment. We identify the occupied and unoccupied electronic states that are most responsible for the formation of the large anisotropy barrier and use a recently developed full-space and full-potential method for calculating the spin-orbit coupling interaction and anisotropy energies. Our calculated second-order anisotropy energy is in excellent agreement with experiment. (c) 2000 American Institute of Physics.

  18. Interaction between water cluster ions and mica surface

    SciTech Connect (OSTI)

    Ryuto, Hiromichi, E-mail: ryuto@kuee.kyoto-u.ac.jp; Ohmura, Yuki; Nakagawa, Minoru; Takeuchi, Mitsuaki; Takaoka, Gikan H. [Photonics and Electronics Science and Engineering Center, Kyoto University, Nishikyo, Kyoto 615-8510 (Japan)

    2014-03-15T23:59:59.000Z

    Water cluster ion beams were irradiated on mica surfaces to investigate the interaction between molecular cluster ions and a mica surface. The contact angle of the mica surface increased with increasing dose of the water cluster ion beam, but the increase in the contact angle was smaller than that induced by an ethanol cluster ion beam. The surface roughness also increased with increasing dose of the water cluster ion beam, whereas the intensity of K 2p x-ray photoelectron spectroscopy peaks decreased with increasing dose of the water cluster ion beam. The decrease in the number of potassium atoms together with the increase in the surface roughness may be the causes of the increase in the contact angle.

  19. UBIQUITOUS COMPUTING AND INTERACTION Kaj Grnbk, Professor,

    E-Print Network [OSTI]

    Equipment (Kinesthetic Interaction) > PosLogistics (Positioning and Logistics) > VPP4SGR ­ SmartGrid project

  20. PHASE TRANSFORMATIONS, STABILITY AND MATERIALS INTERACTIONS

    E-Print Network [OSTI]

    Morris, Jr., J.W.

    2010-01-01T23:59:59.000Z

    engine) Environmental Interactions Ceramic Membrane Development Research Opportunities: •Fundamentals of hydrogen-

  1. Cosmology constrains gravitational four-fermion interaction

    SciTech Connect (OSTI)

    Khriplovich, I.B.; Rudenko, A.S., E-mail: khriplovich@inp.nsk.su, E-mail: a.s.rudenko@inp.nsk.su [Budker Institute of Nuclear Physics, Novosibirsk State University, 630090 Novosibirsk (Russian Federation)

    2012-11-01T23:59:59.000Z

    If torsion exists, it generates gravitational four-fermion interaction (GFFI). This interaction gets dominating on the Planck scale. If one confines to the regular, axial-axial part of this interaction, the results do not comply with the Friedmann-Robertson-Walker (FRW) cosmology for the spatial flat or closed Universe. In principle, the anomalous, vector-vector interaction could restore the agreement.

  2. Cosmology constrains gravitational four-fermion interaction

    E-Print Network [OSTI]

    I. B. Khriplovich; A. S. Rudenko

    2012-10-27T23:59:59.000Z

    If torsion exists, it generates gravitational four-fermion interaction (GFFI). This interaction gets dominating on the Planck scale. If one confines to the regular, axial-axial part of this interaction, the results do not comply with the Friedmann-Robertson-Walker (FRW) cosmology for the spatial flat or closed Universe. In principle, the anomalous, vector-vector interaction could restore the agreement.

  3. A deep near-infrared survey toward the Aquila molecular cloud - I. Molecular hydrogen outflows

    E-Print Network [OSTI]

    Zhang, Miaomiao; Wang, Hongchi; Sun, Jia; Wang, Min; Jiang, Zhibo; Anathipindika, Sumedh

    2015-01-01T23:59:59.000Z

    We have performed an unbiased deep near-infrared survey toward the Aquila molecular cloud with a sky coverage of ~1 deg2. We identified 45 molecular hydrogen emission-line objects(MHOs), of which only 11 were previously known. Using the Spitzer archival data we also identified 802 young stellar objects (YSOs) in this region. Based on the morphology and the location of MHOs and YSO candidates, we associate 43 MHOs with 40 YSO candidates. The distribution of jet length shows an exponential decrease in the number of outflows with increasing length and the molecular hydrogen outflows seem to be oriented randomly. Moreover, there is no obvious correlation between jet lengths, jet opening angles, or jet H2 1-0 S(1) luminosities and spectral indices of the possible driving sources in this region. We also suggest that molecular hydrogen outflows in the Aquila molecular cloud are rather weak sources of turbulence, unlikely to generate the observed velocity dispersion in the region of survey.

