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. PDF icon symbiosis_conference_ronning.pdf 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. (Berkeley, CA); Baksh, Michael M. (Fremont, CA); Jaros, Michal (Brno, CH)

    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 collection and release, and the chemical composition of astrophysical icy bodies in space.

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

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

    efficiency and clinical performance among VEGFR TK inhibitors Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors Print Monday, 17 September 2012 00:00 Pictured are crystals that contain VEGFR2 tyrosine kinase in complex with an inhibitor from a class of potent anticancer

  11. Molecular Simulation of Carbon Dioxide Brine and Clay Mineral Interactions

    Office of Scientific and Technical Information (OSTI)

    and Determination of Contact Angles. (Journal Article) | SciTech Connect Journal Article: Molecular Simulation of Carbon Dioxide Brine and Clay Mineral Interactions and Determination of Contact Angles. Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide Brine and Clay Mineral Interactions and Determination of Contact Angles. Abstract not provided. Authors: Tenney, Craig M ; Cygan, Randall T. Publication Date: 2013-08-01 OSTI Identifier: 1106710 Report Number(s):

  12. Ab initio molecular orbital-configuration interaction based quantum master

    Office of Scientific and Technical Information (OSTI)

    equation (MOQME) approach to the dynamic first hyperpolarizabilities of asymmetric π-conjugated systems (Journal Article) | SciTech Connect Ab initio molecular orbital-configuration interaction based quantum master equation (MOQME) approach to the dynamic first hyperpolarizabilities of asymmetric π-conjugated systems Citation Details In-Document Search Title: Ab initio molecular orbital-configuration interaction based quantum master equation (MOQME) approach to the dynamic first

  13. Electrostatic interactions between peptides and the molecular chaperone

    Office of Scientific and Technical Information (OSTI)

    DnaK (Journal Article) | SciTech Connect Electrostatic interactions between peptides and the molecular chaperone DnaK Citation Details In-Document Search Title: Electrostatic interactions between peptides and the molecular chaperone DnaK No abstract prepared. Authors: Liu, Wei ; Bratko, Dusan ; Prausnitz, J.M. ; Blanch, H.W. Publication Date: 2003-01-30 OSTI Identifier: 824843 Report Number(s): LBNL--52181 R&D Project: 402201; TRN: US200419%%371 DOE Contract Number: AC03-76SF00098

  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.

    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 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 competition among different nutrient consumers. Although we used as many observations as we could obtain, more nutrient addition experiments in tropical systems would greatly benefit model testing and calibration. In summary, the N-COM model provides an ecologically consistent representation of nutrient competition appropriate for land BGC models integrated in Earth System Models.« less

  15. 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.

  16. 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.

  17. Molecular Interaction between Botulinum Neurotoxin B and Its Protein

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

    Receptor Revealed 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 (contoured at 1.5 s) around Syt-II, overlaid with the final refined model (Syt-II: red and green; HcB: grey). Please note that this map is model-bias free since it is calculated from the phases of the atomic model prior to the inclusion of the Syt-II peptide (using a lower resolution diffraction data

  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 of three classes of ''super molecular'' nanostructured materials. These included (1) dendrimers, (2) DNA bonded nano-particles, and (3) colloids, all of which form solution-based self-organizing systems. To this end, our goals were, first, to learn how to modify models of epitaxy in small molecule systems so that they are useful, efficient, and applicable to assembly of super-molecular species; and, second, to learn how systematic variations in the structure and bonding of the building blocks affect the surface kinetics and energetics that control the assembly process and the subsequent dynamic behavior of the assembled structures. AFM imaging provided experimental data on morphology and kinetics, while kinetic Monte Carlo (KMC) simulations related these data to molecular-scale processes and features.

  20. Collective many-body van der Waals interactions in molecular systems

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Journal Article: Collective many-body van der Waals interactions in molecular systems Citation Details In-Document Search Title: Collective many-body van der Waals interactions in molecular systems Authors: DeStasio, Jr., R.A. ; von Lilienfeld, O.A. ; Tkatchenko, A. [1] + Show Author Affiliations (LCF) [LCF Publication Date: 2012-09-11 OSTI Identifier: 1132743 Report Number(s): ANL/LCF/JA-72880 Journal ID: 0027-8424 DOE Contract Number: DE-AC02-06CH11357

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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 follow the same evolutionary patterns found in our broad sample.

  7. 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 cellular environments.

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

    Office of Scientific and Technical Information (OSTI)

    Genetics; I.3.6 Computer Graphics: Methodology and Techniques-Interaction Techniques; ... Institute for Quantitative Biomedical Research, Berkeley, California, tlu@lbl.gov, ...

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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 hybridization and the conventional mode for cocaine detection, the lowest detectable concentration was determined by binding activity between the ligand and receptor molecules. In order to overcome this limitation for cocaine detection, a novel competition sensing mode that relies on rate of aptamers unbinding from the cantilever due to either diffusion or reaction with cocaine as target ligands in solution was investigated. The rate of unbinding is found to be dependent on the concentration of cocaine molecules. A model based on diffusion-reaction equation was developed to explain the experimental observation. Experimental results indicate that the competition mode reduces the lowest detectable threshold to 200 nM which is comparable to that achieved analytical techniques such as mass spectrometry.

  14. 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 ?/2? field components the selective ionization of oriented toluene molecules can be used as a tool to control the directional emission of the H{sub 2}{sup +}, H{sub 3}{sup +} species.

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

    DOE Patents [OSTI]

    Laurence, Ted A. (Livermore, CA); Weiss, Shimon (Los Angels, CA)

    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.

  16. 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.

  17. 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.

  18. 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%.

  19. 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.

  20. 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

    The presence of short-lived radionuclides (t {sub 1/2} < 10 Myr) in the early solar system provides important information about the astrophysical environment in which the solar system formed. The discovery of now extinct {sup 10}Be (t {sub 1/2} = 1.4 Myr) in calcium-aluminum-rich inclusions (CAIs) with Fractionation and Unidentified Nuclear isotope anomalies (FUN-CAIs) suggests that a baseline concentration of {sup 10}Be in the early solar system was inherited from the protosolar molecular cloud. In this paper, we investigate various astrophysical contexts for the nonthermal nucleosynthesis of {sup 10}Be by cosmic-ray-induced reactions. We first show that the {sup 10}Be recorded in FUN-CAIs cannot have been produced in situ by irradiation of the FUN-CAIs themselves. We then show that trapping of Galactic cosmic rays (GCRs) in the collapsing presolar cloud core induced a negligible {sup 10}Be contamination of the protosolar nebula, the inferred {sup 10}Be/{sup 9}Be ratio being at least 40 times lower than that recorded in FUN-CAIs ({sup 10}Be/{sup 9}Be ? 3 × 10{sup –4}). Irradiation of the presolar molecular cloud by background GCRs produced a steady-state {sup 10}Be/{sup 9}Be ratio ? 1.3 × 10{sup –4} at the time of the solar system formation, which suggests that the presolar cloud was irradiated by an additional source of CRs. Considering a detailed model for CR acceleration in a supernova remnant (SNR), we find that the {sup 10}Be abundance recorded in FUN-CAIs can be explained within two alternative scenarios: (1) the irradiation of a giant molecular cloud by CRs produced by ? 50 supernovae exploding in a superbubble of hot gas generated by a large star cluster of at least 20,000 members, and (2) the irradiation of the presolar molecular cloud by freshly accelerated CRs escaped from an isolated SNR at the end of the Sedov-Taylor phase. In the second picture, the SNR resulted from the explosion of a massive star that ran away from its parent OB association, 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.

  1. 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.

  2. 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.

  3. Molecular Foundry

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

    The Molecular Foundry Lawrence Berkeley National Laboratory One Cyclotron Road Building 67 Berkeley, CA 94720 Berkeley Lab Visitor Information Berkeley Lab Interactive Map View Larger Map Foundry Staff FOUNDRY ADMINISTRATION Director Jeff Neaton email 510.486.4527 Director of Strategy and External Relations Branden Brough email 510.486.4206 Senior Administrator Meg Holm email 510.486.5135 User Program Director Alison Hatt email 510.486.7154 User Program Administrator Dmitry Soustin email

  4. 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.

  5. 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.

  6. 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...

  7. 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.

  8. Molecular Foundry

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

    The Molecular Foundry is a Department of Energy-funded nanoscience research facility that provides users from around the world with access to cutting-edge expertise and instrumentation in a collaborative, multidisciplinary environment. Read about the Molecular Foundry's research themes in its recently updated Strategic Plan Learn about the Advanced Materials Special Issue on the Molecular Foundry Call for Proposals: The next deadline for standard proposals is March 31, 2016 Molecular Foundry

  9. 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.

  10. Molecular Foundry

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

    SEMINARS 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. To be added to the Molecular Foundry's seminar mailing list, please email Jason Sweet. Recent Seminar Series Winter 2016 Fall 2015 Spring/Summer 2015 Winter 2015 < Full Seminar Archive EVENTS < events archive Upcoming Events Molecular Foundry

  11. 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...

  12. 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...

  13. Molecular Foundry

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

    transport properties of oligothiophene-based molecular films studied by current sensing atomic force microscopy. Nano Lett. 11, 4107-4112 (2011). Schwartzberg, A. M., Aloni, S.,...

  14. 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.

  15. 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.

  16. 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.

  17. 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 ...

  18. 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...

  19. Molecular Foundry

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

    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...

  20. 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 postdoc. Dr. Hatt received a B.S. in Physics from the University of Utah and a Ph.D. in Materials from the University of California, Santa Barbara. As User Program Director, Dr. Hatt is responsible for overseeing the Molecular Foundry's scientific proposal process, including administration associated with User proposal

  1. Molecular Foundry

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    Behzad Rad Rad Senior Scientific Engineering Associate, Biological Nanostructures BRad@lbl.gov 510.486.5795 Biography Education Postdoctoral Fellow Molecular Foundry Lawrence Berkeley National Labs Ph.D. in Biophysics University of California at Davis Dissertation Title: "The Unwinding Mechanism of the E. coli RecQ helicase" Dissertation Advisor: Dr. Stephen C. Kowalczykowski Bachelor's in Molecular and Cellular Biology University of California at Berkeley Expertise Behzad's interests

  2. Molecular Foundry

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

    Neaton Jeff Neaton Director, Molecular Foundry Senior Faculty Scientist, 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 Nanoscale Science Research Center. He is also a Senior Faculty Scientist at Lawrence Berkeley National Laboratory, Professor of Physics at UC Berkeley, and member of the Kavli Energy NanoSciences Institute at Berkeley. He received his Ph.D. in physics from

  3. Molecular Foundry

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

    Careers Information about current openings at the Molecular Foundry and complete application information is available from LBNL Human Resources. Please follow the application instructions at the bottom of the job posting. Inquiries about opportunities to work in specific areas of the Molecular Foundry can be sent to the following: Imaging and Manipulation of Nanostructures Facility P. Jim Schuck 510.486.4822 Nanofabrication Facility Stefano Cabrini 510.486.7339 Theory of Nanostructured Materials

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. Molecular Foundry

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

    Agenda March 24, 2016 Lawrence Berkeley National Laboratory Building 50 Auditorium Registration: Free Registration 8:30 am - 9:00 am The Molecular Foundry's History and Impact 9:00 am - 10:30 am Jeff Neaton, Molecular Foundry Paul Alivisatos, Berkeley Lab/UC Berkeley Michael Witherell, Berkeley Lab Brian Schowengerdt, Magic Leap Pat Dehmer, DOE Office of Science Representative Mike Honda (D-CA) Break 10:30 am - 11:00 am Session 1 11:00 am - 12:00 pm Moderated by David Prendergast, Andy Minor Jim

  9. 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

  10. 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 administrator, three facility support staff, and two matrixed IT support staff. As part of the management and operations team, she provides operational management, budget, strategy and policy support to the Foundry Director

  11. 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, March 8, 2016 at 11am Utilizing Inelastically Scattered Electrons in the Transmission Electron Microscope Christian Dwyer, Arizona State University [MORE] Tuesday, March 1, 2016 at 11am Noncovalent Binding

  12. Molecular Foundry

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

    See the Foundry's full equipment list Nanofabrication Capabilities & Tools Instrument Scheduler Major Capabilities: Instruments and Labs Zeiss Crossbeam 1540 EsB The Molecular Foundry Zeiss Cross-beam is one of the most versatile lithographic and inspection tools allowing fabrication of complex prototypes for nanoelectronics, nano-optical antenna, modifying scanning probe tips, rapid electrical contacting and many other applications. The 1500XB Cross Beam combines the Gemini field emission

  13. 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 External Relations. In this role, Dr. Brough is responsible for the organization's strategic planning and management. He also facilitates internal and external communications to promote the Foundry's mission and showcase its accomplishments to the DOE, the nanoscience research community and the public. Before joining the

  14. Molecular Foundry

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

    David Prendergast David Prendergast Director, Theory of Nanostructured Materials dgprendergast@lbl.gov 510.486.4948 personal website Biography Education 2002 Ph.D., Physics, University College Cork, Ireland 1999 B.Sc., Physics and Mathematics, University College Cork, Ireland Research Interests My research focuses on employing and developing first-principles electronic structure theory and molecular dynamics simulations on high-performance computing infrastructure to reveal energy relevant

  15. 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 manages proposals throughout the processes of submission, review, and execution, and is a resource for proposal administration, user on-boarding, user agreements, coordinating user access and reporting publications. He also assists with event planning and coordination, including meetings of the Proposal Review Board

  16. 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

  17. Molecular Foundry

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

    Tracy Mattox TMMattox Senior Scientific Engineering Associate, Inorganic Nanostructures TMMattox@lbl.gov 510.495.2649 Biography Education M.S. in Chemistry, Miami University, 2006 B.S. in Chemistry, University of Portland, 2003 Tracy Mattox has been a member of the Inorganic Facility 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 and analyze results). She is well

  18. 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 Prepare responses to proposal questions Create and submit your proposal through the online proposal portal After your proposal is approved* Complete secondary safety screening Become a badged LBNL "affiliate" Contact your assigned Foundry scientist When you arrive* Go to your appointment with the Affiliate

  19. molecular foundry

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

    molecular foundry - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense Waste Management Programs Advanced

  20. Molecular Foundry

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

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

  1. 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

  2. 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,

  3. Molecular Foundry

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

    NEWS New Form of Electron-beam Imaging Can See Elements that are 'Invisible' to Common Methods Molecular Foundry-pioneered 'MIDI-STEM' produces high-resolution views of lightweight atoms [MORE] Foundry Users Developing Paint-on Coating for Energy Efficient Windows Low-cost coating is based on brush block copolymers that rapidly self-assemble to photonics crystals and could disrupt the building retrofit market and potentially save billions in electricity. [MORE] Modernizing a Technology From the

  4. 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 March 31, 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

  5. 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.

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

    Office of Scientific and Technical Information (OSTI)

    Title: Molecular Simulation of Carbon Dioxide Brine and Clay Mineral Interactions and Determination of Contact Angles. Abstract not provided. Authors: Tenney, Craig M ; Cygan, ...

  7. Molecular Foundry

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

    Brett A. Helms Helms Staff Scientist, Organic and Macromolecular Synthesis bahelms@lbl.gov 510.486.7729 personal website Biography Brett A. Helms received his B.S. (2000) from Harvey Mudd College and his Ph.D. (2006) with Jean M. J. Fréchet at the University of California, Berkeley. He joined the staff of the Molecular Foundry in 2007, after postdoctoral research at the Technische Universiteit Eindhoven with E. W. (Bert) Meijer. His research interests include structure of and reactivity at

  8. Molecular Foundry

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

    Caroline M. Ajo-Franklin Ajo-Franklin Staff Scientist, Biological Nanostructures cajo-franklin@lbl.gov 510.486.4299 personal website Biography Dr. Ajo-Franklin has been a Staff Scientist at the Molecular Foundry since 2007. Before that, she received her Ph.D. in Chemistry from Stanford University with Prof. Steve Boxer and was a post-doctoral fellow with Prof. Pam Silver in the Department of Systems Biology at Harvard Medical School. Dr. Ajo-Franklin is fascinated by the incredible, diverse

  9. 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 operations through a broad range of responsibilities including space management/maintenance and modification of the building and lab equipment, both institutional and programatic. Gil also serves as the Building Emergency Team lead. Gil came to the Lab in 2006 after a twenty-eight year career in the specialty gases and

  10. Interactive Jobs

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

    Interactive Jobs Interactive Jobs Interactive Batch Jobs The login nodes on Genepool should not be used for heavy interactive work. These login nodes are shared amoungst all Genepool users so heavy CPU or memory usage will affect other Genepool users. 10 nodes have been reserved on Genepool for high priority and interactive work. Each user can use up to 2 slots at a time in the high priority queue. Use the qlogin command to run jobs interactively. The example below shows how to request an

  11. 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...

  12. 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

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

  13. 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

  14. 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...

  15. Structural Molecular Biology, SSRL

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

    Highlights Training Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating Biological Structures at the Atomic and Molecular Levels Your browser...

  16. 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. % salloc -N 2 -p debug -t 00:30:00 salloc may be issued with several options. For the complete list of all options for salloc, refer to the SLURM salloc

  17. 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.

  18. 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

  19. Interaction and Coalescence of Nanovoids and Dynamic Fracture in Silica

    Office of Scientific and Technical Information (OSTI)

    Glass: Multimiilion-to-Billion Atom Molecular Dynamics Simulations (Journal Article) | SciTech Connect Interaction and Coalescence of Nanovoids and Dynamic Fracture in Silica Glass: Multimiilion-to-Billion Atom Molecular Dynamics Simulations Citation Details In-Document Search Title: Interaction and Coalescence of Nanovoids and Dynamic Fracture in Silica Glass: Multimiilion-to-Billion Atom Molecular Dynamics Simulations Authors: Nomura, K ; Chen, Y C ; Kalia, R K ; Nakano, A ; Vashishta, P ;

  20. 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.

  1. 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 ...

  2. 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 ...

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

    Office of Scientific and Technical Information (OSTI)

    A paper copy of this document is also available for sale to the public from the National ... a minor component in goethite, because goethite rarely exists as a pure phase in nature. ...

  4. 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 definition of nonlinear optical susceptibility, using the frequency domain system ...

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

    Office of Scientific and Technical Information (OSTI)

    DOE Contract Number: DE-AC02-05CH11231; NIH:CHE-0205170 Resource Type: Conference Resource Relation: Conference: IEEE Visualization 2005 (submitted to),Minneapolis, MN, October ...

  6. 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.

  7. 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 ...

  8. 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.

  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. 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.

  11. 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

  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

    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.

  14. 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.

  15. Structural Interactions within Lithium Salt Solvates: Acyclic Carbonates

    Office of Scientific and Technical Information (OSTI)

    and Esters (Journal Article) | SciTech Connect Structural Interactions within Lithium Salt Solvates: Acyclic Carbonates and Esters Citation Details In-Document Search Title: Structural Interactions within Lithium Salt Solvates: Acyclic Carbonates and Esters Solvate crystal structures serve as useful models for the molecular-level interactions within the diverse solvates present in liquid electrolytes. Although acyclic carbonate solvents are widely used for Li-ion battery electrolytes, only

  16. The Role of Solvent Heterogeneity in Determining the Dispersion Interaction

    Office of Scientific and Technical Information (OSTI)

    Between Nanoassemblies (Journal Article) | SciTech Connect The Role of Solvent Heterogeneity in Determining the Dispersion Interaction Between Nanoassemblies Citation Details In-Document Search Title: The Role of Solvent Heterogeneity in Determining the Dispersion Interaction Between Nanoassemblies Understanding fundamental nanoassembly processes on intermediate scales beween the molecular and the continuum requires an in-depth analysis of the coupling between particle interactions and

  17. 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 development and scientific focus: Macromolecular Crystallography (MC) Small Angle X-ray Scattering/Diffraction (SAXS) X-ray Absorption Spectroscopy (XAS) Central to the core technological developments in all three of these areas is the development and utilization of improved detectors and instrumentation, especially to be

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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...

  3. 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.

  4. 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

  5. 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

  6. 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 morphological aggregates that can form on the surface.Again, these structures result from the optimization of chemical redox equilibrium, conformational entropy, electrostatic and hydrophobic interactions. Furthermore, changes in domains structure can manifest themselves in the capacitance-potential curves and then provide a link between macroscopic measurements and the formation of nanoscopic domains. It is clear that chemical engineers are in a unique position to use these switchable surfaces in the molecular design of sensors, biosensors, separation devices, microfluidic devices with on-off environmental switches and drug delivery systems among many others. Finally, we want to stress that the application of molecular theories, where the coupling between chemical equilibrium, physical interactions and molecular organization are explicitly included provide with quantitative predictions of the layers properties, as compared with experimental observations, and enable the fundamental understanding of the observed behavior. Moreover, the theory provides with a detailed microscopic picture and should be used as an integral part in the design of functional and responsive surfaces. It is important to emphasize that the molecular approaches are not exact, and, therefore, there is a need to continue their development and the incorporation of improved approximations to further broaden their applicability.

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

    DOE Patents [OSTI]

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

    1997-01-01

    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.

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

    DOE Patents [OSTI]

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

    1997-01-07

    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.

  9. The Molecular Foundry Turns 10

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

    The Molecular Foundry Turns 10 The Molecular Foundry, a nanoscience user facility that has served thousands of scientists from all over the world, will celebrate the 10th anniversary of the dedication of its iconic building on March 24 with a symposium and dinner. A timeline of scientific milestones of the last decade was also created. ← Previous

  10. 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

  11. 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

  12. 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...

  13. 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).

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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)

  1. Apparatus for molecular weight separation

    DOE Patents [OSTI]

    Smith, Richard D. (Richland, WA); Liu, Chuanliang (Haverhill, MA)

    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).

  2. Steven Weinberg, Weak Interactions, and Electromagnetic Interactions

    Office of Scientific and Technical Information (OSTI)

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

  3. 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

  4. Synchrotrons Explore Water's Molecular Mysteries

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

    Synchrotrons Explore Water's Molecular Mysteries Synchrotrons Explore Water's Molecular Mysteries Print Friday, 01 February 2013 00:00 In experiments at SLAC National Accelerator Laboratory and Lawrence Berkeley National Laboratory's Advanced Light Source, scientists observed a surprisingly dense form of water that remained liquid well beyond its typical freezing point. Researchers applied a superthin coating of water-no deeper than a few molecules-to the surface of a barium fluoride crystal.

  5. 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,

  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 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,

  7. 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,

  8. 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,

  9. 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...

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

    Office of Scientific and Technical Information (OSTI)

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

  11. 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...

  12. 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...

  13. PIA - Environmental Molecular Sciences Laboratory (EMSL) User...

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

    Molecular Sciences Laboratory (EMSL) User System (ESU) PDF icon PIA - Environmental Molecular Sciences Laboratory (EMSL) User System (ESU) More Documents & Publications PIA - WEB ...

  14. 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.

  15. Running Interactive Batch Jobs

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

    if the node of choice is not immediately available Start an interactive session in the debug queue qsh -l debug1 -now no qlogin -l debug1 -now no This is useful when the cluster...

  16. 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

  17. Human-machine interactions

    DOE Patents [OSTI]

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

    2009-04-28

    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.

  18. Impact of the Fuel Molecular Structure on the Oxidation Process of Real

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

    Diesel fuels According to Storage Conditions and Biodiesel Content | Department of Energy the Fuel Molecular Structure on the Oxidation Process of Real Diesel fuels According to Storage Conditions and Biodiesel Content Impact of the Fuel Molecular Structure on the Oxidation Process of Real Diesel fuels According to Storage Conditions and Biodiesel Content Hydrocarbon profilers can provide a clear understanding of complex interactions between fuel chemistry, storage conditions, and quantity

  19. 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

  20. Molecular separation method and apparatus

    DOE Patents [OSTI]

    Villa-Aleman, Eliel (3108 Roses Run, Aiken, SC 29803)

    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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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).

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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``).

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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.

  17. 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.

  18. Interactive optical panel

    DOE Patents [OSTI]

    Veligdan, James T. (Manorville, NY)

    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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Nanoplasmonic molecular ruler for nuclease activity and DNA footprinting

    DOE Patents [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.

  4. 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.

