National Library of Energy BETA

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

    1992-12-31

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

  2. Plant Microbe Interactions | Department of Energy

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

    Plant Microbe Interactions Plant Microbe Interactions This presentation was given by Catherine Ronning at the Symbiosis Conference. symbiosis_conference_ronning.pdf (632.71 KB) More Documents & Publications Symbiosis: Addressing Biomass Production Challenges and Climate Change Symbiosis Conference Speaker and Attendee List Biosystems Design

  3. Multiple soil nutrient competition between plants, microbes,...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several...

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

    SciTech Connect (OSTI)

    Schadt, Christopher [ORNL

    2013-03-01

    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.

  5. Detection of molecular interactions

    DOE Patents [OSTI]

    Groves, John T.; Baksh, Michael M.; Jaros, Michal

    2012-02-14

    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.

  6. Theoretical studies of molecular interactions

    SciTech Connect (OSTI)

    Lester, W.A. Jr.

    1993-12-01

    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.

  7. Spin–orbit interaction mediated molecular dissociation

    SciTech Connect (OSTI)

    Kokkonen, E. Jänkälä, K.; Kettunen, J. A.; Heinäsmäki, S.; Karpenko, A.; Huttula, M.; Löytynoja, T.; Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm

    2014-05-14

    The effect of the spin–orbit interaction to photofragmentation is investigated in the mercury(II) bromide (HgBr{sub 2}) molecule. Changes in the fragmentation between the two spin–orbit components of Hg 5d photoionization, as well as within the molecular-field-splitted levels of these components are observed. Dissociation subsequent to photoionization is studied with synchrotron radiation and photoelectron-photoion coincidence spectroscopy. The experimental results are accompanied by relativistic ab initio analysis of the photoelectron spectrum.

  8. 2010 Atomic & Molecular Interactions Gordon Research Conference

    SciTech Connect (OSTI)

    Todd Martinez

    2010-07-23

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

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

    SciTech Connect (OSTI)

    Gibson, K. D.; Langlois, Grant G.; Li, Wenxin; Sibener, S. J.; Killelea, Daniel R.

    2014-11-14

    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

  10. Molecular Interaction between Botulinum Neurotoxin B and Its...

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

    Molecular Interaction between Botulinum Neurotoxin B and Its Protein Receptor Revealed Figure 1 Structure of the HcB-Syt-II complex. a, sA-weighted FO - FC electron density map ...

  11. Speeding up biomolecular interactions by molecular sledding

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

    Turkin, Alexander; Zhang, Lei; Marcozzi, Alessio; Mangel, Walter F.; Herrmann, Andreas; van Oijen, Antoine M.

    2015-10-07

    In numerous biological processes associations involve a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Moreover, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We also demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptidemore » and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.« less

  12. Speeding up biomolecular interactions by molecular sledding

    SciTech Connect (OSTI)

    Turkin, Alexander; Zhang, Lei; Marcozzi, Alessio; Mangel, Walter F.; Herrmann, Andreas; van Oijen, Antoine M.

    2015-10-07

    In numerous biological processes associations involve a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Moreover, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We also demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptide and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.

  13. Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests

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

    Zhu, Q.; Riley, W. J.; Tang, J.; Koven, C. D.

    2015-03-05

    Soil is a complex system where biotic (e.g., plant roots, micro-organisms) and abiotic (e.g., mineral surfaces) consumers compete for resources necessary for life (e.g., nitrogen, phosphorus). This competition is ecologically significant, since it regulates the dynamics of soil nutrients and controls aboveground plant productivity. Here we develop, calibrate, and test a nutrient competition model that accounts for multiple soil nutrients interacting with multiple biotic and abiotic consumers. As applied here for tropical forests, the Nutrient COMpetition model (N-COM) includes three primary soil nutrients (NH4+, NO3?, and POx (representing the sum of PO43?, HPO42?, and H2PO4?)) and five potential competitors (plantmore »roots, decomposing microbes, nitrifiers, denitrifiers, and mineral surfaces). The competition is formulated with a quasi-steady-state chemical equilibrium approximation to account for substrate (multiple substrates share one consumer) and consumer (multiple consumers compete for one substrate) effects. N-COM successfully reproduced observed soil heterotrophic respiration, N2O emissions, free phosphorus, sorbed phosphorus, and free NH4+ at a tropical forest site (Tapajos). The overall model posterior uncertainty was moderately well constrained. Our sensitivity analysis revealed that soil nutrient competition was primarily regulated by consumer-substrate affinity rather than environmental factors such as soil temperature or soil moisture. Our results imply that the competitiveness (from most to least competitive) followed this order: (1) for NH4+, nitrifiers ~ decomposing microbes > plant roots, (2) for NO3?, denitrifiers ~ decomposing microbes > plant roots, (3) for POx, mineral surfaces > decomposing microbes ~ plant roots. Although smaller, plant relative competitiveness is of the same order of magnitude as microbes. We then applied the N-COM model to analyze field nitrogen and phosphorus perturbation experiments in two tropical forest sites (in

  14. Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests

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

    Zhu, Q.; Riley, W. J.; Tang, J.; Koven, C. D.

    2016-01-18

    Soil is a complex system where biotic (e.g., plant roots, micro-organisms) and abiotic (e.g., mineral surfaces) consumers compete for resources necessary for life (e.g., nitrogen, phosphorus). This competition is ecologically significant, since it regulates the dynamics of soil nutrients and controls aboveground plant productivity. Here we develop, calibrate and test a nutrient competition model that accounts for multiple soil nutrients interacting with multiple biotic and abiotic consumers. As applied here for tropical forests, the Nutrient COMpetition model (N-COM) includes three primary soil nutrients (NH4+, NO3− and POx; representing the sum of PO43−, HPO42− and H2PO4−) and five potential competitors (plantmore » roots, decomposing microbes, nitrifiers, denitrifiers and mineral surfaces). The competition is formulated with a quasi-steady-state chemical equilibrium approximation to account for substrate (multiple substrates share one consumer) and consumer (multiple consumers compete for one substrate) effects. N-COM successfully reproduced observed soil heterotrophic respiration, N2O emissions, free phosphorus, sorbed phosphorus and NH4+ pools at a tropical forest site (Tapajos). The overall model uncertainty was moderately well constrained. Our sensitivity analysis revealed that soil nutrient competition was primarily regulated by consumer–substrate affinity rather than environmental factors such as soil temperature or soil moisture. Our results also imply that under strong nutrient limitation, relative competitiveness depends strongly on the competitor functional traits (affinity and nutrient carrier enzyme abundance). We then applied the N-COM model to analyze field nitrogen and phosphorus perturbation experiments in two tropical forest sites (in Hawaii and Puerto Rico) not used in model development or calibration. Under soil inorganic nitrogen and phosphorus elevated conditions, the model accurately replicated the experimentally observed

  15. Interaction between Cassiopeia A and nearby molecular clouds

    SciTech Connect (OSTI)

    Kilpatrick, C. D.; Bieging, J. H.; Rieke, G. H.

    2014-12-01

    We present spectroscopy of the supernova remnant Cassiopeia A (Cas A) observed at infrared wavelengths from 10 to 40 ?m with the Spitzer Space Telescope and at millimeter wavelengths in {sup 12}CO and {sup 13}CO J =2-1 (230 and 220 GHz) with the Heinrich Hertz Submillimeter Telescope. The IR spectra demonstrate high-velocity features toward a molecular cloud coincident with a region of bright radio continuum emission along the northern shock front of Cas A. The millimeter observations indicate that CO emission is broadened by a factor of two in some clouds toward Cas A, particularly to the south and west. We believe that these features trace interactions between the Cas A shock front and nearby molecular clouds. In addition, some of the molecular clouds that exhibit broadening in CO lie 1'-2' away from the furthest extent of the supernova remnant shock front. We propose that this material may be accelerated by ejecta with velocity significantly larger than the observed free-expansion velocity of the Cas A shock front. These observations may trace cloud interactions with fast-moving outflows such as the bipolar outflow along the southwest to northeast axis of the Cas A supernova remnant, as well as fast-moving knots seen emerging in other directions.

  16. Plant Molecular Biology 2008 Gordon Research Conference - July 13-18, 2008

    SciTech Connect (OSTI)

    Richard M. Amasino

    2009-08-28

    The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2008 conference will continue in that tradition. There will be sessions on metabolism; new methods to study genomes, proteomes and metabolomes; plant-microbe interactions; plant hormones; epigenetics. A new topic for the conference this year will be bioenergy. Thus this conference will bring together a range of disciplines to foster the exchange ideas and to permit the participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner.

  17. DockingShop: A Tool for Interactive Molecular Docking (Conference...

    Office of Scientific and Technical Information (OSTI)

    Country of Publication: United States Language: English Subject: 59 BASIC BIOLOGICAL ... FEEDBACK; FORECASTING; MOLECULAR STRUCTURE; NAVIGATION; OPTIMIZATION; PROTEINS; ...

  18. 2010 Plant Molecular Biology Gordon Research Conference

    SciTech Connect (OSTI)

    Michael Sussman

    2010-07-23

    The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2010 conference will continue in that tradition. Emerging concerns about food security have inspired a program with three main themes: (1) genomics, natural variation and breeding to understand adaptation and crop improvement, (2) hormonal cross talk, and (3) plant/microbe interactions. There are also sessions on epigenetics and proteomics/metabolomics. Thus this conference will bring together a range of disciplines, will foster the exchange of ideas and enable participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner. In particular, this conference plays a key role in enabling students and postdocs (the next generation of research leaders) to mingle with pioneers in multiple areas of plant science.

  19. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    SciTech Connect (OSTI)

    De Yoreo, J J; Bartelt, M C; Orme, C A; Villacampa, A; Weeks, B L; Miller, A E

    2002-01-31

    Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

  20. Parallel implementation of three-dimensional molecular dynamic simulation for laser-cluster interaction

    SciTech Connect (OSTI)

    Holkundkar, Amol R.

    2013-11-15

    The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of the experiments reported in the literature. Scaling laws for the computational time is established by varying the number of processor cores and number of macroparticles used. The capabilities of the code are highlighted by implementing various diagnostic tools. To study the dynamics of the laser-cluster interactions, the executable version of the code is available from the author.

  1. Quantum computations with atoms in optical lattices: Marker qubits and molecular interactions

    SciTech Connect (OSTI)

    Calarco, T.; Dorner, U.; Zoller, P.; Julienne, P.S.; Williams, C.J.

    2004-07-01

    We develop a scheme for quantum computation with neutral atoms, based on the concept of 'marker' atoms, i.e., auxiliary atoms that can be efficiently transported in state-independent periodic external traps to operate quantum gates between physically distant qubits. This allows for relaxing a number of experimental constraints for quantum computation with neutral atoms in microscopic potential, including single-atom laser addressability. We discuss the advantages of this approach in a concrete physical scenario involving molecular interactions.

  2. Molecular theory and the effects of solute attractive forces on hydrophobic interactions

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

    Chaudhari, Mangesh I.; Rempe, Susan B.; Asthagiri, D.; Tan, L.; Pratt, L. R.

    2015-12-22

    The role of solute attractive forces on hydrophobic interactions is studied by coordinated development of theory and simulation results for Ar atoms in water. We present a concise derivation of the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions, a derivation that clarifies the close relation of LMF theory to the EXP approximation applied to this problem long ago. The simulation results show that change from purely repulsive atomic solute interactions to include realistic attractive interactions diminishes the strength of hydrophobic bonds. For the Ar–Ar rdfs considered pointwise, the numerical results for themore » effects of solute attractive forces on hydrophobic interactions are opposite in sign and larger in magnitude than predicted by LMF theory. That comparison is discussed from the point of view of quasichemical theory, and it is suggested that the first reason for this difference is the incomplete evaluation within LMF theory of the hydration energy of the Ar pair. With a recent suggestion for the system-size extrapolation of the required correlation function integrals, the Ar–Ar rdfs permit evaluation of osmotic second virial coefficients B2. Those B2’s also show that incorporation of attractive interactions leads to more positive (repulsive) values. With attractive interactions in play, B2 can change from positive to negative values with increasing temperatures. Furthermore, this is consistent with the puzzling suggestions of decades ago that B2 ≈ 0 for intermediate cases of temperature or solute size. In all cases here, B2 becomes more attractive with increasing temperature.« less

  3. Molecular theory and the effects of solute attractive forces on hydrophobic interactions

    SciTech Connect (OSTI)

    Chaudhari, Mangesh I.; Rempe, Susan B.; Asthagiri, D.; Tan, L.; Pratt, L. R.

    2015-12-22

    The role of solute attractive forces on hydrophobic interactions is studied by coordinated development of theory and simulation results for Ar atoms in water. We present a concise derivation of the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions, a derivation that clarifies the close relation of LMF theory to the EXP approximation applied to this problem long ago. The simulation results show that change from purely repulsive atomic solute interactions to include realistic attractive interactions diminishes the strength of hydrophobic bonds. For the Ar–Ar rdfs considered pointwise, the numerical results for the effects of solute attractive forces on hydrophobic interactions are opposite in sign and larger in magnitude than predicted by LMF theory. That comparison is discussed from the point of view of quasichemical theory, and it is suggested that the first reason for this difference is the incomplete evaluation within LMF theory of the hydration energy of the Ar pair. With a recent suggestion for the system-size extrapolation of the required correlation function integrals, the Ar–Ar rdfs permit evaluation of osmotic second virial coefficients B2. Those B2’s also show that incorporation of attractive interactions leads to more positive (repulsive) values. With attractive interactions in play, B2 can change from positive to negative values with increasing temperatures. Furthermore, this is consistent with the puzzling suggestions of decades ago that B2 ≈ 0 for intermediate cases of temperature or solute size. In all cases here, B2 becomes more attractive with increasing temperature.

  4. Phonon-magnon interactions in body centered cubic iron: A combined molecular and spin dynamics study

    SciTech Connect (OSTI)

    Perera, Dilina Landau, David P.; Nicholson, Don M.; Malcolm Stocks, G.; Eisenbach, Markus; Yin, Junqi; Brown, Gregory

    2014-05-07

    Combining an atomistic many-body potential with a classical spin Hamiltonian parameterized by first principles calculations, molecular-spin dynamics computer simulations were performed to investigate phonon-magnon interactions in body centered cubic iron. Results obtained for spin-spin and density-density dynamic structure factors show that noticeable softening and damping of magnon modes occur due to the presence of lattice vibrations. Furthermore, as a result of the phonon-magnon coupling, additional longitudinal spin wave excitations are observed, with the same frequencies as the longitudinal phonon modes.

  5. 2012 ATOMIC AND MOLECULAR INTERACTIONS GORDON RESEARCH CONFERENCE AND GORDON RESEARCH SEMINAR, JULY 15-20, 2012

    SciTech Connect (OSTI)

    Zwier, Timothy

    2012-07-20

    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.

