Powered by Deep Web Technologies
Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


1

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

SciTech Connect (OSTI)

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

Not Available

1992-12-31T23:59:59.000Z

2

Plant Microbe Interactions | Department of Energy  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankCombustion | Department ofT ib l L d F SSalesOE0000652GrowE-mail onThe2 DOE11.4 Planning andPlant Microbe

3

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

SciTech Connect (OSTI)

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.

Schadt, Christopher [ORNL

2013-03-01T23:59:59.000Z

4

Environmental restoration using plant-microbe bioaugmentation  

SciTech Connect (OSTI)

Land farming, for the purpose of bioremediation, refers traditionally to the spreading of contaminated soil, sediments, or other material over land; mechanically mixing it; incorporating various amendments, such as fertilizer or mulch; and sometimes inoculating with degradative microorganisms. Populations of bacteria added to soils often decline rapidly and become metabolically inactive. To efficiently degrade contaminants, microorganisms must be metabolically active. Thus, a significant obstacle to the successful use of microorganisms for environmental applications is their long-term survival and the expression of their degradative genes in situ. Rhizosphere microorganisms are known to be more metabolically active than those in bulk soil, because they obtain carbon and energy from root exudates and decaying root matter. Rhizosphere populations are also more abundant, often containing 10[sup 8] or more culturable bacteria per gram of soil, and bacterial populations on the rhizoplane can exceed 10[sup 9]/g root. Many of the critical parameters that influence the competitive ability of rhizosphere bacteria have not been identified, but microorganisms have frequently been introduced into soil (bioaugmentation) as part of routine or novel agronomic practices. However, the use of rhizosphere bacteria and their in situ stimulation by plant roots for degrading organic contaminants has received little attention. Published studies have demonstrated the feasibility of using rhizobacteria (Pseudomonas putida) for the rapid removal of chlorinated pesticides from contaminated soil, and to promote germination of radish seeds in the presence of otherwise phytotoxic levels of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and phenoxyacetic acid (PAA). The present investigation was undertaken to determine if these strains (Pseudomonas putida PP0301/pRO101 and PP0301/pRO103) could be used to bioremediate 2,4-D-amended soil via plant-microbe bioaugmentation.

Kingsley, M.T.; Metting, F.B.; Fredrickson, J.K.; Seidler, R.J.

1993-04-01T23:59:59.000Z

5

Environmental restoration using plant-microbe bioaugmentation  

SciTech Connect (OSTI)

Land farming, for the purpose of bioremediation, refers traditionally to the spreading of contaminated soil, sediments, or other material over land; mechanically mixing it; incorporating various amendments, such as fertilizer or mulch; and sometimes inoculating with degradative microorganisms. Populations of bacteria added to soils often decline rapidly and become metabolically inactive. To efficiently degrade contaminants, microorganisms must be metabolically active. Thus, a significant obstacle to the successful use of microorganisms for environmental applications is their long-term survival and the expression of their degradative genes in situ. Rhizosphere microorganisms are known to be more metabolically active than those in bulk soil, because they obtain carbon and energy from root exudates and decaying root matter. Rhizosphere populations are also more abundant, often containing 10{sup 8} or more culturable bacteria per gram of soil, and bacterial populations on the rhizoplane can exceed 10{sup 9}/g root. Many of the critical parameters that influence the competitive ability of rhizosphere bacteria have not been identified, but microorganisms have frequently been introduced into soil (bioaugmentation) as part of routine or novel agronomic practices. However, the use of rhizosphere bacteria and their in situ stimulation by plant roots for degrading organic contaminants has received little attention. Published studies have demonstrated the feasibility of using rhizobacteria (Pseudomonas putida) for the rapid removal of chlorinated pesticides from contaminated soil, and to promote germination of radish seeds in the presence of otherwise phytotoxic levels of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and phenoxyacetic acid (PAA). The present investigation was undertaken to determine if these strains (Pseudomonas putida PPO301/pRO101 and PPO301/pRO103) could be used to bioremediate 2,4-D-amended soil via plant-microbe bioaugmentation.

Kingsley, M.T.; Fredrickson, J.K.; Metting, F.B.; Seidler, R.J.

1993-04-01T23:59:59.000Z

6

Detection of molecular interactions  

DOE Patents [OSTI]

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.

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

2012-02-14T23:59:59.000Z

7

Theoretical studies of molecular interactions  

SciTech Connect (OSTI)

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.

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

1993-12-01T23:59:59.000Z

8

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

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

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

9

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

SciTech Connect (OSTI)

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.