  5. 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 transition temperature T m and the ordered moment, magnetic heat capacity, and anisotropic magnetic susceptibility χ versus temperature T . The anisotropic Weiss temperature θ p in the Curie-Weiss law for T>T m is calculated. A quantitative study of the competition between FM and AFM ordering on cubic Bravais lattices versus the demagnetization factor in the absence of FM domain effects is presented. The contributions of Heisenberg exchange interactions and of the MDIs to T m and to θ p are found to be additive, which simplifies analysis of experimental data. Some properties in the magnetically-ordered state versus T are presented, including the ordered moment and magnetic heat capacity and, for AFMs, the dipolar anisotropy of the free energy and the perpendicular critical field. The anisotropic χ for dipolar AFMs is calculated both above and below the Néel temperature T N and the results are illustrated for a simple tetragonal lattice with c/a>1, c/a=1 (cubic), and c/a<1 , where a change in sign of the χ anisotropy is found at c/a=1 . Finally, following the early work of Keffer [Phys. Rev. 87, 608 (1952)], the dipolar anisotropy of χ above T N =69 K of the prototype collinear Heisenberg-exchange-coupled tetragonal compound MnF 2 is calculated and found to be in excellent agreement with experimental single-crystal literature data above 130 K, where the smoothly increasing deviation of the experimental data from the theory on cooling from 130 K to T N is deduced to arise from dynamic short-range collinear c -axis AFM ordering in this temperature range driven by the exchange interactions.« less

  6. 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

  7. 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

  8. 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.

  9. 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...

  10. Sandia Energy - Atomistic Molecular Dynamics of Ion-Containing...

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

    Atomistic Molecular Dynamics of Ion-Containing Polymers Home Highlights - HPC Atomistic Molecular Dynamics of Ion-Containing Polymers Previous Next Atomistic Molecular Dynamics of...

  11. 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.

  12. 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.

  13. 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.

  14. 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}

  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 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. Accelerated Molecular Dynamics Methods | Department of Energy

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

    Molecular Dynamics Methods Accelerated Molecular Dynamics Methods This presentation on Accelerated Molecular Dynamics Methods was given at the DOE Theory Focus Session on Hydrogen Storage Materials on May 18, 2006. PDF icon storage_theory_session_voter.pdf More Documents & Publications Simulations of Kinetic Events at the Atomic Scale Transportation, Aging and Disposal Canister System Performance Specification: Revision 1 Waste Characterization, Reduction, and Repackaging Facility (WCRRF)

  2. 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.

  3. Production of high molecular weight polylactic acid

    DOE Patents [OSTI]

    Bonsignore, Patrick V. (Joilet, IL)

    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.

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

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

    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...

  5. 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 conversion. Quarterly report You are accessing a document from the Department of Energy's (DOE)...

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

    Office of Scientific and Technical Information (OSTI)

    report Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. Quarterly status report In this Quarter, the research was focused continually on the...

  7. 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 The research was...

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

    Office of Scientific and Technical Information (OSTI)

    October--December 1994 Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. Quarterly report, October--December 1994 You are accessing a...

  9. 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...

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

    Office of Scientific and Technical Information (OSTI)

    October--December 1994 Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. Quarterly report, October--December 1994 In this Quarter, the...

  11. 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 conversion. Quarterly report In this Quarter, the research was focused continually on the two...

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

    Office of Scientific and Technical Information (OSTI)

    report Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion. Quarterly status report You are accessing a document from the Department of...

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

    Office of Scientific and Technical Information (OSTI)

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

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

    Office of Scientific and Technical Information (OSTI)

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

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

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

    Using Hydrogenase Enzymes to Guide Creating Fast and Efficient Molecular Electrocatalysts January 2011 To create solar assemblies that use sunlight to split water and create...

  16. 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.

  17. 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...

  18. 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...

  19. 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 Authors: Kane, J ...

  20. Signature molecular descriptor : advanced applications.

    SciTech Connect (OSTI)

    Visco, Donald Patrick, Jr.

    2010-04-01

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

  1. Surprising Quasiparticle Interactions in Graphene

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

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

  2. Industry Interactive Procurement System (IIPS)

    Broader source: Energy.gov [DOE]

    Presentation on DOE’s Industry Interactive Procurement System (IIPS) presented at the PEM fuel cell pre-solicitation meeting held May 26, 2005 in Arlington, VA.

  3. Strong interactions in air showers

    SciTech Connect (OSTI)

    Dietrich, Dennis D.

    2015-03-02

    We study the role new gauge interactions in extensions of the standard model play in air showers initiated by ultrahigh-energy cosmic rays. Hadron-hadron events remain dominated by quantum chromodynamics, while projectiles and/or targets from beyond the standard model permit us to see qualitative differences arising due to the new interactions.

  4. Eighth international congress on nitrogen fixation

    SciTech Connect (OSTI)

    Not Available

    1990-01-01

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

  5. Eighth international congress on nitrogen fixation. Final program

    SciTech Connect (OSTI)

    Not Available

    1990-12-31

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

  6. Photo of the Week: Studying the Rhizosphere | Department of Energy

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

    Studying the Rhizosphere Photo of the Week: Studying the Rhizosphere December 18, 2013 - 4:48pm Addthis Scientists at Pacific Northwest National Laboratory study the microbial interactions in the plant root systems, the rhizosphere. The rhizosphere represents a critical zone where plant roots, microbes and minerals interface, and where biogeochemical weathering provides nutrients to plants. This research program will broaden our understanding of the biogeochemistry of plant-microbe-soil

  7. Note: Nonpolar solute partial molar volume response to attractive interactions with water

    SciTech Connect (OSTI)

    Williams, Steven M.; Ashbaugh, Henry S.

    2014-01-07

    The impact of attractive interactions on the partial molar volumes of methane-like solutes in water is characterized using molecular simulations. Attractions account for a significant 20% volume drop between a repulsive Weeks-Chandler-Andersen and full Lennard-Jones description of methane interactions. The response of the volume to interaction perturbations is characterized by linear fits to our simulations and a rigorous statistical thermodynamic expression for the derivative of the volume to increasing attractions. While a weak non-linear response is observed, an average effective slope accurately captures the volume decrease. This response, however, is anticipated to become more non-linear with increasing solute size.

  8. 2012 CELLULAR & MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 17 - 22, 2012

    SciTech Connect (OSTI)

    Judith Berman

    2012-06-22

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

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

    SciTech Connect (OSTI)

    Black, Jennifer M; Walters, Deron; Labuda, Aleksander; Feng, Guang; Hillesheim, Patrick C; Dai, Sheng; Cummings, Peter T; Kalinin, Sergei V; Proksch, Roger; Balke, Nina

    2013-01-01

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

  10. Simulation studies of self-organization of microtubules and molecular motors.

    SciTech Connect (OSTI)

    Jian, Z.; Karpeev, D.; Aranson, I. S.; Bates, P. W.; Michigan State Univ.

    2008-05-01

    We perform Monte Carlo type simulation studies of self-organization of microtubules interacting with molecular motors. We model microtubules as stiff polar rods of equal length exhibiting anisotropic diffusion in the plane. The molecular motors are implicitly introduced by specifying certain probabilistic collision rules resulting in realignment of the rods. This approximation of the complicated microtubule-motor interaction by a simple instant collision allows us to bypass the 'computational bottlenecks' associated with the details of the diffusion and the dynamics of motors and the reorientation of microtubules. Consequently, we are able to perform simulations of large ensembles of microtubules and motors on a very large time scale. This simple model reproduces all important phenomenology observed in in vitro experiments: Formation of vortices for low motor density and raylike asters and bundles for higher motor density.

  11. Molecular dynamics of a dilute solution of hydrogen in palladium

    SciTech Connect (OSTI)

    Pratt, L. R.; Eckert, J.

    1989-06-15

    Molecular-dynamics results on a dilute solution of H in Pd are presentedand compared with available incoherent inelastic neutron-scattering results.The embedded-atom model adopted here does a good job of describing the H-Pdatomic forces probed by incoherent inelastic neutron scattering. The timecorrelation functions associated with the computed spectra are strongly dampedand indicative of the anharmonicity that has been suggested as the principalcontribution to the anomalous isotope dependence of the superconductingtransition temperature in PdH. These results highlight the fact that the H-atomvibrations in Pd-H solutions are low-frequency, large-amplitude vibrationsrelative to vibrations of H atoms in usual covalent interactions. The rmsdisplacement of the H atom from its mean position in the center of the Pdoctahedron compares favorably with the available neutron-diffraction results.

  12. Collective alignment of polar filaments by molecular motors.

    SciTech Connect (OSTI)

    Ziebert, F.; Aranson, I. S.; Vershinin, M.; Gross, S. P.; Materials Science Division; Univ. of California at Irvine

    2009-04-01

    We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm model of only two filaments interacting with multiple motors, we were able to investigate in detail the alignment dynamics. While almost no alignment occurs in the case of a single motor, the filaments become rapidly aligned due to the collective action of the motors. Our analysis shows that the alignment time is governed by the number of bound motors and the magnitude of the motors stepping fluctuations. We predict that the time scale of alignment is in the order of seconds, much faster than that reported for passive crosslink-induced bundling. In vitro experiments on the alignment of microtubules by multiple-motor covered beads are in qualitative agreement. We also discuss another mode of fast alignment of filaments, namely the cooperation between motors and passive crosslinks.

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

    ScienceCinema (OSTI)

    Bozek, John

    2014-06-03

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

  14. Method and apparatus to image biological interactions in plants

    DOE Patents [OSTI]

    Weisenberger, Andrew; Bonito, Gregory M.; Reid, Chantal D.; Smith, Mark Frederick

    2015-12-22

    A method to dynamically image the actual translocation of molecular compounds of interest in a plant root, root system, and rhizosphere without disturbing the root or the soil. The technique makes use of radioactive isotopes as tracers to label molecules of interest and to image their distribution in the plant and/or soil. The method allows for the study and imaging of various biological and biochemical interactions in the rhizosphere of a plant, including, but not limited to, mycorrhizal associations in such regions.

  15. Niobate-based octahedral molecular sieves

    DOE Patents [OSTI]

    Nenoff, Tina M.; Nyman, May D.

    2006-10-17

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

  16. Niobate-based octahedral molecular sieves

    DOE Patents [OSTI]

    Nenoff, Tina M.; Nyman, May D.

    2003-07-22

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

  17. B13+: Photodriven Molecular Wankel Engine

    SciTech Connect (OSTI)

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

    2012-07-09

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

  18. Quantum-information analysis of electronic states of different molecular structures

    SciTech Connect (OSTI)

    Barcza, G.; Legeza, Oe.; Marti, K. H.; Reiher, M. [Fachbereich Physik, Philipps-Universitaet Marburg, D-35032 Marburg (Germany); Research Institute for Solid State Physics and Optics, H-1525 Budapest, P. O. Box 49 (Hungary); Laboratorium fuer Physikalische Chemie, ETH Zurich, CH-8093 Zurich (Switzerland)

    2011-01-15

    We have studied transition metal clusters from a quantum information theory perspective using the density-matrix renormalization group (DMRG) method. We demonstrate the competition between entanglement and interaction localization and discuss the application of the configuration interaction-based dynamically extended active space procedure, which significantly reduces the effective system size and accelerates the speed of convergence for complicated molecular electronic structures. Our results indicate the importance of taking entanglement among molecular orbitals into account in order to devise an optimal DMRG orbital ordering and carry out efficient calculations on transition metal clusters. Apart from these algorithmic observations, which lead to a recipe for black-box DMRG calculations, our work provides physical understanding of electron correlation in molecular and cluster structures in terms of entropy measures of relevance also to recent work on tensor-network representations of electronic states. We also identify those molecular orbitals which are highly entangled and discuss the consequences for chemical bonding and for the structural transition from an dioxygen binding copper cluster to an bis-oxygen-bridged system with broken O-O bond.

  19. COLD WATER VAPOR IN THE BARNARD 5 MOLECULAR CLOUD

    SciTech Connect (OSTI)

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

    2014-06-20

    After more than 30 yr of investigations, the nature of gas-grain interactions at low temperatures remains an unresolved issue in astrochemistry. Water ice is the dominant ice found in cold molecular clouds; however, there is only one region where cold (?10 K) water vapor has been detected—L1544. This study aims to shed light on ice desorption mechanisms under cold cloud conditions by expanding the sample. The clumpy distribution of methanol in dark clouds testifies to transient desorption processes at work—likely to also disrupt water ice mantles. Therefore, the Herschel HIFI instrument was used to search for cold water in a small sample of prominent methanol emission peaks. We report detections of the ground-state transition of o-H{sub 2}O (J = 1{sub 10}-1{sub 01}) at 556.9360 GHz toward two positions in the cold molecular cloud, Barnard 5. The relative abundances of methanol and water gas support a desorption mechanism which disrupts the outer ice mantle layers, rather than causing complete mantle removal.

  20. Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

    SciTech Connect (OSTI)

    Mullick, Shanta; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, SummerHill, Shimla - 171005 (India); Pathania, Y. [Chitkara University, Atal Shiksha Kunj, Atal Nagar, Barotiwala, Dist Solan, Himachal Pradesh - 174103 (India)

    2011-12-12

    This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12{sigma}, 14{sigma} and 16{sigma} and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.

  1. Measuring the Monitoring User Interactive Experiences on Franklin Interactive Nodes

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

    Interactive Node Responsiveness Richard Gerber User Services Group National Energy Research Scientific Computing Center Lawrence Berkeley National Laboratory Berkeley, CA June 9, 2008 Introduction Anecdotal reports of slow interactive response on Franklin's login nodes have been documented via comments on the 2007 NERSC User Survey. Users report that sluggish command-line response at times makes it difficult to work. The cause, or causes, of the poor response time is unknown. In an attempt to

  2. Interactions between silver nanoparticles and polyvinyl alcohol nanofibers

    SciTech Connect (OSTI)

    Chou, H. L.; Wu, C. M.; Lin, F. D.; Rick, J.

    2014-08-15

    The interaction of polyvinylalcohol (PVA) nanofibers with silver (Ag) nanoparticles (mean diameter 8nm) has been modeled using density functional theory (DFT) calculations. The physical adsorption of PVA through the hydroxyl group, to the Ag, and its corresponding molecular orientation was compared with experimental results obtained from surface-enhanced Raman scattering (SERS) studies of the same material. A good agreement was found between the computational model of the vibrational spectrum of the adsorbate and the experimentally observed SERS. In general, aliphatic capping molecules are used to passivate the surface of Ag{sub 55} nanocrystals (55 = atomic number of Ag). In this study, a DFT simulation was employed to show binding energies and electron contour map analyses of Ag{sub 55} with PVA. Here we show that the PVA interacts with the Ag nanoparticle's surface, through the OH group, thereby contributing significantly to the increase in SERS activity.

  3. Detailed Investigations of Interactions between Ionizing Radiation and Neutral Gases

    SciTech Connect (OSTI)

    Landers, Allen L

    2014-03-31

    We are investigating phenomena that stem from the many body dynamics associated with ionization of an atom or molecule by photon or charged particle. Our program is funded through the Department of Energy EPSCoR Laboratory Partnership Award in collaboration with Lawrence Berkeley National Laboratory. We are using variations on the well established COLTRIMS technique to measure ions and electrons ejected during these interactions. Photoionization measurements take place at the Advanced Light Source at LBNL as part of the ALS-COLTRIMS collaboration with the groups of Reinhard Dörner at Frankfurt and Ali Belkacem at LBNL. Additional experiments on charged particle impact are conducted locally at Auburn University where we are studying the dissociative molecular dynamics following interactions with either ions or electrons over a velocity range of 1 to 12 atomic units.

  4. Actinide Dioxides in Water: Interactions at the Interface

    SciTech Connect (OSTI)

    Alexandrov, Vitaly; Shvareva, Tatiana Y.; Hayun, Shmuel; Asta, Mark; Navrotsky, Alexandra

    2011-12-15

    A comprehensive understanding of chemical interactions between water and actinide dioxide surfaces is critical for safe operation and storage of nuclear fuels. Despite substantial previous research, understanding the nature of these interactions remains incomplete. In this work, we combine accurate calorimetric measurements with first-principles computational studies to characterize surface energies and adsorption enthalpies of water on two fluorite-structured compounds, ThO? and CeO?, that are relevant for understanding the behavior of water on actinide oxide surfaces more generally. We determine coverage-dependent adsorption enthalpies and demonstrate a mixed molecular and dissociative structure for the first hydration layer. The results show a correlation between the magnitude of the anhydrous surface energy and the water adsorption enthalpy. Further, they suggest a structural model featuring one adsorbed water molecule per one surface cation on the most stable facet that is expected to be a common structural signature of water adsorbed on actinide dioxide compounds.

  5. ENERGETIC PHOTON AND ELECTRON INTERACTIONS WITH POSITIVE IONS

    SciTech Connect (OSTI)

    Phaneuf, Ronald A.

    2013-07-01

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

  6. Nonequilibrium Molecular Dynamics Simulations of the Rheology...

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

    Classical Molecular Dynamics Codes and Coupling of Length Scales Peter T. Cummings 1,2 , Normand Modine 3 and Randy Cygan 4 1 Chemical and Biomolecular Engineering, Vanderbilt U. 2...

  7. Yuan T. Lee's Crossed Molecular Beam Experiment

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

    The above illustration was drawn by Professor Yuan T. Lee, who shared the 1986 Nobel Prize in Chemistry. It shows the design for his crossed molecular beam experiment described in ...

  8. Environmental Molecular Sciences Laboratory 2007 Annual Report

    SciTech Connect (OSTI)

    Showalter, Mary Ann; Foster, Nancy S.

    2008-03-19

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

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

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

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

  10. Genetics and molecular biology of breast cancer

    SciTech Connect (OSTI)

    King, M.C.; Lippman, M.

    1992-12-31

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

  11. Microdialysis unit for molecular weight separation

    DOE Patents [OSTI]

    Smith, Richard D. (Richland, WA); Liu, Chuanliang (Richland, WA)

    1999-01-01

    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, or (4) any combination of (1), (2), and (3).

  12. SECTION IV: ATOMIC, MOLECULAR AND MATERIALS SCIENCE

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

    ATOMIC, MOLECULAR AND MATERIALS SCIENCE A semiempirical scaling law for target K x-ray production in heavy ion collisions... IV-1 R. L. Watson, Y. Peng, V. Horvat, and A....

  13. 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 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 recruit and deposit helicases has remained unclear. To better understand this

  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 Print 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 recruit and deposit helicases has remained unclear. To better understand this

  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 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 recruit and deposit helicases has remained unclear. To better understand this

  16. 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 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 recruit and deposit helicases has remained unclear. To better understand this

  17. Decoding the Molecular Mysteries of Photosynthesis

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

    Decoding Photosynthesis' Molecular Mysteries Decoding the Molecular Mysteries of Photosynthesis Understanding the inner workings of photosynthesis is key to building new man-made energy resources February 14, 2014 Contact: Kathy Kincade, +1 510 495 2124, kkincade@lbl.gov grana_2.jpg Two protein assemblies in a plant cell's chloroplasts -- Photosystem II (blue and red) and light-harvesting complex II (green and purple) -- are key to initiating photosynthesis. This visualization illustrates how

  18. Dudley Herschbach: Chemical Reactions and Molecular Beams

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

    Dudley Herschbach: Chemical Reactions and Molecular Beams Resources with Additional Information Dudley Herschbach Courtesy of Texas A&M University As a co-recipient of the 1986 Nobel Prize in Chemistry, 'Dudley Herschbach was cited for "providing a much more detailed understanding of how chemical reactions take place". Using molecular beams, he studied elementary reactions such as K + CH3I and K + Br2, where it became possible to correlate reaction dynamics with the electronic

  19. Molecular Dynamics Simulation Studies of Electrolytes and

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

    Electrolyte/Electrode Interfaces | Department of Energy Dynamics Simulation Studies of Electrolytes and Electrolyte/Electrode Interfaces Molecular Dynamics Simulation Studies of Electrolytes and Electrolyte/Electrode Interfaces 2010 DOE Vehicle Technologies and Hydrogen Programs Annual Merit Review and Peer Evaluation Meeting, June 7-11, 2010 -- Washington D.C. PDF icon es058_smith_2010_p.pdf More Documents & Publications Molecular dynamics simulation and ab intio studies of electrolytes

  20. Molecular dynamics simulation studies of electrolytes and

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

    electrolyte/electrode interfaces | Department of Energy studies of electrolytes and electrolyte/electrode interfaces Molecular dynamics simulation studies of electrolytes and electrolyte/electrode interfaces 2009 DOE Hydrogen Program and Vehicle Technologies Program Annual Merit Review and Peer Evaluation Meeting, May 18-22, 2009 -- Washington D.C. PDF icon es_40_smith.pdf More Documents & Publications Molecular Dynamics Simulation Studies of Electrolytes and Electrolyte/Electrode

  1. PNNL: Center for Molecular Electrocatalysis About Us

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

    Dr. Morris Bullock, CME Director About Us About the Center for Molecular Electrocatalysis To improve reactions important for solar energy storage and fuel cells, the Center for Molecular Electrocatalysis seeks to transform our ability to design electrocatalysts that convert electrical energy into the chemical bonds of fuels, or the reverse, convert chemical energy into electrical energy. Our researchers seek to understand, predict, and control the intra- and intermolecular flow of protons in

  2. MEIS: Molecular Environmental & Interface Science

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

    People BL 11-2 Reports &Publications Model Compound Library SixPACK Glitch Curves MES User Resources & Instrumentation Environmental Remediation Science at SSRL MEIS Home SSRL Stanford EMSI SLAC Beam line resources and instrumentation Fundamental and applied research Why synchrotrons for environmental science? Molecular Environmental Science (MES) research at SSRL focuses on the fundamental interfacial, molecular- and nano-scale processes that control contaminant and nutrient cycling in

  3. Bilayer membrane interactions with nanofabricated scaffolds

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

    Collier, Patrick C.

    2015-07-29

    Membrane function is facilitated by lateral organization within the lipid bilayer, including phase-separation of lipids into more ordered domains (lipid rafts) and anchoring of the membrane to a cytoskeleton. These features have proven difficult to reproduce in model membrane systems such as black lipid membranes, unilamellar vesicles and supported bilayers. However, advances in micro/nanofabrication have resulted in more realistic synthetic models of membrane-cytoskeleton interactions that can help uncover the design rules responsible for biological membrane formation and organization. This review will focus on describing micro-/nanostructured scaffolds that can emulate the connections of a cellular membrane to an underlying “cytoskeleton”. Thismore » includes molecular-based scaffolds anchored to a solid substrate through surface chemistry, solid-state supports modified by material deposition, lithography and etching, the creation of micro/nanoporous arrays, integration with microfluidics, and droplet-based bilayers at interfaces.Model systems such as these are increasing our understanding of structure and organization in cell membranes, and how they result in the emergence of functionality at the nanoscale.« less

  4. Interactive Map Shows Geothermal Resources

    Broader source: Energy.gov [DOE]

    The free interactive online map posted recently by the Oregon Department of Geology and Mineral Industries is part of a U.S. Department of Energy project to expand the knowledge of geothermal energy potential nationwide.

  5. Groundwater Report Goes Online, Interactive

    Broader source: Energy.gov [DOE]

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

  6. Surprising Quasiparticle Interactions in Graphene

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

    that suggest new kinds of devices. Particle Physics in Your Pencil Quantum electrodynamics, or QED, is the theory of many-body interactions first invented in the 1950s by...

  7. Sandia Energy - Molecular Dynamics Simulations Predict Fate of...

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

    Molecular Dynamics Simulations Predict Fate of Uranium in Sediments Home Highlights - Energy Research Molecular Dynamics Simulations Predict Fate of Uranium in Sediments Previous...

  8. PNNL: Center for Molecular Electrocatalysis - Research: An Assessment...

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

    December 2010 molecular-level understanding of the energetic and mechanistic factors The rational design of improved catalysts requires a detailed molecular-level understanding of ...

  9. The Influence of Molecular Structure of Distillate Fuels on HFRR...

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

    The Influence of Molecular Structure of Distillate Fuels on HFRR Lubricity The Influence of Molecular Structure of Distillate Fuels on HFRR Lubricity Presentation given at 2007...

  10. Deflagration Rates and Molecular Bonding Trends of Statically...

    Office of Scientific and Technical Information (OSTI)

    Molecular Bonding Trends of Statically Compressed Secondary Explosives Citation Details In-Document Search Title: Deflagration Rates and Molecular Bonding Trends of Statically ...

  11. Final Report: Ionization chemistry of high temperature molecular...

    Office of Scientific and Technical Information (OSTI)

    chemistry of high temperature molecular fluids Citation Details In-Document Search Title: Final Report: Ionization chemistry of high temperature molecular fluids With the ...

  12. Validation of Hydrogen Exchange Methodology on Molecular Sieves...

    Office of Environmental Management (EM)

    Validation of Hydrogen Exchange Methodology on Molecular Sieves for Tritium Removal from Contaminated Water Validation of Hydrogen Exchange Methodology on Molecular Sieves for...

  13. Molecular replacement and model-building using distant homology...

    Office of Scientific and Technical Information (OSTI)

    Molecular replacement and model-building using distant homology models as templates Citation Details In-Document Search Title: Molecular replacement and model-building using...