  6. Advanced Characterization of Molecular Interactions in TALSPEAK-like Separations Systems

    SciTech Connect (OSTI)

    Nash, Kenneth; Guelis, Artem; Lumetta, Gregg J.; Sinkov, Sergey

    2015-10-21

    Combining unit operations in advanced aqueous reprocessing schemes brings obvious process compactness advantages, but at the same time greater complexity in process design and operation. Unraveling these interactions requires increasingly sophisticated analytical tools and unique approaches for adequate analysis and characterization that probe molecular scale interactions. Conventional slope analysis methods of solvent extraction are too indirect to provide much insight into such interactions. This project proposed the development and verification of several analytical tools based on studies of TALSPEAK-like aqueous processes. As such, the chemistry of trivalent fission product lanthanides, americium, curium, plutonium, neptunium and uranium figure prominently in these studies. As the project was executed, the primary focus fell upon the chemistry or trivalent lanthanides and actinides. The intent of the investigation was to compare and contrast the results from these various complementary techniques/studies to provide a stronger basis for predicting the performance of extractant/diluent mixtures as media for metal ion separations. As many/most of these techniques require the presence of metal ions at elevated concentrations, it was expected that these studies would take this investigation into the realm of patterns of supramolecular organization of metal complexes and extractants in concentrated aqueous/organic media. We expected to advance knowledge of the processes that enable and limit solvent extraction reactions as a result of the application of fundamental chemical principles to explaining interactions in complex media.

  7. Molecular dynamics for 400 million particles with short-range interactions

    SciTech Connect (OSTI)

    Deng, Y.; McCoy, R.A.; Marr, R.B.

    1995-07-01

    We report the design and performance of a computational molecular dynamics (MD) code for 400 million particles interacting through the standard pairwise 6-12 Lennard-Jones potential on a 1024-node Intel Paragon, a distributed-memory MIMD parallel computer. The initially recorded {open_quotes}particle-step time{close_quotes} was .4 microseconds. A new inter-node communication strategy ensures high parallel efficiency for a large number of nodes. Besides the ability to tackle large problems, our implementation incorporates a novel method for dynamic load balancing. Our communication and load balancing enhancements provide increased efficiency and flexibility for our MD code. vet are general enough for use in other parallel algorithms.

  8. 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.; Wei, Lisa H.; Baker, Andrew J.; Leroy, Adam K.; Vogel, Stuart N.

    2013-05-20

    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

  9. Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

    SciTech Connect (OSTI)

    Kekenes-Huskey, P. M.; Gillette, A. K.; McCammon, J. A.; Department of Chemistry, Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0636

    2014-05-07

    The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute “obstacles” and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as “buffers” that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded

  10. Molecular sled is an eleven-amino acid vehicle facilitating biochemical interactions via sliding components along DNA

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

    Mangel, Walter F.; McGrath, William J.; Xiong, Kan; Graziano, Vito; Blainey, Paul C.

    2016-02-02

    Recently, we showed the adenovirus proteinase interacts productively with its protein substrates in vitro and in vivo in nascent virus particles via one-dimensional diffusion along the viral DNA. The mechanism by which this occurs has heretofore been unknown. We show sliding of these proteins along DNA occurs on a new vehicle in molecular biology, a ‘molecular sled’ named pVIc. This 11-amino acid viral peptide binds to DNA independent of sequence. pVIc slides on DNA, exhibiting the fastest one-dimensional diffusion constant, 26±1.8 × 106 (bp)2 s−1. pVIc is a ‘molecular sled,’ because it can slide heterologous cargos along DNA, for example, amore » streptavidin tetramer. Similar peptides, for example, from the C terminus of β-actin or NLSIII of the p53 protein, slide along DNA. Finally, characteristics of the ‘molecular sled’ in its milieu (virion, nucleus) have implications for how proteins in the nucleus of cells interact and imply a new form of biochemistry, one-dimensional biochemistry.« less

  11. Molecular simulation study of role of polymer–particle interactions in the strain-dependent viscoelasticity of elastomers (Payne effect)

    SciTech Connect (OSTI)

    Chen, Yulong; Li, Ziwei; Wen, Shipeng; Zhang, Liqun; Yang, Qingyuan E-mail: LiuL@mail.buct.edu.cn; Zhong, Chongli; Liu, Li E-mail: LiuL@mail.buct.edu.cn

    2014-09-14

    The strain-amplitude dependence of viscoelastic behavior of model crosslinked elastomers containing various concentrations of spherical nanoparticles (NPs) was studied by non-equilibrium molecular dynamics simulation. All the filler NPs were in monodispersed state and the interactions between these particles were purely repulsive. The polymer–particle interactions were attractive and their interaction energies were tuned in a broad range. Through the computational study, many important features of the behavior of particle-reinforced elastomers observed in experiments, including the Payne effect, were successfully reproduced. It was shown that the magnitude of the Payne effect was found to depend on the polymer–particle interaction and the filler loading. By examining the microstructures of the simulation systems and their evolution during oscillatory shear, four different mechanisms for the role of the polymer–particle interactions in the Payne effect were revealed that consist of the debonding of polymer chains from NP surfaces, the breakage of polymer-shell-bridged NP network, the rearrangement of the NPs in the network into different layers and the shear-induced yielding of the rigid polymer shell in-between neighboring NPs.

  12. 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

    2013-03-01

    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.

  13. Multi-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interaction

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

    Larsen, Peter E.; Sreedasyam, Avinash; Trivedi, Geetika; Desai, Shalaka D.; Dai, Yang; Cseke, Leland; Collart, Frank R.

    2016-01-19

    In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root – mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensormore » systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with fifteen transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and, jasmonic acid. Lastly, this multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.« less

  14. 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

    2014-05-14

    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.

  15. NGC 7538 IRS. 1. Interaction of a polarized dust spiral and a molecular outflow

    SciTech Connect (OSTI)

    Wright, M. C. H.; Hull, Charles L. H. [Department of Astronomy, University of California, Berkeley, CA 94720 (United States); Pillai, Thushara [Max Planck Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Zhao, Jun-Hui [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Sandell, Göran, E-mail: jzhao@cfa.harvard.edu [SOFIA-USRA, NASA Ames Research Center, MS 232-12, Building N232, Room 146, PO Box 1, Moffett Field, CA 94035-0001 (United States)

    2014-12-01

    We present dust polarization and CO molecular line images of NGC 7538 IRS 1. We combined data from the Submillimeter Array, the Combined Array for Research in Millimeter-wave Astronomy, and the James Clerk Maxwell Telescope to make images with ?2.''5 resolution at 230 and 345 GHz. The images show a remarkable spiral pattern in both the dust polarization and molecular outflow. These data dramatically illustrate the interplay between a high infall rate onto IRS 1 and a powerful outflow disrupting the dense, clumpy medium surrounding the star. The images of the dust polarization and the CO outflow presented here provide observational evidence for the exchange of energy and angular momentum between the infall and the outflow. The spiral dust pattern, which rotates through over 180° from IRS 1, may be a clumpy filament wound up by conservation of angular momentum in the infalling material. The redshifted CO emission ridge traces the dust spiral closely through the MM dust cores, several of which may contain protostars. We propose that the CO maps the boundary layer where the outflow is ablating gas from the dense gas in the spiral.

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

    SciTech Connect (OSTI)

    Kang, Kyung

    2011-05-11

    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

  17. 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.

    2014-09-14

    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 ω/2ω 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.

  18. Monitoring molecular interactions using photon arrival-time interval distribution analysis

    DOE Patents [OSTI]

    Laurence, Ted A.; Weiss, Shimon

    2009-10-06

    A method for analyzing/monitoring the properties of species that are labeled with fluorophores. A detector is used to detect photons emitted from species that are labeled with one or more fluorophores and located in a confocal detection volume. The arrival time of each of the photons is determined. The interval of time between various photon pairs is then determined to provide photon pair intervals. The number of photons that have arrival times within the photon pair intervals is also determined. The photon pair intervals are then used in combination with the corresponding counts of intervening photons to analyze properties and interactions of the molecules including brightness, concentration, coincidence and transit time. The method can be used for analyzing single photon streams and multiple photon streams.

  19. Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system

    SciTech Connect (OSTI)

    Fukuda, Ikuo

    2013-11-07

    The zero-multipole summation method has been developed to efficiently evaluate the electrostatic Coulombic interactions of a point charge system. This summation prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large amounts of energetic noise and significant artifacts. The resulting energy function is represented by a constant term plus a simple pairwise summation, using a damped or undamped Coulombic pair potential function along with a polynomial of the distance between each particle pair. Thus, the implementation is straightforward and enables facile applications to high-performance computations. Any higher-order multipole moment can be taken into account in the neutrality principle, and it only affects the degree and coefficients of the polynomial and the constant term. The lowest and second moments correspond respectively to the Wolf zero-charge scheme and the zero-dipole summation scheme, which was previously proposed. Relationships with other non-Ewald methods are discussed, to validate the current method in their contexts. Good numerical efficiencies were easily obtained in the evaluation of Madelung constants of sodium chloride and cesium chloride crystals.

  20. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    SciTech Connect (OSTI)

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-03-07

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper—the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO—it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

  1. Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

    SciTech Connect (OSTI)

    Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der

    2014-12-14

    Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.

  2. 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

    2006-04-21

    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%.

  3. Technical Report Department of Energy Grant #SC0004335 “Tracking Down Cheaters. Molecular Analysis of Carbon Consumption by Organisms That Do Not Contribute to Extracellular Enzyme Pools”

    SciTech Connect (OSTI)

    Blackwood, Christopher

    2015-05-31

    The overriding objective of our work is to integrate physiological and community ecology of belowground organisms into understanding of soil carbon dynamics to improve predictions of terrestrial ecosystem models. This includes using metagenomics and metatranscriptomics-based methods to understand microbial interactions affecting decomposition and soil carbon dynamics. The focus of the majority of the work directly related to this project was on “cheating”, a poorly understood microbial interaction with a potentially large effect on decomposition. Model organisms were used to determine the types of organisms that cheat based on their known niche and genomic characteristics. In addition, we study plant and microbial traits and plant-microbe interactions that affect species distributions and soil carbon, and also develop bioinformatics tools to increase the power of ecological inferences that can be obtained from omics-based sequence data.

  4. Spectroscopic and computational analysis of the molecular interactions in the ionic liquid ion pair [BMP]{sup +}[TFSI]{sup -}

    SciTech Connect (OSTI)

    Mao, James X; Nulwala, Hunaid B; Luebke, David R; Damodaran, Krishnan

    2012-11-01

    1-Butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([BMP]{sup +}[TFSI]{sup −}) ion pairs were studied using DFT at the B3LYP/6-31 + G(d) level. Nine locally stable conformations of the ion pair were located. In the most stable conformation, [TFSI]{sup −} takes a cis conformation and lies below the pyrrolidinium ring. Atoms-in-molecules (AIM) and electron density analysis indicated the existence of nine hydrogen bonds. Interaction energies were recalculated at the Second-order Møller–Plesset (MP2) level to show the importance of dispersion interaction. Further investigation through natural bond orbital (NBO) analysis provided insight into the importance of charge transfer interactions in the ion pair. Harmonic vibrations of the ion pair were calculated and compared with vibrations of the free ions as well as the experimental infrared spectrum. Assignments and frequency shifts are discussed in light of the inter-ionic interactions.

  5. 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.

  6. Light-element nucleosynthesis in a molecular cloud interacting with a supernova remnant and the origin of beryllium-10 in the protosolar nebula

    SciTech Connect (OSTI)

    Tatischeff, Vincent; Duprat, Jean [Centre de Sciences Nucléaires et de Sciences de la Matière, IN2P3-CNRS and Univ Paris-Sud, F-91405 Orsay Cedex (France); De Séréville, Nicolas, E-mail: Vincent.Tatischeff@csnsm.in2p3.fr [Institut de Physique Nucléaire d'Orsay, IN2P3-CNRS and Univ Paris-Sud, F-91405 Orsay Cedex (France)

    2014-12-01

    , expanded during most of its adiabatic phase in an intercloud medium of density of about 1 H-atom cm{sup –3}, and eventually interacted with the presolar molecular cloud only during the radiative stage. This model naturally provides an explanation for the injection of other short-lived radionuclides of stellar origin into the cold presolar molecular cloud ({sup 26}Al, {sup 41}Ca, and {sup 36}Cl) and is in agreement with the solar system originating from the collapse of a molecular cloud shocked by a supernova blast wave.

  7. Ab initio molecular orbital-configuration interaction based quantum master equation (MOQME) approach to the dynamic first hyperpolarizabilities of asymmetric π-conjugated systems

    SciTech Connect (OSTI)

    Kishi, Ryohei; Fujii, Hiroaki; Minami, Takuya; Shigeta, Yasuteru; Nakano, Masayoshi

    2015-01-22

    In this study, we apply the ab initio molecular orbital - configuration interaction based quantum master equation (MOQME) approach to the calculation and analysis of the dynamic first hyperpolarizabilities (β) of asymmetric π-conjugated molecules. In this approach, we construct the excited state models by the ab initio configuration interaction singles method. Then, time evolutions of system reduced density matrix ρ(t) and system polarization p(t) are calculated by the QME approach. Dynamic β in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(ω). Spatial contributions of electrons to β are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2ω. We apply the present method to the calculation of the dynamic β of a series of donor/acceptor substituted polyene oligomers, and then discuss the applicability of the MOQME method to the calculation and analysis of dynamic NLO properties of molecular systems.

  8. A Density Functional Approach to Polarizable Models: A Kim-Gordon-Response Density Interaction Potential for Molecular Simulations

    SciTech Connect (OSTI)

    Tabacchi, G; Hutter, J; Mundy, C

    2005-04-07

    A combined linear response--frozen electron density model has been implemented in a molecular dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory, and a response contribution determined by the instaneous ionic configuration of the system. The method is free from empirical pair-potentials and the parameterization protocol involves only calculations on properly chosen subsystems. They apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparable to Kohn-Sham density functional calculations.

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

    SciTech Connect (OSTI)

    Bond, Stephen D.

    2014-01-01

    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.