  4. Molecular dynamics of excited state intramolecular proton transfer: 3-hydroxyflavone in solution

    SciTech Connect (OSTI)

    Bellucci, Michael A.; Coker, David F. [Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215 (United States)

    2012-05-21T23:59:59.000Z

    The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 3-hydroxyflavone is investigated using classical molecular dynamics in conjunction with empirical valence bond (EVB) potentials for the description of intramolecular interactions, and a molecular mechanics and variable partial charge model, dependent on transferring proton position, for the description of solute-solvent interactions. A parallel multi-level genetic program was used to accurately fit the EVB potential energy surfaces to high level ab initio data. We have studied the excited state intramolecular proton transfer (ESIPT) reaction in three different solvent environments: methylcyclohexane, acetonitrile, and methanol. The effects of the environment on the proton transfer time and the underlying mechanisms responsible for the varied time scales of the ESIPT reaction rates are analyzed. We find that simulations with our EVB potential energy surfaces accurately reproduce experimentally determined reaction rates, fluorescence spectra, and vibrational frequency spectra in all three solvents. Furthermore, we find that the ultrafast ESIPT process results from a combination of ballistic transfer, and intramolecular vibrational redistribution, which leads to the excitation of a set of low frequency promoting vibrational modes. From this set of promoting modes, we find that an O-O in plane bend and a C-H out of plane bend are present in all three solvents, indicating that they are fundamental to the ultrafast proton transfer. Analysis of the slow proton transfer trajectories reveals a solvent mediated proton transfer mechanism, which is diffusion limited.

  5. Molecular-level Design of Heterogeneous Chiral Catalysts

    SciTech Connect (OSTI)

    Gellman, Andrew John [Carnegie Mellon University; Sholl, David S. [Georgia Institute of Technology; Tysoe, Wilfred T. [University of Wisconsin - Milwaukee; Zaera, Francisco [University of California at Riverside

    2013-04-28T23:59:59.000Z

    Understanding and controlling selectivity is one of the key challenges in heterogeneous catalysis. Among problems in catalytic selectivity enantioselectivity is perhaps the most the most challenging. The primary goal of the project on “Molecular-level Design of Heterogeneous Chiral Catalysts” is to understand the origins of enantioselectivity on chiral heterogeneous surfaces and catalysts. The efforts of the project team include preparation of chiral surfaces, characterization of chiral surfaces, experimental detection of enantioselectivity on such surfaces and computational modeling of the interactions of chiral probe molecules with chiral surfaces. Over the course of the project period the team of PI’s has made some of the most detailed and insightful studies of enantioselective chemistry on chiral surfaces. This includes the measurement of fundamental interactions and reaction mechanisms of chiral molecules on chiral surfaces and leads all the way to rationale design and synthesis of chiral surfaces and materials for enantioselective surface chemistry. The PI’s have designed and prepared new materials for enantioselective adsorption and catalysis. Naturally Chiral Surfaces • Completion of a systematic study of the enantiospecific desorption kinetics of R-3-methylcyclohexanone (R-3-MCHO) on 9 achiral and 7 enantiomeric pairs of chiral Cu surfaces with orientations that span the stereographic triangle. • Discovery of super-enantioselective tartaric acid (TA) and aspartic acid (Asp) decomposition as a result of a surface explosion mechanism on Cu(643)R&S. Systematic study of super-enantiospecific TA and Asp decomposition on five enantiomeric pairs of chiral Cu surfaces. • Initial observation of the enantiospecific desorption of R- and S-propylene oxide (PO) from Cu(100) imprinted with {3,1,17} facets by L-lysine adsorption. Templated Chiral Surfaces • Initial observation of the enantiospecific desorption of R- and S-PO from Pt(111) and Pd(111) modified by a variety of chiral templates. • Demonstrated enantioselective separation of racemic PO on chemically synthesized chiral gold nanoparticles. • Discovery of zwitterionic adsorption states of amino acids on Pd(111). • First structure determinations of adsorbed amino acids and identification of tetrameric chiral template structures. • Exploration of the enantiospecific interaction of PO and R-3-MCHO adsorption on chirally modified Cu(100), Cu(110) and Cu(111). One-to-One Interactions • Determination of cinchona orientation on Pt surfaces in situ at the solid-liquid interface using FT-IRAS. • Systematic study of the influence of solution properties on the adsorption of modified cinchonas alkaloids onto Pt surfaces. • Correlation of cinchona adsorption with catalytic activity, as affected by concentration, the nature of the solvent, and dissolved gases in the liquid phase. • Measurement of enantioselective chemisorption on 1-(1-naphthyl) ethylamine (NEA) modified Pt(111) and Pd(111) surfaces. • Imaging of chiral docking complexes between NEA and methyl pyruvate on Pd(111). Chiral Catalyst Synthesis • Anchoring of cinchona alkaloid to surfaces • Synthesis of chiral Au nanoparticles and demonstration of their enantiospecific interactions with R- and S-PO. • Elucidation of the driving forces for chiral imprinting of Cu(100) by L- and D-lysine to form Cu(3,1,17)R&S facets.