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

2014-11-14T23:59:59.000Z

10

DockingShop: A Tool for Interactive Molecular Docking  

SciTech Connect (OSTI)

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

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

2005-04-24T23:59:59.000Z

11

Bacterial indole-3-acetic acid production: a key mediator of plant-microbe interactions between Phaseolus vulgaris and the foliar epiphyte Pantoea agglomerans 299R  

E-Print Network [OSTI]

and Xanthomonas campestris pv vesicatoria. Plant Physiology.and Xanthomonas campestris pv vesicatoria. Plant Physiology.P. syringae pv. tomato DC3000: plants unable to repress

Powell, Tracy Kathleen

2011-01-01T23:59:59.000Z

12

Three Dimensional Molecular Imaging for Lignocellulosic Materials  

SciTech Connect (OSTI)

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

Bohn, Paul W.; Sweedler, Jonathan V.

2011-06-09T23:59:59.000Z

13

2010 Plant Molecular Biology Gordon Research Conference  

SciTech Connect (OSTI)

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.

Michael Sussman

2010-07-23T23:59:59.000Z

14

Assembling, analyzing, refining, and cataloging molecular interaction network  

E-Print Network [OSTI]

ASSEMBLING, ANALYZING, REFINING, AND CATALOGING MOLECULARASSEMBLING, ANALYZING, REFINING, AND CATALOGING MOLECULAR

Mak, Huajiang Craig

2008-01-01T23:59:59.000Z

15

Molecular surface electrostatic potentials in the analysis of non-hydrogen-bonding noncovalent interactions  

SciTech Connect (OSTI)

Electrostatic potentials computed on molecular surfaces are used to analyze some noncovalent interactions that are not in the category of hydrogen bonding, e.g. halogen bonding. The systems examined include halogenated methanes, substituted benzenes, s-tetrazine and 1,3-bisphenylurea. The data were obtained by ab initio SCF calculations. Electrostatic potentials, Non-hydrogen-bonding noncovalent interactions, Molecular surfaces.

Murray, J.S.; Paulsen, K.; Politzer, P.

1993-12-27T23:59:59.000Z

16

Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies  

SciTech Connect (OSTI)

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

Gary J. Blanchard

2009-06-30T23:59:59.000Z

17

assessing molecular interaction: Topics by E-print Network  

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

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

18

Efficiency at maximum power of interacting molecular machines  

E-Print Network [OSTI]

We investigate the efficiency of systems of molecular motors operating at maximum power. We consider two models of kinesin motors on a microtubule: for both the simplified and the detailed model, we find that the many-body exclusion effect enhances the efficiency at maximum power of the many-motor system, with respect to the single motor case. Remarkably, we find that this effect occurs in a limited region of the system parameters, compatible with the biologically relevant range.

N. Golubeva; A. Imparato

2012-10-22T23:59:59.000Z

19

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

E-Print Network [OSTI]

Alpha-D-Glucose GTP Guanosine-5'-Triphosphate GTPCHI GTP-cyclohydrolase I GV Gap Volume HB Hydrogen Bond HBA Hydrogen Bond Acceptor HBD Hydrogen Bond Donor HBPLUS Software to calculate hydrogen bonds in proteins HEM Heme HIV-1 Human Immunodeficiency... Methyllysine mmCIF Macromolecular Crystallographic Information Files MSE Selenomethionine MW Molecular Weight MySQL Open source database engine NAD Nicotinamide Adenine Dinucleotide NAP Nicotinamide Adenine Dinucleotide Phosphate NCC Neighbouring Chemical...

Higueruelo, Alicia Perez

2012-05-08T23:59:59.000Z

20

Molecular force spectroscopy of homophilic nectin-1 interactions  

SciTech Connect (OSTI)

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

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

2007-11-03T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Molecular Interaction between Botulinum Neurotoxin B and Its Protein  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recovery challenge fundProject8Mistakes to AvoidKinetics Molecular Beam

22

Molecular conformations, interactions, and properties associated with drug  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recovery challenge fundProject8Mistakes toMolecular Structure of Water

23

Optimum protein-excipient interactions using molecular docking simulations  

E-Print Network [OSTI]

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

Tarar, Haider

2014-04-01T23:59:59.000Z

24

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

E-Print Network [OSTI]

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

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

2015-01-01T23:59:59.000Z

25

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

E-Print Network [OSTI]

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

Southern California, University of

26

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

SciTech Connect (OSTI)

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

Holkundkar, Amol R. [Department of Physics, Birla Institute of Technology and Science, Pilani-333 031 (India)] [Department of Physics, Birla Institute of Technology and Science, Pilani-333 031 (India)

2013-11-15T23:59:59.000Z

27

Interaction potentials of molecular clusters with applications to collision rate calculations  

E-Print Network [OSTI]

: William H. Marlow (Chair of Commitee) on R. Hart (M her) Marko aric (M r) J. W, Poston (Head of Department) December 1989 ABSTRACT Interaction Potentials of Molecular Clusters with Applications to Collision Rates. (December 1989) Alexis Sylvain... Parents. . . ACKNOWLEDGEMENTS I would like to thank the persons without whom this work would not have been possible. Among those, I would like to express my gratitude to my Conunittee Chairman Dr, W. H. Marlow for his guidance, kindness and dedication...