  10. Magnetic properties and hyperfine interactions in Cr8, Cr7Cd, and Cr7Ni molecular rings from 19F-NMR

    SciTech Connect (OSTI)

    Bordonali, L; Garlatti, E; Casadei, C M; Furukawa, Y; Lascialfari, A; Carretta, S; Troiani, F; Timco, G; Winpenny, R E; Borsa, F

    2014-04-14

    A detailed experimental investigation of the 19F nuclear magnetic resonance is made on single crystals of the homometallic Cr8 antiferromagnetic molecular ring and heterometallic Cr7Cd and Cr7 Ni rings in the low temperature ground state. Since the F? ion is located midway between neighboring magnetic metal ions in the ring, the 19F-NMR spectra yield information about the local electronic spin density and 19F hyperfine interactions. In Cr8, where the ground state is a singlet with total spin S T = 0, the 19F-NMR spectra at 1.7 K and low external magnetic field display a single narrow line, while when the magnetic field is increased towards the first level crossing field, satellite lines appear in the 19F-NMR spectrum, indicating a progressive increase in the Boltzmann population of the first excited state S T = 1. In the heterometallic rings, Cr7Cd and Cr7 Ni, whose ground state is magnetic with S T = 3/2 and S T = 1/2, respectively, the 19F-NMR spectrum has a complicated structure which depends on the strength and orientation of the magnetic field, due to both isotropic and anisotropic transferred hyperfine interactions and classical dipolar interactions. From the 19F-NMR spectra in single crystals we estimated the transferred hyperfine constants for both the F?-Ni2+ and the F?-Cd2+ bonds. The values of the hyperfine constants compare well to the ones known for F?-Ni2+ in KNiF3 and NiF2 and for F?-Cr3+ in K2NaCrF6. The results are discussed in terms of hybridization of the 2s, 2p orbitals of the F? ion and the d orbitals of the magnetic ion. Finally, we discuss the implications of our results for the electron-spin decoherence.

  11. FERMI-LAT OBSERVATIONS OF SUPERNOVA REMNANTS INTERACTING WITH MOLECULAR CLOUDS: W41, MSH 17-39, AND G337.7-0.1

    SciTech Connect (OSTI)

    Castro, Daniel; Figueroa-Feliciano, Enectali; Slane, Patrick; Carlton, Ashley

    2013-09-01

    We report the detection of {gamma}-ray emission coincident with three supernova remnants (SNRs) using data from the Large Area Telescope on board the Fermi Gamma-ray Space Telescope. W41, G337.7-0.1, and MSH 17-39 are SNRs known to be interacting with molecular clouds, as evidenced by observations of hydroxyl (OH) maser emission at 1720 MHz in their directions and other observational information. SNR shocks are expected to be sites of cosmic-ray acceleration, and clouds of dense material can provide effective targets for production of {gamma}-rays from {pi}{sup 0}-decay. The observations reveal unresolved sources in the direction of G337.7-0.1 and MSH 17-39 and an extended source coincident with W41. We model their broadband emission (radio to {gamma}-ray) using a simple one-zone model, and after considering scenarios in which the MeV-TeV sources originate from either {pi}{sup 0}-decay or leptonic emission, we conclude that the {gamma}-rays are most likely produced through the hadronic channel.

  12. 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

    2014-05-28

    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.

  13. Molecular Dynameomics

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

    Dynameomics Molecular Dynameomics DaggettHiResWhitebg.png Key Challenges: Perform molecular dynamics simulations to characterize both native (i.e. biologically active) and...

  14. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect (OSTI)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  15. Molecular Foundry

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

    Mike Brady ed_barnard Joint Molecular Foundry/ALS Project Scientist mabrady@lbl.gov 510.486.6548

  16. Molecular Science

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

    Molecular Science NETL's Molecular Science competency provides technology-enabling computational and experimental insight into the atomic-level processes occurring in condensed matter and gas phase systems or at the heterogeneous surface-gas interfaces used for energy applications. Research includes molecular optimization as well as both classical and high-throughput material design, specifically: Molecular Optimization Development and application of new computational approaches in the general

  17. Nonequilibrium molecular dynamics simulations of confined fluids...

    Office of Scientific and Technical Information (OSTI)

    A nonequilibrium molecular dynamics (MD) ... in a single simulation upon compression, whereas fluid molecules in the bulk ... for weak fluid -- wall interactions. ...

  18. 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.

    2011-01-10

    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.

  19. Molecular Foundry

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

    NEWS Subatomic Microscopy Key to Building New Classes of Materials Molecular Foundry users from Penn State University and Cornell University have worked with staff to describe the first atomic scale evidence for strain-induced ferroelectricity in a layered oxide. [MORE] Molecular Foundry User Featured in MIT's Technology Review Cyclotron Road's Kendra Kuhl Featured in '35 Innovators Under 35' for 2016. [MORE] Foundry Fall Seminar Series Begins September 13 The next Molecular Foundry seminar

  20. Molecular Foundry

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

    Branden Brough Branden Director of Strategy and External Relations bbrough@lbl.gov 510.486.4206 Biography Branden Brough is the Molecular Foundry's Director of Strategy and...

  1. Molecular Foundry

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

    at the Molecular Foundry as a Scientific Engineering Associate since 2007. Expertise Tracy's main focus is assisting users with their research projects (helping design reactions ...

  2. Molecular Foundry

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

    Liu's research aims to achieve coherent control of functionality and properties across different scales through molecular level design and synthesis. With the developed materials ...

  3. Molecular Foundry

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

    Jeff Urban of the Molecular. Both of these positions involved the application of his laser physics and chemistry knowledge to implement various spectroscopic imaging techniques. ...

  4. Molecular Foundry

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

    sources, as well as lasers that can be used in total internal reflectance mode (TIRF). ... to aid in work with biomolecules, microbes, molecular biology techniques and cell culture. ...

  5. Molecular Foundry

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

    User Guide Download the complete Users' Guide (PDF) Submit a Proposal Learn about the Molecular Foundry and its user program Explore Foundry capabilities and plan your proposal...

  6. Molecular Foundry

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

    Facility RLGarcia@lbl.gov 510.486.4125 Biography Education B.A. Molecular Biology, Scripps College, Claremont, CA, 2005 Previous Professional Positions Principal...

  7. Molecular Foundry

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

    Flatter and Faster: Transition Metal Dichalcogendies at the Molecular Foundry (Part II) Brain Imaging and Optical Manipulation Active Nanointerfaces for Electrochemistry SAXS-WAXS...

  8. Molecular Foundry

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

    Dmitry Soustin dmitry User Program Administrator dsoustin@lbl.gov 510.486.7687 Biography Dmitry Soustin is the Molecular Foundry's User Program Administrator. In this role, Dmitry...

  9. Molecular Foundry

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

    Theory of Nanostructured Materials jbneaton@lbl.gov 510.486.4527 personal website Biography Jeffrey B. Neaton is Director of the Molecular Foundry, a Department of Energy...

  10. All-Optical Molecular Orientation

    SciTech Connect (OSTI)

    Oda, Keita; Hita, Masafumi; Minemoto, Shinichirou; Sakai, Hirofumi [Department of Physics, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)

    2010-05-28

    We report clear evidence of all-optical orientation of carbonyl sulfide molecules with an intense nonresonant two-color laser field in the adiabatic regime. The technique relies on the combined effects of anisotropic hyperpolarizability interaction and anisotropic polarizability interaction and does not rely on the permanent dipole interaction with an electrostatic field. It is demonstrated that the molecular orientation can be controlled simply by changing the relative phase between the two wavelength fields. The present technique brings researchers a new steering tool of gaseous molecules and will be quite useful in various fields such as electronic stereodynamics in molecules and ultrafast molecular imaging.

  11. Parallel Molecular Dynamics Program for Molecules

    Energy Science and Technology Software Center (OSTI)

    1995-03-07

    ParBond is a parallel classical molecular dynamics code that models bonded molecular systems, typically of an organic nature. It uses classical force fields for both non-bonded Coulombic and Van der Waals interactions and for 2-, 3-, and 4-body bonded (bond, angle, dihedral, and improper) interactions. It integrates Newton''s equation of motion for the molecular system and evaluates various thermodynamical properties of the system as it progresses.

  12. Magnetic properties and hyperfine interactions in Cr{sub 8}, Cr{sub 7}Cd, and Cr{sub 7}Ni molecular rings from {sup 19}F-NMR

    SciTech Connect (OSTI)

    Bordonali, L.; Borsa, F.; Consorzio INSTM, Via Giusti 9, I-50121 Firenze; Department of Physics and Astronomy, Ames Laboratory, Iowa State University, Ames, Iowa 50011 ; Garlatti, E.; Dipartimento di Fisica e Scienze della Terra, Università di Parma, Viale G. P. Usberti 7 Casadei, C. M.; Department of Physics and Astronomy, Ames Laboratory, Iowa State University, Ames, Iowa 50011 ; Furukawa, Y.; Lascialfari, A.; Consorzio INSTM, Via Giusti 9, I-50121 Firenze; Department of Physics, Università degli Studi di Milano, Via Celoria 16, 20133 Milano ; Carretta, S.; Timco, G.; Winpenny, R. E. P.

    2014-04-14

    A detailed experimental investigation of the {sup 19}F nuclear magnetic resonance is made on single crystals of the homometallic Cr{sub 8} antiferromagnetic molecular ring and heterometallic Cr{sub 7}Cd and Cr{sub 7}Ni rings in the low temperature ground state. Since the F{sup −} ion is located midway between neighboring magnetic metal ions in the ring, the {sup 19}F-NMR spectra yield information about the local electronic spin density and {sup 19}F hyperfine interactions. In Cr{sub 8}, where the ground state is a singlet with total spin S{sub T} = 0, the {sup 19}F-NMR spectra at 1.7 K and low external magnetic field display a single narrow line, while when the magnetic field is increased towards the first level crossing field, satellite lines appear in the {sup 19}F-NMR spectrum, indicating a progressive increase in the Boltzmann population of the first excited state S{sub T} = 1. In the heterometallic rings, Cr{sub 7}Cd and Cr{sub 7}Ni, whose ground state is magnetic with S{sub T} = 3/2 and S{sub T} = 1/2, respectively, the {sup 19}F-NMR spectrum has a complicated structure which depends on the strength and orientation of the magnetic field, due to both isotropic and anisotropic transferred hyperfine interactions and classical dipolar interactions. From the {sup 19}F-NMR spectra in single crystals we estimated the transferred hyperfine constants for both the F{sup −}-Ni{sup 2+} and the F{sup −}-Cd{sup 2+} bonds. The values of the hyperfine constants compare well to the ones known for F{sup −}-Ni{sup 2+} in KNiF{sub 3} and NiF{sub 2} and for F{sup −}-Cr{sup 3+} in K{sub 2}NaCrF{sub 6}. The results are discussed in terms of hybridization of the 2s, 2p orbitals of the F{sup −} ion and the d orbitals of the magnetic ion. Finally, we discuss the implications of our results for the electron-spin decoherence.

  13. Molecular Foundry

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

    Agenda March 24, 2016 Lawrence Berkeley National Laboratory AGENDA Registration 8:30 am - 9:00 am The Molecular Foundry's History and Impact 9:00 am - 10:30 am Jeff Neaton, Molecular Foundry Welcome Paul Alivisatos, Berkeley Lab/UC Berkeley The Creation of the Molecular Foundry Michael Witherell, Berkeley Lab Berkeley Lab Impact Brian Schowengerdt, Magic Leap Industry Impact Representative Mike Honda (D-CA) National Impact Break 10:30 am - 11:00 am Session 1: Functional Nanointerfaces 11:00 am -

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

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

    contain VEGFR2 tyrosine kinase in complex with an inhibitor from a class of potent anticancer drugs. Michele McTigue et al. produced these and similar crystals to determine the...

  15. Electrostatic interactions between peptides and the molecular...

    Office of Scientific and Technical Information (OSTI)

    Close Cite: Bibtex Format Close 0 pages in this document matching the terms "" Search For Terms: Enter terms in the toolbar above to search the full text of this document for ...

  16. Molecular Foundry

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

    Basic understanding of this nature is required to achieve the mission of the Molecular Foundry, the atomic-level design, creation and control of energy-relevant materials. My group ...

  17. Molecular Foundry

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

    Seminars occur on Tuesdays at 11:00 am, in Building 67, Room 3111 unless otherwise noted. To be added to the Molecular Foundry's seminar mailing list, please email Jason Sweet. ...

  18. Molecular Foundry

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

    Meg Holm Meg Senior Administrator mcholm@lbl.gov 510.486.5135 Biography Meg is the Molecular Foundry's Senior Administrator. In this role, she supervises the Foundry budget...

  19. Molecular Foundry

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

    Alison Hatt allison User Program Director ajhatt@lbl.gov 510.486.7154 Biography Alison Hatt is the Director of the User Program at the Molecular Foundry and a former Foundry...

  20. Molecular Foundry

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

    Gil Torres Gil Torres gjtorres@lbl.gov 510.486.4395 Biography Gil is the Building Manager for MSD in buildings 62, 66, 2, 30, JCAP and the Molecular Foundry. Gil supports Foundry...

  1. Molecular Foundry

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

    See the Foundry's full equipment list Organic and Macromolecular Synthesis Capabilities & Tools Instrument Scheduler Major Instruments and Capabilities AB SCIEX TF4800 MALDI TOF-TOF Mass Spectrometer This instrument is the tandem time-of-flight mass spectrometer systems, providing the excellent level of molecular mass coverage in the range of molecular masses 500 and 150,000 Da, high throughput, and confidence in both qualitative and quantitative analyses. The analyzer combines all of the

  2. Molecular Foundry

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

    Foundry Molecular Foundry HOME REGISTRATION AGENDA SYMPOSIA POSTERS EXHIBITOR INFO TRAVEL & LODGING Molecular Foundry User Meeting: August 11-12, 2016 This conference focuses on frontier research topics in nanoscale science, providing a forum for discussion and development of new results and ideas. Whether you are a returning user, a prospective user, or someone who is curious about the Foundry, you are encouraged to attend the User Meeting. Participants are invited to submit abstracts for

  3. Molecular Foundry

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

    Media and Resources MEDIA Molecular Foundry Youtube Channel Berkeley Lab Youtube Channel Berkeley Lab Photo Archive Webcam The Molecular Foundry and its users benefit from its location at Berkeley Lab within the Bay Area's vibrant scientific ecosystem. The expansive views serve to fuel the imagination and build connections among the Foundry's diverse research community. Baycam Click here for a full screen view from our webcam. RESOURCES Style Guide PDF 308 KB Logos Signature Preferred 41 KB ZIP

  4. Molecular Foundry

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

    Publications Advanced Materials Special Issue » The Molecular Foundry publication database lists peer-reviewed work that has resulted from internal and user research. New publications can be added to the database here. All published work resulting from the use of this facility must acknowledge the Molecular Foundry, regardless of whether Foundry staff are included as authors. Proper acknowledgement text can be found here. Citation Year Facility User Loading data from server

  5. Molecular fountain.

    SciTech Connect (OSTI)

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  6. Interface-assisted molecular spintronics

    SciTech Connect (OSTI)

    Raman, Karthik V.