  14. Accuracy of density functionals for molecular electronics: The...

    Office of Scientific and Technical Information (OSTI)

    Accuracy of density functionals for molecular electronics: The Anderson junction Prev Next Title: Accuracy of density functionals for molecular electronics: The Anderson ...

  15. Molecular catalytic coal liquid conversion (Conference) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Conference: Molecular catalytic coal liquid conversion Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion This research, which is relevant to the...

  16. Molecular catalytic coal liquid conversion (Conference) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Conference: Molecular catalytic coal liquid conversion Citation Details In-Document Search Title: Molecular catalytic coal liquid conversion You are accessing a document from...

  17. Remarkable Effect of Molecular Architecture on Chain Exchange...

    Office of Scientific and Technical Information (OSTI)

    Remarkable Effect of Molecular Architecture on Chain Exchange in Triblock Copolymer Micelles Citation Details In-Document Search Title: Remarkable Effect of Molecular Architecture...

  18. Molecular Structure of the Brucella abortus Metalloprotein RicA...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Molecular Structure of the Brucella abortus Metalloprotein RicA, a Rab2-Binding Virulence Effector Citation Details In-Document Search Title: Molecular Structure ...

  19. Molecular Weight Effects on Particle and Polymer Microstructure...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Molecular Weight Effects on Particle and Polymer Microstructure in Concentrated Polymer Solutions Citation Details In-Document Search Title: Molecular Weight ...

  20. Surprising Quasiparticle Interactions in Graphene

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

    Surprising Quasiparticle Interactions in Graphene Surprising Quasiparticle Interactions in Graphene Print Wednesday, 31 October 2007 00:00 Until now, the world's electronics have been dominated by silicon, whose properties, while excellent, significantly limit the size and power consumption of today's computer chips. In order to develop ever smaller and more efficient devices, scientists have turned their attention to carbon, which can be formed into nanostructures like nanotubes, whose

  1. Fundamental Interactions - Research - Cyclotron Institute

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

    Fundamental Interactions Production of 46V with MARS. Energy loss versus position on Y axis. The Standard Model, which unifies the strong, electromagnetic and weak forces, has been remarkably successful in describing the interactions of quarks and leptons. However, the model is incomplete, and it is the goal of this research program to sensitively probe its limits. Though in most cases we use the nucleus as a micro-laboratory for testing the Standard Model, the implications of the results extend

  2. Interactive Grid | Department of Energy

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

    Educational Resources » Interactive Grid Interactive Grid Each time you flick a light switch or press a power button, you enjoy the benefits of the nation's incredible electric grid. The grid is a complex network of people and machinery working around the clock to produce and deliver electricity to millions of homes across the nation. The electric grid works so well, Americans often think about it only when they receive their electric bills, or in those rare instances when there is a power

  3. Rotating fiber array molecular driver and molecular momentum transfer device constructed therewith

    DOE Patents [OSTI]

    Milleron, Norman (1854 San Juan, Berkeley, CA 94707)

    1983-01-01

    A rotating fiber array molecular driver is disclosed which includes a magnetically suspended and rotated central hub to which is attached a plurality of elongated fibers extending radially therefrom. The hub is rotated so as to straighten and axially extend the fibers and to provide the fibers with a tip speed which exceeds the average molecular velocity of fluid molecules entering between the fibers. Molecules colliding with the sides of the rotating fibers are accelerated to the tip speed of the fiber and given a momentum having a directional orientation within a relatively narrow distribution angle at a point radially outward of the hub, which is centered and peaks at the normal to the fiber sides in the direction of fiber rotation. The rotating fiber array may be used with other like fiber arrays or with other stationary structures to form molecular momentum transfer devices such as vacuum pumps, molecular separators, molecular coaters, or molecular reactors.

  4. Unconventional interaction between vortices in a polarized Fermi gas

    SciTech Connect (OSTI)

    Stojanovic, Vladimir M.; Vincent Liu, W. Kim, Yong Baek

    2008-04-15

    Recently, a homogeneous superfluid state with a single gapless Fermi surface was predicted to be the ground state of an ultracold Fermi gas with spin population imbalance in the regime of molecular Bose-Einstein condensation. We study vortices in this novel state using a symmetry-based effective field theory, which captures the low-energy physics of gapless fermions and superfluid phase fluctuations. This theory is applicable to all spin-imbalanced ultracold Fermi gases in the superfluid regime, regardless of whether the original fermion-pairing interaction is weak or strong. We find a remarkable, unconventional form of the interaction between vortices. The presence of gapless fermions gives rise to a spatially oscillating potential, akin to the RKKY indirect-exchange interaction in non-magnetic metals. We compare the parameters of the effective theory to the experimentally measurable quantities and further discuss the conditions for the verification of the predicted new feature. Our study opens up an interesting question as to the nature of the vortex lattice resulting from the competition between the usual repulsive logarithmic (2D Coulomb) and predominantly attractive fermion-induced interactions.

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

    SciTech Connect (OSTI)

    Tian, W. W.; Leahy, D. A.

    2011-03-10

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

  6. Determining the Overpotential for a Molecular Electrocatalyst

    SciTech Connect (OSTI)

    Appel, Aaron M.; Helm, Monte L.

    2014-02-07

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

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

    DOE Patents [OSTI]

    Kurnit, Norman A. (Santa Fe, NM)

    1980-01-01

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

  8. Experimental and Modeling Investigation of Radionuclide Interaction...

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

    interactions with clay minerals with results suggesting that iodide may directly interact with clays by forming ion-pairs which may concentrate within the interlayer space as...

  9. Structural Interactions within Lithium Salt Solvates: Acyclic...

    Office of Scientific and Technical Information (OSTI)

    Structural Interactions within Lithium Salt Solvates: Acyclic Carbonates and Esters Citation Details In-Document Search Title: Structural Interactions within Lithium Salt Solvates: ...

  10. Elementary Particles and Weak Interactions

    DOE R&D Accomplishments [OSTI]

    Lee, T. D.; Yang, C. N.

    1957-01-01

    Some general patterns of interactions between various elementary particles are reviewed and some general questions concerning the symmetry properties of these particles are studied. Topics are included on the theta-tau puzzle, experimental limits on the validity of parity conservation, some general discussions on the consequences due to possible non-invariance under P, C, and T, various possible experimental tests on invariance under P, C, and T, a two-component theory of the neutrino, a possible law of conservation of leptons and the universal Fermi interactions, and time reversal invariance and Mach's principle. (M.H.R.)

  11. Method of making molecularly doped composite polymer material

    DOE Patents [OSTI]

    Affinito, John D. (Tucson, AZ) [Tucson, AZ; Martin, Peter M. (Kennewick, WA) [Kennewick, WA; Graff, Gordon L. (West Richland, WA) [West Richland, WA; Burrows, Paul E. (Kennewick, WA) [Kennewick, WA; Gross, Mark E. (Pasco, WA), Sapochak, Linda S. (Henderson, NV)

    2005-06-21

    A method of making a composite polymer of a molecularly doped polymer. The method includes mixing a liquid polymer precursor with molecular dopant forming a molecularly doped polymer precursor mixture. The molecularly doped polymer precursor mixture is flash evaporated forming a composite vapor. The composite vapor is cryocondensed on a cool substrate forming a composite molecularly doped polymer precursor layer, and the cryocondensed composite molecularly doped polymer precursor layer is cross linked thereby forming a layer of the composite polymer layer of the molecularly doped polymer.

  12. Discovery of a pre-existing molecular filament associated with supernova remnant G127.1+0.5

    SciTech Connect (OSTI)

    Zhou, Xin; Yang, Ji; Fang, Min; Su, Yang

    2014-08-20

    We performed millimeter observations in CO lines toward the supernova remnant (SNR) G127.1+0.5. We found a molecular filament at 4-13 km s{sup –1} consisting of two distinct parts: a straight part coming out of the remnant region and a curved part in the remnant region. The curved part is coincides well with the bright SNR shell detected in 1420 MHz radio continuum and mid-infrared observations in the northeastern region. In addition, redshifted line wing broadening is found only in the curved part of the molecular filament, which indicates a physical interaction. These provide strong evidences, for the first time, to confirm the association between an SNR and a pre-existing long molecular filament. Multi-band observations in the northeastern remnant shell could be explained by the interaction between the remnant shock and the dense molecular filament. RADEX radiative transfer modeling of the quiet and shocked components yield physical conditions consistent with the passage of a non-dissociative J-type shock. We argue that the curved part of the filament is fully engulfed by the remnant's forward shock. A spatial correlation between aggregated young stellar objects (YSOs) and the adjacent molecular filament close to the SNR is also found, which could be related to the progenitor's activity.

  13. Force transduction and lipid binding in MscL: A continuum-molecular approach

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

    Vanegas, Juan M.; Arroyo, Marino; Fotiadis, Dimitrios

    2014-12-01

    The bacterial mechanosensitive channel MscL, a small protein mainly activated by membrane tension, is a central model system to study the transduction of mechanical stimuli into chemical signals. Mutagenic studies suggest that MscL gating strongly depends on both intra-protein and interfacial lipid-protein interactions. However, there is a gap between this detailed chemical information and current mechanical models of MscL gating. Here, we investigate the MscL bilayer-protein interface through molecular dynamics simulations, and take a combined continuum-molecular approach to connect chemistry and mechanics. We quantify the effect of membrane tension on the forces acting on the surface of the channel, andmore » identify interactions that may be critical in the force transduction between the membrane and MscL. We find that the local stress distribution on the protein surface is largely asymmetric, particularly under tension, with the cytoplasmic side showing significantly larger and more localized forces, which pull the protein radially outward. The molecular interactions that mediate this behavior arise from hydrogen bonds between the electronegative oxygens in the lipid headgroup and a cluster of positively charged lysine residues on the amphipathic S1 domain and the C-terminal end of the second trans-membrane helix. We take advantage of this strong interaction (estimated to be 10–13 kT per lipid) to actuate the channel (by applying forces on protein-bound lipids) and explore its sensitivity to the pulling magnitude and direction. We conclude by highlighting the simple motif that confers MscL with strong anchoring to the bilayer, and its presence in various integral membrane proteins including the human mechanosensitive channel K2P1 and bovine rhodopsin.« less

  14. Towards reproducible, scalable lateral molecular electronic devices

    SciTech Connect (OSTI)

    Durkan, Colm Zhang, Qian

    2014-08-25

    An approach to reproducibly fabricate molecular electronic devices is presented. Lateral nanometer-scale gaps with high yield are formed in Au/Pd nanowires by a combination of electromigration and Joule-heating-induced thermomechanical stress. The resulting nanogap devices are used to measure the electrical properties of small numbers of two different molecular species with different end-groups, namely 1,4-butane dithiol and 1,5-diamino-2-methylpentane. Fluctuations in the current reveal that in the case of the dithiol molecule devices, individual molecules conduct intermittently, with the fluctuations becoming more pronounced at larger biases.

  15. PNNL: Center for Molecular Electrocatalysis - Publications

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

    Publications Check out our publications on molecular electrocatalysts 2016 Publications Raugei S, ML Helm, S Hammes-Schiffer, AM Appel, M O'Hagan, ES Wiedner, and RM Bullock. 2016. "Experimental and Computational Mechanistic Studies Guiding the Rational Design of Molecular Electrocatalysts for the Production and Oxidation of Hydrogen." Inorganic Chemistry 55(2):445-460. DOI: 10.1021/acs.inorgchem.5b02262 Wiedner ES, HJS Brown, and ML Helm. 2016. "Kinetic Analysis of Competitive

  16. Molecular-Frame Angular Distributions of Resonant Auger Electrons

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

    Molecular-Frame Angular Distributions of Resonant Auger Electrons Molecular-Frame Angular Distributions of Resonant Auger Electrons Print Wednesday, 27 May 2009 00:00 Molecular-frame electron angular distribution (MFAD) measurements provide access to an unprecedented level of detailed information about phenomena involving quantum coherence, such as phases of photoelectron waves, symmetry breaking in molecular dissociation, core-hole localization in molecules, and molecular double-slit

  17. Grid Interaction Technical Team Roadmap

    SciTech Connect (OSTI)

    2013-06-01

    The mission of the Grid Interaction Technical Team (GITT) is to support a transition scenario to large scale grid-connected vehicle charging with transformational technology, proof of concept and information dissemination. The GITT facilitates technical coordination and collaboration between vehicle-grid connectivity and communication activities among U.S. DRIVE government and industry partners.

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

    SciTech Connect (OSTI)

    Dixon, David Adams

    2013-06-27

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

  19. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    SciTech Connect (OSTI)

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  20. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

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

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

  1. Molecular sieving silica membrane fabrication process

    DOE Patents [OSTI]

    Raman, Narayan K. (400 Maple St. SE., Apartment 112, Albuquerque, NM 87106); Brinker, Charles Jeffrey (14 Eagle Nest Dr., NE., Albuquerque, NM 87122)

    1998-01-01

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

  2. Berkeley Lab Scientists Create Molecular Paper

    SciTech Connect (OSTI)

    2010-01-01

    These fluorescence microscope images show free-floating peptoid nanosheets in liquid. Each peptoid sheet is just two molecules thick yet up to hundreds of square micrometers in area—a molecular paper large enough to be visible to the naked eye.

  3. Geochemical Reaction Mechanism Discovery from Molecular Simulation

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

    Stack, Andrew G.; Kent, Paul R. C.

    2014-11-10

    Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

  4. Molecular sieving silica membrane fabrication process

    DOE Patents [OSTI]

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

    1999-08-10

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

  5. Molecular sieving silica membrane fabrication process

    DOE Patents [OSTI]

    Raman, Narayan K. (Monroeville, PA); Brinker, Charles Jeffrey (Albuquerque, NM)

    1999-01-01

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

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

    SciTech Connect (OSTI)

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

    2011-12-31

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

  7. Surprising Quasiparticle Interactions in Graphene

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

    Surprising Quasiparticle Interactions in Graphene Print Until now, the world's electronics have been dominated by silicon, whose properties, while excellent, significantly limit the size and power consumption of today's computer chips. In order to develop ever smaller and more efficient devices, scientists have turned their attention to carbon, which can be formed into nanostructures like nanotubes, whose properties can be tuned from metallic to semiconducting. However, using carbon nanotubes

  8. Strongly interacting parton matter equilibration

    SciTech Connect (OSTI)

    Ozvenchuk, V.; Linnyk, O.; Bratkovskaya, E.; Gorenstein, M.; Cassing, W.

    2012-07-15

    We study the kinetic and chemical equilibration in 'infinite' parton matter within the Parton-Hadron-String Dynamics transport approach. The 'infinite' matter is simulated within a cubic box with periodic boundary conditions initialized at different energy densities. Particle abundances, kinetic energy distributions, and the detailed balance of the off-shell quarks and gluons in the strongly-interacting quarkgluon plasma are addressed and discussed.

  9. Surprising Quasiparticle Interactions in Graphene

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

    Surprising Quasiparticle Interactions in Graphene Print Until now, the world's electronics have been dominated by silicon, whose properties, while excellent, significantly limit the size and power consumption of today's computer chips. In order to develop ever smaller and more efficient devices, scientists have turned their attention to carbon, which can be formed into nanostructures like nanotubes, whose properties can be tuned from metallic to semiconducting. However, using carbon nanotubes

  10. Surprising Quasiparticle Interactions in Graphene

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

    Surprising Quasiparticle Interactions in Graphene Print Until now, the world's electronics have been dominated by silicon, whose properties, while excellent, significantly limit the size and power consumption of today's computer chips. In order to develop ever smaller and more efficient devices, scientists have turned their attention to carbon, which can be formed into nanostructures like nanotubes, whose properties can be tuned from metallic to semiconducting. However, using carbon nanotubes

  11. Surprising Quasiparticle Interactions in Graphene

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

    Surprising Quasiparticle Interactions in Graphene Print Until now, the world's electronics have been dominated by silicon, whose properties, while excellent, significantly limit the size and power consumption of today's computer chips. In order to develop ever smaller and more efficient devices, scientists have turned their attention to carbon, which can be formed into nanostructures like nanotubes, whose properties can be tuned from metallic to semiconducting. However, using carbon nanotubes

  12. Surprising Quasiparticle Interactions in Graphene

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

    Surprising Quasiparticle Interactions in Graphene Print Until now, the world's electronics have been dominated by silicon, whose properties, while excellent, significantly limit the size and power consumption of today's computer chips. In order to develop ever smaller and more efficient devices, scientists have turned their attention to carbon, which can be formed into nanostructures like nanotubes, whose properties can be tuned from metallic to semiconducting. However, using carbon nanotubes

  13. Simulating Turbine-Turbine Interaction

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

    Turbine-Turbine Interaction - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us Employee Locator Energy & Climate Secure & Sustainable Energy Future Stationary Power Energy Conversion Efficiency Solar Energy Wind Energy Water Power Supercritical CO2 Geothermal Natural Gas Safety, Security & Resilience of the Energy Infrastructure Energy Storage Nuclear Power & Engineering Grid Modernization Battery Testing Nuclear Fuel Cycle Defense Waste Management Programs

  14. Designing π-stacked molecular structures to control heat transport through molecular junctions

    SciTech Connect (OSTI)

    Kiršanskas, Gediminas; Li, Qian; Solomon, Gemma C.; Flensberg, Karsten; Leijnse, Martin

    2014-12-08

    We propose and analyze a way of using π stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.

  15. Probing Adsorption Interactions In Metal-Organic Framework Using X-ray

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

    Spectroscopy | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Probing Adsorption Interactions In Metal-Organic Framework Using X-ray Spectroscopy Previous Next List Walter S. Drisdell, Roberta Poloni, Thomas M. McDonald, Jeffrey R. Long, Berend Smit, Jeffrey B. Neaton, David Prendergast, Jeffrey B. Kortright, J. Am. Chem. Soc., 135, 18183-18190 (2013) DOI: 10.1021/ja408972f Abstract: We explore the local electronic signatures of molecular adsorption at

  16. Weak interactions at the SSC

    SciTech Connect (OSTI)

    Chanowitz, M.S.

    1986-03-01

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

  17. A coarse-grained model for the simulations of biomolecular interactions in cellular environments

    SciTech Connect (OSTI)

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

    2014-02-07

    The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments.

  18. Growth of bi- and tri-layered graphene on silicon carbide substrate via molecular dynamics simulation

    SciTech Connect (OSTI)

    Min, Tjun Kit; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    Molecular dynamics (MD) simulation with simulated annealing method is used to study the growth process of bi- and tri-layered graphene on a 6H-SiC (0001) substrate via molecular dynamics simulation. Tersoff-Albe-Erhart (TEA) potential is used to describe the inter-atomic interactions among the atoms in the system. The formation temperature, averaged carbon-carbon bond length, pair correlation function, binding energy and the distance between the graphene formed and the SiC substrate are quantified. The growth mechanism, graphitization of graphene on the SiC substrate and characteristics of the surface morphology of the graphene sheet obtained in our MD simulation compare well to that observed in epitaxially grown graphene experiments and other simulation works.

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

    SciTech Connect (OSTI)

    Hummer, G.

    1999-07-07

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

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

    SciTech Connect (OSTI)

    Wang, Yusu

    2013-03-25

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

  1. Dense molecular clumps associated with the Large Magellanic Cloud supergiant shells LMC 4 and LMC 5

    SciTech Connect (OSTI)

    Fujii, Kosuke; Mizuno, Norikazu [Department of Astronomy, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 133-0033 (Japan); Minamidani, Tetsuhiro [Nobeyama Radio Observatory, 462-2 Nobeyama Minamimaki-mura, Minamisaku-gun, Nagano 384-1305 (Japan); Onishi, Toshikazu; Muraoka, Kazuyuki [Department of Physical Science, Osaka Prefecture University, Gakuen 1-1, Sakai, Osaka 599-8531 (Japan); Kawamura, Akiko; Muller, Erik; Tatematsu, Ken'ichi; Hasegawa, Tetsuo; Miura, Rie E.; Ezawa, Hajime [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Dawson, Joanne [Australia Telescope National Facility, CSIRO Astronomy and Space Science, P.O. Box 76, Epping, NSW 1710 (Australia); Tosaki, Tomoka [Joetsu University of Education, Yamayashiki-machi, Joetsu, Niigata 943-8512 (Japan); Sakai, Takeshi [Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585 (Japan); Tsukagoshi, Takashi [College of Science, Ibaraki University, Bunkyo 2-1-1, Mito 310-8512 (Japan); Tanaka, Kunihiko [Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Yokohama, Kanagawa 223-8522 (Japan); Fukui, Yasuo, E-mail: kosuke.fujii@nao.ac.jp [Department of Astrophysics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

    2014-12-01

    We investigate the effects of supergiant shells (SGSs) and their interaction on dense molecular clumps by observing the Large Magellanic Cloud (LMC) star-forming regions N48 and N49, which are located between two SGSs, LMC 4 and LMC 5. {sup 12}CO (J = 3-2, 1-0) and {sup 13}CO(J = 1-0) observations with the ASTE and Mopra telescopes have been carried out toward these regions. A clumpy distribution of dense molecular clumps is revealed with 7 pc spatial resolution. Large velocity gradient analysis shows that the molecular hydrogen densities (n(H{sub 2})) of the clumps are distributed from low to high density (10{sup 3}-10{sup 5} cm{sup –3}) and their kinetic temperatures (T {sub kin}) are typically high (greater than 50 K). These clumps seem to be in the early stages of star formation, as also indicated from the distribution of H?, young stellar object candidates, and IR emission. We found that the N48 region is located in the high column density H I envelope at the interface of the two SGSs and the star formation is relatively evolved, whereas the N49 region is associated with LMC 5 alone and the star formation is quiet. The clumps in the N48 region typically show high n(H{sub 2}) and T {sub kin}, which are as dense and warm as the clumps in LMC massive cluster-forming areas (30 Dor, N159). These results suggest that the large-scale structure of the SGSs, especially the interaction of two SGSs, works efficiently on the formation of dense molecular clumps and stars.

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

    SciTech Connect (OSTI)

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

    2014-10-28

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

  3. Interaction of water with epoxy.

    SciTech Connect (OSTI)

    Powers, Dana Auburn

    2009-07-01

    The chemistries of reactants, plasticizers, solvents and additives in an epoxy paint are discussed. Polyamide additives may play an important role in the absorption of molecular iodine by epoxy paints. It is recommended that the unsaturation of the polyamide additive in the epoxy cure be determined. Experimental studies of water absorption by epoxy resins are discussed. These studies show that absorption can disrupt hydrogen bonds among segments of the polymers and cause swelling of the polymer. The water absorption increases the diffusion coefficient of water within the polymer. Permanent damage to the polymer can result if water causes hydrolysis of ether linkages. Water desorption studies are recommended to ascertain how water absorption affects epoxy paint.

  4. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect (OSTI)

    Nesbitt, David J.

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor Yuan T. Lee & Professor George Schatz. Professor Lee’s research has been based on the development & use of advanced chemical kinetics & molecular beams to investigate & manipulate the behavior of fundamental chemical reactions. Lee’s work has been recognized by many awards, including the Nobel Prize for Chemistry in 1986, as well as Sloan Fellow, Dreyfus Scholar, Fellowship in the American Academy of Arts & Sciences, Fellowship in the American Physical Society, Guggenheim Fellow, Member National Academy of Sciences, Member Academia Sinica, E.O. Lawrence Award, Miller Professor, Berkeley, Fairchild Distinguished Scholar, Harrison Howe Award, Peter Debye Award, & the National Medal of Science. Lee also has served as the President of the Academia Sinica in Taiwan (ROC). Professor Schatz’s research group is interested in using theory & computation to describe physical phenomena in a broad range of applications relevant to chemistry, physics, biology & engineering. Among the types of applications that we interested are: optical properties of nanoparticles & nanoparticle assemblies; using theory to model polymer properties; DNA structure, thermodynamics & dynamics; modeling self assembly & nanopatterning; & gas phase reaction dynamics. Among his many awards & distinctions have been appointment as an Alfred P. Sloan Research Fellow, Camille & Henry Dreyfus Teacher-Scholar, the Fresenius Award, Fellow of the American Physical Society, the Max Planck Research Award, Fellowship in the American Association for the Advancement of Science, & election to the International Academy of Quantum Molecular Sciences & the American Academy of Arts & Sciences. Dr Schatz is also lauded for his highly successful work as Editor for the Journal of Physical Chemistry. We requested $10,000 from DOE in support of this meeting. The money was distributed widely among the student & post doctoral fellows & some used to attract the very best scientists in the field. The organizers were committed to encouraging women & minorities as well as encourage the field of Chemical Physics in scientific

  5. Institute for Molecular Medicine Research Program

    SciTech Connect (OSTI)

    Phelps, Michael E

    2012-12-14

    The objectives of the project are the development of new Positron Emission Tomography (PET) imaging instrumentation, chemistry technology platforms and new molecular imaging probes to examine the transformations from normal cellular and biological processes to those of disease in pre-clinical animal models. These technology platforms and imaging probes provide the means to: 1. Study the biology of disease using pre-clinical mouse models and cells. 2. Develop molecular imaging probes for imaging assays of proteins in pre-clinical models. 3. Develop imaging assays in pre-clinical models to provide to other scientists the means to guide and improve the processes for discovering new drugs. 4. Develop imaging assays in pre-clinical models for others to use in judging the impact of drugs on the biology of disease.