Amadon, Alexis Sylvain

2012-06-07T23:59:59.000Z

28

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

SciTech Connect (OSTI)

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.

Zwier, Timothy

2012-07-20T23:59:59.000Z

29

Realizing strong light-matter interactions between single nanoparticle plasmons and molecular excitons at ambient conditions  

E-Print Network [OSTI]

Realizing strong light-matter interactions between individual 2-level systems and resonating cavities in atomic and solid state systems opens up possibilities to study optical nonlinearities on a single photon level, which can be useful for future quantum information processing networks. However, these efforts have been hampered by the unfavorable experimental conditions, such as cryogenic temperatures and ultrahigh vacuum, required to study such systems and phenomena. Although several attempts to realize strong light-matter interactions at room-temperature using so-called plasmon resonances have been made, successful realizations on the single nanoparticle level are still lacking. Here, we demonstrate strong coupling between plasmons confined within a single silver nanoprism and excitons in molecular J-aggregates at ambient conditions. Our findings show that the deep subwavelength mode volumes, $V$, together with high quality factors, $Q$, associated with plasmons in the nanoprisms result in strong coupling ...

Zengin, Gülis; Nilsson, Sara; Antosiewicz, Tomasz J; Käll, Mikael; Shegai, Timur

2015-01-01T23:59:59.000Z

30

Molecular Dynamics - Solvated Interaction Energy Studies of Protein-Protein Interactions; The MP1-p14 Scaffolding Complex  

SciTech Connect (OSTI)

Using the MP1-p14 scaffolding complex from the mitogen-activated protein kinase signaling pathway as model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. Hot spots are located by virtual alanine-scanning consensus predictions over three different energy functions and two different single-structure representations of the complex. Refined binding affinity predictions for select hot-spot mutations are carried out by applying first-principle methods such as the molecular mechanics generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) to the molecular dynamics (MD) trajectories for mutated and wild-type complexes. Here, predicted hot-spot residues were actually mutated to alanine, and crystal structures of the mutated complexes were determined. Two mutated MP1-p14 complexes were investigated, the p14(Y56A)-mutated complex and the MP1(L63A, L65A)-mutated complex. Alternative ways to generate MD ensembles for mutant complexes, not relying on crystal structures for mutated complexes, were also investigated. The SIE function, fitted on protein-ligand binding affinities, gave absolute binding affinity predictions in excellent agreement with experiment and outperformed standard MM-GBSA predictions when tested on the MD ensembles of Ras-Raf and Ras-RalGDS protein-protein complexes. For wild-type and mutant MP1-p14 complexes, SIE predictions of relative binding affinities were supported by a yeast two-hybrid assay that provided semiquantitative relative interaction strengths. Results on the MP1-mutated complex suggested that SIE predictions deteriorate if mutant MD ensembles are approximated by just mutating the wild-type MD trajectory. The SIE data on the p14-mutated complex indicated feasibility for generating mutant MD ensembles from mutated wild-type crystal structure, despite local structural differences observed upon mutation. For energetic considerations, this would circumvent costly needs to produce and crystallize mutated complexes. The sensitized protein-protein interface afforded by the p14(Y56A) mutation identified here has practical applications in screening-based discovery of first-generation small-molecule hits for further development into specific modulators of the mitogen-activated protein kinase signaling pathway.

Cui,Q.; Sulea, T.; Schrag, J.; Munger, C.; Hung, M.; Naim, M.; Cygler, M.; Purisima, E.

2008-01-01T23:59:59.000Z

31

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

E-Print Network [OSTI]

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

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

2014-01-01T23:59:59.000Z

32

Interaction potential for silicon carbide: A molecular dynamics study of elastic constants and vibrational density of states for crystalline  

E-Print Network [OSTI]

Interaction potential for silicon carbide: A molecular dynamics study of elastic constants and vibrational density of states for crystalline and amorphous silicon carbide Priya Vashishta,a Rajiv K. Kalia Silicon carbide SiC has been proposed for a wide range of technological applications

Southern California, University of

33

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

E-Print Network [OSTI]

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

34

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

SciTech Connect (OSTI)

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.