    2014-09-15

    Molecular spintronics, a field that utilizes the spin state of organic molecules to develop magneto-electronic devices, has shown an enormous scientific activity for more than a decade. But, in the last couple of years, new insights in understanding the fundamental phenomena of molecular interaction on magnetic surfaces, forming a hybrid interface, are presenting a new pathway for developing the subfield of interface-assisted molecular spintronics. The recent exploration of such hybrid interfaces involving carbon based aromatic molecules shows a significant excitement and promise over the previously studied single molecular magnets. In the above new scenario, hybridization of the molecular orbitals with the spin-polarized bands of the surface creates new interface states with unique electronic and magnetic character. This study opens up a molecular-genome initiative in designing new handles to functionalize the spin dependent electronic properties of the hybrid interface to construct spin-functional tailor-made devices. Through this article, we review this subject by presenting a fundamental understanding of the interface spin-chemistry and spin-physics by taking support of advanced computational and spectroscopy tools to investigate molecular spin responses with demonstration of new interface phenomena. Spin-polarized scanning tunneling spectroscopy is favorably considered to be an important tool to investigate these hybrid interfaces with intra-molecular spatial resolution. Finally, by addressing some of the recent findings, we propose novel device schemes towards building interface tailored molecular spintronic devices for applications in sensor, memory, and quantum computing.

  7. Molecular Foundry

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

    See the Foundry's full equipment list Research Themes Discovering the Future, Atom by Atom The six-story, 94,000 square-foot Molecular Foundry building at LBNL overlooks the UC Berkeley campus and, from a distance, the San Francisco Bay. Directly adjacent to the Foundry is the NCEM complex that was established in 1983 to maintain a forefront research center for electron microscopy with state-of-the-art instrumentation and expertise. Merged with the Molecular Foundry in 2014 to take advantage of

  8. Molecular Foundry

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

    My research is focused on understanding the nano- and meso-scale interactions between ... These are typically grounded in (nano)optical and scan-probe techniques, exploiting the ...

  9. Molecular Foundry

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

    SEMINARS ARCHIVE The Molecular Foundry regularly offers seminars and events that feature compelling research and information for those who investigate at the nanoscale. Seminars occur on Tuesdays at 11:00 am, in Building 67, Room 3111 unless otherwise noted. < seminars and events Tuesday, June 28, 2016 at 11am Revealing the Mechanisms of Deformation in Structural Materials Using Advanced Characterization Techniques Mike Mills, The Ohio State University [MORE] Tuesday, June 14, 2016 at 11am

  10. Molecular Foundry

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

    Emory Chan Brand Staff Scientist, Inorganic Nanostructures EMChan@lbl.gov 510.486.7874 personal website Biography Education Postdoctoral fellow, Molecular Foundry with Dr. Delia Milliron Ph. D., Chemistry, UC Berkeley with Prof. Paul Alivisatos and Prof. Richard Mathies, B. S., Chemistry, Stanford University with Prof. Hongjie Dai Expertise Dr. Chan's expertise lies in the combinatorial and high-throughput synthesis of colloidal inorganic nanoparticles. As part of the Foundry's Combinatorial

  11. Molecular Foundry

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

    Molecular Foundry User Policies and Definitions Download the complete User Policies and Definitions (PDF) Guiding principles Safety Costs 50/50 staff time model User proposal types Proposal questions and evaluation criteria Proposal Review Board (PRB) and review process User agreements with Berkeley Lab Access to other user facilities at LBNL Final project report Publications and acknowledgement User feedback and end-of-project survey Users' Executive Committee (UEC) Scientific Advisory Board

  12. Molecular Foundry

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

    and Dinner On March 24, 2016, the Molecular Foundry celebrated the 10th anniversary of the dedication of its iconic building with a full day scientific symposium and dinner event. This celebration recognized the Foundry's major scientific and operational milestones and looked forward to the promising future of nanoscience. Leaders from Congress, DOE, academia, industry, and Berkeley Lab joined prominent Foundry users and staff, both past and present, to participate in this celebration.

  13. Molecular Foundry

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

    One of the World's Premier Nanoscience Research Institutions Supported by the Department of Energy Office of Basic Energy Sciences (BES) through their Nanoscale Science Research Center (NSRC) program, the Molecular Foundry is a national User Facility for nanoscale science serving hundreds of academic, industrial and government scientists around the world each year. Users come to the Foundry to perform multidisciplinary research beyond the scope of an individual's own laboratory. By taking

  14. Molecular Foundry

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

    Theory of Nanostructured Materials The Theory of Nanostructured Materials Facility at the Molecular Foundry is focused on expanding our understanding of materials at the nanoscale. Our research connects the structural and dynamical properties of materials to their functions, such as electrical conductivity and storage, light-harvesting for electricity and fuel, or gas separation and sequestration. We develop and employ a broad range of tools, including advanced electronic-structure theory,

  15. Molecular Foundry

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

    POLICIES AND DEFINITIONS PROPOSAL GUIDE USER GUIDE USER PROGRAM SUBMIT A PROPOSAL » Reviewer Login » Proposal Deadline September 30, 2016 Instrument Scheduler Nanofabrication Instrument Scheduler User Program The Molecular Foundry user program gives researchers access to expertise and equipment for cutting-edge nanoscience in a collaborative, multidisciplinary environment. The program is open to scientists from academia, industry, and research institutes worldwide. These users join a vibrant

  16. Modern concepts in molecular modeling

    SciTech Connect (OSTI)

    Bajorath, J.; Klein, T.E.

    1996-12-31

    This session focused on the application of computer models and the development and application of various energy functions to study the structure, energetics and dynamics of proteins and their interactions with ligands. These studies provide an exciting view of current developments in computer-aided molecular modeling and theoretical analysis of biological molecules.

  17. Molecular Simulation of Carbon Dioxide Brine and Clay Mineral...

    Office of Scientific and Technical Information (OSTI)

    of Carbon Dioxide Brine and Clay Mineral Interactions and Determination of Contact Angles. Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide ...

  18. Interactive Jobs

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

    Interactive Jobs Interactive Jobs Interactive Jobs The login nodes (genepool13 and genepool14) on Genepool should not be used for heavy interactive work. These login nodes are shared amongst all Genepool users, so heavy CPU or memory usage will affect other Genepool users. Instead, you should run intensive interactive sessions via the scheduler with the "qlogin" command, or on a group-dedicated gpint server. Scheduled Interactive Sessions PLEASE NOTE: As of May 2016, qlogin sessions

  19. Molecular Foundry

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

    Nanofabrication Our facility strives to gain insight into fundamental nanofabrication processes, as well as the generation of structures that control light, electron, or energy flow, and how those, and other, nanoscale structures interact with light on ultrafast time scales. Measuring plasmonic structures High yield and performance optical transformers are fabricated by nanoimprint lithography for near-field probe and ultra-resolution sub-surface imaging (a). The new ultrafast laser lab uses

  20. Interactive Jobs

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

    The following command requests 2 nodes using the interactive queue. hopper% qsub -I -q debug -l mppwidth48 The -I flag specifies an interactive job. The -q flag specifies the...

  1. 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

    2014-11-26

    spatially structured microbial partnerships, including other syntrophic associations, microbial mats, biofilms, and plant-microbe or animal-microbe symbioses in nature.

  2. Interactive Jobs

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

    Interactive Jobs Interactive Jobs To run an interactive job on Hopper's compute nodes you must request the number of nodes you want and have the system allocate resources from the pool of free nodes. The following command requests 2 nodes using the interactive queue. hopper% qsub -I -q debug -l mppwidth=48 The -I flag specifies an interactive job. The -q flag specifies the name of the queue and -l mppwidth determines the number of nodes to allocate for your job, but not as you might expect. The

  3. Interaction and Coalescence of Nanovoids and Dynamic Fracture...

    Office of Scientific and Technical Information (OSTI)

    of Nanovoids and Dynamic Fracture in Silica Glass: Multimiilion-to-Billion Atom Molecular Dynamics Simulations Citation Details In-Document Search Title: Interaction and...

  4. Interactive Jobs

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

    Interactive Jobs Interactive Jobs Overview To run interactive jobs on Cori, you must request the number of nodes you want and have the system allocate resources from the pool of free nodes. To request an interactive session, the salloc command must be issued. For example, the following command requests 2 nodes in the debug partition for 30 min, and it requests a license to run on the $SCRATCH file system. More details on requesting file system license can be found here. % salloc -N 2 -p debug -t

  5. Interactive Jobs

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

    Interactive Jobs Interactive Jobs Overview There are two types of interactive jobs. The first type runs on a login node. These applications are typically pre- and post-processing jobs, data management programs, or some other type of "tool". Note that it is not possible to run any MPI application on Carver login nodes. The second type of interactive job runs on one or more Carver compute nodes. Because the only way to gain access to the compute nodes is through the batch system, these

  6. Physics with fast molecular-ion beams

    SciTech Connect (OSTI)

    Kanter, E.P.

    1980-01-01

    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.

  7. Interactive Jobs

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

    Interactive Jobs Interactive Jobs To run an interactive job on Edison's compute nodes you must request the number of nodes you want and have the batch system allocate resources from the pool of free nodes. The following command requests two nodes using the debug partition, and it requests a license to run on the $SCRATCH file system. More details on requesting file system license can be found here. edison% salloc -N 2 -p debug -L SCRATCH The -p flag specifies the name of the partition and the -N

  8. Interactive Jobs

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

    Interactive Jobs Interactive Jobs Serial Code or Commands Franklin is a massively parallel high-performance computing platform and is intended and designed to run large parallel codes. While it is possible to run serial jobs on Franklin, it is discouraged. Any code or command that is not preceeded by the aprun command will execute serially on a service (usually login) node. The login nodes are for executing general UNIX shell commands, building code, and submitting jobs intended to run on the

  9. Weak Interactions

    DOE R&D Accomplishments [OSTI]

    Lee, T. D.

    1957-06-01

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

  10. Solution-Processed Molecular Opto-Ferroic Crystals | Argonne National

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

    Laboratory Solution-Processed Molecular Opto-Ferroic Crystals Title Solution-Processed Molecular Opto-Ferroic Crystals Publication Type Journal Article Year of Publication 2016 Authors Xu, B, Luo, Z, Gao, W, Wilson, AJ, He, C, Chen, X, Yuan, G, Dai, H-L, Rao, Y, Willets, K, Ren, S Journal Chemistry of Materials Volume 28 Start Page 2441 Issue 7 Pagination 9 Date Published 03182016 Abstract Supramolecular assembly utilizing noncovalent interaction to construct ordered molecular

  11. HIV Molecular Immunology 2014

    SciTech Connect (OSTI)

    Yusim, Karina; Korber, Bette Tina Marie; Barouch, Dan; Koup, Richard; de Boer, Rob; Moore, John P.; Brander, Christian; Haynes, Barton F.; Walker, Bruce D.

    2015-02-03

    HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2014 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as crossreactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins are provided.

  12. Structural Molecular Biology, SSRL

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

    Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating ... major experimental driver for structural biology research, serving the needs of a large ...

  13. Structural Molecular Biology, SSRL

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

    Our Mission Our Mission The SSRL Structural Molecular Biology program operates as a integrated resource and has three primary areas (or cores) of technological research and ...

  14. Accelerated Molecular Dynamics Methods

    Broader source: Energy.gov [DOE]

    This presentation on Accelerated Molecular Dynamics Methods was given at the DOE Theory Focus Session on Hydrogen Storage Materials on May 18, 2006.

  15. Committee on Atomic, Molecular and Optical Sciences

    SciTech Connect (OSTI)

    Lancaster, James

    2015-06-30

    The Committee on Atomic, Molecular, and Optical Sciences (CAMOS) is a standing activity of the National Research Council (NRC) that operates under the auspices of the Board on Physics and Astronomy. CAMOS is one of five standing committees of the BPA that are charged with assisting it in achieving its goals—monitoring the health of physics and astronomy, identifying important new developments at the scientific forefronts, fostering interactions with other fields, strengthening connections to technology, facilitating effective service to the nation, and enhancing education in physics. CAMOS provides these capabilities for the atomic, molecular and optical (AMO) sciences.

  16. Rigorous theory of molecular orientational nonlinear optics

    SciTech Connect (OSTI)

    Kwak, Chong Hoon Kim, Gun Yeup

    2015-01-15

    Classical statistical mechanics of the molecular optics theory proposed by Buckingham [A. D. Buckingham and J. A. Pople, Proc. Phys. Soc. A 68, 905 (1955)] has been extended to describe the field induced molecular orientational polarization effects on nonlinear optics. In this paper, we present the generalized molecular orientational nonlinear optical processes (MONLO) through the calculation of the classical orientational averaging using the Boltzmann type time-averaged orientational interaction energy in the randomly oriented molecular system under the influence of applied electric fields. The focal points of the calculation are (1) the derivation of rigorous tensorial components of the effective molecular hyperpolarizabilities, (2) the molecular orientational polarizations and the electronic polarizations including the well-known third-order dc polarization, dc electric field induced Kerr effect (dc Kerr effect), optical Kerr effect (OKE), dc electric field induced second harmonic generation (EFISH), degenerate four wave mixing (DFWM) and third harmonic generation (THG). We also present some of the new predictive MONLO processes. For second-order MONLO, second-order optical rectification (SOR), Pockels effect and difference frequency generation (DFG) are described in terms of the anisotropic coefficients of first hyperpolarizability. And, for third-order MONLO, third-order optical rectification (TOR), dc electric field induced difference frequency generation (EFIDFG) and pump-probe transmission are presented.

  17. Ab initio molecular orbital-configuration interaction based quantum...

    Office of Scientific and Technical Information (OSTI)

    Dynamic in the second harmonic generation is calculated based on the nonperturbative ... Country of Publication: United States Language: English Subject: 71 CLASSICAL AND QUANTUM ...

  18. Collective many-body van der Waals interactions in molecular...

    Office of Scientific and Technical Information (OSTI)

    Research Org: Argonne National Laboratory (ANL) Sponsoring Org: SC OFFICE OF BASIC ENERGY SCIENCES Country of Publication: United States Language: ENGLISH Word Cloud More Like This ...

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

    Office of Scientific and Technical Information (OSTI)

    We chose to study the influence of manganese as a minor component in goethite, because goethite rarely exists as a pure phase in nature. Manganese X-ray absorption near-edge ...

  20. Computational methods for molecular docking

    SciTech Connect (OSTI)

    Klebe, G.; Lengauer, T.

    1995-12-31

    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.