  6. Counting molecular-beam grown graphene layers

    SciTech Connect (OSTI)

    Plaut, Annette S.; Wurstbauer, Ulrich; Pinczuk, Aron; Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027 ; Garcia, Jorge M.; Pfeiffer, Loren N.

    2013-06-17

    We have used the ratio of the integrated intensity of graphene's Raman G peak to that of the silicon substrate's first-order optical phonon peak, accurately to determine the number of graphene layers across our molecular-beam (MB) grown graphene films. We find that these results agree well both, with those from our own exfoliated single and few-layer graphene flakes, and with the results of Koh et al.[ACS Nano 5, 269 (2011)]. We hence distinguish regions of single-, bi-, tri-, four-layer, etc., graphene, consecutively, as we scan coarsely across our MB-grown graphene. This is the first, but crucial, step to being able to grow, by such molecular-beam-techniques, a specified number of large-area graphene layers, to order.

  7. Self-doped molecular composite battery electrolytes

    DOE Patents [OSTI]

    Harrup, Mason K.; Wertsching, Alan K.; Stewart, Frederick F.

    2003-04-08

    This invention is in solid polymer-based electrolytes for battery applications. It uses molecular composite technology, coupled with unique preparation techniques to render a self-doped, stabilized electrolyte material suitable for inclusion in both primary and secondary batteries. In particular, a salt is incorporated in a nano-composite material formed by the in situ catalyzed condensation of a ceramic precursor in the presence of a solvated polymer material, utilizing a condensation agent comprised of at least one cation amenable to SPE applications. As such, the counterion in the condensation agent used in the formation of the molecular composite is already present as the electrolyte matrix develops. This procedure effectively decouples the cation loading levels required for maximum ionic conductivity from electrolyte physical properties associated with condensation agent loading levels by utilizing the inverse relationship discovered between condensation agent loading and the time domain of the aging step.

  8. Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach

    SciTech Connect (OSTI)

    Hyeon-Deuk, Kim; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 ; Ando, Koji

    2014-05-07

    Liquid para-hydrogen (p-H{sub 2}) is a typical quantum liquid which exhibits strong nuclear quantum effects (NQEs) and thus anomalous static and dynamic properties. We propose a real-time simulation method of wave packet (WP) molecular dynamics (MD) based on non-empirical intra- and inter-molecular interactions of non-spherical hydrogen molecules, and apply it to condensed-phase p-H{sub 2}. The NQEs, such as WP delocalization and zero-point energy, are taken into account without perturbative expansion of prepared model potential functions but with explicit interactions between nuclear and electron WPs. The developed MD simulation for 100 ps with 1200 hydrogen molecules is realized at feasible computational cost, by which basic experimental properties of p-H{sub 2} liquid such as radial distribution functions, self-diffusion coefficients, and shear viscosities are all well reproduced.

  9. Frontiers of NMR in Molecular Biology

    SciTech Connect (OSTI)

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  10. Sandia Pursues Biotechnology Molecular Integrated Microsystems

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

    Pursues Biotechnology Molecular Integrated Microsystems Powering Devices from Living Systems A QUARTERLY RESEARCH & DEVELOPMENT JOURNAL VOLUME 4, NO. 4 S A N D I A T E C H N O L O G Y Sandia Technology is a quarterly journal published by Sandia National Laboratories. Sandia is a multiprogram engineering and science laboratory operated by Sandia Corporation, a Lockheed Martin company, for the Department of Energy. With main facilities in Albuquerque, New Mexico, and Livermore, California,

  11. PNNL: Center for Molecular Electrocatalysis - Research Team

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

    Research Team Morris Bullock Morris Bullock Director Aaron Appel Aaron Appel Deputy Director Dan DuBois Dan DuBois Scientific Advisor Monte L. Helm Monte L. Helm Mike Mock Mike Mock Molly O'Hagan Molly O'Hagan Simone Raugei Simone Raugei Eric Wiedner Eric Wiedner Collaborators Sharon Hammes-Schiffer Sharon Hammes-Schiffer University of Illinois Jim Mayer Jim Mayer Yale University Shannon Stahl Shannon Stahl University of Wisconsin - Madison Center for Molecular Electrocatalysis Home Scientific

  12. Molecular Mechanism of Biological Proton Transport

    SciTech Connect (OSTI)

    Pomes, R.

    1998-09-01

    Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

  13. Nanoscale molecularly imprinted polymers and method thereof

    DOE Patents [OSTI]

    Hart, Bradley R. (Brentwood, CA); Talley, Chad E. (Brentwood, CA)

    2008-06-10

    Nanoscale molecularly imprinted polymers (MIP) having polymer features wherein the size, shape and position are predetermined can be fabricated using an xy piezo stage mounted on an inverted microscope and a laser. Using an AMF controller, a solution containing polymer precursors and a photo initiator are positioned on the xy piezo and hit with a laser beam. The thickness of the polymeric features can be varied from a few nanometers to over a micron.

  14. Molecular Science Research Center 1992 annual report

    SciTech Connect (OSTI)

    Knotek, M.L.

    1994-01-01

    The Molecular Science Research Center is a designated national user facility, available to scientists from universities, industry, and other national laboratories. After an opening section, which includes conferences hosted, appointments, and projects, this document presents progress in the following fields: chemical structure and dynamics; environmental dynamics and simulation; macromolecular structure and dynamics; materials and interfaces; theory, modeling, and simulation; and computing and information sciences. Appendices are included: MSRC staff and associates, 1992 publications and presentations, activities, and acronyms and abbreviations.

  15. Molecular Structure of Water at Gold Electrodes Revealed

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

    Molecular Structure of Water at Gold Electrodes Revealed Molecular Structure of Water at Gold Electrodes Revealed Print Wednesday, 25 March 2015 00:00 The structure of liquid water...

  16. The Molecular Ingenuity of a Unique Fish Scale

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

    The Molecular Ingenuity of a Unique Fish Scale The Molecular Ingenuity of a Unique Fish Scale Print Monday, 25 November 2013 12:06 Arapaima gigas, a freshwater fish found in the...

  17. Probing Core-Hole Localization in Molecular Nitrogen

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

    Probing Core-Hole Localization in Molecular Nitrogen Probing Core-Hole Localization in Molecular Nitrogen Print Wednesday, 25 February 2009 00:00 The behavior of the core hole...

  18. Supercritical fluid molecular spray film deposition and powder formation

    DOE Patents [OSTI]

    Smith, Richard D.

    1986-01-01

    Solid films are deposited, or fine powders formed, by dissolving a solid material into a supercritical fluid solution at an elevated pressure and then rapidly expanding the solution through a short orifice into a region of relatively low pressure. This produces a molecular spray which is directed against a substrate to deposit a solid thin film thereon, or discharged into a collection chamber to collect a fine powder. Upon expansion and supersonic interaction with background gases in the low pressure region, any clusters of solvent are broken up and the solvent is vaporized and pumped away. Solute concentration in the solution is varied primarily by varying solution pressure to determine, together with flow rate, the rate of deposition and to control in part whether a film or powder is produced and the granularity of each. Solvent clustering and solute nucleation are controlled by manipulating the rate of expansion of the solution and the pressure of the lower pressure region. Solution and low pressure region temperatures are also controlled.

  19. T Cell Allorecognition via Molecular Mimicry

    SciTech Connect (OSTI)

    Macdonald, Whitney A.; Chen, Zhenjun; Gras, Stephanie; Archbold, Julia K.; Tynan, Fleur E.; Clements, Craig S.; Bharadwaj, Mandvi; Kjer-Nielsen, Lars; Saunders, Philippa M.; Wilce, Matthew C.J.; Crawford, Fran; Stadinsky, Brian; Jackson, David; Brooks, Andrew G.; Purcell, Anthony W.; Kappler, John W.; Burrows, Scott R.; Rossjohn, Jamie; McCluskey, James

    2010-08-16

    T cells often alloreact with foreign human leukocyte antigens (HLA). Here we showed the LC13 T cell receptor (TCR), selected for recognition on self-HLA-B*0801 bound to a viral peptide, alloreacts with B44 allotypes (HLA-B*4402 and HLA-B*4405) bound to two different allopeptides. Despite extensive polymorphism between HLA-B*0801, HLA-B*4402, and HLA-B*4405 and the disparate sequences of the viral and allopeptides, the LC13 TCR engaged these peptide-HLA (pHLA) complexes identically, accommodating mimicry of the viral peptide by the allopeptide. The viral and allopeptides adopted similar conformations only after TCR ligation, revealing an induced-fit mechanism of molecular mimicry. The LC13 T cells did not alloreact against HLA-B*4403, and the single residue polymorphism between HLA-B*4402 and HLA-B*4403 affected the plasticity of the allopeptide, revealing that molecular mimicry was associated with TCR specificity. Accordingly, molecular mimicry that is HLA and peptide dependent is a mechanism for human T cell alloreactivity between disparate cognate and allogeneic pHLA complexes.

  20. Structural Interactions within Lithium Salt Solvates: Acyclic Carbonates and Esters

    SciTech Connect (OSTI)

    Afroz, Taliman; Seo, D. M.; Han, Sang D.; Boyle, Paul D.; Henderson, Wesley A.

    2015-03-06

    Solvate crystal structures serve as useful models for the molecular-level interactions within the diverse solvates present in liquid electrolytes. Although acyclic carbonate solvents are widely used for Li-ion battery electrolytes, only three solvate crystal structures with lithium salts are known for these and related solvents. The present work, therefore, reports six lithium salt solvate structures with dimethyl and diethyl carbonate: (DMC)2:LiPF6, (DMC)1:LiCF3SO3, (DMC)1/4:LiBF4, (DEC)2:LiClO4, (DEC)1:LiClO4 and (DEC)1:LiCF3SO3 and four with the structurally related methyl and ethyl acetate: (MA)2:LiClO4, (MA)1:LiBF4, (EA)1:LiClO4 and (EA)1:LiBF4.

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

    SciTech Connect (OSTI)

    Lu, Gui; Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104 ; Hu, Han; Sun, Ying E-mail: ysun@coe.drexel.edu; Duan, Yuanyuan E-mail: ysun@coe.drexel.edu

    2013-12-16

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

  2. Molecular-Frame Angular Distributions of Resonant Auger Electrons

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

    Molecular-Frame Angular Distributions of Resonant Auger Electrons Print Molecular-frame electron angular distribution (MFAD) measurements provide access to an unprecedented level of detailed information about phenomena involving quantum coherence, such as phases of photoelectron waves, symmetry breaking in molecular dissociation, core-hole localization in molecules, and molecular double-slit interference, all of which are hidden in conventional gas-phase electron spectroscopy, owing to the

  3. Molecular-Frame Angular Distributions of Resonant Auger Electrons

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

    Molecular-Frame Angular Distributions of Resonant Auger Electrons Print Molecular-frame electron angular distribution (MFAD) measurements provide access to an unprecedented level of detailed information about phenomena involving quantum coherence, such as phases of photoelectron waves, symmetry breaking in molecular dissociation, core-hole localization in molecules, and molecular double-slit interference, all of which are hidden in conventional gas-phase electron spectroscopy, owing to the

  4. Probing Core-Hole Localization in Molecular Nitrogen

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

    Probing Core-Hole Localization in Molecular Nitrogen Probing Core-Hole Localization in Molecular Nitrogen Print Wednesday, 25 February 2009 00:00 The behavior of the core hole created in molecular x-ray photoemission experiments has provided molecular scientists with a valuable window through which to probe the electronic structure and dynamics of molecules. But the answer to one fundamental quantum question-whether the core hole is localized or delocalized-has remained elusive for diatomic

  5. 2010-2011 SECTION IV: ATOMIC, MOLECULAR AND MATERIALS SCIENCE

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

    Kinetic energy release in the dissociations of doubly and triply charged molecular ions V. Horvat and R. L. Watson

  6. PARTICLE ACCELERATORS; 74 ATOMIC AND MOLECULAR PHYSICS; ATOMS...

    Office of Scientific and Technical Information (OSTI)

    74 ATOMIC AND MOLECULAR PHYSICS; ATOMS; ELECTRONS; HELIUM; LIGHT SOURCES; RADIATIONS; STORAGE RINGS; SYNCHROTRONS SYNCHROTRON RADIATION SYNCHROTRONLIGHT SOURCES QUANTUM CHAOS...

  7. Understanding Porosity in Amorphous Porous Molecular Solids | Center for

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

    Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome Understanding Porosity in Amorphous Porous Molecular Solids

  8. Molecular-Frame Angular Distributions of Resonant Auger Electrons

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

    Molecular-Frame Angular Distributions of Resonant Auger Electrons Print Molecular-frame electron angular distribution (MFAD) measurements provide access to an unprecedented level of detailed information about phenomena involving quantum coherence, such as phases of photoelectron waves, symmetry breaking in molecular dissociation, core-hole localization in molecules, and molecular double-slit interference, all of which are hidden in conventional gas-phase electron spectroscopy, owing to the

  9. Molecular-Frame Angular Distributions of Resonant Auger Electrons

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

    Molecular-Frame Angular Distributions of Resonant Auger Electrons Print Molecular-frame electron angular distribution (MFAD) measurements provide access to an unprecedented level of detailed information about phenomena involving quantum coherence, such as phases of photoelectron waves, symmetry breaking in molecular dissociation, core-hole localization in molecules, and molecular double-slit interference, all of which are hidden in conventional gas-phase electron spectroscopy, owing to the

  10. Molecular-Frame Angular Distributions of Resonant Auger Electrons

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

    Molecular-Frame Angular Distributions of Resonant Auger Electrons Print Molecular-frame electron angular distribution (MFAD) measurements provide access to an unprecedented level of detailed information about phenomena involving quantum coherence, such as phases of photoelectron waves, symmetry breaking in molecular dissociation, core-hole localization in molecules, and molecular double-slit interference, all of which are hidden in conventional gas-phase electron spectroscopy, owing to the

  11. Molecular-Frame Angular Distributions of Resonant Auger Electrons

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

    Molecular-Frame Angular Distributions of Resonant Auger Electrons Print Molecular-frame electron angular distribution (MFAD) measurements provide access to an unprecedented level of detailed information about phenomena involving quantum coherence, such as phases of photoelectron waves, symmetry breaking in molecular dissociation, core-hole localization in molecules, and molecular double-slit interference, all of which are hidden in conventional gas-phase electron spectroscopy, owing to the

  12. PIA - Environmental Molecular Sciences Laboratory (EMSL) User System (ESU)

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

    | Department of Energy Molecular Sciences Laboratory (EMSL) User System (ESU) PIA - Environmental Molecular Sciences Laboratory (EMSL) User System (ESU) PIA - Environmental Molecular Sciences Laboratory (EMSL) User System (ESU) PDF icon PIA - Environmental Molecular Sciences Laboratory (EMSL) User System (ESU) More Documents & Publications PIA - WEB iPASS System DOE PIA Integrated Safety Management Workshop Registration, PIA, Idaho National Laboratory PIA - Advanced Test Reactor National

  13. Supporting collaborative computing and interaction

    SciTech Connect (OSTI)

    Agarwal, Deborah; McParland, Charles; Perry, Marcia

    2002-05-22

    To enable collaboration on the daily tasks involved in scientific research, collaborative frameworks should provide lightweight and ubiquitous components that support a wide variety of interaction modes. We envision a collaborative environment as one that provides a persistent space within which participants can locate each other, exchange synchronous and asynchronous messages, share documents and applications, share workflow, and hold videoconferences. We are developing the Pervasive Collaborative Computing Environment (PCCE) as such an environment. The PCCE will provide integrated tools to support shared computing and task control and monitoring. This paper describes the PCCE and the rationale for its design.

  14. The Determination of Molecular Structure from Rotational Spectra

    DOE R&D Accomplishments [OSTI]

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  15. Compact submanifolds supporting singular interactions

    SciTech Connect (OSTI)

    Kaynak, Burak Tevfik Teoman Turgut, O.

    2013-12-15

    A quantum particle moving under the influence of singular interactions on embedded surfaces furnish an interesting example from the spectral point of view. In these problems, the possible occurrence of a bound-state is perhaps the most important aspect. Such systems can be introduced as quadratic forms and generically they do not require renormalization. Yet an alternative path through the resolvent is also beneficial to study various properties. In the present work, we address these issues for compact surfaces embedded in a class of ambient manifolds. We discover that there is an exact bound state solution written in terms of the heat kernel of the ambient manifold for a range of coupling strengths. Moreover, we develop techniques to estimate bounds on the ground state energy when several surfaces, each of which admits a bound state solution, coexist. -- Highlights: •Schrödinger operator with singular interactions supported on compact submanifolds. •Exact bound-state solution in terms of the heat kernel of the ambient manifold. •Generalization of the variational approach to a collection of submanifolds. •Existence of a lower bound for a unique ground state energy.

  16. Molecular-level Design of Heterogeneous Chiral Catalysts

    SciTech Connect (OSTI)

    Gellman, Andrew John; Sholl, David S.; Tysoe, Wilfred T.; Zaera, Francisco

    2013-04-28

    Understanding and controlling selectivity is one of the key challenges in heterogeneous catalysis. Among problems in catalytic selectivity enantioselectivity is perhaps the most the most challenging. The primary goal of the project on “Molecular-level Design of Heterogeneous Chiral Catalysts” is to understand the origins of enantioselectivity on chiral heterogeneous surfaces and catalysts. The efforts of the project team include preparation of chiral surfaces, characterization of chiral surfaces, experimental detection of enantioselectivity on such surfaces and computational modeling of the interactions of chiral probe molecules with chiral surfaces. Over the course of the project period the team of PI’s has made some of the most detailed and insightful studies of enantioselective chemistry on chiral surfaces. This includes the measurement of fundamental interactions and reaction mechanisms of chiral molecules on chiral surfaces and leads all the way to rationale design and synthesis of chiral surfaces and materials for enantioselective surface chemistry. The PI’s have designed and prepared new materials for enantioselective adsorption and catalysis. Naturally Chiral Surfaces • Completion of a systematic study of the enantiospecific desorption kinetics of R-3-methylcyclohexanone (R-3-MCHO) on 9 achiral and 7 enantiomeric pairs of chiral Cu surfaces with orientations that span the stereographic triangle. • Discovery of super-enantioselective tartaric acid (TA) and aspartic acid (Asp) decomposition as a result of a surface explosion mechanism on Cu(643)R&S. Systematic study of super-enantiospecific TA and Asp decomposition on five enantiomeric pairs of chiral Cu surfaces. • Initial observation of the enantiospecific desorption of R- and S-propylene oxide (PO) from Cu(100) imprinted with {3,1,17} facets by L-lysine adsorption. Templated Chiral Surfaces • Initial observation of the enantiospecific desorption of R- and S-PO from Pt(111) and Pd(111) modified by a variety of chiral templates. • Demonstrated enantioselective separation of racemic PO on chemically synthesized chiral gold nanoparticles. • Discovery of zwitterionic adsorption states of amino acids on Pd(111). • First structure determinations of adsorbed amino acids and identification of tetrameric chiral template structures. • Exploration of the enantiospecific interaction of PO and R-3-MCHO adsorption on chirally modified Cu(100), Cu(110) and Cu(111). One-to-One Interactions • Determination of cinchona orientation on Pt surfaces in situ at the solid-liquid interface using FT-IRAS. • Systematic study of the influence of solution properties on the adsorption of modified cinchonas alkaloids onto Pt surfaces. • Correlation of cinchona adsorption with catalytic activity, as affected by concentration, the nature of the solvent, and dissolved gases in the liquid phase. • Measurement of enantioselective chemisorption on 1-(1-naphthyl) ethylamine (NEA) modified Pt(111) and Pd(111) surfaces. • Imaging of chiral docking complexes between NEA and methyl pyruvate on Pd(111). Chiral Catalyst Synthesis • Anchoring of cinchona alkaloid to surfaces • Synthesis of chiral Au nanoparticles and demonstration of their enantiospecific interactions with R- and S-PO. • Elucidation of the driving forces for chiral imprinting of Cu(100) by L- and D-lysine to form Cu(3,1,17)R&S facets.

  17. Dynamical Study of Guest-Host Orientational Interaction in LiquidCrystalline Materials

    SciTech Connect (OSTI)

    Truong, Thai Viet

    2005-12-20

    Guest-host interaction has long been a subject of interest in many disciplines. Emphasis is often on how a small amount of guest substance could significantly affect the properties of a host material. This thesis describe our work in studying a guest-host effect where dye-doping of liquid crystalline materials greatly enhances the optical Kerr nonlinearity of the material. The dye molecules, upon excitation and via intermolecular interaction, provides an extra torque to reorient the host molecules, leading to the enhanced optical Kerr nonlinearity. We carried out a comprehensive study on the dynamics of the photoexcited dye-doped liquid crystalline medium. Using various experimental techniques, we separately characterized the dynamical responses of the relevant molecular species present in the medium following photo-excitation, and thus were able to follow the transient process in which photo-excitation of the dye molecules exert through guest-host interaction a net torque on the host LC material, leading to the observed enhanced molecular reorientation. We also observed for the first time the enhanced reorientation in a pure liquid crystal system, where the guest population is created through photoexcitation of the host molecules themselves. Experimental results agree quantitatively with the time-dependent theory based on a mean-field model of the guest-host interaction.

  18. Ocean current wave interaction study

    SciTech Connect (OSTI)

    Hayes, J.G.

    1980-09-20

    A numerical model has been developed to incorporate refraction of ocean surface gravity waves by major ocean currents. The model is initialized with directional wave spectra and verified with aircraft synthetic aperture radar X band spectra, laser profilometer spectra, and pitch and roll buoy data. Data collected during the Marineland test experiment are used as surface truth observations for the wave-current study. Evidence of Gulf Stream refraction and trapping of surface waves as well as caustics in the current is shown and modeled assuming a nonuniform Gulf Stream distribution. Frequency and directional resolution of the wave spectral distribution and the current refraction patterns illustrates the need for further study of ocean current-wave interaction in wave refraction studies.

  19. Development of Molecular Electrocatalysts for Energy Storage

    SciTech Connect (OSTI)

    DuBois, Daniel L.

    2014-02-20

    Molecular electrocatalysts can play an important role in energy storage and utilization reactions needed for intermittent renewable energy sources. This manuscript describes three general themes that our laboratories have found useful in the development of molecular electrocatalysts for reduction of CO2 to CO and for H2 oxidation and production. The first theme involves a conceptual partitioning of catalysts into first, second, and outer coordination spheres. This is illustrated with the design of electrocatalysts for CO2 reduction to CO using first and second coordination spheres and for H2 production catalysts using all three coordination spheres. The second theme focuses on the development of thermodynamic models that can be used to design catalysts to avoid high energy and low energy intermediates. In this research, new approaches to the measurement of thermodynamic hydride donor and acceptor abilities of transition metal complexes were developed. Combining this information with other thermodynamic information such as pKa values and redox potentials led to more complete thermodynamic descriptions of transition metal hydride, dihydride, and related species. Relationships extracted from this information were then used to develop models that are powerful tools for predicting and understanding the relative free energies of intermediates in catalytic reactions. The third theme is the control of proton movement during electrochemical fuel generation and utilization reactions. This research involves the incorporation of pendant amines in the second coordination sphere that can facilitate H-H bond heterolysis and heteroformation, intramolecular and intermolecular proton transfer steps, and the coupling of proton and electron transfer steps. Studies also indicate an important role for outer coordination sphere in the delivery of protons to the second coordination sphere. Understanding these proton transfer reactions and their associated energy barriers are key to the design of faster and more efficient molecular electrocatalysts for energy storage. Funding for the research described in this manuscript was provided as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center supported by the U.S. Department of Energy, Office of Science and through individual grants from the Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Biosciences, and Geosciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  20. SECTION IV. ATOMIC AND MOLECULAR SCIENCE

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

    IV. ATOMIC AND MOLECULAR SCIENCE Cross Sections for Cu K-Vacancy Production in Fast Heavy Ion Collisions R.L. Watson, J.M. Blackadar and V. Horvat Enhancement of the Cu Kα x-ray Diagram Lines in Fast Heavy Ion Collisions R.L. Watson, V. Horvat and J.M. Blackadar K-shell Ionization by Secondary Electrons V. Horvat, R.L. Watson and J.M. Blackadar Target-atom Inner-shell Vacancy Distributions Created in Collisions with Heavy Ion Projectiles V. Horvat, R.L. Watson and J.M. Blackadar Systematics of

  1. Phonon interference effects in molecular junctions

    SciTech Connect (OSTI)

    Markussen, Troels

    2013-12-28

    We study coherent phonon transport through organic, ?-conjugated molecules. Using first principles calculations and Green's function methods, we find that the phonon transmission function in cross-conjugated molecules, like meta-connected benzene, exhibits destructive quantum interference features very analogous to those observed theoretically and experimentally for electron transport in similar molecules. The destructive interference features observed in four different cross-conjugated molecules significantly reduce the thermal conductance with respect to linear conjugated analogues. Such control of the thermal conductance by chemical modifications could be important for thermoelectric applications of molecular junctions.