  6. Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models

    E-Print Network [OSTI]

    M. R. Ejtehadi; S. P. Avall; S. S. Plotkin

    2004-07-14T23:59:59.000Z

    Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pair-wise interactions only, we have found 1) a significantly increased correlation with experimental phi-values and folding rates, 2) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ~ 20%, and 3) a considerably larger amount of 3-body energy present in Chymotripsin inhibitor than other proteins studied.

  7. Synthetic Diamond and Wurtzite Structures Self-Assemble with Isotropic Pair Interactions

    E-Print Network [OSTI]

    Mikael C. Rechtsman; Frank H. Stillinger; Salvatore Torquato

    2007-09-24T23:59:59.000Z

    Using inverse statistical-mechanical optimization techniques, we have discovered isotropic pair interaction potentials with strongly repulsive cores that cause the tetrahedrally coordinated diamond and wurtzite lattices to stabilize, as evidenced by lattice sums, phonon spectra, positive-energy defects, and self-assembly in classical molecular dynamics simulations. These results challenge conventional thinking that such open lattices can only be created via directional covalent interactions observed in nature. Thus, our discovery adds to fundamental understanding of the nature of the solid state by showing that isotropic interactions enable the self-assembly of open crystal structures with a broader range of coordination number than previously thought. Our work is important technologically because of its direct relevance generally to the science of self-assembly and specifically to photonic crystal fabrication.

  8. Temperature Dependent Interaction Non-Additivity in the Inorganic Ionic Clusters

    E-Print Network [OSTI]

    Chaban, Vitaly V

    2015-01-01T23:59:59.000Z

    Interaction non-additivity in the chemical context means that binding of certain atom to a reference atom cannot be fully predicted from the interactions of these two atoms with other atoms. This constitutes one of key phenomena determining an identity of our world, which would have been much poorer otherwise. Ionic systems provide a good example of the interaction non-additivity in most cases due to electron transfer and delocalization effects. We report Born-Oppenheimer molecular dynamics (BOMD) simulations of LiCl, NaCl, and KCl at 300, 1500, and 2000 K. We show that our observations originate from interplay of thermal motion during BOMD and cation nature. In the case of alkali cations, ionic nature plays a more significant role than temperature. Our results bring fundamental understanding of electronic effects in the condensed phase of ionic systems and foster progress in physical chemistry and engineering.

  9. Digital Soil Mapping: Interactions with

    E-Print Network [OSTI]

    Grunwald, Sabine

    Chapter 21 Digital Soil Mapping: Interactions with and Applications for Hydropedology J.A. Thompson,1, * S. Roecker,2 S. Grunwald3 and P.R. Owens4 ABSTRACT Spatial information on soils, particularly hydrologic and hydromorphic soil properties, is used to understand and assess soil water retention, flooding

  10. Rotational ratchets with dipolar interactions

    E-Print Network [OSTI]

    Sebastian Jäger; Sabine H. L. Klapp

    2012-10-12T23:59:59.000Z

    We report results from a computer simulation study on the rotational ratchet effect in systems of magnetic particles interacting via dipolar interactions. The ratchet effect consists of directed rotations of the particles in an oscillating magnetic field, which lacks a net rotating component. Our investigations are based on Brownian dynamics simulations of such many-particle systems. We investigate the influence of both, the random and deterministic contributions to the equations of motion on the ratchet effect. As a main result, we show that dipolar interactions can have an enhancing as well as a dampening effect on the ratchet behavior depending on the dipolar coupling strength of the system under consideration. The enhancement is shown to be caused by an increase in the effective field on a particle generated by neighboring magnetic particles, while the dampening is due to restricted rotational motion in the effective field. Moreover, we find a non-trivial influence of the short-range, repulsive interaction between the particles.

  11. Giant amplification of tunnel magnetoresistance in a molecular junction: Molecular spin-valve transistor

    SciTech Connect (OSTI)

    Dhungana, Kamal B.; Pati, Ranjit, E-mail: patir@mtu.edu [Department of Physics, Michigan Technological University, Houghton, Michigan 49931 (United States)

    2014-04-21T23:59:59.000Z

    Amplification of tunnel magnetoresistance by gate field in a molecular junction is the most important requirement for the development of a molecular spin valve transistor. Herein, we predict a giant amplification of tunnel magnetoresistance in a single molecular spin valve junction, which consists of Ru-bis-terpyridine molecule as a spacer between two ferromagnetic nickel contacts. Based on the first-principles quantum transport approach, we show that a modest change in the gate field that is experimentally accessible can lead to a substantial amplification (320%) of tunnel magnetoresistance. The origin of such large amplification is attributed to the spin dependent modification of orbitals at the molecule-lead interface and the resultant Stark effect induced shift in channel position with respect to the Fermi energy.