  1. Wetting properties of molecularly rough surfaces

    SciTech Connect (OSTI)

    Svoboda, Martin; Lísal, Martin; Malijevský, Alexandr

    2015-09-14

    We employ molecular dynamics simulations to study the wettability of nanoscale rough surfaces in systems governed by Lennard-Jones (LJ) interactions. We consider both smooth and molecularly rough planar surfaces. Solid substrates are modeled as a static collection of LJ particles arranged in a face-centered cubic lattice with the (100) surface exposed to the LJ fluid. Molecularly rough solid surfaces are prepared by removing several strips of LJ atoms from the external layers of the substrate, i.e., forming parallel nanogrooves on the surface. We vary the solid-fluid interactions to investigate strongly and weakly wettable surfaces. We determine the wetting properties by measuring the equilibrium droplet profiles that are in turn used to evaluate the contact angles. Macroscopic arguments, such as those leading to Wenzel’s law, suggest that surface roughness always amplifies the wetting properties of a lyophilic surface. However, our results indicate the opposite effect from roughness for microscopically corrugated surfaces, i.e., surface roughness deteriorates the substrate wettability. Adding the roughness to a strongly wettable surface shrinks the surface area wet with the liquid, and it either increases or only marginally affects the contact angle, depending on the degree of liquid adsorption into the nanogrooves. For a weakly wettable surface, the roughness changes the surface character from lyophilic to lyophobic due to a weakening of the solid-fluid interactions by the presence of the nanogrooves and the weaker adsorption of the liquid into the nanogrooves.

  2. Structural Molecular Biology, SSRL

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

    Molecular Biology Group hosted a 3-day comprehensive workshop on the use of non-crystalline small-angle x-ray scattering and diffraction techniques in structural biology research. ...

  3. THE DARK MOLECULAR GAS

    SciTech Connect (OSTI)

    Wolfire, Mark G.; Hollenbach, David; McKee, Christopher F. E-mail: dhollenbach@seti.or

    2010-06-20

    The mass of molecular gas in an interstellar cloud is often measured using line emission from low rotational levels of CO, which are sensitive to the CO mass, and then scaling to the assumed molecular hydrogen H{sub 2} mass. However, a significant H{sub 2} mass may lie outside the CO region, in the outer regions of the molecular cloud where the gas-phase carbon resides in C or C{sup +}. Here, H{sub 2} self-shields or is shielded by dust from UV photodissociation, whereas CO is photodissociated. This H{sub 2} gas is 'dark' in molecular transitions because of the absence of CO and other trace molecules, and because H{sub 2} emits so weakly at temperatures 10 K molecular component. This component has been indirectly observed through other tracers of mass such as gamma rays produced in cosmic-ray collisions with the gas and far-infrared/submillimeter wavelength dust continuum radiation. In this paper, we theoretically model this dark mass and find that the fraction of the molecular mass in this dark component is remarkably constant ({approx}0.3 for average visual extinction through the cloud A-bar{sub V{approx_equal}}8) and insensitive to the incident ultraviolet radiation field strength, the internal density distribution, and the mass of the molecular cloud as long as A-bar{sub V}, or equivalently, the product of the average hydrogen nucleus column and the metallicity through the cloud, is constant. We also find that the dark mass fraction increases with decreasing A-bar{sub V}, since relatively more molecular H{sub 2} material lies outside the CO region in this case.

  4. Optical Modulation of Molecular Conductance

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

    Transient absorption spectra of these molecular layers are consistent with formation of a long-lived charge separated state, a finding with implications for the design of molecular ...

  5. Controlling Molecular Ordering in Solution-State Conjugated Polymers

    SciTech Connect (OSTI)

    Zhu, Jiahua; Han, Youngkyu; Kumar, Rajeev; Hong, Kunlun; Bonnesen, Peter V.; Sumpter, Bobby G.; Smith, Gregory Scott; Ivanov, Ilia N.; Do, Changwoo

    2015-07-17

    Rationally encoding molecular interactions that can control the assembly structure and functional expression in solution of conjugated polymers holds great potential for enabling optimal organic optoelectronic and sensory materials. In this work, we show that thermally-controlled and surfactant-guided assembly of water-soluble conjugated polymers in aqueous solution is a simple and effective strategy to generate optoelectronic materials with desired molecular ordering. We have studied a conjugated polymer consisting of a hydrophobic thiophene backbone and hydrophilic, thermo-responsive ethylene oxide side groups, which shows a step-wise, multi-dimensional assembly in water. By incorporating the polymer into phase-segregated domains of an amphiphilic surfactant in solution, we demonstrate that both chain conformation and degree of molecular ordering of the conjugated polymer can be tuned in hexagonal, micellar and lamellar phases of the surfactant solution. The controlled molecular ordering in conjugated polymer assembly is demonstrated as a key factor determining the electronic interaction and optical function.

  6. The interactions of peripheral membrane proteins with biological membranes

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

    Johs, Alexander; Whited, A. M.

    2015-01-01

    The interactions of peripheral proteins with membrane surfaces are critical to many biological processes, including signaling, recognition, membrane trafficking, cell division and cell structure. On a molecular level, peripheral membrane proteins can modulate lipid composition, membrane dynamics and protein-protein interactions. Biochemical and biophysical studies have shown that these interactions are in fact highly complex, dominated by several different types of interactions, and have an interdependent effect on both the protein and membrane. Here we examine three major mechanisms underlying the interactions between peripheral membrane proteins and membranes: electrostatic interactions, hydrophobic interactions, and fatty acid modification of proteins. While experimental approachesmore » continue to provide critical insights into specific interaction mechanisms, emerging bioinformatics resources and tools contribute to a systems-level picture of protein-lipid interactions. Through these recent advances, we begin to understand the pivotal role of protein-lipid interactions underlying complex biological functions at membrane interfaces.« less

  7. The interactions of peripheral membrane proteins with biological membranes

    SciTech Connect (OSTI)

    Johs, Alexander; Whited, A. M.

    2015-01-01

    The interactions of peripheral proteins with membrane surfaces are critical to many biological processes, including signaling, recognition, membrane trafficking, cell division and cell structure. On a molecular level, peripheral membrane proteins can modulate lipid composition, membrane dynamics and protein-protein interactions. Biochemical and biophysical studies have shown that these interactions are in fact highly complex, dominated by several different types of interactions, and have an interdependent effect on both the protein and membrane. Here we examine three major mechanisms underlying the interactions between peripheral membrane proteins and membranes: electrostatic interactions, hydrophobic interactions, and fatty acid modification of proteins. While experimental approaches continue to provide critical insights into specific interaction mechanisms, emerging bioinformatics resources and tools contribute to a systems-level picture of protein-lipid interactions. Through these recent advances, we begin to understand the pivotal role of protein-lipid interactions underlying complex biological functions at membrane interfaces.

  8. Hole Localization in Molecular Crystals from Hybrid Density Functional Theory

    SciTech Connect (OSTI)

    Sai, Na; Barbara, Paul F.; Leung, Kevin

    2011-06-02

    We use first-principles computational methods to examine hole trapping in organic molecular crystals. We present a computational scheme based on the tuning of the fraction of exact exchange in hybrid density functional theory to eliminate the many-electron self-interaction error. With small organic molecules, we show that this scheme gives accurate descriptions of ionization and dimer dissociation. We demonstrate that the excess hole in perfect molecular crystals forms self-trapped molecular polarons. The predicted absolute ionization potentials of both localized and delocalized holes are consistent with experimental values.

  9. 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.

    2006-11-01

    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.

  10. Molecular Foundry Bay Cam

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

    Baycam The Molecular Foundry is a Department of Energy-funded nanoscience research facility at Berkeley Lab that provides users from around the world with access to cutting-edge expertise and instrumentation in a collaborative, multidisciplinary environment. twitter instagram facebook

  11. ENERGY DERIVATIVES FOR CONFIGURATION INTERACTION WAVEFUNCTIONS

    SciTech Connect (OSTI)

    Dupuis, M.

    1980-09-01

    Equations providing the first and second derivatives of a configuration interaction (CI) energy with respect to an external parameter are provided. We assume no restriction on the form of the CI expansion built from molecular orbitals obtained in a multiconfiguration Hartree-Fock (MCHF) calculation. Also the coupled perturbed multi-configuration Hartree-Fock formalism is presented for a general MCHF wavefunction and provides the first order and second order changes of the molecular orbital expansion coefficients with respect to an external parameter.

  12. 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

    2014-01-01

    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.

  13. Aqua-vanadyl ion interaction with Nafion® membranes

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

    Vijayakumar, Murugesan; Govind, Niranjan; Li, Bin; Wei, Xiaoliang; Nie, Zimin; Thevuthasan, Suntharampillai; Sprenkle, Vince L.; Wang, Wei

    2015-03-23

    Lack of comprehensive understanding about the interactions between Nafion membrane and battery electrolytes prevents the straightforward tailoring of optimal materials for redox flow battery applications. In this work, we analyzed the interaction between aqua-vanadyl cation and sulfonic sites within the pores of Nafion membranes using combined theoretical and experimental X-ray spectroscopic methods. Molecular level interactions, namely, solvent share and contact pair mechanisms are discussed based on Vanadium and Sulfur K-edge spectroscopic analysis.

  14. Aqua-vanadyl ion interaction with Nafion® membranes

    SciTech Connect (OSTI)

    Vijayakumar, Murugesan; Govind, Niranjan; Li, Bin; Wei, Xiaoliang; Nie, Zimin; Thevuthasan, Suntharampillai; Sprenkle, Vince L.; Wang, Wei

    2015-03-23

    Lack of comprehensive understanding about the interactions between Nafion membrane and battery electrolytes prevents the straightforward tailoring of optimal materials for redox flow battery applications. In this work, we analyzed the interaction between aqua-vanadyl cation and sulfonic sites within the pores of Nafion membranes using combined theoretical and experimental X-ray spectroscopic methods. Molecular level interactions, namely, solvent share and contact pair mechanisms are discussed based on Vanadium and Sulfur K-edge spectroscopic analysis.

  15. Laser Plasma Interactions

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

    Laser Plasma Interactions Laser Plasma Interactions Understanding and controlling laser produced plasmas for fusion and basic science Contact David Montgomery (505) 665-7994 Email ...

  16. Molecular-beam scattering

    SciTech Connect (OSTI)

    Vernon, M.F.

    1983-07-01

    The molecular-beam technique has been used in three different experimental arrangements to study a wide range of inter-atomic and molecular forces. Chapter 1 reports results of a low-energy (0.2 kcal/mole) elastic-scattering study of the He-Ar pair potential. The purpose of the study was to accurately characterize the shape of the potential in the well region, by scattering slow He atoms produced by expanding a mixture of He in N/sub 2/ from a cooled nozzle. Chapter 2 contains measurements of the vibrational predissociation spectra and product translational energy for clusters of water, benzene, and ammonia. The experiments show that most of the product energy remains in the internal molecular motions. Chapter 3 presents measurements of the reaction Na + HCl ..-->.. NaCl + H at collision energies of 5.38 and 19.4 kcal/mole. This is the first study to resolve both scattering angle and velocity for the reaction of a short lived (16 nsec) electronic excited state. Descriptions are given of computer programs written to analyze molecular-beam expansions to extract information characterizing their velocity distributions, and to calculate accurate laboratory elastic-scattering differential cross sections accounting for the finite apparatus resolution. Experimental results which attempted to determine the efficiency of optically pumping the Li(2/sup 2/P/sub 3/2/) and Na(3/sup 2/P/sub 3/2/) excited states are given. A simple three-level model for predicting the steady-state fraction of atoms in the excited state is included.

  17. Molecular dynamics of membrane proteins.

    SciTech Connect (OSTI)

    Woolf, Thomas B.; Crozier, Paul Stewart; Stevens, Mark Jackson

    2004-10-01

    Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.

  18. MOLECULAR VACUUM PUMP

    DOE Patents [OSTI]

    Eckberg, E.E.

    1960-09-27

    A multiple molecular vacuum pump capable of producing a vacuum of the order of 10/sup -9/ mm Hg is described. The pump comprises a casing of an aggregate of paired and matched cylindrical plates, a recessed portion on one face of each plate concentrically positioned formed by a radially extending wall and matching the similarly recessed portion of its twin plate of that pair of plates and for all paired and matched plates; a plurality of grooves formed in the radially extending walls of each and all recesses progressing in a spiral manner from their respective starting points out at the periphery of the recess inwardly to the central area; a plurality of rotors rotatably mounted to closely occupy the spaces as presented by the paired and matched recesses between all paired plates; a hollowed drive-shaft perforated at points adjacent to the termini of all spiral grooves; inlet ports at the starting points of all grooves and through all plates at common points to each respectively; and a common outlet passage presented by the hollow portion of the perforated hollowed drive-shaft of the molecular pump. (AEC)

  19. Interacting dark sector with transversal interaction

    SciTech Connect (OSTI)

    Chimento, Luis P.; Richarte, Martín G.

    2015-03-26

    We investigate the interacting dark sector composed of dark matter, dark energy, and dark radiation for a spatially flat Friedmann-Robertson-Walker (FRW) background by introducing a three-dimensional internal space spanned by the interaction vector Q and solve the source equation for a linear transversal interaction. Then, we explore a realistic model with dark matter coupled to a scalar field plus a decoupled radiation term, analyze the amount of dark energy in the radiation era and find that our model is consistent with the recent measurements of cosmic microwave background anisotropy coming from Planck along with the future constraints achievable by CMBPol experiment.

  20. Engineering Molecular Transformations for Sustainable Energy...

    Office of Scientific and Technical Information (OSTI)

    Engineering Molecular Transformations for Sustainable Energy Conversion Citation Details In-Document Search Title: Engineering Molecular Transformations for Sustainable Energy ...

  1. Assessment of Molecular Modeling & Simulation

    SciTech Connect (OSTI)

    2002-01-03

    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.

  2. Mysteries of 'molecular machines' revealed

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

    Mysteries of 'molecular machines' revealed Mysteries of 'molecular machines' revealed Scientists are making it easier for pharmaceutical companies and researchers to see the detailed inner workings of molecular machines. December 22, 2014 A picture of a membrane protein called cysZ determined with Phenix software using data that could not previously be analyzed. A picture of a membrane protein called cysZ determined with Phenix software using data that could not previously be analyzed. Contact

  3. Lubricant characterization by molecular simulation

    SciTech Connect (OSTI)

    Moore, J.D.; Cui, S.T.; Cummings, P.T.; Cochran, H.D.

    1997-12-01

    The authors have reported the calculation of the kinematic viscosity index of squalane from nonequilibrium molecular dynamics simulations. This represents the first accurate quantitative prediction of this measure of lubricant performance by molecular simulation. Using the same general alkane potential model, this computational approach offers the possibility of predicting the performance of potential lubricants prior to synthesis. Consequently, molecular simulation is poised to become an important tool for future lubricant development.