  2. Environmental Molecular Sciences Laboratory 2004 Annual Report

    SciTech Connect (OSTI)

    White, Julia C.

    2005-04-17

    This 2004 Annual Report describes the research and accomplishments of staff and users of the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL), located in Richland, Washington. EMSL is a multidisciplinary, national scientific user facility and research organization, operated by Pacific Northwest National Laboratory (PNNL) for the U.S. Department of Energy's Office of Biological and Environmental Research. The resources and opportunities within the facility are an outgrowth of the U.S. Department of Energy's (DOE) commitment to fundamental research for understanding and resolving environmental and other critical scientific issues.

  3. Stressor Interactions in Ecological Systems

    SciTech Connect (OSTI)

    Clements, Will; Luoma, Samuel N.; Gerritsen, Jeroen; Hatch, Audrey; Jepson, Paul; Reynoldson, Trefor; Thom, Ronald M.

    2001-12-03

    Here we ask what types of field studies can best detect interactions among stressors and allow us to separate and rank the relative importance of individual stressors in systems receiving multiple disturbances (natural and/or anthropogenic). If multiple stressor responses are common in nature, then single variable tests, such as analysis of a biomarker in isolation or along a surmised gradient, or studies that exclude variables other than pollutants, could be insensitive to all but the most extreme influences of contamination. Preponderance of evidence approaches will be similarly insensitive if designs are too simplistic. A combination of persistent and intensive study of exposure and response in the field, study of critical ecosystem-specific and organism-specific processes, as well as iteration with experimental studies, are useful (and perhaps necessary) strategies to discern interactions among stressors. As our understanding of the mechanisms responsible for changes at lower levels of organization improves, responses to complex stressors become more predictable. This improved mechanistic understanding could lead to a similar degree of understanding for responses at higher levels of biological organization. Below we discuss three examples where researchers have attempted to identify and quantify the relative importance of individual stressors in systems receiving complex stressors. The first example demonstrates how intensive field studies identified multiple stressors and how a management plan resulted in mitigation of these stressors. The second example describes a series of field experiments designed to identify the relative importance of water quality and substrate quality on benthic macroinvertebrates in a metal-polluted stream. The final example illustrates the difficulty of sorting out the direct and indirect influences of global climate change on populations.

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

    SciTech Connect (OSTI)

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

    2015-01-01

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

  5. Molecular Aspects of Transport in Thin Films of Controlled Architecture

    SciTech Connect (OSTI)

    Paul W. Bohn

    2009-04-16

    Our laboratory focuses on developing spatially localized chemistries which can produce structures of controlled architecture on the supermolecular length scale -- structures which allow us to control the motion of molecular species with high spatial resolution, ultimately on nanometer length scales. Specifically, nanocapillary array membranes (NCAMs) contain an array of nanometer diameter pores connecting vertically separated microfluidic channels. NCAMs can manipulate samples with sub-femtoliter characteristic volumes and attomole sample amounts and are opening the field of chemical analysis of mass-limited samples, because they are capable of digital control of fluid switching down to sub-attoliter volumes; extension of analytical “unit operations” down to sub-femtomole sample sizes; and exerting spatiotemporal control over fluid mixing to enable studies of reaction dynamics. Digital flow switching mediated by nanocapillary array membranes can be controlled by bias, ionic strength, or pore diameter and is being studied by observing the temporal characteristics of transport across a single nanopore in thin PMMA membranes. The control of flow via nanopore surface characteristics, charge density and functional group presentation, is being studied by coupled conductivity and laser-induced fluorescence (LIF) measurements. Reactive mixing experiments previously established low millisecond mixing times for NCAM-mediated fluid transfer, and this has been exploited to demonstrate capture of mass-limited target species by Au colloids. Voltage and thermally-activated polymer switches have been developed for active control of transport in NCAMs. Thermally-switchable and size-selective transport was achieved by grafting poly(N-isopropylacrylamide) brushes onto the exterior surface of a Au-coated polycarbonate track-etched membrane, while the voltage-gated properties of poly(hydroxyethylmethacrylate) were characterized dynamically. Electrophoretic separations have been coupled to analyte sampling both by LIF and mass spectrometry. Detection of electrophoresis separation products by electrospray mass spectrometry was achieved through direct interfacing to an electrospray mass spectrometer. Pb(II) interactions with the DNAzyme have been realized in an NCAM-coupled integrated microfluidic structure allowing cation separations to be coupled to molecular beacon detection motifs for the determination of Pb(II) in an electroplating sludge reference material. By changing the DNAzyme to select for other compounds of interest, it is possible to incorporate multiple sensing systems within a single device, thereby achieving great flexibility.

  6. Directed nanoscale self-assembly of molecular wires interconnecting nodal points using Monte Carlo simulations

    SciTech Connect (OSTI)

    Boscoboinik, A. M.; Manzi, S. J.; Tysoe, W. T.; Pereyra, V. D.; Boscoboinik, J. A.

    2015-09-10

    The influence of directing agents in the self-assembly of molecular wires to produce two-dimensional electronic nanoarchitectures is studied here using a Monte Carlo approach to simulate the effect of arbitrarily locating nodal points on a surface, from which the growth of self-assembled molecular wires can be nucleated. This is compared to experimental results reported for the self-assembly of molecular wires when 1,4-phenylenediisocyanide (PDI) is adsorbed on Au(111). The latter results in the formation of (Au-PDI)n organometallic chains, which were shown to be conductive when linked between gold nanoparticles on an insulating substrate. The present study analyzes, by means of stochastic methods, the influence of variables that affect the growth and design of self-assembled conductive nanoarchitectures, such as the distance between nodes, coverage of the monomeric units that leads to the formation of the desired architectures, and the interaction between the monomeric units. As a result, this study proposes an approach and sets the stage for the production of complex 2D nanoarchitectures using a bottom-up strategy but including the use of current state-of-the-art top-down technology as an integral part of the self-assembly strategy.

  7. Computational Molecular Simulation of the Oxidative Adsorption of Ferrous Iron at the Hematite (001)-Water Interface

    SciTech Connect (OSTI)

    Kerisit, Sebastien N.; Zarzycki, Piotr P.; Rosso, Kevin M.

    2015-04-30

    The interaction of Fe(II) with ferric oxide/oxyhydroxide phases is central to the biogeochemical redox chemistry of iron. Molecular simulation techniques were employed to determine the mechanisms and quantify the rates of Fe(II) oxidative adsorption at the hematite (001)-water interface. Molecular dynamics potential of mean force calculations of Fe(II) adsorbing on the hematite surface revealed the presence of three free energy minima corresponding to Fe(II) adsorbed in an outersphere complex, a monodentate innersphere complex, and a tridentate innersphere complex. The free energy barrier for adsorption from the outersphere position to the monodentate innersphere site was calculated to be similar to the activation enthalpy for water exchange around aqueous Fe(II). Adsorption at both innersphere sites was predicted to be unfavorable unless accompanied by release of protons. Molecular dynamics umbrella sampling simulations and ab initio cluster calculations were performed to determine the rates of electron transfer from Fe(II) adsorbed as an innersphere and outersphere complex. The electron transfer rates were calculated to range from 10^-4 to 10^2 s-1, depending on the adsorption site and the potential parameter set, and were generally slower than those obtained in the bulk hematite lattice. The most reliable estimate of the rate of electron transfer from Fe(II) adsorbed as an outersphere complex to lattice Fe(III) was commensurate with the rate of adsorption as an innersphere complex suggesting that adsorption does not necessarily need to precede oxidation.

  8. Directed nanoscale self-assembly of molecular wires interconnecting nodal points using Monte Carlo simulations

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

    Boscoboinik, A. M.; Manzi, S. J.; Tysoe, W. T.; Pereyra, V. D.; Boscoboinik, J. A.

    2015-09-10

    The influence of directing agents in the self-assembly of molecular wires to produce two-dimensional electronic nanoarchitectures is studied here using a Monte Carlo approach to simulate the effect of arbitrarily locating nodal points on a surface, from which the growth of self-assembled molecular wires can be nucleated. This is compared to experimental results reported for the self-assembly of molecular wires when 1,4-phenylenediisocyanide (PDI) is adsorbed on Au(111). The latter results in the formation of (Au-PDI)n organometallic chains, which were shown to be conductive when linked between gold nanoparticles on an insulating substrate. The present study analyzes, by means of stochasticmore » methods, the influence of variables that affect the growth and design of self-assembled conductive nanoarchitectures, such as the distance between nodes, coverage of the monomeric units that leads to the formation of the desired architectures, and the interaction between the monomeric units. As a result, this study proposes an approach and sets the stage for the production of complex 2D nanoarchitectures using a bottom-up strategy but including the use of current state-of-the-art top-down technology as an integral part of the self-assembly strategy.« less

  9. An Efficient Molecular Dynamics Scheme for Predicting Dopant Implant Profiles in Semiconductors

    SciTech Connect (OSTI)

    Beardmore, K.M.; Gronbech-Jensen, N.

    1998-09-15

    The authors present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. The program incorporates methods for reducing computational overhead, plus a rare event algorithm to give statistical accuracy over several orders of magnitude change in the dopant concentration. The code uses a molecular dynamics (MD) model, instead of the binary collision approximation (BCA) used in implant simulators such as TRIM and Marlowe, to describe ion-target interactions. Atomic interactions are described by a combination of 'many-body' and screened Coulomb potentials. Inelastic energy loss is accounted for using a Firsov model, and electronic stopping is described by a Brandt-Kitagawa model which contains the single adjustable parameter for the entire scheme. Thus, the program is easily extensible to new ion-target combinations with the minimum of tuning, and is predictive over a wide range of implant energies and angles. The scheme is especially suited for calculating profiles due to low energy, large angle implants, and for situations where a predictive capability is required with the minimum of experimental validation. They give examples of using their code to calculate concentration profiles and 2D 'point response' profiles of dopants in crystalline silicon, silicon-germanium blends, and gallium-arsenide. They can predict the experimental profiles over five orders of magnitude for <100> and <110> channeling and for non-channeling implants at energies up to hundreds of keV.

  10. Predicting Low Energy Dopant Implant Profiles in Semiconductors using Molecular Dynamics

    SciTech Connect (OSTI)

    Beardmore, K.M.; Gronbech-Jensen, N.

    1999-05-02

    The authors present a highly efficient molecular dynamics scheme for calculating dopant density profiles in group-IV alloy, and III-V zinc blende structure materials. Their scheme incorporates several necessary methods for reducing computational overhead, plus a rare event algorithm to give statistical accuracy over several orders of magnitude change in the dopant concentration. The code uses a molecular dynamics (MD) model to describe ion-target interactions. Atomic interactions are described by a combination of 'many-body' and pair specific screened Coulomb potentials. Accumulative damage is accounted for using a Kinchin-Pease type model, inelastic energy loss is represented by a Firsov expression, and electronic stopping is described by a modified Brandt-Kitagawa model which contains a single adjustable ion-target dependent parameter. Thus, the program is easily extensible beyond a given validation range, and is therefore truly predictive over a wide range of implant energies and angles. The scheme is especially suited for calculating profiles due to low energy and to situations where a predictive capability is required with the minimum of experimental validation. They give examples of using the code to calculate concentration profiles and 2D 'point response' profiles of dopants in crystalline silicon and gallium-arsenide. Here they can predict the experimental profile over five orders of magnitude for <100> and <110> channeling and for non-channeling implants at energies up to hundreds of keV.

  11. Interactivity vs. fairness in networked linux systems

    SciTech Connect (OSTI)

    Wu, Wenji; Crawford, Matt; ,

    2007-01-01

    In general, the Linux 2.6 scheduler can ensure fairness and provide excellent interactive performance at the same time. However, our experiments and mathematical analysis have shown that the current Linux interactivity mechanism tends to incorrectly categorize non-interactive network applications as interactive, which can lead to serious fairness or starvation issues. In the extreme, a single process can unjustifiably obtain up to 95% of the CPU! The root cause is due to the facts that: (1) network packets arrive at the receiver independently and discretely, and the 'relatively fast' non-interactive network process might frequently sleep to wait for packet arrival. Though each sleep lasts for a very short period of time, the wait-for-packet sleeps occur so frequently that they lead to interactive status for the process. (2) The current Linux interactivity mechanism provides the possibility that a non-interactive network process could receive a high CPU share, and at the same time be incorrectly categorized as 'interactive.' In this paper, we propose and test a possible solution to address the interactivity vs. fairness problems. Experiment results have proved the effectiveness of the proposed solution.

  12. Molecular beam mass spectrometry with tunable vacuum ultraviolet (VUV) synchrotron radiation

    SciTech Connect (OSTI)

    Golan, Amir; Ahmed, Musahid

    2012-01-01

    Tunable soft ionization coupled to mass spectroscopy is a powerful method to investigate isolated molecules, complexes and clusters and their spectroscopy and dynamics.[1-4] Fundamental studies of photoionization processes of biomolecules provide information about electronic structure of these systems. Furthermore determinations of ionization energies and other properties of biomolecules in the gas phase are not trivial, and these experiments provide a platform to generate these data. We have developed a thermal vaporization technique coupled with supersonic molecular beams that provides a gentle way to transport these species into the gas phase. Judicious combination of source gas and temperature allows for formation of dimers and higher clusters of the DNA bases. The focus of this particular work is on the effects of non-covalent interactions, i.e., hydrogen bonding, stacking, and electrostatic interactions, on the ionization energies and proton transfer of individual biomolecules, their complexes and upon micro-hydration by water.[1, 5-9] We have performed experimental and theoretical characterization of the photoionization dynamics of gas-phase uracil and 1,3-methyluracil dimers using molecular beams coupled with synchrotron radiation at the Chemical Dynamics Beamline[10] located at the Advanced Light Source and the experimental details are visualized here. This allowed us to observe the proton transfer in 1,3-dimethyluracil dimers, a system with pi stacking geometry and with no hydrogen bonds[1]. Molecular beams provide a very convenient and efficient way to isolate the sample of interest from environmental perturbations which in return allows accurate comparison with electronic structure calculations[11, 12]. By tuning the photon energy from the synchrotron, a photoionization efficiency (PIE) curve can be plotted which informs us about the cationic electronic states. These values can then be compared to theoretical models and calculations and in turn, explain in detail the electronic structure and dynamics of the investigated species [1, 3].

  13. L3 Interactive Data Language

    Energy Science and Technology Software Center (OSTI)

    2006-09-05

    The L3 system is a computational steering environment for image processing and scientific computing. It consists of an interactive graphical language and interface. Its purpose is to help advanced users in controlling their computational software and assist in the management of data accumulated during numerical experiments. L3 provides a combination of features not found in other environments; these are: - textual and graphical construction of programs - persistence of programs and associated data - directmore » mapping between the scripts, the parameters, and the produced data - implicit hierarchial data organization - full programmability, including conditionals and functions - incremental execution of programs The software includes the l3 language and the graphical environment. The language is a single-assignment functional language; the implementation consists of lexer, parser, interpreter, storage handler, and editing support, The graphical environment is an event-driven nested list viewer/editor providing graphical elements corresponding to the language. These elements are both the represenation of a users program and active interfaces to the values computed by that program.« less

  14. STRUCTURE-SOIL-STRUCTURE INTERACTION AT SRS | Department of Energy

    Office of Environmental Management (EM)

    STRUCTURE-SOIL-STRUCTURE INTERACTION AT SRS STRUCTURE-SOIL-STRUCTURE INTERACTION AT SRS Structure-Soil-Structure Interaction at SRS Structural Mechanics - SRS October 25, 2011 PDF...

  15. Unified molecular field theory for collinear and noncollinear Heisenberg antiferromagnets

    SciTech Connect (OSTI)

    Johnston, David C.

    2015-02-27

    In this study, a unified molecular field theory (MFT) is presented that applies to both collinear and planar noncollinear Heisenberg antiferromagnets (AFs) on the same footing. The spins in the system are assumed to be identical and crystallographically equivalent. This formulation allows calculations of the anisotropic magnetic susceptibility χ versus temperature T below the AF ordering temperature TN to be carried out for arbitrary Heisenberg exchange interactions Jij between arbitrary neighbors j of a given spin i without recourse to magnetic sublattices. The Weiss temperature θp in the Curie-Weiss law is written in terms of the Jij values and TN in terms of the Jij values and an assumed AF structure. Other magnetic and thermal properties are then expressed in terms of quantities easily accessible from experiment as laws of corresponding states for a given spin S. For collinear ordering these properties are the reduced temperature t=T/TN, the ratio f = θp/TN, and S. For planar noncollinear helical or cycloidal ordering, an additional parameter is the wave vector of the helix or cycloid. The MFT is also applicable to AFs with other AF structures. The MFT predicts that χ(T ≤ TN) of noncollinear 120° spin structures on triangular lattices is isotropic and independent of S and T and thus clarifies the origin of this universally observed behavior. The high-field magnetization and heat capacity for fields applied perpendicular to the ordering axis (collinear AFs) and ordering plane (planar noncollinear AFs) are also calculated and expressed for both types of AF structures as laws of corresponding states for a given S, and the reduced perpendicular field versus reduced temperature phase diagram is constructed.

  16. Unified molecular field theory for collinear and noncollinear Heisenberg antiferromagnets

    SciTech Connect (OSTI)

    Johnston, David C.

    2015-02-27

    In this study, a unified molecular field theory (MFT) is presented that applies to both collinear and planar noncollinear Heisenberg antiferromagnets (AFs) on the same footing. The spins in the system are assumed to be identical and crystallographically equivalent. This formulation allows calculations of the anisotropic magnetic susceptibility ? versus temperature T below the AF ordering temperature TN to be carried out for arbitrary Heisenberg exchange interactions Jij between arbitrary neighbors j of a given spin i without recourse to magnetic sublattices. The Weiss temperature ?p in the Curie-Weiss law is written in terms of the Jij values and TN in terms of the Jij values and an assumed AF structure. Other magnetic and thermal properties are then expressed in terms of quantities easily accessible from experiment as laws of corresponding states for a given spin S. For collinear ordering these properties are the reduced temperature t=T/TN, the ratio f = ?p/TN, and S. For planar noncollinear helical or cycloidal ordering, an additional parameter is the wave vector of the helix or cycloid. The MFT is also applicable to AFs with other AF structures. The MFT predicts that ?(T ? TN) of noncollinear 120° spin structures on triangular lattices is isotropic and independent of S and T and thus clarifies the origin of this universally observed behavior. The high-field magnetization and heat capacity for fields applied perpendicular to the ordering axis (collinear AFs) and ordering plane (planar noncollinear AFs) are also calculated and expressed for both types of AF structures as laws of corresponding states for a given S, and the reduced perpendicular field versus reduced temperature phase diagram is constructed.

  17. Unified molecular field theory for collinear and noncollinear Heisenberg antiferromagnets

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

    Johnston, David C.

    2015-02-27

    In this study, a unified molecular field theory (MFT) is presented that applies to both collinear and planar noncollinear Heisenberg antiferromagnets (AFs) on the same footing. The spins in the system are assumed to be identical and crystallographically equivalent. This formulation allows calculations of the anisotropic magnetic susceptibility χ versus temperature T below the AF ordering temperature TN to be carried out for arbitrary Heisenberg exchange interactions Jij between arbitrary neighbors j of a given spin i without recourse to magnetic sublattices. The Weiss temperature θp in the Curie-Weiss law is written in terms of the Jij values and TNmore » in terms of the Jij values and an assumed AF structure. Other magnetic and thermal properties are then expressed in terms of quantities easily accessible from experiment as laws of corresponding states for a given spin S. For collinear ordering these properties are the reduced temperature t=T/TN, the ratio f = θp/TN, and S. For planar noncollinear helical or cycloidal ordering, an additional parameter is the wave vector of the helix or cycloid. The MFT is also applicable to AFs with other AF structures. The MFT predicts that χ(T ≤ TN) of noncollinear 120° spin structures on triangular lattices is isotropic and independent of S and T and thus clarifies the origin of this universally observed behavior. The high-field magnetization and heat capacity for fields applied perpendicular to the ordering axis (collinear AFs) and ordering plane (planar noncollinear AFs) are also calculated and expressed for both types of AF structures as laws of corresponding states for a given S, and the reduced perpendicular field versus reduced temperature phase diagram is constructed.« less

  18. An NMR (Nuclear Magnetic Resonance) Investigation of the Chemical Association and Molecular Dynamics in Asphalt Ridge Tar Sand Ore and Bitumen

    DOE R&D Accomplishments [OSTI]

    Netzel, D. A.; Coover, P. T.

    1987-09-01

    Preliminary studies on tar sand bitumen given in this report have shown that the reassociation of tar sand bitumen to its original molecular configuration after thermal stressing is a first-order process requiring nearly a week to establish equilibrium. Studies were also conducted on the dissolution of tar sand bitumen in solvents of varying polarity. At a high-weight fraction of solute to solvent the apparent molecular weight of the bitumen molecules was greater than that of the original bitumen when dissolved in chloroform-d{sub 1} and benzene-d{sub 6}. This increase in the apparent molecular weight may be due to micellar formation or a weak solute-solvent molecular complex. Upon further dilution with any of the solvents studied, the apparent molecular weight of the tar sand bitumen decreased because of reduced van der Waals forces of interaction and/or hydrogen bonding. To define the exact nature of the interactions, it will be necessary to have viscosity measurements of the solutions.

  19. Synthesis and stability of liquid molecular DT

    SciTech Connect (OSTI)

    Souers, P.C.; Fearon, E.M.; Garza, R.G.; Griffith, C.M.; Mayhugh, S.R.; Mapoles, E.R.; Tsurgawa, R.T.; Sater, J.D.; Collins, G.W.; Gaines, J.R.

    1988-01-01

    Regular equimolar deuterium-tritium is a mixture of 25 mol% T/sub 2/-50% DT-25% D/sub 2/. We have synthesized molecular DT of greater purity by the reaction LiT + CH/sub 3/OD ..-->.. DT + LiOCH/sub 3/, run at 243/degree/K. With both the alcohol and reactor-to-cryostat transfer lines at room temperature, we obtain 88 mol% DT purity. By cooling the alcohol and holding the transfer lines at 80/degree/K, the yield rose to 95% DT. The DT disproportionated to D/sub 2/ and T/sub 2/ with a le-time constant of about 100 hours in the liquid at 20.5/degree/K. Nuclear magnetic resonance data showed that the eventual T/sub 2/-DT-D/sub 2/ equilibrium is probably a /open quotes/hot-atom/close quotes/ one.

  20. Synthesis and stability of liquid molecular DT

    SciTech Connect (OSTI)

    Souers, P.C.; Fearon, E.M.; Garza, R.G.; Friffith, C.M.; Mayhugh, S.R.; Mapoles, E.R.; Tsugawa, R.T.; Sater, J.D.; Collins, G.W.; Gaines, J.R.

    1988-05-01

    Regular equimolar deuterium-tritium is a mixture of 25 mol% T/sub 2/-50% DT-25% D/sub 2/. We have synthesized molecular DT of greater purity by the reaction LiT + CH/sub 3/OD ..-->.. DT + LiOCH/sub 3/, run at 243/degree/K. With both the alcohol and reactor-to-cryostat transfer lines at room temperature, we obtain 88 mol% DT purity. By cooling the alcohol and holding the transfer lines at 80/degree/K, the yield rose to 95% DT. The DT disproportionated to D/sub 2/ and T/sub 2/ with a 1e time constant of about 100 h in the liquid at 20.5/degree/K. Nuclear magnetic resonance data showed that the eventual T/sub 2/-DT-D/sub 2/ equilibrium is probably a /open quotes/hot-atom/close quotes/ one. 15 refs., 4 figs., 1 tab.

  1. Synthesis and stability of liquid molecular DT

    SciTech Connect (OSTI)

    Pearon, E.M.; Garza, R.G.; Griffith, C.M.; Mayhugh, S.R.; Mapoles, E.R.; Sater, J.D.; Souers, P.C.; Tsugawa, R.T.; Gaines, J.R.; Collins, G.W.