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

2013-05-20T23:59:59.000Z

35

Self-interaction corrected density functional calculations of molecular Rydberg states  

SciTech Connect (OSTI)

A method is presented for calculating the wave function and energy of Rydberg excited states of molecules. A good estimate of the Rydberg state orbital is obtained using ground state density functional theory including Perdew-Zunger self-interaction correction and an optimized effective potential. The total energy of the excited molecule is obtained using the Delta Self-Consistent Field method where an electron is removed from the highest occupied orbital and placed in the Rydberg orbital. Results are presented for the first few Rydberg states of NH{sub 3}, H{sub 2}O, H{sub 2}CO, C{sub 2}H{sub 4}, and N(CH{sub 3}){sub 3}. The mean absolute error in the energy of the 33 molecular Rydberg states presented here is 0.18 eV. The orbitals are represented on a real space grid, avoiding the dependence on diffuse atomic basis sets. As in standard density functional theory calculations, the computational effort scales as NM{sup 2} where N is the number of orbitals and M is the number of grid points included in the calculation. Due to the slow scaling of the computational effort with system size and the high level of parallelism in the real space grid approach, the method presented here makes it possible to estimate Rydberg electron binding energy in large molecules.

Gudmundsdóttir, Hildur [Science Institute of the University of Iceland, 107 Reykjavík (Iceland)] [Science Institute of the University of Iceland, 107 Reykjavík (Iceland); Zhang, Yao; Weber, Peter M. [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States)] [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States); Jónsson, Hannes [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States) [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States); Faculty of Physical Sciences, VR-III, University of Iceland, 107 Reykjavík (Iceland)

2013-11-21T23:59:59.000Z

36

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

SciTech Connect (OSTI)

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

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

2014-03-14T23:59:59.000Z

37

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

SciTech Connect (OSTI)

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

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

1994-01-01T23:59:59.000Z

38

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)

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.

Larsen, Peter [Argonne

2013-03-01T23:59:59.000Z

39

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

E-Print Network [OSTI]

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

Barch, Mariya

2009-01-01T23:59:59.000Z

40

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

E-Print Network [OSTI]

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

Wang, Wei

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

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

E-Print Network [OSTI]

Chemistry 685 (CHE 685) Advanced Organic Chemistry: Organic Reaction Mechanisms and Molecular and physical chemistry Course description and rationale CHE685 is a graduate-level organic chemistry course. These two courses focus on physical organic chemistry, which deals with the structure and reactivity

Mather, Patrick T.

42

Interaction between the molecular coherent states for a discrete variable harmonic oscillator and the coherent radiation  

SciTech Connect (OSTI)

We used the dicrete variable three-dimmensional Charlier oscillator. For a system of molecules interacting with the coherent radiation field the temporal variation of the refractive index has been established.

Draganescu, Gheorghe Eugen [Department of Mechanics, Polytechnic University of Timisoara, Bd M Viteazu No1, Timisoara and Department of Physics, West University of Timisoara (Romania)

2012-08-17T23:59:59.000Z

43

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

E-Print Network [OSTI]

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

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

2014-01-01T23:59:59.000Z

44

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

SciTech Connect (OSTI)

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.

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

2014-09-14T23:59:59.000Z

45

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

SciTech Connect (OSTI)

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

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

2014-06-07T23:59:59.000Z

46

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

SciTech Connect (OSTI)

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.

Kang, Kyung

2011-05-11T23:59:59.000Z

47

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

E-Print Network [OSTI]

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

Sander Woutersen

2007-03-06T23:59:59.000Z

48

Monitoring molecular interactions using photon arrival-time interval distribution analysis  

SciTech Connect (OSTI)

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.

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

2009-10-06T23:59:59.000Z

49

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

SciTech Connect (OSTI)

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

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

2010-11-15T23:59:59.000Z

50

An STM Study of Molecular Self-Assemblies on Cu(111): Structure, Interaction, and Effects of Confinement  

E-Print Network [OSTI]

mechanism for molecular self?assembly  on metal substrates: Heim, D.  et al.  Self?Assembly of Flexible One?Dimensional coordination chemistry and self?assembly.   Dalton T, 2794?

Luo, Miaomiao

2012-01-01T23:59:59.000Z

51

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

SciTech Connect (OSTI)

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%.

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

2006-04-21T23:59:59.000Z

52

Interaction potential for aluminum nitride: A molecular dynamics study of mechanical and thermal properties of crystalline and amorphous  

E-Print Network [OSTI]

for AlN is proposed. The potential consists of two-body and three-body covalent interactions. The two-body are described by the three-body potential. The proposed three-body interaction potential is a modificationN for several densities and temperatures. The structural energy for wurtzite 2H structure has the lowest energy

Southern California, University of

53

Theoretical Studies of Solid-Liquid Interfaces: Molecular Interactions at the MgO(001)-Water Interface  

E-Print Network [OSTI]

as these compounds are major components of rocks, soils, and airborne dust particles. In addition, metal oxides often groups.2-6 Recently, classical molecular mechanical models appeared which can address the structural chemistry are needed. A few quantum mechanical calculations concerning the properties of water and hydroxyl

Truong, Thanh N.