  12. STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

    SciTech Connect (OSTI)

    Eisenberg, David S.

    2008-07-15T23:59:59.000Z

    The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages. The development of publicly accessible, web-based servers, including the HOTPATCH server, the ProKnow Server and the SAVEs server. All of these are accessible from the home page of the Institute. Advancing the science of bioenergy, in the laboratories of the Principal Investigators of the Institute, including the laboratories of Shimon Weiss, James Liao, James Bowie, Todd Yeates, Rob Gunsalus.

  13. Molecular Aspects of Transport in Thin Films of Controlled Architecture

    SciTech Connect (OSTI)

    Paul W. Bohn

    2009-04-16T23:59:59.000Z

    Our laboratory focuses on developing spatially localized chemistries which can produce structures of controlled architecture on the supermolecular length scale -- structures which allow us to control the motion of molecular species with high spatial resolution, ultimately on nanometer length scales. Specifically, nanocapillary array membranes (NCAMs) contain an array of nanometer diameter pores connecting vertically separated microfluidic channels. NCAMs can manipulate samples with sub-femtoliter characteristic volumes and attomole sample amounts and are opening the field of chemical analysis of mass-limited samples, because they are capable of digital control of fluid switching down to sub-attoliter volumes; extension of analytical “unit operations” down to sub-femtomole sample sizes; and exerting spatiotemporal control over fluid mixing to enable studies of reaction dynamics. Digital flow switching mediated by nanocapillary array membranes can be controlled by bias, ionic strength, or pore diameter and is being studied by observing the temporal characteristics of transport across a single nanopore in thin PMMA membranes. The control of flow via nanopore surface characteristics, charge density and functional group presentation, is being studied by coupled conductivity and laser-induced fluorescence (LIF) measurements. Reactive mixing experiments previously established low millisecond mixing times for NCAM-mediated fluid transfer, and this has been exploited to demonstrate capture of mass-limited target species by Au colloids. Voltage and thermally-activated polymer switches have been developed for active control of transport in NCAMs. Thermally-switchable and size-selective transport was achieved by grafting poly(N-isopropylacrylamide) brushes onto the exterior surface of a Au-coated polycarbonate track-etched membrane, while the voltage-gated properties of poly(hydroxyethylmethacrylate) were characterized dynamically. Electrophoretic separations have been coupled to analyte sampling both by LIF and mass spectrometry. Detection of electrophoresis separation products by electrospray mass spectrometry was achieved through direct interfacing to an electrospray mass spectrometer. Pb(II) interactions with the DNAzyme have been realized in an NCAM-coupled integrated microfluidic structure allowing cation separations to be coupled to molecular beacon detection motifs for the determination of Pb(II) in an electroplating sludge reference material. By changing the DNAzyme to select for other compounds of interest, it is possible to incorporate multiple sensing systems within a single device, thereby achieving great flexibility.

  14. Effective interactions between fluid membranes

    E-Print Network [OSTI]

    Bing-Sui Lu; Rudolf Podgornik

    2015-05-01T23:59:59.000Z

    A self-consistent theory is proposed for the general problem of interacting undulating fluid membranes subject to the constraint that they do not interpenetrate. The steric constraint is implemented via a representation of the Heaviside function, which enables one to transform it into a novel effective steric potential. The steric potential is found to consist of two contributions: one generated by zero mode fluctuations of the membranes, and the other by thermal bending fluctuations. For membranes of cross-sectional area $S$, we find that the bending fluctuation part scales with the inter-membrane separation $d$ as $d^{-2}$ for $d \\ll \\sqrt{S}$, but crosses over to $d^{-4}$ scaling for $d \\gg \\sqrt{S}$, whereas the zero mode part of the steric potential always scales as $d^{-2}$. For membranes interacting exclusively via the steric potential, we obtain exact nonlinear expressions for the effective interaction potential and for the rms undulation amplitude $\\sigma$, which becomes small at low temperatures $T$ and/or large bending stiffnesses $\\kappa$. Moreover, $\\sigma$ scales as $d$ for $d \\ll \\sqrt{S}$, but saturates at $\\sqrt{k_{{\\rm B}} T S/\\kappa}$ for $d \\gg \\sqrt{S}$. In addition, using variational Gaussian theory, we apply our self-consistent treatment to study inter-membrane interactions subject to three different types of potential: (i)~the Moreira-Netz potential for a pair of strongly charged membranes with an intervening solution of multivalent counterions, (ii)~an attractive square well, (iii)~the Morse potential, and (iv)~a combination of hydration and van der Waals interactions.