  4. Electron Trapping by Molecular Vibration

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

    Electron Trapping by Molecular Vibration Electron Trapping by Molecular Vibration Print Wednesday, 27 April 2005 00:00 In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can

  5. Molecular Foundry User Meeting - JCAP

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

    Molecular Foundry User Meeting Molecular Foundry User Meeting Thu, Aug 11, 2016 5:00pm 17:00 Fri, Aug 12, 2016 6:00pm 18:00 Lawrence Berkeley National Laboratory Berkeley, CA USA The Molecular Foundry is hosting its annual Users' Meeting - a nanoscience conference at Lawrence Berkeley National Lab - on August 11-12, 2016. The Molecular Foundry is a Department of Energy user facility for academic, national laboratory and industrial researchers. Whether you are a returning user, a prospective

  6. Electron Trapping by Molecular Vibration

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

    Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally...

  7. Running 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 or qsh. This can be useful if you are doing something that is potentially disruptive or if the interactive nodes are overloaded. qlogin will give you an interactive session in the same window as your original session on PDSF, however, you must have your ssh keys in place. You can do this locally on PDSF by following

  8. Interactive (login) 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, pdsf[6-8].nersc.gov, that should be accessed via ssh to pdsf.nersc.gov. These are the gateways to accessing the rest of PDSF. Users can submit batch jobs as well as view and manipulate their files and directories from the interactive nodes. The configuration of the interactive nodes is shown in the table below. Processor Clock Speed (GHz) Architecture Cores Total Memory (GB) Scratch Space (GB) Intel Xeon

  9. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect (OSTI)

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  10. Molecular modeling of responsive polymer films

    SciTech Connect (OSTI)

    Tagliazucchi, Mario; Calvo, Ernesto J; Szleifer, Igal

    2010-06-29

    In this perspective, we have shown three different cases of responsive polymers at surfaces where the properties of the surface can be varied in response to cues from the bulk solution or in the presence of an external field. The most important conclusion in all three cases is that the chemical reaction equilibrium, physical interactions and molecular organization are strongly coupled, and it is imperative to consider the global and local changes that occur to the surface structure and properties due to this coupling. In particular acid-base and redox equilibrium are very different in polymer-modified surfaces than in the corresponding bulk solutions. Moreover, the definition of ‘‘apparent redox potentials’’ and ‘‘apparent pKa’’results from the averaging over highly inhomogeneous values,and, therefore, they do not necessarily represent the state of the layer and the local values and their variation are very important for the design of functional surfaces. The very large variation on chemical equilibrium results from the optimization of all the interactions. The picture that emerges is that trying to deduce what the final state of the system is by looking at the individual optimization of each contribution leads to qualitative incorrect assumptions and only the minimization of the complete free energy leads to the proper behavior in these complex systems.In the cases where domain formation is possible in grafted weak polyacid layers charge regulation may lead to regimes of coexistence between aggregates with relatively low fraction of charged polymer segments surrounded by highly stretched chains that have a relatively high fraction of charged groups.Therefore, one can control the state of charge, local electrostatic potential and local pH in all three dimensions with im-portant gradients on length scales of nanometers. For hydrophobic redox polymers we show how the application of an electrode potential can lead to changes in the structure and type of

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

    DOE Patents [OSTI]

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

    1997-01-07

    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.

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

    DOE Patents [OSTI]

    King, David E.; Herdt, Gregory C.; Czanderna, Alvin W.

    1997-01-01

    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.

  13. CX-005436: Categorical Exclusion Determination

    Broader source: Energy.gov [DOE]

    Beneficial Plant Microbe Interactions and their Potential to Increase Biomass Production in Prairie CordgrassCX(s) Applied: B3.6, B3.8, B5.1Date: 03/08/2011Location(s): South DakotaOffice(s): Energy Efficiency and Renewable Energy, Golden Field Office

  14. Learning from Semantic Interactions

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

    Learning from Semantic Interactions Most machine learning tools used in geospatial mapping can only learn from labels. Learning from Semantic Interactions LANL's new machine learning tools can learn from semantic user interactions to produce more accurate mappings Point of Contact: Reid Porter, ISR Division, 665-7508, rporter@lanl.gov Current Phase - LDRD: * Develop theory and algorithms for tools and demonstrate impact in image analysis applications in materials microscopy. Phase 2 - Geospatial

  15. ERHIC INTERACTION REGION DESIGN.

    SciTech Connect (OSTI)

    MONTAG,C.PARKER,B.PTITSYN,V.TEPIKIAN,S.WANG,D.WANG,F.

    2003-10-13

    This paper presents the current interaction region design status of the ring-ring version of the electron-ion collider eRHIC (release 2.0).

  16. Nerve-pulse interactions

    SciTech Connect (OSTI)

    Scott, A.C.

    1982-01-01

    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.

  17. Weak Interaction | Jefferson Lab

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

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

  18. Optically induced transport through semiconductor-based molecular electronics

    SciTech Connect (OSTI)

    Li, Guangqi; Seideman, Tamar; Fainberg, Boris D.

    2015-04-21

    A tight binding model is used to investigate photoinduced tunneling current through a molecular bridge coupled to two semiconductor electrodes. A quantum master equation is developed within a non-Markovian theory based on second-order perturbation theory with respect to the molecule-semiconductor electrode coupling. The spectral functions are generated using a one dimensional alternating bond model, and the coupling between the molecule and the electrodes is expressed through a corresponding correlation function. Since the molecular bridge orbitals are inside the bandgap between the conduction and valence bands, charge carrier tunneling is inhibited in the dark. Subject to the dipole interaction with the laser field, virtual molecular states are generated via the absorption and emission of photons, and new tunneling channels open. Interesting phenomena arising from memory are noted. Such a phenomenon could serve as a switch.

  19. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    SciTech Connect (OSTI)

    Dr. Julie Maupin- Furlow

    2009-07-26

    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.

  20. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    SciTech Connect (OSTI)

    Keneth Stedman

    2011-08-05

    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.

  1. Molecular recognition of nitrated fatty acids by PPAR[gamma

    SciTech Connect (OSTI)

    Li, Yong; Zhang, Jifeng; Schopfer, Francisco J.; Martynowski, Dariusz; Garcia-Barrio, Minerva T.; Kovach, Amanda; Suino-Powell, Kelly; Baker, Paul R.S.; Freeman, Bruce A.; Chen, Y. Eugene; Xu, H. Eric

    2010-03-08

    Peroxisome proliferator activated receptor-{gamma} (PPAR{gamma}) regulates metabolic homeostasis and adipocyte differentiation, and it is activated by oxidized and nitrated fatty acids. Here we report the crystal structure of the PPAR{gamma} ligand binding domain bound to nitrated linoleic acid, a potent endogenous ligand of PPAR{gamma}. Structural and functional studies of receptor-ligand interactions reveal the molecular basis of PPAR{gamma} discrimination of various naturally occurring fatty acid derivatives.

  2. Industry Interactive Procurement System (IIPS)

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

    Interactive Industry Interactive Procurement System Procurement System (IIPS) (IIPS) Douglas Baptist, Project Manager Information Management Systems Division US Department of ...

  3. Controlling Molecular Ordering in Solution-State Conjugated Polymers

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

    Zhu, Jiahua; Han, Youngkyu; Kumar, Rajeev; Hong, Kunlun; Bonnesen, Peter V.; Sumpter, Bobby G.; Smith, Gregory Scott; Ivanov, Ilia N.; Do, Changwoo

    2015-07-17

    Rationally encoding molecular interactions that can control the assembly structure and functional expression in solution of conjugated polymers holds great potential for enabling optimal organic optoelectronic and sensory materials. In this work, we show that thermally-controlled and surfactant-guided assembly of water-soluble conjugated polymers in aqueous solution is a simple and effective strategy to generate optoelectronic materials with desired molecular ordering. We have studied a conjugated polymer consisting of a hydrophobic thiophene backbone and hydrophilic, thermo-responsive ethylene oxide side groups, which shows a step-wise, multi-dimensional assembly in water. By incorporating the polymer into phase-segregated domains of an amphiphilic surfactant in solution,more » we demonstrate that both chain conformation and degree of molecular ordering of the conjugated polymer can be tuned in hexagonal, micellar and lamellar phases of the surfactant solution. The controlled molecular ordering in conjugated polymer assembly is demonstrated as a key factor determining the electronic interaction and optical function.« less

  4. Elementary particle interactions

    SciTech Connect (OSTI)

    Bugg, W.M.; Condo, G.T.; Handler, T.; Hart, E.L.; Ward, B.F.L.; Close, F.E.; Christophorou, L.G.

    1990-10-01

    This report discusses freon bubble chamber experiments exposed to {mu}{sup +} and neutrinos, photon-proton interactions; shower counter simulations; SLD detectors at the Stanford Linear Collider, and the detectors at the Superconducting Super Collider; elementary particle interactions; physical properties of dielectric materials used in High Energy Physics detectors; and Nuclear Physics. (LSP)

  5. Application of optimal prediction to molecular dynamics

    SciTech Connect (OSTI)

    Barber IV, John Letherman

    2004-12-01

    Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is {delta}-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.

  6. Molecular resonance phenomena. [Calculation of resonance widths

    SciTech Connect (OSTI)

    Hazi, A.U.

    1980-01-01

    It is attempted to show that the Stieltjes-moment-theory provides a practical and a reasonably accurate method for calculating the widths of molecular resonances. The method seems to possess a number of advantages for molecular applications, since it avoids the explicit construction of continuum wavefunctions. It is very simple to implement the technique numerically, because it requires only existing bound-state electronic structure codes. Through the use of configuration interaction techniques, many-electron correlation and polarization effects can be included in the description of both the resonance and the non-resonant background continuum. To illustrate the utility and the accuracy of the Stieltjes-moment-theory technique, used in conjunction with configuration interaction (CI) wave functions, recent applications to the /sup 1/..sigma../sub u/(1sigma/sub u/ 2sigma/sub g/) autoionizing resonance state of H/sub 2/ and the well known /sup 2/PI/sub g/ state of N/sub 2//sup -/ are discussed. The choices of the one-electron basis sets and the types of many-electron configurations appropriate for these two cases are described. Also, guidelines for the selection of the projection operators defining the resonant and non-resonant subspaces in the case of both Feshbach and shape-resonances are given. The numerical results indicate that the Stieltjes-moment-theory technique, which employs L/sup 2/ basis functions exclusively, produces as accurate resonance parameters as can be extracted from direct electron-molecule scattering calculations, provided approximately the same approximations are used to describe important physical effects such as target polarization. Furthermore the method provides sufficiently accurate fixed-nuclei electronic resonance parameters to be used in ab initio calculation of resonant vibrational excitation cross sections. (WHK)

  7. Molecular Science Research Center annual report

    SciTech Connect (OSTI)

    Knotek, M.L.

    1991-01-01

    The Chemical Structure and Dynamics group is studying chemical kinetics and reactions dynamics of terrestrial and atmospheric processes as well as the chemistry of complex waste forms and waste storage media. Staff are using new laser systems and surface-mapping techniques in combination with molecular clusters that mimic adsorbate/surface interactions. The Macromolecular Structure and Dynamics group is determining biomolecular structure/function relationships for processes the control the biological transformation of contaminants and the health effects of toxic substances. The Materials and Interfaces program is generating information needed to design and synthesize advanced materials for the analysis and separation of mixed chemical waste, the long-term storage of concentrated hazardous materials, and the development of chemical sensors for environmental monitoring of various organic and inorganic species. The Theory, Modeling, and Simulation group is developing detailed molecular-level descriptions of the chemical, physical, and biological processes in natural and contaminated systems. Researchers are using the full spectrum of computational techniques. The Computer and Information Sciences group is developing new approaches to handle vast amounts of data and to perform calculations for complex natural systems. The EMSL will contain a high-performance computing facility, ancillary computing laboratories, and high-speed data acquisition systems for all major research instruments.

  8. Molecular dynamics simulations of microscale fluid transport

    SciTech Connect (OSTI)

    Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.

    1998-02-01

    Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.

  9. Apparatus for molecular weight separation

    DOE Patents [OSTI]

    Smith, Richard D.; Liu, Chuanliang

    2001-01-01

    The present invention relates generally to an apparatus and method for separating high molecular weight molecules from low molecular weight molecules. More specifically, the invention relates to the use of microdialysis for removal of the salt (low molecular weight molecules) from a nucleotide sample (high molecular weight molecules) for ESI-MS analysis. The dialysis or separation performance of the present invention is improved by (1) increasing dialysis temperature thereby increasing desalting efficiency and improving spectrum quality; (2) adding piperidine and imidazole to the dialysis buffer solution and reducing charge states and further increasing detection sensitivity for DNA; (3) using low concentrations (0-2.5 mM NH4OAc) of dialysis buffer and shifting the DNA negative ions to higher charge states, producing a nearly 10-fold increase in detection sensitivity and a slightly decreased desalting efficiency, (4) conducting a two-stage separation or (5) any combination of (1), (2), (3) and (4).

  10. Institute for Molecular Engineering | Argonne National Laboratory

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

    Learn more about the Institute for Molecular Engineering. When completed in early 2015, the William Eckhardt Research Center at the University of Chicago will be the home of the Institute of Molecular Engineering. Institute for Molecular Engineering The new Institute for Molecular Engineering explores innovative technologies that address fundamental societal problems through advances in nanoscale manipulation and design at a molecular scale. Addressing Societal Problems with Molecular Science

  11. Electron Trapping by Molecular Vibration

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

    Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping,

  12. Electron Trapping by Molecular Vibration

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

    Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping,

  13. Electron Trapping by Molecular Vibration

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

    Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping,

  14. Electron Trapping by Molecular Vibration

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

    Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping,

  15. 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...

  16. Protein Structure Suggests Role as Molecular Adapter

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

    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...

  17. Connecting the Molecular and the Continuum Scales

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

    range of phenomena, from climate change to contaminant remediation. Accomplishments: Used molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients of...

  18. SPITZER INFRARED SPECTROGRAPH DETECTION OF MOLECULAR HYDROGEN...

    Office of Scientific and Technical Information (OSTI)

    MOLECULAR HYDROGEN ROTATIONAL EMISSION TOWARDS TRANSLUCENT CLOUDS Citation Details In-Document Search Title: SPITZER INFRARED SPECTROGRAPH DETECTION OF MOLECULAR HYDROGEN ...

  19. Size-exclusion chromatography system for macromolecular interaction analysis

    DOE Patents [OSTI]

    Stevens, Fred J.

    1988-01-01

    A low pressure, microcomputer controlled system employing high performance liquid chromatography (HPLC) allows for precise analysis of the interaction of two reversibly associating macromolecules such as proteins. Since a macromolecular complex migrates faster than its components during size-exclusion chromatography, the difference between the elution profile of a mixture of two macromolecules and the summation of the elution profiles of the two components provides a quantifiable indication of the degree of molecular interaction. This delta profile is used to qualitatively reveal the presence or absence of significant interaction or to rank the relative degree of interaction in comparing samples and, in combination with a computer simulation, is further used to quantify the magnitude of the interaction in an arrangement wherein a microcomputer is coupled to analytical instrumentation in a novel manner.