54

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.

55

Role of PeptidePeptide Interactions in Stabilizing Peptide-Wrapped Single-Walled Carbon Nanotubes: A Molecular Dynamics Study  

E-Print Network [OSTI]

, and energy conservation devices.2 Unfortunately, car- bon nanotubes are extremely hydrophobic which leadsRole of Peptide­Peptide Interactions in Stabilizing Peptide-Wrapped Single-Walled Carbon Nanotubes at biopolymers@wiley. com INTRODUCTION S ingle-walled carbon nanotubes (SWNTs) are hollow cylinders formed

Nielsen, Steven O.

56

E-Print Network 3.0 - alternaria alternata fungo Sample Search...  

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

phus... oxysporum and Alternaria alternata. Mol Plant-Microbe Interact 13:130-139 Armstrong CL, Chongo G, Gossen BD... in MAT loci of several loculoascomycete fungi,...

57

An efficient method for visualization and growth of fluorescent Xanthomonas oryzae pv. oryzae in planta.  

E-Print Network [OSTI]

strains, plants and growth conditions Xanthomonas oryzae pv.Xanthomonas oryzae pv. oryzae. Mol Plant Microbe InteractOryzae sativa L. ) plants. X. oryzae pv. oryzae infection

Han, Sang-Wook; Park, Chang-Jin; Lee, Sang-Won; Ronald, Pamela C

2008-01-01T23:59:59.000Z

58

Purification of soluble and active RaxH, a transmembrane histidine protein kinase from Xanthomonas oryzae pv. oryzae required for AvrXa21 activity.  

E-Print Network [OSTI]

of the plant pathogenic bacterium Xanthomonas campestris pv.oryzae pv. oryzae isolates in transgenic plants. Mol. Plant–Xanthomonas oryzae pv. oryzae. Mol. Plant–Microbe Interact.

Stolov, Avital; Valverde, Angel; Ronald, Pamela; Burdman, Saul

2007-01-01T23:59:59.000Z

59

Biochemical and Functional Characterization of the GH3 Amino Acid-Conjugase PBS3 of Arabidopsis thaliana  

E-Print Network [OSTI]

with the plant pathogen Pseudomonas syringae pv. tomatosyringae pv. Phaseolicola. Mol Plant Microbe Interact 8,plants were treated with elicitors such as Pseudomonas syringae pv.

Okrent, Rachel Allegra

2010-01-01T23:59:59.000Z

60

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

SciTech Connect (OSTI)

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.

Bond, Stephen D.

2014-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

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

E-Print Network [OSTI]

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

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

2007-10-27T23:59:59.000Z

62

Self-interaction-free time-dependent density-functional theory for molecular processes in strong fields: High-order harmonic generation of H2 in intense laser fields  

E-Print Network [OSTI]

Self-interaction-free time-dependent density-functional theory for molecular processes in strong work of Hohenberg and Kohn 1 and Kohn and Sham 2 , the steady-state density-functional theory DFT has-electron systems, within the density-functional theory, is much less developed. The central theme of the modern

Chu, Shih-I

63

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

SciTech Connect (OSTI)

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

Wolk, C.P.

1992-07-01T23:59:59.000Z

64

Interdisciplinary Research and Training Program in the Plant Sciences  

SciTech Connect (OSTI)

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

Wolk, C.P.

1992-01-01T23:59:59.000Z

65

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

SciTech Connect (OSTI)

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

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

2013-01-01T23:59:59.000Z

66

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

E-Print Network [OSTI]

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

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

2010-06-01T23:59:59.000Z

67

Homogeneous Cooling with Repulsive and Attractive Long-range Interactions  

E-Print Network [OSTI]

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

Luding, Stefan

68

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

E-Print Network [OSTI]

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

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

2015-01-01T23:59:59.000Z

69

MSU-DOE Plant Research Laboratory  

SciTech Connect (OSTI)

This document is the compiled progress reports of research funded through the Michigan State University/Department of Energy Plant Research Laboratory. Fourteen reports are included, covering the molecular basis of plant/microbe symbiosis, cell wall biosynthesis and proteins, gene expression, stress responses, plant hormone biosynthesis, interactions between the nuclear and organelle genomes, sensory transduction and tropisms, intracellular sorting and trafficking, regulation of lipid metabolism, molecular basis of disease resistance and plant pathogenesis, developmental biology of Cyanobacteria, and hormonal involvement in environmental control of plant growth. 320 refs., 26 figs., 3 tabs. (MHB)

Not Available

1991-01-01T23:59:59.000Z

70

Interaction of copper oxides with reaction medium in heterogeneous catalytic oxidation of carbon monoxide by molecular oxygen. IV. IR spectroscopic study of carbon monoxide interaction with copper oxide surface  