    1988-09-01

    Regular equimolar deuterium-tritium is a mixture of 25 mol% T/sub 2/-50% DT-25% D/sub 2/. The authors have synthesized molecular DT of greater purity by the reaction LiT + CH/sub 3/OD /yields/ DT + LiOCH/sub 3/, run at 243 K. With both the alcohol and reactor-to-cryostat transfer lines at room temperature, they obtain the 88 mol% DT purity. By cooling the alcohol and holding the transfer lines at 80 K, the yield rose to 95% DT. The DT disproportionated to D/sub 2/ and T/sub 2/ with a 1/e time constant of about 100 hr in the liquid at 20.5 K. Nuclear magnetic resonance data showed that the eventual T/sub 2/-DT-D/sub 2/ equilibrium is probably a hot-atom one.

  2. Octahedral molecular sieve sorbents and catalysts

    DOE Patents [OSTI]

    Li, Liyu [Richland, WA; King, David L [Richland, WA

    2010-04-20

    Octahedral molecular sieve sorbents and catalysts are disclosed, including silver hollandite and cryptomelane. These materials can be used, for example, to catalyze the oxidation of CO.sub.x (e.g., CO), NO.sub.x (e.g., NO), hydrocarbons (e.g., C.sub.3H.sub.6) and/or sulfur-containing compounds. The disclosed materials also may be used to catalyze other reactions, such as the reduction of NO.sub.2. In some cases, the disclosed materials are capable of sorbing certain products from the reactions they catalyze. Silver hollandite, in particular, can be used to remove a substantial portion of certain sulfur-containing compounds from a gas or liquid by catalysis and/or sorption. The gas or liquid can be, for example, natural gas or a liquid hydrocarbon.

  3. Silicotitanate molecular sieve and condensed phases

    DOE Patents [OSTI]

    Nenoff, Tina M. (Albuquerque, NM); Nyman, May D. (Albuquerque, NM)

    2002-01-01

    A new microporous crystalline molecular sieve material having the formula Cs.sub.3 TiSi.sub.3 O.sub.95.cndot.3H.sub.2 O and its hydrothermally condensed phase, Cs.sub.2 TiSi.sub.6 O.sub.15, are disclosed. The microporous material can adsorb divalent ions of radionuclides or other industrial metals such as chromium, nickel, lead, copper, cobalt, zinc, cadmium, barium, and mercury, from aqueous or hydrocarbon solutions. The adsorbed metal ions can be leached out for recovery purposes or the microporous material can be hydrothermally condensed to a radiation resistant, structurally and chemically stable phase which can serve as a storage waste form for radionuclides.

  4. Integrated Multiscale Modeling of Molecular Computing Devices

    SciTech Connect (OSTI)

    Weinan E

    2012-03-29

    The main bottleneck in modeling transport in molecular devices is to develop the correct formulation of the problem and efficient algorithms for analyzing the electronic structure and dynamics using, for example, the time-dependent density functional theory. We have divided this task into several steps. The first step is to developing the right mathematical formulation and numerical algorithms for analyzing the electronic structure using density functional theory. The second step is to study time-dependent density functional theory, particularly the far-field boundary conditions. The third step is to study electronic transport in molecular devices. We are now at the end of the first step. Under DOE support, we have made subtantial progress in developing linear scaling and sub-linear scaling algorithms for electronic structure analysis. Although there has been a huge amount of effort in the past on developing linear scaling algorithms, most of the algorithms developed suffer from the lack of robustness and controllable accuracy. We have made the following progress: (1) We have analyzed thoroughly the localization properties of the wave-functions. We have developed a clear understanding of the physical as well as mathematical origin of the decay properties. One important conclusion is that even for metals, one can choose wavefunctions that decay faster than any algebraic power. (2) We have developed algorithms that make use of these localization properties. Our algorithms are based on non-orthogonal formulations of the density functional theory. Our key contribution is to add a localization step into the algorithm. The addition of this localization step makes the algorithm quite robust and much more accurate. Moreover, we can control the accuracy of these algorithms by changing the numerical parameters. (3) We have considerably improved the Fermi operator expansion (FOE) approach. Through pole expansion, we have developed the optimal scaling FOE algorithm.

  5. Final Report for Integrated Multiscale Modeling of Molecular Computing Devices

    SciTech Connect (OSTI)

    Glotzer, Sharon C.

    2013-08-28

    In collaboration with researchers at Vanderbilt University, North Carolina State University, Princeton and Oakridge National Laboratory we developed multiscale modeling and simulation methods capable of modeling the synthesis, assembly, and operation of molecular electronics devices. Our role in this project included the development of coarse-grained molecular and mesoscale models and simulation methods capable of simulating the assembly of millions of organic conducting molecules and other molecular components into nanowires, crossbars, and other organized patterns.

  6. Probing Core-Hole Localization in Molecular Nitrogen

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

    Probing Core-Hole Localization in Molecular Nitrogen Print The behavior of the core hole created in molecular x-ray photoemission experiments has provided molecular scientists with a valuable window through which to probe the electronic structure and dynamics of molecules. But the answer to one fundamental quantum question-whether the core hole is localized or delocalized-has remained elusive for diatomic molecules in which both atoms are the same element. An international team of scientists

  7. Probing Core-Hole Localization in Molecular Nitrogen

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

    Probing Core-Hole Localization in Molecular Nitrogen Print The behavior of the core hole created in molecular x-ray photoemission experiments has provided molecular scientists with a valuable window through which to probe the electronic structure and dynamics of molecules. But the answer to one fundamental quantum question-whether the core hole is localized or delocalized-has remained elusive for diatomic molecules in which both atoms are the same element. An international team of scientists

  8. Probing Core-Hole Localization in Molecular Nitrogen

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

    Probing Core-Hole Localization in Molecular Nitrogen Print The behavior of the core hole created in molecular x-ray photoemission experiments has provided molecular scientists with a valuable window through which to probe the electronic structure and dynamics of molecules. But the answer to one fundamental quantum question-whether the core hole is localized or delocalized-has remained elusive for diatomic molecules in which both atoms are the same element. An international team of scientists

  9. Nonequilibrium molecular dynamics simulations of confined fluids in contact

    Office of Scientific and Technical Information (OSTI)

    with the bulk (Journal Article) | SciTech Connect Nonequilibrium molecular dynamics simulations of confined fluids in contact with the bulk Citation Details In-Document Search Title: Nonequilibrium molecular dynamics simulations of confined fluids in contact with the bulk A nonequilibrium molecular dynamics (MD) simulation study is reported of the structural and rheological properties of confined n-decane between two Au(111) surfaces in contact with its bulk under constant normal loads or

  10. Applications of molecular replacement to G protein-coupled receptors

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Applications of molecular replacement to G protein-coupled receptors Citation Details In-Document Search Title: Applications of molecular replacement to G protein-coupled receptors The use of molecular replacement in solving the structures of G protein-coupled receptors is discussed, with specific examples being described in detail. G protein-coupled receptors (GPCRs) are a large class of integral membrane proteins involved in regulating virtually every

  11. Probing Core-Hole Localization in Molecular Nitrogen

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

    Probing Core-Hole Localization in Molecular Nitrogen Print The behavior of the core hole created in molecular x-ray photoemission experiments has provided molecular scientists with a valuable window through which to probe the electronic structure and dynamics of molecules. But the answer to one fundamental quantum question-whether the core hole is localized or delocalized-has remained elusive for diatomic molecules in which both atoms are the same element. An international team of scientists

  12. Molecular Structure of Water at Gold Electrodes Revealed

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

    Molecular Structure of Water at Gold Electrodes Revealed Molecular Structure of Water at Gold Electrodes Revealed Print Wednesday, 25 March 2015 00:00 The structure of liquid water has been intensely studied, but until recently, it has not been clear what happens to it when a surface is introduced. ALS researchers have now made a first-ever observation of the molecular structure of liquid water at a gold surface under different charging conditions. This marks the first time that the scientific

  13. 8 Questions for a Scientist: Molecular Biologist Dr. Amanda Barry |

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

    Department of Energy for a Scientist: Molecular Biologist Dr. Amanda Barry 8 Questions for a Scientist: Molecular Biologist Dr. Amanda Barry August 13, 2015 - 9:45am Addthis Molecular biologist Dr. Amanda Barry at Los Alamos National Laboratory's environmental photobioreactor matrix, which simulates microalgal biofuel pond conditions. <a href="/node/1143116">Algal biofuels have big potential</a> for America's clean energy future. | <a

  14. Supercritical Carbon Dioxide / Reservoir Rock Chemical Interactions...

    Open Energy Info (EERE)

    Supercritical Carbon Dioxide Reservoir Rock Chemical Interactions Jump to: navigation, search Geothermal Lab Call Projects for Supercritical Carbon Dioxide Reservoir Rock...

  15. Catalyst Support Interactions | Argonne Leadership Computing...

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

    on the reactivity of metal catalyst particles. The research team will also study the adhesion properties by simulating the interactions between metal particles of different sizes...

  16. Frank Wilczek, Asymptotic Freedom, and Strong Interaction

    Office of Scientific and Technical Information (OSTI)

    of matter under extreme conditions, such as occurred in the earliest moments of the Big Bang. Also, it permits the construction of unified models of particle interactions,...

  17. Apogee Interactive Inc | Open Energy Information

    Open Energy Info (EERE)

    Georgia Zip: GE 30084 Sector: Services Product: Apogee Interactive provides a full-service of online technology solutions and consulting services to the energy industry...

  18. Structural Interactions within Lithium Salt Solvates: Cyclic...

    Office of Scientific and Technical Information (OSTI)

    and ester solvents coordinate Li+ cations in electrolyte solutions for lithium batteries. One approach to gleaning significant insight into these interactions is to examine...

  19. ARM - Publications: Science Team Meeting Documents: Interactions...

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

    Interactions Between Clouds and Radiation in the Multiscale Modelling Framework Cole, Jason Meteorological Service of Canada Barker, Howard Meteorological Service of Canada...

  20. Effects of phenylpropanolamine (PPA) on in vitro human erythrocyte membranes and molecular models

    SciTech Connect (OSTI)

    Suwalsky, Mario; Zambrano, Pablo; Mennickent, Sigrid; Villena, Fernando; Sotomayor, Carlos P.; Aguilar, Luis F.; Bolognin, Silvia

    2011-03-18

    Research highlights: {yields} PPA is a common ingredient in cough-cold medication and appetite suppressants. {yields} Reports on its effects on human erythrocytes are very scarce. {yields} We found that PPA induced in vitro morphological changes to human erythrocytes. {yields} PPA interacted with isolated unsealed human erythrocyte membranes. {yields} PPA interacted with class of lipid present in the erythrocyte membrane outer monolayer. -- Abstract: Norephedrine, also called phenylpropanolamine (PPA), is a synthetic form of the ephedrine alkaloid. After reports of the occurrence of intracranial hemorrhage and other adverse effects, including several deaths, PPA is no longer sold in USA and Canada. Despite the extensive information about PPA toxicity, reports on its effects on cell membranes are scarce. With the aim to better understand the molecular mechanisms of the interaction of PPA with cell membranes, ranges of concentrations were incubated with intact human erythrocytes, isolated unsealed human erythrocyte membranes (IUM), and molecular models of cell membranes. The latter consisted in bilayers built-up of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylethanolamine (DMPE), phospholipid classes present in the outer and inner monolayers of most plasmatic cell membranes, respectively. The capacity of PPA to perturb the bilayer structures of DMPC and DMPE was assessed by X-ray diffraction, DMPC large unilamellar vesicles (LUV) and IUM were studied by fluorescence spectroscopy, and intact human erythrocytes were observed by scanning electron microscopy (SEM). This study presents evidence that PPA affects human red cell membranes as follows: (a) in SEM studies on human erythrocytes it was observed that 0.5 mM PPA induced shape changes; (b) in IUM PPA induced a sharp decrease in the fluorescence anisotropy in the lipid bilayer acyl chains in a concentration range lower than 100 {mu}M; (c) X-ray diffraction studies showed that PPA in the 0.1-0.5 mM range induced increasing structural perturbation to DMPC, but no effects on DMPE multibilayers were detected.

  1. Polarized X-Rays Reveal Molecular Alignment in Printed Electronics

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

    ... These discoveries are valuable in guiding the molecular design of improved polymers for transistors and in gaining a better understanding of charge generation at complex 3D ...

  2. Preparation of Core-Shell Coordination Molecular Assemblies via...

    Office of Scientific and Technical Information (OSTI)

    Title: Preparation of Core-Shell Coordination Molecular Assemblies via the Enrichment of ... Subject: membrane, carbon capture, materials and chemistry by design, synthesis (novel ...

  3. The Role of Additive in Diketopyrrolopyrrole-based Small Molecular...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: The Role of Additive in Diketopyrrolopyrrole-based Small Molecular Bulk Heterojunction Solar Cells Citation Details In-Document Search Title: The Role of Additive ...

  4. Analysis of Molecular Clusters in Simulations of Lithium-Ion...

    Office of Scientific and Technical Information (OSTI)

    Title: Analysis of Molecular Clusters in Simulations of Lithium-Ion Battery Electrolytes. Abstract not provided. Authors: Tenney, Craig M ; Cygan, Randall T. Publication Date: ...

  5. Molecular Simulation of Carbon Dioxide Nanodroplets on Clay in...

    Office of Scientific and Technical Information (OSTI)

    Title: Molecular Simulation of Carbon Dioxide Nanodroplets on Clay in Deep Saline Aquifers. Authors: Tenney, Craig M. Publication Date: 2012-06-01 OSTI Identifier: 1073284 Report ...

  6. Molecular Simulation of Carbon Dioxide Nanodroplets on Clay Surfaces...

    Office of Scientific and Technical Information (OSTI)

    Title: Molecular Simulation of Carbon Dioxide Nanodroplets on Clay Surfaces in Deep Saline Aquifers. Authors: Tenney, Craig M. Publication Date: 2013-01-01 OSTI Identifier: 1063603 ...

  7. Low molecular weight thermostable .beta.-D-glucosidase from acidotherm...

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

    Visual Patent Search Success Stories News Events Find More Like This Return to Search Low molecular weight thermostable .beta.-D-glucosidase from acidothermus cellulolyticus...

  8. Note: High density pulsed molecular beam for cold ion chemistry

    SciTech Connect (OSTI)

    Kokish, M. G.; Rajagopal, V.; Marler, J. P.; Odom, B. C.

    2014-08-15

    A recent expansion of cold and ultracold molecule applications has led to renewed focus on molecular species preparation under ultrahigh vacuum conditions. Meanwhile, molecular beams have been used to study gas phase chemical reactions for decades. In this paper, we describe an apparatus that uses pulsed molecular beam technology to achieve high local gas densities, leading to faster reaction rates with cold trapped ions. We characterize the beam's spatial profile using the trapped ions themselves. This apparatus could be used for preparation of molecular species by reactions requiring excitation of trapped ion precursors to states with short lifetimes or for obtaining a high reaction rate with minimal increase of background chamber pressure.

  9. Exploring the speed and performance of molecular replacement...

    Office of Scientific and Technical Information (OSTI)

    ab initio protein models Citation Details In-Document Search Title: Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models Two ...

  10. Activation of molecular catalysts using semiconductor quantum dots

    DOE Patents [OSTI]

    Meyer, Thomas J. (Chapel Hill, NC); Sykora, Milan (Los Alamos, NM); Klimov, Victor I. (Los Alamos, NM)

    2011-10-04

    Photocatalytic materials based on coupling of semiconductor nanocrystalline quantum dots (NQD) and molecular catalysts. These materials have capability to drive or catalyze non-spontaneous chemical reactions in the presence of visible radiation, ultraviolet radiation, or both. The NQD functions in these materials as a light absorber and charge generator. Following light absorption, the NQD activates a molecular catalyst adsorbed on the surface of the NQD via transfer of one or more charges (either electrons or electron-holes) from the NQD to the molecular catalyst. The activated molecular catalyst can then drive a chemical reaction. A photoelectrolytic device that includes such photocatalytic materials is also described.

  11. MOLECULAR MECHANISM OF MICROBIAL TECHNETIUM REDUCTION FINAL REPORT...

    Office of Scientific and Technical Information (OSTI)

    Title: MOLECULAR MECHANISM OF MICROBIAL TECHNETIUM REDUCTION FINAL REPORT Microbial Tc(VII) reduction is an attractive alternative strategy for bioremediation of...

  12. Graphene nanoribbon molecular sensor based on inelastic transport...

    Office of Scientific and Technical Information (OSTI)

    Citation Details In-Document Search Title: Graphene nanoribbon molecular sensor based on ... School of Physics, Trinity College Dublin, Dublin 2 (Ireland) Instituto de Fsica, ...

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

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

    Vehicle Technologies Program Annual Merit Review and Peer Evaluation PDF icon es058smith2011o.pdf More Documents & Publications Molecular Dynamics Simulation Studies of ...

  14. Picture of the Week: Molecular "dimmer" switches for biomedicine...

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

    and designed to control transmission of information (greenblue) to molecular machines (greyorange) inside living cells. READ MORE: Medical and biofuel advances possible with new...

  15. QUANTUM MECHANICS, GENERAL PHYSICS; 74 ATOMIC AND MOLECULAR PHYSICS...

    Office of Scientific and Technical Information (OSTI)

    of model atoms in fields Milonni, P.W. 71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 74 ATOMIC AND MOLECULAR PHYSICS; ATOMS; OPTICAL MODELS; QUANTUM MECHANICS;...

  16. Elaine Chan Fosters ALS/Molecular Foundry Collaboration

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

    and the Molecular Foundry to a new role as joint ALSFoundry project scientist. Chan's mission will be to foster collaborations between the two facility's users and to communicate...

  17. First-principles molecular dynamics simulations of condensed...

    Office of Scientific and Technical Information (OSTI)

    First-principles molecular dynamics simulations of condensed phase V-type nerve agent reaction pathways and energy barriers Citation Details In-Document Search Title:...

  18. Molecular Weight Distributions of Irradiated Siloxane-Based Elastomers...

    Office of Scientific and Technical Information (OSTI)

    A Complementary Study by Statistical Modeling and Multiple Quantum Nuclear Magnetic Resonance. Citation Details In-Document Search Title: Molecular Weight Distributions...

  19. Strain effect on the adsorption, diffusion, and molecular dissociation...

    Office of Scientific and Technical Information (OSTI)

    Strain effect on the adsorption, diffusion, and molecular dissociation of hydrogen on Mg (0001) surface Citation Details In-Document Search Title: Strain effect on the adsorption,...

  20. Molecular Weight Distributions of Irradiated Siloxane-Based Elastomers...

    Office of Scientific and Technical Information (OSTI)

    Molecular Weight Distributions of Irradiated Siloxane-Based Elastomers: A Complementary Study by Statistical Modeling and Multiple Quantum Nuclear Magnetic Resonance. Citation...

  1. Sequential Activation of Molecular Breathing and Bending during...

    Office of Scientific and Technical Information (OSTI)

    Sequential Activation of Molecular Breathing and Bending during Spin-Crossover Photoswitching Revealed by Femtosecond Optical and X-Ray Absorption Spectroscopy Citation Details...

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

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

    Evaluation Meeting PDF icon es058bedrov2012p.pdf More Documents & Publications High Voltage Electrolytes for Li-ion Batteries Molecular Dynamics Simulation Studies of ...

  3. Reactive Molecular Simulations of Protonation of Water Clusters...

    Office of Scientific and Technical Information (OSTI)

    of Water Clusters and Depletion of Acidity in H-ZSM-5 Zeolite Citation Details In-Document Search Title: Reactive Molecular Simulations of Protonation of Water Clusters ...

  4. New synthetic strategy for porous molecular materials towards gas

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

    separation | Center for Gas SeparationsRelevant to Clean Energy Technologies | Blandine Jerome New synthetic strategy for porous molecular materials towards gas separation

  5. Preparation of Core-Shell Coordination Molecular Assemblies via...

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

    Preparation of Core-Shell Coordination Molecular Assemblies via the Enrichment of Structure-Directing "Codes" of Bridging Ligands and Metathesis of Metal Units Previous Next List...

  6. Molecular biology of signal transduction in plants. Abstracts

    SciTech Connect (OSTI)

    Not Available

    1991-12-31

    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.

  7. Crystal Structure of MC159 Reveals Molecular Mechanism of DISC...

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Search Results Journal Article: Crystal Structure of MC159 Reveals Molecular Mechanism of DISC Assembly and FLIP Inhibition Citation Details In-Document Search ...

  8. Molecular Mechanisms of Uranium Reduction by Clostridia and its Manipulation

    SciTech Connect (OSTI)

    Matin, A. C.

    2006-06-01

    The objective of this grant is to examine and manipulate the molecular mechanisms in Clostridia to make them better agents for uranyl [U(VI)] bioremediation.

  9. Probing Core-Hole Localization in Molecular Nitrogen

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

    molecular scientists with a valuable window through which to probe the electronic structure and dynamics of molecules. But the answer to one fundamental quantum...

  10. Molecular receptors in metal oxide sol-gel materials prepared via molecular imprinting

    DOE Patents [OSTI]

    Sasaki, Darryl Y. (Albuquerque, NM); Brinker, C. Jeffrey (Albuquerque, NM); Ashley, Carol S. (Albuquerque, NM); Daitch, Charles E. (Charlottesville, VA); Shea, Kenneth J. (Irvine, CA); Rush, Daniel J. (Philadelphia, PA)

    2000-01-01

    A method is provided for molecularly imprinting the surface of a sol-gel material, by forming a solution comprised of a sol-gel material, a solvent, an imprinting molecule, and a functionalizing siloxane monomer of the form Si(OR).sub.3-n X.sub.n, wherein n is an integer between zero and three and X is a functional group capable of reacting with the imprinting molecule, evaporating the solvent, and removing the imprinting molecule to form the molecularly imprinted metal oxide sol-gel material. The use of metal oxide sol-gels allows the material porosity, pore size, density, surface area, hardness, electrostatic charge, polarity, optical density, and surface hydrophobicity to be tailored and be employed as sensors and in catalytic and separations operations.

  11. Molecular Dynamics Simulations from SNL's Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)

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

    Plimpton, Steve; Thompson, Aidan; Crozier, Paul

    LAMMPS (http://lammps.sandia.gov/index.html) stands for Large-scale Atomic/Molecular Massively Parallel Simulator and is a code that can be used to model atoms or, as the LAMMPS website says, as a parallel particle simulator at the atomic, meso, or continuum scale. This Sandia-based website provides a long list of animations from large simulations. These were created using different visualization packages to read LAMMPS output, and each one provides the name of the PI and a brief description of the work done or visualization package used. See also the static images produced from simulations at http://lammps.sandia.gov/pictures.html The foundation paper for LAMMPS is: S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995), but the website also lists other papers describing contributions to LAMMPS over the years.

  12. VUV studies of molecular photofragmentation dynamics

    SciTech Connect (OSTI)

    White, M.G.

    1993-12-01

    State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.

  13. Competing interactions in semiconductor quantum dots

    SciTech Connect (OSTI)

    van den Berg, R.; Brandino, G. P.; El Araby, O.; Konik, R. M.; Gritsev, V.; Caux, J. -S.

    2014-10-01

    We introduce an integrability-based method enabling the study of semiconductor quantum dot models incorporating both the full hyperfine interaction as well as a mean-field treatment of dipole-dipole interactions in the nuclear spin bath. By performing free induction decay and spin echo simulations we characterize the combined effect of both types of interactions on the decoherence of the electron spin, for external fields ranging from low to high values. We show that for spin echo simulations the hyperfine interaction is the dominant source of decoherence at short times for low fields, and competes with the dipole-dipole interactions at longer times. On the contrary, at high fields the main source of decay is due to the dipole-dipole interactions. In the latter regime an asymmetry in the echo is observed. Furthermore, the non-decaying fraction previously observed for zero field free induction decay simulations in quantum dots with only hyperfine interactions, is destroyed for longer times by the mean-field treatment of the dipolar interactions.

  14. Dynamical Symmetries Reflected in Realistic Interactions

    SciTech Connect (OSTI)

    Sviratcheva, K.D.; Draayer, J.P.; /Louisiana State U.; Vary, J.P.; /Iowa State U. /LLNL, Livermore /SLAC

    2007-04-06

    Realistic nucleon-nucleon (NN) interactions, derived within the framework of meson theory or more recently in terms of chiral effective field theory, yield new possibilities for achieving a unified microscopic description of atomic nuclei. Based on spectral distribution methods, a comparison of these interactions to a most general Sp(4) dynamically symmetric interaction, which previously we found to reproduce well that part of the interaction that is responsible for shaping pairing-governed isobaric analog 0{sup +} states, can determine the extent to which this significantly simpler model Hamiltonian can be used to obtain an approximate, yet very good description of low-lying nuclear structure. And furthermore, one can apply this model in situations that would otherwise be prohibitive because of the size of the model space. In addition, we introduce a Sp(4) symmetry breaking term by including the quadrupole-quadrupole interaction in the analysis and examining the capacity of this extended model interaction to imitate realistic interactions. This provides a further step towards gaining a better understanding of the underlying foundation of realistic interactions and their ability to reproduce striking features of nuclei such as strong pairing correlations or collective rotational motion.