  15. Blended Interaction Toward a Framework for the Design of Interactive Spaces

    E-Print Network [OSTI]

    Reiterer, Harald

    Blended Interaction ­ Toward a Framework for the Design of Interactive Spaces Hans-Christian Jetter, Florian Geyer, Tobias Schwarz, Harald Reiterer Human-Computer Interaction Group, University of Konstanz In this paper, we propose Blended Interaction as a conceptual framework for the design of interactive spaces. We

  16. Molecular characterization and evolutionary plasticity of protein-protein interfaces

    E-Print Network [OSTI]

    Bickerton, George Richard James

    are the percentage of interfaces having non- zero values for this interaction type. Interaction types per unit area for the overall non-redundant set. . . . . . . . . . . . . . . . 99 3.11 Interaction types per unit area for obligate homodimers. . . . . . 100 3...

  17. Towards reproducible, scalable lateral molecular electronic devices

    E-Print Network [OSTI]

    Durkan, Colm; Zhang, Qian

    2014-08-26T23:59:59.000Z

    of a renaissance in recent years, due in part to the fact that silicon-based devices have continued to decrease in size towards molecular dimensions. Transistors have been fabricated with gate lengths as short as 3 nm [1], and a plethora of new... REFERENCES 1. Hyunjin Lee et al, 2006 Symposium on VLSI Technology, 58, 2006, DOI: 10.1109/VLSIT.2006.1705215 2. K. Tomioka, M. Yoshimura & T. Fukui, Nature, 488, 189 (2012) 3. G. Larrieu & X. –L. Han, Nanoscale, 5, 2437 (2013) 4. A. D. Franklin, S. O...

  18. Thermal Conductivity of Ordered Molecular Water

    SciTech Connect (OSTI)

    W Evans; J Fish; P Keblinski

    2006-02-16T23:59:59.000Z

    We use molecular dynamics simulation to investigate thermal transport characteristics of water with various degree of orientational and translational order induced by the application of an electric field. We observe that orientational ordering of the water dipole moments has a minor effect on the thermal conductivity. However, electric-field induced crystallization and associated translational order results in approximately a 3-fold increase of thermal conductivity with respect to the base water, i.e., to values comparable with those characterizing ice crystal structures.

  19. Intrinsic Shapes of Molecular Cloud Cores

    E-Print Network [OSTI]

    C. E. Jones; Shantanu Basu; John Dubinski

    2001-01-08T23:59:59.000Z

    We conduct an analysis of the shapes of molecular cloud cores using recently compiled catalogs of observed axis ratios of individual cores mapped in ammonia or through optical selection. We apply both analytical and statistical techniques to deproject the observed axis ratios in order to determine the true distribution of cloud core shapes. We find that neither pure oblate nor pure prolate cores can account for the observed distribution of core shapes. Intrinsically triaxial cores produce distributions which agree with observations. The best-fit triaxial distribution contains cores which are more nearly oblate than prolate.

  20. Molecular phosphorus ion source for semiconductor technology

    SciTech Connect (OSTI)

    Gushenets V. I.; Hershcovitch A.; Bugaev, A.S.; Oks, E.M.; Kulevoy, T.V.

    2012-02-15T23:59:59.000Z

    This paper presents results on the generation of molecular phosphorus ion beams in a hot filament ion source. Solid red phosphorous is evaporated mainly as tetra-atomic molecules up to a temperature of 800 C. Thus, one of the main conditions for producing maximum P{sub 4}{sup +} fraction in the beam is to keep the temperature of the phosphorous oven, the steam line and the discharge chamber walls no greater than 800 C. The prior version of our ion source was equipped with a discharge chamber cooling system. The modified source ensured a P{sub 4}{sup +} ion beam current greater than 30% of the total beam current.

  1. Environmental Molecular Sciences Laboratory 2004 Annual Report

    SciTech Connect (OSTI)

    White, Julia C.

    2005-04-17T23:59:59.000Z

    This 2004 Annual Report describes the research and accomplishments of staff and users of the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL), located in Richland, Washington. EMSL is a multidisciplinary, national scientific user facility and research organization, operated by Pacific Northwest National Laboratory (PNNL) for the U.S. Department of Energy's Office of Biological and Environmental Research. The resources and opportunities within the facility are an outgrowth of the U.S. Department of Energy's (DOE) commitment to fundamental research for understanding and resolving environmental and other critical scientific issues.