SciTech Connect (OSTI)

An IR spectroscopic study has been made of the interaction of CO with CuO prepared in different ways, and the interaction of O/sub 2/ with carbon monoxide preadsorbed on CuO. A number of Cu/sup +/CO surface complexes have been detected (2114-2148 cm/sup -1/) with a heat of adsorption about 79.5-180 kJ/mole. From an analysis of the nature of these complexes, we have evaluated the processes taking place on the CuO surface when it interacts with CO and have compared the properties of massive CuO with those of CuO on oxide supports. The data are interpreted on the assumption that extended defects - dislocations - exist and play an important role, determining to a considerable degree the properties of the massive CuO in the reaction of CO oxidation.

Lokhov, Y.A.; Popovskii, V.V.; Sadykov, V.A.; Tikhov, S.F.

1985-08-01T23:59:59.000Z

71

Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations  

SciTech Connect (OSTI)

The behavior of the UO{sub 2}{sup 2+} uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT +U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 A above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d{sub U-O{sub a{sub d{sub s{sub o{sub r{sub p{sub t{sub i{sub o{sub n}}}}}}}}}}}=2.39 A. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

Sebbari, Karim [EDF-R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Ecuelles, 77818 Moret Sur Loing (France); Institut de Physique Nucleaire d'Orsay, Universite Paris-Sud, CNRS UMR 8608, 15 rue Georges Clemenceau, Batiment 100, 91406 Orsay Cedex (France); Roques, Jerome; Simoni, Eric [Institut de Physique Nucleaire d'Orsay, Universite Paris-Sud, CNRS UMR 8608, 15 rue Georges Clemenceau, Batiment 100, 91406 Orsay Cedex (France); Domain, Christophe [EDF-R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Ecuelles, 77818 Moret Sur Loing (France)

2012-10-28T23:59:59.000Z

72

Magnetismo Molecular (Molecular Magentism)  

SciTech Connect (OSTI)

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

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

2010-07-01T23:59:59.000Z

73

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

SciTech Connect (OSTI)

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.

Markutsya, Sergiy [Ames Laboratory; Lamm, Monica H [Ames Laboratory

2014-11-07T23:59:59.000Z

74

INTERACTING COSMIC RAYS WITH MOLECULAR CLOUDS: A BREMSSTRAHLUNG ORIGIN OF DIFFUSE HIGH-ENERGY EMISSION FROM THE INNER 2 Degree-Sign Multiplication-Sign 1 Degree-Sign OF THE GALACTIC CENTER  

SciTech Connect (OSTI)

The high-energy activity in the inner few degrees of the Galactic center is traced by diffuse radio, X-ray, and {gamma}-ray emission. The physical relationship between different components of diffuse gas emitting at multiple wavelengths is a focus of this work. We first present radio continuum observations using the Green Bank Telescope and model the nonthermal spectrum in terms of a broken power-law distribution of {approx}GeV electrons emitting synchrotron radiation. We show that the emission detected by Fermi is primarily due to nonthermal bremsstrahlung produced by the population of synchrotron emitting electrons in the GeV energy range interacting with neutral gas. The extrapolation of the electron population measured from radio data to low and high energies can also explain the origin of Fe I 6.4 keV line and diffuse TeV emission, as observed with Suzaku, XMM-Newton, Chandra, and the H.E.S.S. observatories. The inferred physical quantities from modeling multiwavelength emission in the context of bremsstrahlung emission from the inner {approx}300 Multiplication-Sign 120 pc of the Galactic center are constrained to have the cosmic-ray ionization rate {approx}1-10 Multiplication-Sign 10{sup -15} s{sup -1}, molecular gas heating rate elevating the gas temperature to 75-200 K, fractional ionization of molecular gas 10{sup -6}-10{sup -5}, large-scale magnetic field 10-20 {mu}G, the density of diffuse and dense molecular gas {approx}100 and {approx}10{sup 3} cm{sup -3} over 300 pc and 50 pc path lengths, and the variability of Fe I K{alpha} 6.4 keV line emission on yearly timescales. Important implications of our study are that GeV electrons emitting in radio can explain the GeV {gamma}-rays detected by Fermi and that the cosmic-ray irradiation model, like the model of the X-ray irradiation triggered by past activity of Sgr A*, can also explain the origin of the variable 6.4 keV emission from Galactic center molecular clouds.