  15. TOUGH Pitzer Ion-Interaction Model

    Energy Science and Technology Software Center (OSTI)

    2008-10-23

    The TOUGHREACT Pitzer ion-interaction model version was developed based on the previous versions of TOUGHREACT. The main extensions include the Pitzer ion-interaction model for ionic activity calculation of solutions over a broad range of concentrations and the coupling of the vapor-pressure-lowering effect of salinity to phase partitioning.

  16. Competing interactions in semiconductor quantum dots

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

    van den Berg, R.; Brandino, G. P.; El Araby, O.; Konik, R. M.; Gritsev, V.; Caux, J. -S.

    2014-10-14

    In this study, we introduce an integrability-based method enabling the study of semiconductor quantum dot models incorporating both the full hyperfine interaction as well as a mean-field treatment of dipole-dipole interactions in the nuclear spin bath. By performing free induction decay and spin echo simulations we characterize the combined effect of both types of interactions on the decoherence of the electron spin, for external fields ranging from low to high values. We show that for spin echo simulations the hyperfine interaction is the dominant source of decoherence at short times for low fields, and competes with the dipole-dipole interactions atmore » longer times. On the contrary, at high fields the main source of decay is due to the dipole-dipole interactions. In the latter regime an asymmetry in the echo is observed. Furthermore, the non-decaying fraction previously observed for zero field free induction decay simulations in quantum dots with only hyperfine interactions, is destroyed for longer times by the mean-field treatment of the dipolar interactions.« less

  17. JET-SHOCKED H{sub 2} AND CO IN THE ANOMALOUS ARMS OF MOLECULAR HYDROGEN EMISSION GALAXY NGC 4258

    SciTech Connect (OSTI)

    Ogle, P. M.; Lanz, L.; Appleton, P. N.

    2014-06-20

    We present a Spitzer Infrared Spectrograph map of H{sub 2} emission from the nearby galaxy NGC 4258 (Messier 106). The H{sub 2} emission comes from 9.4 ± 0.4 × 10{sup 6} M {sub ?} of warm molecular hydrogen heated to 240-1040 K in the inner anomalous arms, a signature of jet interaction with the galaxy disk. The spectrum is that of a molecular hydrogen emission galaxy (MOHEG), with a large ratio of H{sub 2} over 7.7 ?m polycyclic aromatic hydrocarbon emission (0.37), characteristic of shocked molecular gas. We find close spatial correspondence between the H{sub 2} and CO emission from the anomalous arms. Our estimate of cold molecular gas mass based on CO emission is 10 times greater than our estimate of 1.0 × 10{sup 8} M {sub ?} based on dust emission. We suggest that the X {sub CO} value is 10 times lower than the Milky Way value because of high kinetic temperature and enhanced turbulence. The H{sub 2} disk has been overrun and is being shocked by the jet cocoon, and much of the gas originally in the disk has been ejected into the galaxy halo in an X-ray hot outflow. We measure a modest star formation rate of 0.08 M {sub ?} yr{sup –1} in the central 3.4 kpc{sup 2} that is consistent with the remaining gas surface density.

  18. Molecular structure and motion in zero field magnetic resonance

    SciTech Connect (OSTI)

    Jarvie, T.P.

    1989-10-01

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed.

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

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

    electrolyte/electrode interfaces | Department of Energy 1 DOE Hydrogen and Fuel Cells Program, and Vehicle Technologies Program Annual Merit Review and Peer Evaluation PDF icon es058_smith_2011_o.pdf More Documents & Publications Molecular Dynamics Simulation Studies of Electrolytes and Electrolyte/Electrode Interfaces Molecular dynamics simulation studies of electrolytes and electrolyte/electrode interfaces

  20. Vibrationally excited molecular hydrogen near Herschel 36

    SciTech Connect (OSTI)

    Rachford, Brian L. [Department of Physics, Embry-Riddle Aeronautical University, 3700 Willow Creek Road, Prescott, AZ 86301-3720 (United States); Snow, Theodore P. [Center for Astrophysics and Space Astronomy, Department of Astrophysical and Planetary Sciences, University of Colorado, Boulder, CO 80309-0389 (United States); Ross, Teresa L., E-mail: rachf7ac@erau.edu [Department of Astronomy, New Mexico State University, Las Cruces, NM 88003-8001 (United States)

    2014-05-10

    We present the first high resolution UV spectra toward Herschel 36, a Trapezium-like system of high-mass stars contained within the Lagoon Nebula (M8, NGC 6523). The spectra reveal extreme rovibrational excitation of molecular hydrogen in material at a single velocity or very small range of velocities, with this component presumably lying near the star system and undergoing fluorescent excitation. The overall H{sub 2} excitation is similar to, but apparently larger than, that seen toward HD 37903 which previously showed the largest vibrationally excited H{sub 2} column densities seen in UV absorption spectra. While the velocities of the highly excited H{sub 2} lines are consistent within each observation, it appears that they underwent a ?60 km s{sup –1} redshift during the 3.6 yr between observations. In neither case does the velocity of the highly excited material match the velocity of the bulk of the line-of-sight material which appears to mostly be in the foreground of M8. Recent work shows unusually excited CH and CH{sup +} lines and several unusually broad diffuse interstellar bands toward Herschel 36. Along with the H{sub 2} excitation, all of these findings appear to be related to the extreme environment within ?0.1 pc of the massive young stellar system.

  1. Molecular beam studies of reaction dynamics

    SciTech Connect (OSTI)

    Lee, Y.T.

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  2. Star formation relations in nearby molecular clouds

    SciTech Connect (OSTI)

    Evans, Neal J. II; Heiderman, Amanda; Vutisalchavakul, Nalin

    2014-02-20

    We test some ideas for star formation relations against data on local molecular clouds. On a cloud by cloud basis, the relation between the surface density of star formation rate and surface density of gas divided by a free-fall time, calculated from the mean cloud density, shows no significant correlation. If a crossing time is substituted for the free-fall time, there is even less correlation. Within a cloud, the star formation rate volume and surface densities increase rapidly with the corresponding gas densities, faster than predicted by models using the free-fall time defined from the local density. A model in which the star formation rate depends linearly on the mass of gas above a visual extinction of 8 mag describes the data on these clouds, with very low dispersion. The data on regions of very massive star formation, with improved star formation rates based on free-free emission from ionized gas, also agree with this linear relation.

  3. New hydroprocessing catalysts prepared from molecular complexes

    SciTech Connect (OSTI)

    Ho, T.C.

    1994-12-31

    Current commercial hydroprocessing catalysts are transition metal sulfides (TMS) based on Group 8 and 11 metals. They are prepared by dispersing MoO{sub 3} and a promoter metal oxide, either CoO or NiO, on {gamma}-Al{sub 2}O{sub 3} or SiO{sub 2}-modified Al{sub 2}O{sub 3}. This is followed by sulfiding with a sulfur-bearing stream such as H{sub 2}S at high temperatures. The thus formed MoS{sub 2} crystallites are the backbone of the working catalysts. A potentially fruitful approach to new catalysts would be to molecularly incorporate promoter metals into the structure of MoS{sub 2} edge planes. As a first step, it would seem reasonable to exploit the use of heterometallic metal sulfur complexes as hydroprocessing catalyst precursors. The authors have developed several families of new catalysts along this line. In this paper the authors restrict themselves to the metal amine thiomolybdate-derived catalysts. Specifically, they give an overview of the performance of the bulk (unsupported) FeMo sulfide prepared from MAT. This low-surface-area catalyst shows a high HDN-to-HDS volumetric activity ratio and is also active for HDA. While most of the results are taken from their previous publications, some new results are reported here.

  4. Molecular beam surface analysis. 1993 Summary report

    SciTech Connect (OSTI)

    Appelhans, A.D.; Ingram, J.C.; Groenewold, G.S.; Dahl, D.A.; Delmore, J.E.

    1993-09-01

    The Molecular Beam Surface Analysis (MBSA) program is developing both laboratory-based and potentially field-portable chemical analyses systems taking advantage of new surface analysis technology developed at the Idaho National Engineering Laboratory (INEL). The objective is to develop the means to rapidly detect and identify, with high specificity and high sensitivity, nonvolatile and low volatile organics found in Chemical Weapons (CW) and High Explosives (HE) feedstocks, agents, and decomposition products on surfaces of plants, rocks, paint chips, filters, smears of buildings, vehicles, equipment, etc.. Ideally, the method would involve no sample preparation and no waste generation, and would have the potential for being implemented as a field-portable instrument. In contrast to existing analytical methods that rely on sample volatility, MBSA is optimized for nonvolatile and low volatile compounds. This makes it amenable for rapidly screening field samples for CW agent decomposition products and feedstock chemicals and perhaps actual agents. In its final configuration (benchtop size) it could be operated in a non-laboratory environment (such as an office building) requiring no sample preparation chemistry or chemical supplies. It could also be included in a mobile laboratory used in on-site, ore remote site cooperative surveys, or in a standard laboratory, where it would provide fast screening of samples at minimal cost.

  5. Non-orthogonal configuration interaction for the calculation of multielectron excited states

    SciTech Connect (OSTI)

    Sundstrom, Eric J. Head-Gordon, Martin

    2014-03-21

    We apply Non-orthogonal Configuration Interaction (NOCI) to molecular systems where multielectron excitations, in this case double excitations, play a substantial role: the linear polyenes and ?-carotene. We demonstrate that NOCI when applied to systems with extended conjugation, provides a qualitatively correct wavefunction at a fraction of the cost of many other multireference treatments. We also present a new extension to this method allowing for purification of higher-order spin states by utilizing Generalized Hartree-Fock Slater determinants and the details for computing ?S{sup 2}? for the ground and excited states.

  6. Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

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

    Giera, Brian; Lawrence Livermore National Lab.; Henson, Neil; Kober, Edward M.; Shell, M. Scott; Squires, Todd M.

    2015-02-27

    We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drivemore » strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.« less

  7. High-energy cosmic ray interactions

    SciTech Connect (OSTI)

    Engel, Ralph; Orellana, Mariana; Reynoso, Matias M.; Vila, Gabriela S.

    2009-04-30

    Research into hadronic interactions and high-energy cosmic rays are closely related. On one hand--due to the indirect observation of cosmic rays through air showers--the understanding of hadronic multiparticle production is needed for deriving the flux and composition of cosmic rays at high energy. On the other hand the highest energy particles from the universe allow us to study the characteristics of hadronic interactions at energies far beyond the reach of terrestrial accelerators. This is the summary of three introductory lectures on our current understanding of hadronic interactions of cosmic rays.

  8. Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions

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

    Zhang, Yugang; Pal, Suchetan; Srinivasan, Babji; Vo, Thi; Kumar, Sanat; Gang, Oleg

    2015-05-25

    The rapid development of self-assembly approaches has enabled the creation of materials with desired organization of nanoscale components. However, achieving dynamic control, wherein the system can be transformed on demand into multiple entirely different states, is typically absent in atomic and molecular systems and has remained elusive in designed nanoparticle systems. Here, we demonstrate with in situ small-angle x-ray scattering that, by using DNA strands as inputs, the structure of a three-dimensional lattice of DNA-coated nanoparticles can be switched from an initial 'mother' phase into one of multiple 'daughter' phases. The introduction of different types of re-programming DNA strands modifiesmore » the DNA shells of the nanoparticles within the superlattice, thereby shifting interparticle interactions to drive the transformation into a particular daughter phase. We mapped quantitatively with free-energy calculations the selective re-programming of interactions onto the observed daughter phases.« less

  9. Interactions in 1-ethyl-3-methyl imidazolium tetracyanoborate ion pair: Spectroscopic and density functional study

    SciTech Connect (OSTI)

    Mao, James X.; Lee, Anita S.; Kitchin, John R.; Nulwala, Hunaid B; Luebke, David R.; Damodaran, Krishnan

    2013-04-24

    Density Functional Theory is used to investigate a weakly coordinating room-temperature ionic liquid, 1-ethyl-3-methyl imidazolium tetracyanoborate ([Emim]{sup +}[TCB]{sup -}). Four locally stable conformers of the ion pair were located. Atoms-in-molecules (AIM) and electron density analysis indicated the existence of several hydrogen bonds. Further investigation through the Natural Bond Orbital (NBO) and Natural Energy Decomposition Analysis (NEDA) calculations provided insight into the origin of interactions in the [Emim]{sup +}[TCB]{sup -} ion pair. Strength of molecular interactions in the ionic liquid was correlated with frequency shifts of the characteristic vibrations of the ion pair. Harmonic vibrations of the ion pair were also compared with the experimental Raman and Infrared spectra. Vibrational frequencies were assigned by visualizing displacements of atoms around their equilibrium positions and through Potential Energy Distribution (PED) analysis.

  10. Structure of a BRCA1/BARD1 Complex: a Heterodimeric RING-RING Interaction

    SciTech Connect (OSTI)

    Brzovic, Peter S.; Rajagopal, Ponni; Hoyt, David W.; King, Mary-Claire; Klevit, Rachel E.

    2001-10-01

    The N-terminal RING domain of the breast and ovarian cancer tumor suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein, BARD1. Proper function of the BRCA1 RING domain is critical, as evidenced by the many cancer-predisposing mutations found within this domain. We present the solution structure of the N-terminal RING domain heterodimer of BRCA1 and BARD1. Comparison with the RAG1 RING homodimer reveals the structural diversity of complexes formed by interactions between different RING domains. The BRCA1/BARD1 structure provides a model for its ubiquitin ligase activity, illustrates how the BRCA1 RING domain can be involved in associations with multiple protein partners, and provdes a framework for understanding cancer-causing mutations at the molecular level.

  11. Third international congress of plant molecular biology: Molecular biology of plant growth and development

    SciTech Connect (OSTI)

    Hallick, R.B.

    1995-02-01

    The Congress was held October 6-11, 1991 in Tucson with approximately 3000 scientists attending and over 300 oral presentations and 1800 posters. Plant molecular biology is one of the most rapidly developing areas of the biological sciences. Recent advances in the ability to isolate genes, to study their expression, and to create transgenic plants have had a major impact on our understanding of the many fundamental plant processes. In addition, new approaches have been created to improve plants for agricultural purposes. This is a book of presentation and posters from the conference.

  12. Decomposition of amino diazeniumdiolates (NONOates): Molecular mechanisms

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

    Shaikh, Nizamuddin; Valiev, Marat; Lymar, Sergei V.

    2014-08-23

    Although diazeniumdiolates (X[N(O)NO]-) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a quantitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO]-, where R = —N(C2H5)2(1), —N(C3H4NH2)2(2), or —N(C2H4NH2)2(3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO]- group with the apparent pKa and decomposition rate constants of 4.6 and 1 s-1 for 1; 3.5 and 0.083 s-1 for 2; andmore » 3.8 and 0.0033 s-1 for 3. Although protonation occurs mainly on the O atoms of the functional group, only the minor R2N(H)N(O)NO tautomer (population ~ 10-7, for 1) undergoes the N—N heterolytic bond cleavage (kd ~ 107 s-1 for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. Thus, the bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH < 2, decompositions of all three NONOates that have been investigated are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO]- group.« less

  13. Corn Storage Protein - A Molecular Genetic Model

    SciTech Connect (OSTI)

    Messing, Joachim

    2013-05-31

    Corn is the highest yielding crop on earth and probably the most valuable agricultural product of the United States. Because it converts sun energy through photosynthesis into starch and proteins, we addressed energy savings by focusing on protein quality. People and animals require essential amino acids derived from the digestion of proteins. If proteins are relatively low in certain essential amino acids, the crop becomes nutritionally defective and has to be supplemented. Such deficiency affects meat and fish production and countries where corn is a staple. Because corn seed proteins have relatively low levels of lysine and methionine, a diet has to be supplemented with soybeans for the missing lysine and with chemically synthesized methionine. We therefore have studied genes expressed during maize seed development and their chromosomal organization. A critical technical requirement for the understanding of the molecular structure of genes and their positional information was DNA sequencing. Because of the length of sequences, DNA sequencing methods themselves were insufficient for this type of analysis. We therefore developed the so-called “DNA shotgun sequencing” strategy, where overlapping DNA fragments were sequenced in parallel and used to reconstruct large DNA molecules via overlaps. Our publications became the most frequently cited ones during the decade of 1981-1990 and former Associate Director of Science for the Office of Basic Energy Sciences Patricia M. Dehmer presented our work as one of the great successes of this program. A major component of the sequencing strategy was the development of bacterial strains and vectors, which were also used to develop the first biotechnology crops. These crops possessed new traits thanks to the expression of foreign genes in plants. To enable such expression, chimeric genes had to be constructed using our materials and methods by the industry. Because we made our materials and methods freely available to academia and industry, progress in plant research and new crop development could accelerate and benefit the public.

  14. Radioprotectors and Tumors: Molecular Studies in Mice

    SciTech Connect (OSTI)

    Gayle Woloschak, David Grdina

    2010-03-10

    This proposal investigated effects of radiation using a set of archival tissues. Main interests of this proposal were to investigate effects of irradiation alone or in the presence or radioprotectors; to investigate these effects on different tissues; and to use/develop molecular biology techniques that would be suitable for work with archived tissues. This work resulted in several manuscripts published or in preparation. Approach for evaluation of gene copy numbers by quantitative real time PCR has been developed and we are striving to establish methods to utilize Q-RT-PCR data to evaluate genomic instability caused by irradiation(s) and accompanying treatments. References: 1. Paunesku D, Paunesku T, Wahl A, Kataoka Y, Murley J, Grdina DJ, Woloschak GE. Incidence of tissue toxicities in gamma ray and fission neutron-exposed mice treated with Amifostine. Int J Radiat Biol. 2008, 84(8):623-34. PMID: 18661379, http://informahealthcare.com/doi/full/10.1080/09553000802241762?cookieSet=1 2. Wang Q, Paunesku T and Woloschak GE. Tissue and data archives from irradiation experiments conducted at Argonne National Laboratory over a period of four decades, in press in Radiation and Environmental Biophysics. 3. Alcantara M, Paunesku D, Rademaker A, Paunesku T and Woloschak GE. A RETROSPECTIVE ANALYSIS OF TISSUE TOXICITIES IN B6CF1 MICE IRRADIATED WITH FISSION NEUTRONS OR COBALT 60 GAMMA RAYS: Gender modulates accumulation of tissue toxicities caused by low dose rate fractionated irradiation; in preparation; this document has been uploaded as STI product 4. Wang Q, Paunesku T Wanzer B and Woloschak GE. Mitochondrial gene copy number differences in different tissues of irradiated and control mice with lymphoid cancers; in preparation 5. Wang Q, Raha, S, Paunesku T and Woloschak GE. Evaluation of gene copy number differences in different tissues of irradiated and control mice; in preparation

  15. Decomposition of Amino Diazeniumdiolates (NONOates): Molecular Mechanisms

    SciTech Connect (OSTI)

    Shaikh, Nizamuddin; Valiev, Marat; Lymar, Sergei V.

    2014-08-23

    Although diazeniumdiolates (X[N(O)NO]-) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to slowly release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a qualitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO]-, where R = -N(C2H5)2 (1), -N(C3H4NH2)2 (2), or -N(C2H4NH2)2 (3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO]- group with apparent pKa and decomposition rate constants of 4.6 and 1 s-1 for 1-H, 3.5 and 83 x 10-3 s-1 for 2-H, and 3.8 and 3.3 x 10-3 s-1 for 3-H. Although protonation occurs mainly on the O atoms of the functional group, only the minor R2N(H)N(O)NO tautomer (population ~0.01%, for 1) undergoes the N-N heterolytic bond cleavage (k ~102 s-1 for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. The bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH < 2, decompositions of all these NONOates are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO]- group.

  16. Molecular orientation of copper phthalocyanine thin films on different monolayers of fullerene on SiO{sub 2} or highly oriented pyrolytic graphite

    SciTech Connect (OSTI)

    Wang, Chenggong; Wang, Congcong; Liu, Xiaoliang; Xu, Xumei; Li, Youzhen; Xie, Fangyan; Gao, Yongli

    2015-03-23

    The interface electronic structures of copper phthalocyanine (CuPc) have been studied using ultraviolet photoemission spectroscopy as different monolayers of C{sub 60} were inserted between CuPc and a SiO{sub 2} or highly ordered pyrolytic graphite (HOPG) substrate. The results show that CuPc has standing up configuration with one monolayer of C{sub 60} insertion on SiO{sub 2} while lying down on HOPG, indicating that the insertion layer propagates the CuPc-substrate interaction. Meanwhile, CuPc on more than one monolayers of C{sub 60} on different substrates show that the substrate orientation effect quickly vanished. Our study elucidates intriguing molecular interactions that manipulate molecular orientation and donor-acceptor energy level alignment.

  17. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect (OSTI)

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A.

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  18. Interacting vacuum energy in the dark sector

    SciTech Connect (OSTI)

    Chimento, L. P.; Carneiro, S.

    2015-03-26

    We analyse three cosmological scenarios with interaction in the dark sector, which are particular cases of a general expression for the energy flux from vacuum to matter. In the first case the interaction leads to a transition from an unstable de Sitter phase to a radiation dominated universe, avoiding in this way the initial singularity. In the second case the interaction gives rise to a slow-roll power-law inflation. Finally, the third scenario is a concordance model for the late-time universe, with the vacuum term decaying into cold dark matter. We identify the physics behind these forms of interaction and show that they can be described as particular types of the modified Chaplygin gas.

  19. Computes Generalized Electromagnetic Interactions Between Structures

    Energy Science and Technology Software Center (OSTI)

    1999-02-20

    Object oriented software for computing generalized electromagnetic interactions between structures in the frequency domains. The software is based on integral equations. There is also a static integral equation capability.

  20. Recent Neutrino Interaction Measurements Mike Wilking TRIUMF

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

    Neutrino Interaction Measurements Mike Wilking TRIUMF PIC Conference, 3-Sept-2010 Neutrinos: more than just missing E T ... ! Interactions and Oscillations * Neutrino oscillation experiments have now moved into the realm of precision physics * Cross section uncertainties are now becoming an important factor in interpreting oscillation data * The next generation of accelerator-based neutrino experiments all take place at the ~1 GeV neutrino energy scale * In the last few years, several new cross

  1. Frank Wilczek, Asymptotic Freedom, and Strong Interaction

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

    Frank Wilczek, Asymptotic Freedom, and Strong Interaction Resources with Additional Information H. David Politzer Photo Credit: Donna Coveney, MIT Frank Wilczek, a winner of the 2004 Nobel Prize in Physics "for the discovery of asymptotic freedom in the theory of the strong interaction", has had multiple connections with Brookhaven National Laboratory (BNL). These include his being the Leland J. Haworth Distinguished Scientist from 1994 - 1997. Wilczek shares the Nobel prize with David

  2. Layered Atlantic Smoke Interactions with Clouds

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

    Layered Atlantic Smoke Interactions with Clouds Island in the South Atlantic Ocean. Warm African winds combine with the cool sea surface temperatures and form a large stratocumulus deck, transitioning to year-round trade-wind shallow cumulus at the location of Ascension Island. These clouds and myriad aerosol-cloud-radiation interactions will be studied. Using a portable observatory, or ARM Mobile Facility (AMF), that contains some of most advanced atmospheric research instrumentation for cloud,

  3. Understanding Radionuclide Interactions with Layered Materials.

    Office of Scientific and Technical Information (OSTI)

    (Conference) | SciTech Connect Understanding Radionuclide Interactions with Layered Materials. Citation Details In-Document Search Title: Understanding Radionuclide Interactions with Layered Materials. Abstract not provided. Authors: Wang, Yifeng Publication Date: 2014-10-01 OSTI Identifier: 1241847 Report Number(s): SAND2014-18612C 540411 DOE Contract Number: AC04-94AL85000 Resource Type: Conference Resource Relation: Conference: Proposed for presentation at the Materials Science &

  4. BETO Quiz - Interactive Content | Department of Energy

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

    BETO Quiz - Interactive Content BETO Quiz - Interactive Content Welcome to the Bioenergy Quiz! Navigate through the quiz by clicking on the circular buttons and selecting the correct answers to the questions. Use the scrollbar to move down the page and view all of the information displayed. Hover over words and phrases highlighted in orange for an explanation of terms. Share the information by clicking on the buttons in the Share This block. Use the arrow button found in the bottom right-hand

  5. Molecular simulations of heterogeneous ice nucleation. I. Controlling ice nucleation through surface hydrophilicity

    SciTech Connect (OSTI)

    Cox, Stephen J.; Kathmann, Shawn M.; Slater, B.; Michaelides, Angelos

    2015-05-14

    Ice formation is one of the most common and important processes on earth and almost always occurs at the surface of a material. A basic understanding of how the physicochemical properties of a material’s surface affect its ability to form ice has remained elusive. Here, we use molecular dynamics simulations to directly probe heterogeneous ice nucleation at a hexagonal surface of a nanoparticle of varying hydrophilicity. Surprisingly, we find that structurally identical surfaces can both inhibit and promote ice formation and analogous to a chemical catalyst, it is found that an optimal interaction between the surface and the water exists for promoting ice nucleation.We use our microscopic understanding of the mechanism to design a modified surface in silico with enhanced ice nucleating ability. C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

  6. Receptor tyrosine kinase EphA5 is a functional molecular target in human lung cancer

    SciTech Connect (OSTI)

    Staquicini, Fernanda I.; Qian, Ming D.; Salameh, Ahmad; Dobroff, Andrey S.; Edwards, Julianna K.; Cimino, Daniel F.; Moeller, Benjamin J.; Kelly, Patrick; Nunez, Maria I.; Tang, Ximing; Liu, Diane D.; Lee, J. Jack; Hong, Waun Ki; Ferrara, Fortunato; Bradbury, Andrew R. M.; Lobb, Roy R.; Edelman, Martin J.; Sidman, Richard L.; Wistuba, Ignacio I.; Arap, Wadih; Pasqualini, Renata

    2015-03-20

    Lung cancer is often refractory to radiotherapy, but molecular mechanisms of tumor resistance remain poorly defined. Here we show that the receptor tyrosine kinase EphA5 is specifically overexpressed in lung cancer and is involved in regulating cellular responses to genotoxic insult. In the absence of EphA5, lung cancer cells displayed a defective G1/S cell cycle checkpoint, were unable to resolve DNA damage, and became radiosensitive. Upon irradiation, EphA5 was transported into the nucleus where it interacted with activated ATM (ataxia-telangiectasia mutated) at sites of DNA repair. In conclusion, we demonstrate that a new monoclonal antibody against human EphA5 sensitized lung cancer cells and human lung cancer xenografts to radiotherapy and significantly prolonged survival, thus suggesting the likelihood of translational applications.