  2. Phonon interference effects in molecular junctions

    SciTech Connect (OSTI)

    Markussen, Troels, E-mail: troels.markussen@gmail.com [Center for Atomic-scale Materials Design (CAMD), Department of Physics, Technical University of Denmark, DK-2800 Kgs. Lyngby (Denmark)] [Center for Atomic-scale Materials Design (CAMD), Department of Physics, Technical University of Denmark, DK-2800 Kgs. Lyngby (Denmark)

    2013-12-28T23:59:59.000Z

    We study coherent phonon transport through organic, ?-conjugated molecules. Using first principles calculations and Green's function methods, we find that the phonon transmission function in cross-conjugated molecules, like meta-connected benzene, exhibits destructive quantum interference features very analogous to those observed theoretically and experimentally for electron transport in similar molecules. The destructive interference features observed in four different cross-conjugated molecules significantly reduce the thermal conductance with respect to linear conjugated analogues. Such control of the thermal conductance by chemical modifications could be important for thermoelectric applications of molecular junctions.

  3. Yuan T. Lee's Crossed Molecular Beam Experiment

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengtheningWildfires mayYuan T. Lee's Crossed Molecular Beam Experiment Home |

  4. Accelerated Molecular Dynamics Methods | Department of Energy

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't Your Destiny: The Future of1 AAccelerated aging of roofing surfaces Hugo Destaillats,Molecular

  5. Effects of phenylpropanolamine (PPA) on in vitro human erythrocyte membranes and molecular models

    SciTech Connect (OSTI)

    Suwalsky, Mario, E-mail: msuwalsk@udec.cl [Faculty of Chemical Sciences, University of Concepcion, Concepcion (Chile)] [Faculty of Chemical Sciences, University of Concepcion, Concepcion (Chile); Zambrano, Pablo; Mennickent, Sigrid [Faculty of Pharmacy, University of Concepcion, Concepcion (Chile)] [Faculty of Pharmacy, University of Concepcion, Concepcion (Chile); Villena, Fernando [Faculty of Biological Sciences, University of Concepcion, Concepcion (Chile)] [Faculty of Biological Sciences, University of Concepcion, Concepcion (Chile); Sotomayor, Carlos P.; Aguilar, Luis F. [Instituto de Quimica, Pontificia Universidad Catolica de Valparaiso, Valparaiso (Chile)] [Instituto de Quimica, Pontificia Universidad Catolica de Valparaiso, Valparaiso (Chile); Bolognin, Silvia [CNR-Institute for Biomedical Technologies, University of Padova, Padova (Italy)] [CNR-Institute for Biomedical Technologies, University of Padova, Padova (Italy)

    2011-03-18T23:59:59.000Z

    Research highlights: {yields} PPA is a common ingredient in cough-cold medication and appetite suppressants. {yields} Reports on its effects on human erythrocytes are very scarce. {yields} We found that PPA induced in vitro morphological changes to human erythrocytes. {yields} PPA interacted with isolated unsealed human erythrocyte membranes. {yields} PPA interacted with class of lipid present in the erythrocyte membrane outer monolayer. -- Abstract: Norephedrine, also called phenylpropanolamine (PPA), is a synthetic form of the ephedrine alkaloid. After reports of the occurrence of intracranial hemorrhage and other adverse effects, including several deaths, PPA is no longer sold in USA and Canada. Despite the extensive information about PPA toxicity, reports on its effects on cell membranes are scarce. With the aim to better understand the molecular mechanisms of the interaction of PPA with cell membranes, ranges of concentrations were incubated with intact human erythrocytes, isolated unsealed human erythrocyte membranes (IUM), and molecular models of cell membranes. The latter consisted in bilayers built-up of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylethanolamine (DMPE), phospholipid classes present in the outer and inner monolayers of most plasmatic cell membranes, respectively. The capacity of PPA to perturb the bilayer structures of DMPC and DMPE was assessed by X-ray diffraction, DMPC large unilamellar vesicles (LUV) and IUM were studied by fluorescence spectroscopy, and intact human erythrocytes were observed by scanning electron microscopy (SEM). This study presents evidence that PPA affects human red cell membranes as follows: (a) in SEM studies on human erythrocytes it was observed that 0.5 mM PPA induced shape changes; (b) in IUM PPA induced a sharp decrease in the fluorescence anisotropy in the lipid bilayer acyl chains in a concentration range lower than 100 {mu}M; (c) X-ray diffraction studies showed that PPA in the 0.1-0.5 mM range induced increasing structural perturbation to DMPC, but no effects on DMPE multibilayers were detected.