Yusef-Zadeh, F.; Roberts, D. A.; Royster, M. [Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208 (United States)] [Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208 (United States); Hewitt, J. W. [Code 662, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States)] [Code 662, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Wardle, M. [Department of Physics and Astronomy, and Research Center for Astronomy, Astrophysics and Astrophotonics, Macquarie University, Sydney, NSW 2109 (Australia)] [Department of Physics and Astronomy, and Research Center for Astronomy, Astrophysics and Astrophotonics, Macquarie University, Sydney, NSW 2109 (Australia); Tatischeff, V. [Center de Spectrometrie Nucleaire et de Spectrometrie de Massse, IN2P3/CNRS and Univ. Paris-Sud, F-91405 Orsay Campus (France)] [Center de Spectrometrie Nucleaire et de Spectrometrie de Massse, IN2P3/CNRS and Univ. Paris-Sud, F-91405 Orsay Campus (France); Cotton, W. [NRAO, 520 Edgemont Road, Charlottesville, VA 22903 (United States)] [NRAO, 520 Edgemont Road, Charlottesville, VA 22903 (United States); Uchiyama, H.; Nobukawa, M.; Tsuru, T. G. [Cosmic Ray Group, Physics, Kyoto University, Kitashirakawa-Oiwake-Cho, Sakyo, Kyoto 606-8502 (Japan)] [Cosmic Ray Group, Physics, Kyoto University, Kitashirakawa-Oiwake-Cho, Sakyo, Kyoto 606-8502 (Japan); Heinke, C. [Department of Physics, Room 238 CEB, University of Alberta, Edmonton, AB T6G 2G7 (Canada)] [Department of Physics, Room 238 CEB, University of Alberta, Edmonton, AB T6G 2G7 (Canada)

2013-01-01T23:59:59.000Z

75

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

E-Print Network [OSTI]

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

Poldrack, Russ

76

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

E-Print Network [OSTI]

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

B. J. Smith; C. Struck

2000-11-03T23:59:59.000Z

77

BE.462J Molecular Principles of Biomaterials, Spring 2003  

E-Print Network [OSTI]

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

Irvine, Darrell J.

78

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

E-Print Network [OSTI]

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

Wood, Kris Cameron

2007-01-01T23:59:59.000Z

79

Photoassociative molecular spectroscopy for atomic radiative lifetimes.  

E-Print Network [OSTI]

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

Boyer, Edmond

80

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

SciTech Connect (OSTI)

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.

Orphan, Victoria Jeanne [California Institute of Technology

2014-11-26T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

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

E-Print Network [OSTI]

We examine via molecular simulation the dependence of the crystal-melt interfacial free energy gamma on molecular interaction and crystal structure (fcc vs bcc) for systems interacting with inverse-power repulsive potentials, u...

Davidchack, R. L.; Laird, Brian Bostian

2005-03-01T23:59:59.000Z

82

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

E-Print Network [OSTI]

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

Ferreira, Márcia M. C.

83

Biology is the study of life. Its scope ranges from the molecular to the ecosystem. It deals with fundamental questions such as the origin and evolution of plants and animals, interactions  

E-Print Network [OSTI]

Biology is the study of life. Its scope ranges from the molecular to the ecosystem. It deals diseases, and the operation of the brain and the nervous system. The study of Biology has major practical. The programs in Biology provide students with an introduction to the broad spectrum of Biological Sciences

Barthelat, Francois

84

Modeling Molecular Dynamics from Simulations  

SciTech Connect (OSTI)

Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.

Hinrichs, Nina Singhal (University of Chicago) [University of Chicago

2009-01-28T23:59:59.000Z

85

Molecular Gas in Galaxies  

E-Print Network [OSTI]

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

F. Combes

2000-07-21T23:59:59.000Z

86

Decoding Photosynthesis' Molecular Mysteries  

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...

87

Physics with fast molecular-ion beams  

SciTech Connect (OSTI)

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.

Kanter, E.P.

1980-01-01T23:59:59.000Z

88

Interactive Environments  

E-Print Network [OSTI]

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

89

Molecular information ratchets   

E-Print Network [OSTI]

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

Wilson, Adam Christopher

2012-11-28T23:59:59.000Z

90

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

E-Print Network [OSTI]

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

Van Vliet, Krystyn J.

91

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

E-Print Network [OSTI]

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

Irvine, Darrell J.

92

iscoverD COLLEGE OF AGRICULTURAL AND ENVIRONMENTAL SCIENCES The department strives to be the  

E-Print Network [OSTI]

, the beneficial interactions between microbes and plant roots, and the impacts of farming on soil biology study of the biology and ecology of soil microbes, plant-microbe interactions, and plant pathogens-microbe interactions and the development of innovative approaches to plant disease control. Faculty are international

Ferrara, Katherine W.

93

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

E-Print Network [OSTI]

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

Ferreira, Márcia M. C.