  20. Interactive (login) Nodes

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

    There are 3 interactive nodes at PDSF, pdsf6-8.nersc.gov, that should be accessed via ssh to pdsf.nersc.gov. These are the gateways to accessing the rest of PDSF. Users can ...

  1. Human-machine interactions

    DOE Patents [OSTI]

    Forsythe, J. Chris; Xavier, Patrick G.; Abbott, Robert G.; Brannon, Nathan G.; Bernard, Michael L.; Speed, Ann E.

    2009-04-28

    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.

  2. Measuring Neutrino Interactions

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

    Measuring Neutrino Interactions with MiniBooNE R. Tayloe for the MiniBooNE collaboration Physics Department, Indiana University Bloomington, IN 47405, USA Abstract. The MiniBooNE neutrino oscillation experiment has collected a large sample of charged- and neutral-current neutrino interaction events. These samples are important to understand the normalization and backgrounds in neutrino oscillation searches. They also reveal insight into the structure of the nucleus and nucleon. The MiniBooNE

  3. Laser Plasma Interactions

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

    Laser Plasma Interactions Laser Plasma Interactions Understanding and controlling laser produced plasmas for fusion and basic science Contact David Montgomery (505) 665-7994 Email John Kline (505) 667-7062 Email Thomson scattering is widely used to measure plasma temperature, density, and flow velocity in laser-produced plasmas at Trident, and is also used to detect plasma waves driven by unstable and nonlinear processes. A typical configuration uses a low intensity laser beam (2nd, 3rd, or 4th

  4. United polarizable multipole water model for molecular mechanics simulation

    SciTech Connect (OSTI)

    Qi, Rui; Wang, Qiantao; Ren, Pengyu; Wang, Lee-Ping; Pande, Vijay S.

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

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

    SciTech Connect (OSTI)

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

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobic environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.

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

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

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; et al

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobicmore » environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.« less

  7. Molecular separation method and apparatus

    DOE Patents [OSTI]

    Villa-Aleman, Eliel

    1996-01-01

    A method and apparatus for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve.

  8. Molecular separation method and apparatus

    DOE Patents [OSTI]

    Villa-Aleman, E.

    1996-04-09

    A method and apparatus are disclosed for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular sieve. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve. 2 figs.

  9. Linear Dichroism in Resonant Inelastic X-Ray Scattering to Molecular

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

    Spin-Orbit States Linear Dichroism in Resonant Inelastic X-Ray Scattering to Molecular Spin-Orbit States Linear Dichroism in Resonant Inelastic X-Ray Scattering to Molecular Spin-Orbit States Print Thursday, 17 December 2009 13:47 Schematic representation of linear dichroism observed in KL x-ray emission. Coupling between the spin-orbit interaction and the molecular field, oriented along the chemical bond, leads to different spin-orbit ratios as a function of the angle between the incoming

  10. Charge exchange molecular ion source

    DOE Patents [OSTI]

    Vella, Michael C.

    2003-06-03

    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.

  11. Dike/Drift Interactions

    SciTech Connect (OSTI)

    E. Gaffiney

    2004-11-23

    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).

  12. Achromatic Interaction Point Design

    SciTech Connect (OSTI)

    Guimei Wang,, Yaroslav Derbenev, S.Alex Bogacz, P. Chevtsov, Andre Afanaciev, Charles Ankenbrandt, Valentin Ivanov, Rolland P. Johnson

    2009-05-01

    Designers of high-luminosity energy-frontier muon colliders must provide strong beam focusing in the interaction regions. However, the construction of a strong, aberration-free beam focus is difficult and space consuming, and long straight sections generate an off-site radiation problem due to muon decay neutrinos that interact as they leave the surface of the earth. Without some way to mitigate the neutrino radiation problem, the maximum c.m. energy of a muon collider will be limited to about 3.5 TeV. A new concept for achromatic low beta design is being developed, in which the interaction region telescope and optical correction elements, are installed in the bending arcs. The concept, formulated analytically, combines space economy, a preventative approach to compensation for aberrations, and a reduction of neutrino flux concentration. An analytical theory for the aberration-free, low beta, spatially compact insertion is being developed.

  13. History of Weak Interactions

    DOE R&D Accomplishments [OSTI]

    Lee, T. D.

    1970-07-01

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

  14. Molecular structure in soil humic substances: The new view

    SciTech Connect (OSTI)

    Sutton, Rebecca; Sposito, Garrison

    2005-04-21

    A critical examination of published data obtained primarily from recent nuclear magnetic resonance spectroscopy, X-ray absorption near-edge structure spectroscopy, electrospray ionization-mass spectrometry, and pyrolysis studies reveals an evolving new view of the molecular structure of soil humic substances. According to the new view, humic substances are collections of diverse, relatively low molecular mass components forming dynamic associations stabilized by hydrophobic interactions and hydrogen bonds. These associations are capable of organizing into micellar structures in suitable aqueous environments. Humic components display contrasting molecular motional behavior and may be spatially segregated on a scale of nanometers. Within this new structural context, these components comprise any molecules intimately associated with a humic substance, such that they cannot be separated effectively by chemical or physical methods. Thus biomolecules strongly bound within humic fractions are by definition humic components, a conclusion that necessarily calls into question key biogeochemical pathways traditionally thought to be required for the formation of humic substances. Further research is needed to elucidate the intermolecular interactions that link humic components into supramolecular associations and to establish the pathways by which these associations emerge from the degradation of organic litter.

  15. Relativistic Laser-Matter Interactions

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

    Relativistic Laser-Matter Interactions Relativistic Laser-Matter Interactions Enabling the next generation of intense particle accelerators Contact Juan Fernandez (505) 667-6575 ...

  16. Nucleon-nucleon interactions

    SciTech Connect (OSTI)

    Wiringa, R.B.

    1996-12-31

    Nucleon-nucleon interactions are at the heart of nuclear physics, bridging the gap between QCD and the effective interactions appropriate for the shell model. We discuss the current status of {ital NN} data sets, partial-wave analyses, and some of the issues that go into the construction of potential models. Our remarks are illustrated by reference to the Argonne {ital v}{sub 18} potential, one of a number of new potentials that fit elastic nucleon-nucleon data up to 350 MeV with a {Chi}{sup 2} per datum near 1. We also discuss the related issues of three-nucleon potentials, two-nucleon charge and current operators, and relativistic effects. We give some examples of calculations that can be made using these realistic descriptions of {ital NN} interactions. We conclude with some remarks on how our empirical knowledge of {ital NN} interactions may help constrain models at the quark level, and hence models of nucleon structure.

  17. Double rotation NMR studies of zeolites and aluminophosphate molecular sieves

    SciTech Connect (OSTI)

    Jelinek, R. |

    1993-07-01

    Goal is to study the organization and structures of guest atoms and molecules and their reactions on internal surfaces within pores of zeolites and aluminophosphate molecular sieves. {sup 27}Al and {sup 23}Na double rotation NMR (DOR) is used since it removes the anisotropic broadening in NMR spectra of quadrupolar nuclei, thus increasing resolution. This work concentrates on probing aluminum framework atoms in aluminophosphate molecular sieves and sodium extra framework cations in porous aluminosilicates. In aluminophosphates, ordering and electronic environments of the framework {sup 27}Al nuclei are modified upon adsorption of water molecules within the channels; a relation is sought between the sieve channel topology and the organization of adsorbed water, as well as the interaction between the Al nuclei and the water molecules. Extra framework Na{sup +} cations are directly involved in adsorption processes and reactions in zeolite cavities.

  18. Electron: Cluster interactions

    SciTech Connect (OSTI)

    Scheidemann, A.A.; Kresin, V.V.; Knight, W.D.

    1994-02-01

    Beam depletion spectroscopy has been used to measure absolute total inelastic electron-sodium cluster collision cross sections in the energy range from E {approximately} 0.1 to E {approximately} 6 eV. The investigation focused on the closed shell clusters Na{sub 8}, Na{sub 20}, Na{sub 40}. The measured cross sections show an increase for the lowest collision energies where electron attachment is the primary scattering channel. The electron attachment cross section can be understood in terms of Langevin scattering, connecting this measurement with the polarizability of the cluster. For energies above the dissociation energy the measured electron-cluster cross section is energy independent, thus defining an electron-cluster interaction range. This interaction range increases with the cluster size.

  19. Interactive optical panel

    DOE Patents [OSTI]

    Veligdan, James T.

    1995-10-03

    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.

  20. Interactive optical panel

    DOE Patents [OSTI]

    Veligdan, J.T.

    1995-10-03

    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.

  1. Hierarchical analysis of molecular spectra

    SciTech Connect (OSTI)

    Davis, M.J.

    1996-03-01

    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``).

  2. Molecular engineering with bridged polysilsesquioxanes

    SciTech Connect (OSTI)

    LOY,DOUGLAS A.; SHEA,KENNETH J.

    2000-05-09

    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.

  3. ELEMENTARY PARTICLE INTERACTIONS

    SciTech Connect (OSTI)

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

    2013-07-30

    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.

  4. Interactive Activity Detection Tools

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

    Activity Detection Tools Interactive Activity Detection Tools Tools for detecting specified activities in video data provide a key intelligence capability. High numbers of false alarms, however, reduce tool effectiveness and analyst patience. User feedback reduces false alarms * This project will reduce the number of false alarms generated by activity detection tools (including single vehicle start / stop, multi-vehicle meetings and coordinated driving patterns) by exploiting user feedback in a

  5. Interactive Comparative Analysis

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

    Comparative Analysis Interactive Comparative Analysis We can learn the correlations between sensors and modalities that differentiate activities (or operating modes) by using transfer learning. Our new approach to data fusion and signature discovery has a number of advantages and applications: * Finding correlations that differentiate datasets requires less data than finding correlations that explain datasets. * The differences between datasets are smaller in number, and often easier to

  6. Molecular Science Computing: 2010 Greenbook

    SciTech Connect (OSTI)

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

    2010-04-02

    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.

  7. DNA-Based Optomechanical Molecular Motor

    SciTech Connect (OSTI)

    McCullagh, Martin; Franco, Ignacio; Ratner, Mark A.; Schatz, George C.

    2011-03-16

    An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the unfolding of both isomers along the O5'-O3' extension coordinate is monitored. The potentials of mean force (PMFs) along this coordinate indicate that there are two major differences induced by photoisomerization. The first is that the interbase hydrogen bond and stacking interactions are stable for a greater range of extensions in the trans system than in the cis system. The second difference is due to a decreased chain length of the cis isomer with respect to the trans isomer. These differences are exploited to extract work in optomechanical cycles. The disruption of the hairpin structure gives a maximum of 3.4 kcal mol-1 of extractable work per cycle with an estimated maximum efficiency of 2.4%. Structure-function insights into the operation of this motor are provided, and the effect of the cantilever stiffness on the extractable work is characterized.

  8. Protein Structure Suggests Role as Molecular Adapter

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

    Suggests Role as Molecular Adapter Print Wednesday, 24 June 2009 00:00 To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known...

  9. 14th international symposium on molecular beams

    SciTech Connect (OSTI)

    Not Available

    1992-09-01

    This report discusses research being conducted with molecular beams. The general topic areas are as follows: Clusters I; reaction dynamics; atomic and molecular spectroscopy; clusters II; new techniques; photodissociation & dynamics; and surfaces.

  10. 14th international symposium on molecular beams

    SciTech Connect (OSTI)

    Not Available

    1992-01-01

    This report discusses research being conducted with molecular beams. The general topic areas are as follows: Clusters I; reaction dynamics; atomic and molecular spectroscopy; clusters II; new techniques; photodissociation dynamics; and surfaces.

  11. Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data

    SciTech Connect (OSTI)

    Zhu, Yitan; Xu, Yanxun; Helseth, Donald L.; Gulukota, Kamalakar; Yang, Shengjie; Pesce, Lorenzo L.; Mitra, Riten; Muller, Peter; Sengupta, Subhajit; Guo, Wentian; Foster, Ian; Bullock, JaQuel A.

    2015-08-01

    Background: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. Methods: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.” Results: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC. Conclusions: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.

  12. Nanoplasmonic molecular ruler for nuclease activity and DNA footprinting

    SciTech Connect (OSTI)

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

    2013-10-29

    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.

  13. Magnetic dipole interactions in crystals

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

    Johnston, David

    2016-01-13

    The influence of magnetic dipole interactions (MDIs) on the magnetic properties of local-moment Heisenberg spin systems is investigated. A general formulation is presented for calculating the eigenvalues λ and eigenvectors μ ˆ of the MDI tensor of the magnetic dipoles in a line (one dimension, 1D), within a circle (2D) or a sphere (3D) of radius r surrounding a given moment μ → i for given magnetic propagation vectors k for collinear and coplanar noncollinear magnetic structures on both Bravais and non-Bravais spin lattices. Results are calculated for collinear ordering on 1D chains, 2D square and simple-hexagonal (triangular) Bravais lattices,more » 2D honeycomb and kagomé non-Bravais lattices, and 3D cubic Bravais lattices. The λ and μ ˆ values are compared with previously reported results. Calculations for collinear ordering on 3D simple tetragonal, body-centered tetragonal, and stacked triangular and honeycomb lattices are presented for c/a ratios from 0.5 to 3 in both graphical and tabular form to facilitate comparison of experimentally determined easy axes of ordering on these Bravais lattices with the predictions for MDIs. Comparisons with the easy axes measured for several illustrative collinear antiferromagnets (AFMs) are given. The calculations are extended to the cycloidal noncollinear 120 ° AFM ordering on the triangular lattice where λ is found to be the same as for collinear AFM ordering with the same k. The angular orientation of the ordered moments in the noncollinear coplanar AFM structure of GdB 4 with a distorted stacked 3D Shastry-Sutherland spin-lattice geometry is calculated and found to be in disagreement with experimental observations, indicating the presence of another source of anisotropy. Similar calculations for the undistorted 2D and stacked 3D Shastry-Sutherland lattices are reported. The thermodynamics of dipolar magnets are calculated using the Weiss molecular field theory for quantum spins, including the magnetic

  14. Molecular dynamics simulations of H{sub 2} adsorption in tetramethyl ammonium lithium phthalocyanine crystalline structures.

    SciTech Connect (OSTI)

    Lamonte, K.; Gomez Gualdron, D.; Scanlon, L. G.; Sandi, G.; Feld, W.; Balbuena, P. B.; Chemical Sciences and Engineering Division; Texas A&M Univ.; Wright-Patterson Air Force Base; Wright State Univ.