  6. The Galactic Center: An Interacting System of Unusual Sources

    E-Print Network [OSTI]

    F. Yusef-Zade; F. Melia; M. Wardle

    2000-01-11T23:59:59.000Z

    The region bounded by the inner tens of light years at the center of the Milky Way contains five principal components that coexist within the central deep gravitational potential well. These constituents are a black hole candidate (Sgr~A*) with a mass equivalent to $2.6\\pm0.2\\times 10^6$ suns, a surrounding cluster of evolved stars, a complex of young stars, molecular and ionized gas clouds, and a powerful supernova-like remnant. The interaction of these components is responsible for many of the phenomena occurring in this complex and unique portion of the Galaxy. Developing a consistent picture of the primary interactions between the components at the Galactic Center will improve our understanding of the nature of galactic nuclei in general, and will provide with a better defined set of characteristics of black holes. For example, the accretion of stellar winds by Sgr A* appears to produce far less radiation than indicated by estimates based on models of galactic nuclei.

  7. Final Report for Integrated Multiscale Modeling of Molecular Computing Devices

    SciTech Connect (OSTI)

    Glotzer, Sharon C.

    2013-08-28T23:59:59.000Z

    In collaboration with researchers at Vanderbilt University, North Carolina State University, Princeton and Oakridge National Laboratory we developed multiscale modeling and simulation methods capable of modeling the synthesis, assembly, and operation of molecular electronics devices. Our role in this project included the development of coarse-grained molecular and mesoscale models and simulation methods capable of simulating the assembly of millions of organic conducting molecules and other molecular components into nanowires, crossbars, and other organized patterns.

  8. Interaction of water with epoxy.

    SciTech Connect (OSTI)

    Powers, Dana Auburn

    2009-07-01T23:59:59.000Z

    The chemistries of reactants, plasticizers, solvents and additives in an epoxy paint are discussed. Polyamide additives may play an important role in the absorption of molecular iodine by epoxy paints. It is recommended that the unsaturation of the polyamide additive in the epoxy cure be determined. Experimental studies of water absorption by epoxy resins are discussed. These studies show that absorption can disrupt hydrogen bonds among segments of the polymers and cause swelling of the polymer. The water absorption increases the diffusion coefficient of water within the polymer. Permanent damage to the polymer can result if water causes hydrolysis of ether linkages. Water desorption studies are recommended to ascertain how water absorption affects epoxy paint.

  9. Probing DNA interactions with proteins using a single-molecule toolbox: inside the cell, in a test tube, and in a computer

    E-Print Network [OSTI]

    Wollman, Adam J M; Zhou, Zhaokun; Leake, Mark C

    2015-01-01T23:59:59.000Z

    DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and the proteins that bind to it must ideally be interrogated at a single molecule level in their native in vivo environments, in a time-resolved manner fast to sample the molecular transitions across the free energy landscape. Progress has been made over the past decade in utilising cutting-edge tools of the physical sciences to address challenging biological questions concerning the function and modes of action of several different proteins which bind to DNA. These physiologically relevant assays are technically challenging, but can be complemented by powerful and often more tractable in vitro experiments which confer advantages of the chemical environment with enhanced detection single-to-noise of molecular signatures and transition events. Here, we discuss a range of techniqu...

  10. Magnetic Fields in Molecular Cloud Cores

    E-Print Network [OSTI]

    Shantanu Basu

    2004-10-22T23:59:59.000Z

    Observations of magnetic field strengths imply that molecular cloud fragments are individually close to being in a magnetically critical state, even though both magnetic field and column density measurements range over two orders of magnitude. The turbulent pressure also approximately balances the self-gravitational pressure. These results together mean that the one-dimensional velocity dispersion $\\sigv$ is proportional to the mean \\Alf speed of a cloud $\\va$. Global models of MHD turbulence in a molecular cloud show that this correlation is naturally satisfied for a range of different driving strengths of the turbulence. For example, an increase of turbulent driving causes a cloud expansion which also increases $\\va$. Clouds are in a time averaged balance but exhibit large oscillatory motions, particularly in their outer rarefied regions. We also discuss models of gravitational fragmentation in a sheet-like region in which turbulence has already dissipated, including the effects of magnetic fields and ion-neutral friction. Clouds with near-critical mass-to-flux ratios lead to subsonic infall within cores, consistent with some recent observations of motions in starless cores. Conversely, significantly supercritical clouds are expected to produce extended supersonic infall.