  7. Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations

    SciTech Connect (OSTI)

    Mester, Zoltan; Panagiotopoulos, Athanassios Z.

    2015-01-28

    The mean ionic activity coefficients of aqueous NaCl solutions of varying concentrations at 298.15 K and 1 bar have been obtained from molecular dynamics simulations by gradually turning on the interactions of an ion pair inserted into the solution. Several common non-polarizable water and ion models have been used in the simulations. Gibbs-Duhem equation calculations of the thermodynamic activity of water are used to confirm the thermodynamic consistency of the mean ionic activity coefficients. While the majority of model combinations predict the correct trends in mean ionic activity coefficients, they overestimate their values at high salt concentrations. The solubility predictions also suffer from inaccuracies, with all models underpredicting the experimental values, some by large factors. These results point to the need for further ion and water model development.

  8. Melting behaviour of gold-platinum nanoalloy clusters by molecular dynamics simulations

    SciTech Connect (OSTI)

    Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

    2015-04-24

    The melting behavior of bimetallic gold-platinum nanoclusters is studied by applying Brownian-type isothermal molecular dynamics (MD) simulation, a program modified from the cubic coupling scheme (CCS). The process begins with the ground-state structures obtained from global minimum search algorithm and proceeds with the investigation of the effect of temperature on the thermal properties of gold-platinum nanoalloy clusters. N-body Gupta potential has been employed in order to account for the interactions between gold and platinum atoms. The ground states of the nanoalloy clusters, which are core-shell segregated, are heated until they become thermally segregated. The detailed melting mechanism of the nanoalloy clusters is studied via this approach to provide insight into the thermal stability of the nanoalloy clusters.

  9. Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-08-01

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  10. Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation

    SciTech Connect (OSTI)

    Noe, F [University of Heidelberg; Daidone, Isabella [University of Heidelberg; Smith, Jeremy C [ORNL; DiNola, Alfredo [University of Rome; Amadei, Andrea [University of Rome 'Tor Vergata', Rome, Italy

    2008-06-01

    A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the 'unfolding'. While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.

  11. Receptor tyrosine kinase EphA5 is a functional molecular target in human lung cancer

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

    Staquicini, Fernanda I.; Qian, Ming D.; Salameh, Ahmad; Dobroff, Andrey S.; Edwards, Julianna K.; Cimino, Daniel F.; Moeller, Benjamin J.; Kelly, Patrick; Nunez, Maria I.; Tang, Ximing; et al

    2015-03-20

    Lung cancer is often refractory to radiotherapy, but molecular mechanisms of tumor resistance remain poorly defined. Here we show that the receptor tyrosine kinase EphA5 is specifically overexpressed in lung cancer and is involved in regulating cellular responses to genotoxic insult. In the absence of EphA5, lung cancer cells displayed a defective G1/S cell cycle checkpoint, were unable to resolve DNA damage, and became radiosensitive. Upon irradiation, EphA5 was transported into the nucleus where it interacted with activated ATM (ataxia-telangiectasia mutated) at sites of DNA repair. In conclusion, we demonstrate that a new monoclonal antibody against human EphA5 sensitized lungmore » cancer cells and human lung cancer xenografts to radiotherapy and significantly prolonged survival, thus suggesting the likelihood of translational applications.« less

  12. Defect study in molecular beam epitaxy-grown HgCdTe films with activated and unactivated arsenic

    SciTech Connect (OSTI)

    Izhnin, I. I.; Dvoretsky, S. A.; Mikhailov, N. N.; Varavin, V. S.; Mynbaev, K. D.; Fitsych, O. I.; Pociask-Bialy, M.; Sheregii, E.; Voitsekhovskii, A. V.

    2014-04-28

    A defect study was performed on molecular beam epitaxy-grown HgCdTe films in situ doped with arsenic. Doping was performed from either effusion cell or cracker cell, and studied were both as-grown samples and samples subjected to arsenic activation annealing. Electrical properties of the films were investigated with the use of ion milling as a means of “stirring” defects in the material. As a result of the study, it was confirmed that the most efficient incorporation of electrically active arsenic occurs at the cracking zone temperature of 700?°C. Interaction between arsenic and tellurium during the growth was observed and is discussed in the paper.

  13. Excitation picture of an interacting Bose gas

    SciTech Connect (OSTI)

    Kira, M.

    2014-12-15

    Atomic Bose–Einstein condensates (BECs) can be viewed as macroscopic objects where atoms form correlated atom clusters to all orders. Therefore, the presence of a BEC makes the direct use of the cluster-expansion approach–lucrative e.g. in semiconductor quantum optics–inefficient when solving the many-body kinetics of a strongly interacting Bose. An excitation picture is introduced with a nonunitary transformation that describes the system in terms of atom clusters within the normal component alone. The nontrivial properties of this transformation are systematically studied, which yields a cluster-expansion friendly formalism for a strongly interacting Bose gas. Its connections and corrections to the standard Hartree–Fock–Bogoliubov approach are discussed and the role of the order parameter and the Bogoliubov excitations are identified. The resulting interaction effects are shown to visibly modify number fluctuations of the BEC. Even when the BEC has a nearly perfect second-order coherence, the BEC number fluctuations can still resolve interaction-generated non-Poissonian fluctuations. - Highlights: • Excitation picture expresses interacting Bose gas with few atom clusters. • Semiconductor and BEC many-body investigations are connected with cluster expansion. • Quantum statistics of BEC is identified in terms of atom clusters. • BEC number fluctuations show extreme sensitivity to many-body correlations. • Cluster-expansion friendly framework is established for an interacting Bose gas.

  14. DIP: The Database of Interacting Proteins

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

    The DIP Database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. By interaction, the DIP Database creators mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organisation and complexity of the protein interaction network at the cellular level. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. It is a relational database that can be searched by protein, sequence, motif, article information, and pathBLAST. The website also serves as an access point to a number of projects related to DIP, such as LiveDIP, The Database of Ligand-Receptor Partners (DLRP) and JDIP. Users have free and open access to DIP after login. [Taken from the DIP Guide and the DIP website] (Specialized Interface) (Registration Required)

  15. psu-molecular-basket | netl.doe.gov

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

    CO2 Capture from Flue Gas Using Solid Molecular Basket Sorbents Project No.: FE0000458 Pennsylvania State University (PSU) is developing a new generation of solid polymer-based sorbents for more efficient capture and separation of carbon dioxide (CO2) from flue gas of coal-fired power plants. The project is based on the concept of a "molecular basket" sorbent which was invented and developed at PSU. The idea of a molecular basket sorbent development is to load CO2-philic polymers

  16. CO{sub 2} Capture from Flue Gas Using Solid Molecular Basket Sorbents

    SciTech Connect (OSTI)

    Fillerup, Eric; Zhang, Zhonghua; Peduzzi, Emanuela; Wang, Dongxiang; Guo, Jiahua; Ma, Xiaoliang; Wang, Xiaoxing; Song, Chunshan

    2012-08-31

    The objective of this project is to develop a new generation of solid, regenerable polymeric molecular basket sorbent (MBS) for more cost-efficient capture and separation of CO{sub 2} from flue gas of coal-fired power plants. The primary goal is to develop a cost-effective MBS sorbent with better thermal stability. To improve the cost-effectiveness of MBS, we have explored commercially available and inexpensive support to replace the more expensive mesoporous molecular sieves like MCM-41 and SBA- 15. In addition, we have developed some advanced sorbent materials with 3D pore structure such as hexagonal mesoporous silica (HMS) to improve the CO{sub 2} working capacity of MBS, which can also reduce the cost for the whole CO{sub 2} capture process. During the project duration, the concern regarding the desorption rate of MBS sorbents has been raised, because lower desorption rate increases the desorption time for complete regeneration of the sorbent which in turn leads to a lower working capacity if the regeneration time is limited. Thus, the improvement in the thermal stability of MBS became a vital task for later part of this project. The improvement in the thermal stability was performed via increasing the polymer density either using higher molecular weight PEI or PEI cross-linking with an organic compound. Moreover, we have used the computational approach to estimate the interaction of CO{sub 2} with different MBSs for the fundamental understanding of CO{sub 2} sorption, which may benefit the development, design and modification of the sorbents and the process.

  17. Molecular dynamics simulation of diffusion and electrical conductivity in montmorillonite interlayers

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

    Greathouse, Jeffery A.; Cygan, Randall T.; Fredrich, Joanne T.; Jerauld, Gary R.

    2016-01-20

    In this study, the diffusion of water and ions in the interlayer region of smectite clay minerals represents a direct probe of the type and strength of clay–fluid interactions. Interlayer diffusion also represents an important link between molecular simulation and macroscopic experiments. Here we use molecular dynamics simulation to investigate trends in cation and water diffusion in montmorillonite interlayers, looking specifically at the effects of layer charge, interlayer cation and cation charge (sodium or calcium), water content, and temperature. For Na-montmorillonite, the largest increase in ion and water diffusion coefficients occurs between the one-layer and two-layer hydrates, corresponding to themore » transition from inner-sphere to outer-sphere surface complexes. Calculated activation energies for ion and water diffusion in Na-montmorillonite are similar to each other and to the water hydrogen bond energy, suggesting the breaking of water–water and water–clay hydrogen bonds as a likely mechanism for interlayer diffusion. A comparison of interlayer diffusion with that of bulk electrolyte solutions reveals a clear trend of decreasing diffusion coefficient with increasing electrolyte concentration, and in most cases the interlayer diffusion results are nearly coincident with the corresponding bulk solutions. Trends in electrical conductivities computed from the ion diffusion coefficients are also compared.« less

  18. Decomposition of amino diazeniumdiolates (NONOates): Molecular mechanisms

    SciTech Connect (OSTI)

    Shaikh, Nizamuddin; Valiev, Marat; Lymar, Sergei V.

    2014-12-01

    Although diazeniumdiolates (X[N(O)NO]-) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a quantitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO]-, where R = —N(C2H5)2(1), —N(C3H4NH2)2(2), or —N(C2H4NH2)2(3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO]- group with the apparent pKa and decomposition rate constants of 4.6 and 1 s-1 for 1; 3.5 and 0.083 s-1 for 2; and 3.8 and 0.0033 s-1 for 3. Although protonation occurs mainly on the O atoms of the functional group, only the minor R2N(H)N(O)NO tautomer (population ~ 10-7, for 1) undergoes the N—N heterolytic bond cleavage (kd ~ 107 s-1 for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. The bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH < 2, decompositions of all three NONOates that have been investigated are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO]- group.

  19. Ensemble density variational methods with self- and ghost-interaction-corrected functionals

    SciTech Connect (OSTI)

    Pastorczak, Ewa; Pernal, Katarzyna

    2014-05-14

    Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introduced by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.

  20. Solvation of molecules in superfluid helium enhances the “interaction induced localization” effect

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    Walewski, ?ukasz Forbert, Harald; Marx, Dominik

    2014-04-14

    Atomic nuclei become delocalized at low temperatures as a result of quantum effects, whereas they are point-like in the high temperature (classical) limit. For non-interacting nuclei, the delocalization upon lowering the temperature is quantitatively described in terms of the thermal de Broglie wavelength of free particles. Clearly, light non-interacting nuclei – the proton being a prominent one – are much more delocalized at low temperatures compared to heavy nuclei, such as non-interacting oxygen having water in mind. However, strong interactions due to chemical bonding in conjunction with ultra-low temperatures characteristic to superfluid helium nanodroplets change this common picture substantially for nuclei in molecules or clusters. It turns out that protons shared in hydrogen bonds undergo an extreme “interaction induced localization” at temperatures on the order of 1 K, which compresses the protonic spatial distributions to the size of the much heavier donor or acceptor atoms, such as O or Cl nuclei, corresponding to about 0.1% of the volume occupied by a non-interacting proton at the same temperature. Moreover, applying our recently developed hybrid ab initio path integral molecular dynamics/bosonic path integral Monte Carlo quantum simulation technique to a HCl/water cluster, HCl(H{sub 2}O){sub 4}, we find that helium solvation has a significant additional localizing effect of up to about 30% in volume. In particular, the solvent-induced excess localization is the stronger the lesser the given nucleus is already localized in the gas phase reference situation.

  1. Environmental Molecular Sciences Laboratory Annual Report: Fiscal Year 2006

    SciTech Connect (OSTI)

    Foster, Nancy S.; Showalter, Mary Ann

    2007-03-23

    This report describes the activities and research performed at the Environmental Molecular Sciences Laboratory, a Department of Energy national scientific user facility at Pacific Northwest National Laboratory, during Fiscal Year 2006.

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

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

    on organic bulk heterojunction solar cells The influence of molecular orientation on organic bulk heterojunction solar cells Print Monday, 28 April 2014 09:03 Work done on ALS...

  3. The Molecular Ingenuity of a Unique Fish Scale

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

    The Molecular Ingenuity of a Unique Fish Scale Print Arapaima gigas, a freshwater fish found in the Amazon Basin, has a remarkable ability to resist predation by piranhas through...

  4. First-principles molecular dynamics simulations of condensed...

    Office of Scientific and Technical Information (OSTI)

    phase V-type nerve agent reaction pathways and energy barriers Citation Details In-Document Search Title: First-principles molecular dynamics simulations of condensed phase V-type ...

  5. Molecular Dynamics Simulation Studies of Electrolytes andElectrolyte...

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

    Review and Peer Evaluation Meeting, June 7-11, 2010 -- Washington D.C. PDF icon es058smith2010p.pdf More Documents & Publications Molecular dynamics simulation and ab intio ...

  6. Large-Scale First-Principles Molecular Dynamics Simulations on...

    Office of Scientific and Technical Information (OSTI)

    Conference: Large-Scale First-Principles Molecular Dynamics Simulations on the BlueGeneL Platform using the Qbox Code Citation Details In-Document Search Title: Large-Scale...

  7. PNNL: Center for Molecular Electrocatalysis - Research: A Fast...

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

    of the fastest molecular electrocatalyst for oxidation of hydrogen. Oxidation of hydrogen in fuel cells is an efficient way to convert the chemical energy of an H-H bond...

  8. Chaos in laser-matter interactions

    SciTech Connect (OSTI)

    Ackerhalt, J.; Milonni, P.; Shih, M.L.

    1987-01-01

    This is a set of lecture notes given by the authors at the Universities of Rochester, Arkansas and Puerto Rico. This volume introduces the main ideas of chaos and its applications to a broad range of problems in quantum optics, electronics and laser physics. Contents: Introduction; Nonlinearity; The Period Doubling Route to Chaos; The Duffing Oscillator; Strange Attractors; Two-Frequency Route to Chaos; Intermittency; Dimensions of Attractors; Noise, The Lorenz Model and the Single-Mode Laser; Chaotic Lasers: Theory and Experiment; Hamiltonian Systems; The Henon-Heiles System; The Standard Mapping; Fat Fractals; Ergodicity and Mixing; Chaos and the Microwave Ionization of Hydrogen; The Kicked Pendulum: Classical Theory and Quantum Theory; Chaos and Multiple-Photon Excitation of Molecular Vibrations; Chaos and Molecular Rotations; Ideas in Quantum Chaos; Outlook.

  9. First-principles insights into interaction of CO, NO, and HCN with Ag{sub 8}

    SciTech Connect (OSTI)

    Torbatian, Zahra; Hashemifar, S. Javad, E-mail: hashemifar@cc.iut.ac.ir; Akbarzadeh, Hadi [Department of Physics, Isfahan University of Technology, 84156-83111 Isfahan (Iran, Islamic Republic of)] [Department of Physics, Isfahan University of Technology, 84156-83111 Isfahan (Iran, Islamic Republic of)

    2014-02-28

    We use static as well as time-dependent first-principles computations to study interaction of the CO, NO, and HCN molecules with the Ag{sub 8} nanocluster. The many-body based GW correction is applied for accurate description of the highest occupied (HOMO) and the lowest unoccupied (LUMO) molecular orbital levels. It is argued that the adsorption of these molecules changes the stable structure of Ag{sub 8} from Td to the more chemically active D{sub 2d} symmetry. We discuss that the CO, NO, and HCN molecules prefer to adsorb on the atom of the cluster with significant contribution to both HOMO and LUMO, for the accomplishment of the required charge transfers in the systems. The charge back donation is found to leave an excess energy of about 110 meV on the NO molecular bond, evidencing potential application of silver clusters for NO reduction. It is argued that CO and specially NO exhibit strong physical interaction with the silver cluster and hence significantly modify the electronic and optical properties of the system, while HCN makes very week physical bonds with the cluster. The optical absorption spectra of the Ag{sub 8} cluster before and after molecule adsorption are computed and a nontrivial red shift is observed in the NO and HCN adsorbed clusters.

  10. Molecular Structure of Water at Gold Electrodes Revealed

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

    Molecular Structure of Water at Gold Electrodes Revealed Print The structure of liquid water has been intensely studied, but until recently, it has not been clear what happens to it when a surface is introduced. ALS researchers have now made a first-ever observation of the molecular structure of liquid water at a gold surface under different charging conditions. This marks the first time that the scientific community has shown such high sensitivity in an in-situ environment under working

  11. The influence of molecular orientation on organic bulk heterojunction solar

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

    cells The influence of molecular orientation on organic bulk heterojunction solar cells The influence of molecular orientation on organic bulk heterojunction solar cells Print Monday, 28 April 2014 09:03 Work done on ALS Beamlines 11.0.1.2, 7.3.3, and 5.3.2.2. reveals that preferential orientation of polymer chains with respect to the fullerene domain leads to a high photovoltaic performance. Featured on the cover of Nature Photonics 8. Article link

  12. The Molecular Ingenuity of a Unique Fish Scale

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

    The Molecular Ingenuity of a Unique Fish Scale The Molecular Ingenuity of a Unique Fish Scale Print Monday, 25 November 2013 12:06 Arapaima gigas, a freshwater fish found in the Amazon Basin, has a remarkable ability to resist predation by piranhas through the strength and toughness of their scales, which act as natural dermal armor. Arapaima scales consist of a hard, mineralized outer shell surrounding a more ductile core. This core region is composed of aligned mineralized collagen fibrils

  13. Assembly of a Molecular Needle, from the Bottom Up

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

    Assembly of a Molecular Needle, from the Bottom Up Assembly of a Molecular Needle, from the Bottom Up Print Wednesday, 21 December 2005 00:00 Many pathogenic bacteria use a specialized secretion system to inject virulence proteins directly into the cells they infect. The injected proteins, by mimicking host-cell mechanisms, can then subvert normal cellular function. The type III secretion system (TTSS) is a sophisticated protein complex with an overall shape similar to a hypodermic needle. More

  14. Polarized X-Rays Reveal Molecular Alignment in Printed Electronics

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

    Polarized X-Rays Reveal Molecular Alignment in Printed Electronics Polarized X-Rays Reveal Molecular Alignment in Printed Electronics Print Wednesday, 31 October 2012 00:00 The printing of electronic devices using giant roll-to-roll presses or inkjet-style printers has recently been made possible by the development of solution-processable organic materials with optoelectronic properties. Organic light-emitting diodes (OLEDs) are already being produced commercially, and sensors, organic thin-film

  15. Molecular Structure of Water at Gold Electrodes Revealed

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

    Molecular Structure of Water at Gold Electrodes Revealed Print The structure of liquid water has been intensely studied, but until recently, it has not been clear what happens to it when a surface is introduced. ALS researchers have now made a first-ever observation of the molecular structure of liquid water at a gold surface under different charging conditions. This marks the first time that the scientific community has shown such high sensitivity in an in-situ environment under working

  16. Molecular Simulation of Protein Aggregation (Journal Article) | SciTech

    Office of Scientific and Technical Information (OSTI)

    Connect Molecular Simulation of Protein Aggregation Citation Details In-Document Search Title: Molecular Simulation of Protein Aggregation Authors: Bratko, Dusan ; Cellmer, Troy ; Prausnitz, John M. ; Blanch, Harvey W. Publication Date: 2006-10-01 OSTI Identifier: 926889 Report Number(s): LBNL--61957 R&D Project: 402201; BnR: KC0302040 DOE Contract Number: DE-AC02-05CH11231 Resource Type: Journal Article Resource Relation: Journal Name: Biotechnology and Bioengineering; Journal Volume:

  17. Molecular Weight Distributions of Irradiated Siloxane-Based Elastomers: A

    Office of Scientific and Technical Information (OSTI)

    Complementary Study by Statistical Modeling and Multiple Quantum Nuclear Magnetic Resonance. (Journal Article) | SciTech Connect Molecular Weight Distributions of Irradiated Siloxane-Based Elastomers: A Complementary Study by Statistical Modeling and Multiple Quantum Nuclear Magnetic Resonance. Citation Details In-Document Search Title: Molecular Weight Distributions of Irradiated Siloxane-Based Elastomers: A Complementary Study by Statistical Modeling and Multiple Quantum Nuclear Magnetic

  18. Molecular design for growth of supramolecular membranes with hierarchical

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    structure (Journal Article) | SciTech Connect Molecular design for growth of supramolecular membranes with hierarchical structure Citation Details In-Document Search Title: Molecular design for growth of supramolecular membranes with hierarchical structure Authors: Zha, R. Helen ; Velichko, Yuri S. ; Bitton, Ronit ; Stupp, Samuel I. [1] + Show Author Affiliations (NWU) Publication Date: 2016-02-10 OSTI Identifier: 1237763 Resource Type: Journal Article Resource Relation: Journal Name: Soft

  19. Preparation of Core-Shell Coordination Molecular Assemblies via the

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    Enrichment of Structure-Directing "Codes" of Bridging Ligands and Metathesis of Metal Units (Journal Article) | SciTech Connect Preparation of Core-Shell Coordination Molecular Assemblies via the Enrichment of Structure-Directing "Codes" of Bridging Ligands and Metathesis of Metal Units Citation Details In-Document Search Title: Preparation of Core-Shell Coordination Molecular Assemblies via the Enrichment of Structure-Directing "Codes" of Bridging Ligands and

  20. Reactive Molecular Simulations of Protonation of Water Clusters and

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    Depletion of Acidity in H-ZSM-5 Zeolite (Journal Article) | SciTech Connect Reactive Molecular Simulations of Protonation of Water Clusters and Depletion of Acidity in H-ZSM-5 Zeolite Citation Details In-Document Search Title: Reactive Molecular Simulations of Protonation of Water Clusters and Depletion of Acidity in H-ZSM-5 Zeolite Authors: Joshi, Kaushik L. [1] ; Psofogiannakis, George [1] ; Van Duin, Adri C. T. [2] ; Raman, Sumathy [3] + Show Author Affiliations Pennsylvania State