    2008-11-01

    Tetramethyl ammonium lithium phthalocyanine is explored as a potential material for storage of molecular hydrogen. Density functional theory calculations are used to investigate the molecular structure and the dimer conformation. Additional scans performed to determine the interactions of a H{sub 2} molecule located at various distances from the molecular sites are used to generate a simple force field including dipole-induced-dipole interactions. This force field is employed in molecular dynamics simulations to calculate adsorption isotherms at various pressures. The regions of strongest adsorption are quantified as functions of temperature, pressure, and separation between molecules in the adsorbent phase, and compared to the regions of strongest binding energy as given by the proposed force field. It is found that the total adsorption could not be predicted only from the spatial distribution of the strongest binding energies; the available volume is the other contributing factor even if the volume includes regions of much lower binding energy. The results suggest that the complex anion is primarily involved in the adsorption process with molecular hydrogen, whereas the cation serves to provide access for hydrogen adsorption in both sides of the anion molecular plane, and spacing between the planes.

  15. Bioassays Based on Molecular Nanomechanics

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

    Majumdar, Arun

    2002-01-01

    Recent experiments have shown that when specific biomolecular interactions are confined to one surface of a microcantilever beam, changes in intermolecular nanomechanical forces provide sufficient differential torque to bend the cantilever beam. This has been used to detect single base pair mismatches during DNA hybridization, as well as prostate specific antigen (PSA) at concentrations and conditions that are clinically relevant for prostate cancer diagnosis. Since cantilever motion originates from free energy change induced by specific biomolecular binding, this technique is now offering a common platform for label-free quantitative analysis of protein-protein binding, DNA hybridization DNA-protein interactions, and in general receptor-ligandmore » interactions. Current work is focused on developing “universal microarrays” of microcantilever beams for high-throughput multiplexed bioassays.« less

  16. Clustering effects in ionic polymers: Molecular dynamics simulations

    SciTech Connect (OSTI)

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing the electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.

  17. Clustering effects in ionic polymers: Molecular dynamics simulations

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

    Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

    2015-08-18

    Ionic clusters control the structure, dynamics, and transport in soft matter. Incorporating a small fraction of ionizable groups in polymers substantially reduces the mobility of the macromolecules in melts. Furthermore, these ionic groups often associate into random clusters in melts, where the distribution and morphology of the clusters impact the transport in these materials. Here, using molecular dynamic simulations we demonstrate a clear correlation between cluster size and morphology with the polymer mobility in melts of sulfonated polystyrene. We show that in low dielectric media ladderlike clusters that are lower in energy compared with spherical assemblies are formed. Reducing themore » electrostatic interactions by enhancing the dielectric constant leads to morphological transformation from ladderlike clusters to globular assemblies. Finally, decrease in electrostatic interaction significantly enhances the mobility of the polymer.« less

  18. Transport and Self-Assembly in Molecular Nanosystems

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

    Transport and Self-Assembly in Molecular Nanosystems Key Challenges: Use classical molecular dynamics and coarse grain molecular dynamics to enable "bottom-up" material...

  19. Toward Molecular Catalysts by Computer

    SciTech Connect (OSTI)

    Raugei, Simone; DuBois, Daniel L.; Rousseau, Roger J.; Chen, Shentan; Ho, Ming-Hsun; Bullock, R. Morris; Dupuis, Michel

    2015-02-17

    Rational design of molecular catalysts requires a systematic approach to designing ligands with specific functionality and precisely tailored electronic and steric properties. It then becomes possible to devise computer protocols to predict accurately the required properties and ultimately to design catalysts by computer. In this account we first review how thermodynamic properties such as oxidation-reduction potentials (E0), acidities (pKa), and hydride donor abilities (ΔGH-) form the basis for a systematic design of molecular catalysts for reactions that are critical for a secure energy future (hydrogen evolution and oxidation, oxygen and nitrogen reduction, and carbon dioxide reduction). We highlight how density functional theory allows us to determine and predict these properties within “chemical” accuracy (~ 0.06 eV for redox potentials, ~ 1 pKa unit for pKa values, and ~ 1.5 kcal/mol for hydricities). These quantities determine free energy maps and profiles associated with catalytic cycles, i.e. the relative energies of intermediates, and help us distinguish between desirable and high-energy pathways and mechanisms. Good catalysts have flat profiles that avoid high activation barriers due to low and high energy intermediates. We illustrate how the criterion of a flat energy profile lends itself to the prediction of design points by computer for optimum catalysts. This research was carried out in the Center for Molecular Electro-catalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle.

  20. Uranium molecular laser isotope separation

    SciTech Connect (OSTI)

    Jensen, R.J.; Sullivan, A.

    1982-01-01

    The Molecular Laser Isotope Separation program is moving into the engineering phase, and it is possible to determine in some detail the plant cost terms involved in the process economics. A brief description of the MLIS process physics is given as a motivation to the engineering and economics discussion. Much of the plant cost arises from lasers and the overall optical system. In the paper, the authors discuss lasers as operating units and systems, along with temporal multiplexing and Raman shifting. Estimates of plant laser costs are given.

  1. Molecular pathways of angiogenesis inhibition

    SciTech Connect (OSTI)

    Tabruyn, Sebastien P.; Griffioen, Arjan W. . E-mail: aw.griffioen@path.unimaas.nl

    2007-03-30

    A large body of evidence now demonstrates that angiostatic therapy represents a promising way to fight cancer. This research recently resulted in the approval of First angiostatic agent for clinical treatment of cancer. Progress has been achieved in decrypting the cellular signaling in endothelial cells induced by angiostatic agents. These agents predominantly interfere with the molecular pathways involved in migration, proliferation and endothelial cell survival. In the current review, these pathways are discussed. A thorough understanding of the mechanism of action of angiostatic agents is required to develop efficient anti-tumor therapies.

  2. Relativistic Laser-Matter Interactions

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

    Relativistic Laser-Matter Interactions Relativistic Laser-Matter Interactions Enabling the next generation of intense particle accelerators Contact Juan Fernandez (505) 667-6575 Email Short-pulse ion acceleration The Trident facility is a world-class performer in the area of ion acceleration from laser-solid target interactions. Trident has demonstrated over 100 MeV protons at intensities of 8x1020 W/cm2 with efficiencies approaching 5%. These intense relativistic interactions can be diagnosed

  3. Daejeon16 NN Interaction Software

    SciTech Connect (OSTI)

    Shirokov, A. M.; Shin, I. J.; Kim, Y.; Sosonkina, M.; Maris, P.; Vary, James P.

    2016-01-01

    A Fortran subroutine that generates harmonic oscillator matrix elements of the nucleon-nucleon interaction, Daejeon16, is provided.

  4. Simulation and dynamics of entropy-driven, molecular self-assembly processes

    SciTech Connect (OSTI)

    Mayer, B.; Kohler, G.,; Rasmussen, S.,

    1997-04-01

    Molecular self-assembly is frequently found to generate higher-order functional structures in biochemical systems. One such example is the self-assembly of lipids in aqueous solution forming membranes, micelles, and vesicles; another is the dynamic formation and rearrangement of the cytoskeleton. These processes are often driven by local, short-range forces and therefore the dynamics is solely based on local interactions. In this paper, we introduce a cellular automata based simulation, the lattice molecular automaton, in which data structures, representing different molecular entities such as water and hydrophilic and hydrophobic monomers, share locally propagated force information on a hexagonal, two-dimensional lattice. The purpose of this level of description is the simulation of entropic and enthalpic flows in a microcanonical, molecular ensemble to gain insight about entropy-driven processes in molecular many-particle systems. Three applications are shown, i.e., modeling structural features of a polar solvent, cluster formation of hydrophobic monomers in a polar environment, and the self-assembly of polymers. Processes leading to phase separation on a molecular level are discussed. A thorough discussion of the computational details, advantages, and limitations of the lattice molecular automaton approach is given elsewhere [B. Mayer and S. Rasmussen (unpublished)]. {copyright} {ital 1997} {ital The American Physical Society}

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

    SciTech Connect (OSTI)

    Zhang, Lei; Reynolds, Kellie S.; Zhao, Ping; Huang, Shiew-Mei

    2010-03-01

    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.

  6. Turbulence-chemistry interactions in reacting flows

    SciTech Connect (OSTI)

    Barlow, R.S.; Carter, C.D.

    1993-12-01

    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.

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

    SciTech Connect (OSTI)

    Kirsten Larson Genson

    2005-12-27

    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.

  8. Elasticity of crystalline molecular explosives

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

    Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; Cawkwell, Marc J.

    2015-04-14

    Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, andmore » an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.« less

  9. Elasticity of crystalline molecular explosives

    SciTech Connect (OSTI)

    Hooks, Daniel E.; Ramos, Kyle J.; Bolme, C. A.; Cawkwell, Marc J.

    2015-04-14

    Crystalline molecular explosives are key components of engineered explosive formulations. In precision applications a high degree of consistency and predictability is desired under a range of conditions to a variety of stimuli. Prediction of behaviors from mechanical response and failure to detonation initiation and detonation performance of the material is linked to accurate knowledge of the material structure and first stage of deformation: elasticity. The elastic response of pentaerythritol tetranitrate (PETN), cyclotrimethylene trinitramine (RDX), and cyclotetramethylene tetranitramine (HMX), including aspects of material and measurement variability, and computational methods are described in detail. Experimental determinations of elastic tensors are compared, and an evaluation of sources of error is presented. Furthermore, computed elastic constants are also compared for these materials and for triaminotrinitrobenzene (TATB), for which there are no measurements.

  10. Production of high molecular weight polylactic acid

    DOE Patents [OSTI]

    Bonsignore, Patrick V.

    1995-01-01

    A degradable high molecular weight poly(lactic acid). A poly(lactic acid) has a terminal end group of one of carboxyl or hydroxyl groups with low molecular weight poly(lactic acid) units coupled with linking agents of di-isocyanates, bis-epoxides, bis-oxazolines and bis-ortho esters. The resulting high molecular weight poly(lactic acid) can be used for applications taking advantage of the improved physical properties.

  11. Production of high molecular weight polylactic acid

    DOE Patents [OSTI]

    Bonsignore, P.V.

    1995-11-28

    A degradable high molecular weight poly(lactic acid) is described. The poly(lactic acid) has a terminal end group of one of carboxyl or hydroxyl groups with low molecular weight poly(lactic acid) units coupled with linking agents of di-isocyanates, bis-epoxides, bis-oxazolines and bis-ortho esters. The resulting high molecular weight poly(lactic acid) can be used for applications taking advantage of the improved physical properties.

  12. Towards Using Molecular States as Qubits

    SciTech Connect (OSTI)

    Goswami, Debabrata; Goswami, Tapas; Kumar, S. K. Karthick; Das, Dipak K.

    2011-09-23

    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.

  13. Large rectification in molecular heterojunctions | Argonne National

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

    Laboratory Large rectification in molecular heterojunctions April 19, 2016 Tweet EmailPrint The outstanding challenge in using molecules in optoelectronics devices is to create electrical functionality through molecular design and to go beyond the use of molecules as mere light absorbers and/or resistive elements. The earliest proposal for such non-linear electrical behavior is the Aviram-Ratner molecular diode model, proposed in 1974. However, more than forty years later, the electrical

  14. 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 Protein Structure Suggests Role as Molecular Adapter Print Wednesday, 24 June 2009 00:00 To split and copy DNA during replication, all cellular organisms use a multicomponent molecular machine known as the replisome. An essential step in replisome assembly is the loading of ring-shaped helicases (motor proteins) onto the separated strands of DNA. Dedicated ATP-fueled proteins regulate the loading; however, the mechanism by which these proteins

  15. Dynamics of Molecular Clouds: Observations, Simulations, and...

    Office of Scientific and Technical Information (OSTI)

    Simulations, and NIF Experiments Citation Details In-Document Search Title: Dynamics of Molecular Clouds: Observations, Simulations, and NIF Experiments You are ...

  16. Molecular catalytic coal liquid conversion. Quarterly status...

    Office of Scientific and Technical Information (OSTI)

    July--September 1995 Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. Quarterly status report, July--September 1995 You are accessing...

  17. Nanoscopic Electrode Molecular Probes - Energy Innovation Portal

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

    other molecular sensing Applications and Industries Cancer genome sequencing Comparative genome sequencing Human genotyping Medical sequencing Model systems Parasite and vector...

  18. Molecular Manipulations of Symmetry | The Ames Laboratory

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

    Molecular Manipulations of Symmetry Researchers have studied the effect of concentration on the activity and selectivity in a zirconium-catalyzed hydroamination reaction. In this...

  19. Molecular catalytic coal liquid conversion. Quarterly status...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. ... organic base catalysts for arene hydrogenation and the hydrotreating of the coal liquids. ...

  20. Molecular catalytic coal liquid conversion. Quarterly report...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. ... organic base catalysts for arene hydrogenation and the hydrotreating of the coal liquids. ...

  1. Molecular catalytic coal liquid conversion. Quarterly report...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. ... Task 2, organic base-catalyzed arene hydrogenation and hydrotreating of the coal liquids. ...

  2. Molecular catalytic hydrogenation of aromatic hydrocarbons and...

    Office of Scientific and Technical Information (OSTI)

    and hydrotreating of coal liquids. Citation Details In-Document Search Title: Molecular catalytic hydrogenation of aromatic hydrocarbons and hydrotreating of coal liquids. ...

  3. Nanocrystal and Molecular Precursors for Photovoltaic Applications...

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    Nanocrystal and Molecular Precursors for Photovoltaic Applications The objective in this proposal is to identify factors that limit the efficiency of nanocrystal based solar cells...

  4. Molecular catalytic coal liquid conversion. Quarterly report...

    Office of Scientific and Technical Information (OSTI)

    report Citation Details In-Document Search Title: Molecular catalytic coal liquid ... It was found that the rhodium catalyst works well under biphase conditions rather than ...

  5. Molecular biology of signal transduction in plants

    SciTech Connect (OSTI)

    Not Available

    1991-01-01

    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.

  6. Communication: Quantum molecular dynamics simulation of liquid...

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    Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach Citation Details In-Document Search Title: Communication:...

  7. PNNL: Center for Molecular Electrocatalysis - Using Hydrogenase...

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    and Efficient Molecular Electrocatalysts January 2011 To create solar assemblies that use sunlight to split water and create hydrogen fuel requires designing fast, efficient ...

  8. 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.

    2006-10-31

    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.

  9. DockingShop: A Tool for Interactive Molecular Docking Ting-Cheng...

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    ... Covalent bond Cova lent bond Hydrogen bond Hydro gen bond monitors the position and ... Figure 3. Small blue spheres represent water. Dashed-blue lines represent hydrogen bonds ...

  10. Simulating Turbine-Turbine Interaction

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    Simulating Turbine-Turbine Interaction - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future ...