  11. Molecular basis for amyloid-[beta] polymorphism

    SciTech Connect (OSTI)

    Colletier, Jacques-Philippe; Laganowsky, Arthur; Landau, Meytal; Zhao, Minglei; Soriaga, Angela B.; Goldschmidt, Lukasz; Flot, David; Cascio, Duilio; Sawaya, Michael R.; Eisenberga, David (UCLA); (ESRF)

    2011-10-19T23:59:59.000Z

    Amyloid-beta (A{beta}) aggregates are the main constituent of senile plaques, the histological hallmark of Alzheimer's disease. A{beta} molecules form {beta}-sheet containing structures that assemble into a variety of polymorphic oligomers, protofibers, and fibers that exhibit a range of lifetimes and cellular toxicities. This polymorphic nature of A{beta} has frustrated its biophysical characterization, its structural determination, and our understanding of its pathological mechanism. To elucidate A{beta} polymorphism in atomic detail, we determined eight new microcrystal structures of fiber-forming segments of A{beta}. These structures, all of short, self-complementing pairs of {beta}-sheets termed steric zippers, reveal a variety of modes of self-association of A{beta}. Combining these atomic structures with previous NMR studies allows us to propose several fiber models, offering molecular models for some of the repertoire of polydisperse structures accessible to A{beta}. These structures and molecular models contribute fundamental information for understanding A{beta} polymorphic nature and pathogenesis.

  12. Ice chemistry in starless molecular cores

    E-Print Network [OSTI]

    Kalvans, Juris

    2015-01-01T23:59:59.000Z

    Starless molecular cores are natural laboratories for interstellar molecular chemistry research. The chemistry of ices in such objects was investigated with a three-phase (gas, surface, and mantle) model. We considered the center part of five starless cores, with their physical conditions derived from observations. The ice chemistry of oxygen, nitrogen, sulfur, and complex organic molecules (COMs) was analyzed. We found that an ice-depth dimension, measured, e.g., in monolayers, is essential for modeling of chemistry in interstellar ices. Particularly, the H2O:CO:CO2:N2:NH3 ice abundance ratio regulates the production and destruction of minor species. It is suggested that photodesorption during core collapse period is responsible for high abundance of interstellar H2O2 and O2H, and other species synthesized on the surface. The calculated abundances of COMs in ice were compared to observed gas-phase values. Smaller activation barriers for CO and H2CO hydrogenation may help explain the production of a number of...

  13. Molecular heat pump for rotational states

    E-Print Network [OSTI]

    Lazarou, C; Garraway, B M

    2010-01-01T23:59:59.000Z

    In this work we investigate the theory for three different uni-directional population transfer schemes in trapped multilevel systems which can be utilized to cool molecular ions. The approach we use exploits the laser-induced coupling between the internal and motional degrees of freedom so that the internal state of a molecule can be mapped onto the motion of that molecule in an external trapping potential. By sympathetically cooling the translational motion back into its ground state the mapping process can be employed as part of a cooling scheme for molecular rotational levels. This step is achieved through a common mode involving a laser-cooled atom trapped alongside the molecule. For the coherent mapping we will focus on adiabatic passage techniques which may be expected to provide robust and efficient population transfers. By applying far-detuned chirped adiabatic rapid passage pulses we are able to achieve an efficiency of better than 98% for realistic parameters and including spontaneous emission. Even...

  14. amyloidogenic molecular structures: Topics by E-print Network

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

    the symmetry and phase space distribution of excited electronic states in bulk 10 Fractal Structure of Molecular Clouds Astrophysics (arXiv) Summary: Compelling evidence...

  15. alkane molecular ions: Topics by E-print Network

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

    1977-01-01 25 Blackbody thermometry with cold molecular ions and application to ion-based frequency standards Physics Websites Summary: Blackbody thermometry with cold...

  16. apparent molecular weight: Topics by E-print Network

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

    stability, atomic weights and molecular weights V. Paar, Bijeniccka 32, 10000 Zagreb, Croatia Accepted 15 January 2002 Abstract A power law is introduced weights. The power law...

  17. Molecular simulations of the transport of molecules across the...

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

    simulations of the transport of molecules across the liquidvapor interface of water. Molecular simulations of the transport of molecules across the liquidvapor interface of...

  18. Impact of the Fuel Molecular Structure on the Oxidation Process...

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

    on the Oxidation Process of Real Diesel fuels According to Storage Conditions and Biodiesel Content Impact of the Fuel Molecular Structure on the Oxidation Process of Real...

  19. Molecular dynamics study of interfacial confinement effects of...

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

    Molecular dynamics study of interfacial confinement effects of aqueous NaCl brines in nanoporous carbon Re-direct Destination: In this paper, studies of aqueous electrolyte...

  20. Molecular Dynamics Study of the Proposed Proton Transport Pathways...

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

    Dynamics Study of the Proposed Proton Transport Pathways in FeFe-Hydrogenase. Molecular Dynamics Study of the Proposed Proton Transport Pathways in FeFe-Hydrogenase. Abstract:...