94

developments. interactive  

E-Print Network [OSTI]

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

Jaun, André

95

Calculation of molecular free energies in classical potentials  

E-Print Network [OSTI]

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

Farhi, Asaf

2015-01-01T23:59:59.000Z

96

Molecular electrostatic potentials by systematic molecular fragmentation  

SciTech Connect (OSTI)

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

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

2013-11-14T23:59:59.000Z

97

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

E-Print Network [OSTI]

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

Zyto, Aurore

2008-01-01T23:59:59.000Z

98

E-Print Network 3.0 - atomic interaction networks Sample Search...  

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

Materials Science 3 Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes Summary: on these potentials, interactions between catalytic metals and...

99

Molecular Cluster Perturbation Theory. I. Formalism  

E-Print Network [OSTI]

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

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

2015-03-23T23:59:59.000Z

100

Molecular Cluster Perturbation Theory. I. Formalism  

E-Print Network [OSTI]

We present second-order molecular cluster perturbation theory (MCPT(2)), a methodology to calculate arbitrarily large systems with explicit calculation of individual wavefunctions in a coupled-cluster framework. This new MCPT(2) framework uses coupled-cluster perturbation theory and an expansion in terms of molecular dimer interactions to obtain molecular wavefunctions that are infinite-order in both the electronic fluctuation operator and all possible dimer (and products of dimers) interactions. The MCPT(2) framework has been implemented in the new SIA/ACES parallel architecture, making use of the advanced dynamic memory control and fine grained parallelism to perform very large explicit molecular cluster calculations. To illustrate the power of this method, we have computed energy shifts and lattice site dipole moments via explicit calculation of the bulk system for the polar and non-polar configurations of solid hydrogen fluoride. The explicit lattice size without periodic boundary conditions was expanded up to 1,000 HF molecules, with 32,000 basis functions and 10,000 electrons. Our obtained HF lattice site dipole moments of 2.51 and 2.49 Debye (for the polar and non-polar configurations, respectively) are in good agreement with the existing literature values of 2.51 and 2.47.

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

2014-09-06T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

Molecular Cluster Perturbation Theory. I. Formalism  

E-Print Network [OSTI]

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

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

2015-01-14T23:59:59.000Z

102

Computational methods for molecular docking  

SciTech Connect (OSTI)

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

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

1995-12-31T23:59:59.000Z

103

Molecular heat pump  

E-Print Network [OSTI]

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

Dvira Segal; Abraham Nitzan

2005-10-11T23:59:59.000Z

104

Accelerated molecular dynamics methods  

SciTech Connect (OSTI)

The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.

Perez, Danny [Los Alamos National Laboratory

2011-01-04T23:59:59.000Z

105

Interactive Jobs  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-SeriesFlickrinformation for and NovelFEG-SEM with0, FirstIntelligenceInteractive

106

Theory of Molecular Machines. I. Channel Capacity of Molecular Machines  

E-Print Network [OSTI]

Theory of Molecular Machines. I. Channel Capacity of Molecular Machines running title: Channel Capacity of Molecular Machines Thomas D. Schneider version = 5.76 of ccmm.tex 2004 Feb 3 Version 5.67 was submitted 1990 December 5 Schneider, T. D. (1991). Theory of molecular machines. I. Channel capacity

Schneider, Thomas D.

107

Structure of the Alkali-metal-atom-Strontium molecular ions: towards photoassociation and formation of cold molecular ions  

E-Print Network [OSTI]

The potential energy curves, permanent and transition dipole moments, and the static dipolar polarizability, of molecular ions composed of one alkali-metal atom and a Strontium ion are determined with a quantum chemistry approach. The molecular ions are treated as effective two-electron systems and are treated using effective core potentials including core polarization, large gaussian basis sets, and full configuration interaction. In the perspective of upcoming experiments aiming at merging cold atom and cold ion traps, possible paths for radiative charge exchange, photoassociation of a cold Lithium or Rubidium atom and a Strontium ion are discussed, as well as the formation of stable molecular ions.

Mireille Aymar; Romain Guérout; Olivier Dulieu

2011-02-24T23:59:59.000Z

108

Structure of the alkali-metal-atom + strontium molecular ions: Towards photoassociation and formation of cold molecular ions  

SciTech Connect (OSTI)

The potential energy curves, permanent and transition dipole moments, and the static dipolar polarizability, of molecular ions composed of one alkali-metal atom and a strontium ion are determined with a quantum chemistry approach. The molecular ions are treated as effective two-electron systems and are treated using effective core potentials including core polarization, large gaussian basis sets, and full configuration interaction. In the perspective of upcoming experiments aiming at merging cold atom and cold ion traps, possible paths for radiative charge exchange, photoassociation of a cold lithium or rubidium atom and a strontium ion are discussed, as well as the formation of stable molecular ions.

Aymar, M.; Dulieu, O. [Laboratoire Aime Cotton, CNRS, UPR3321, Ba circumflex t. 505, Univ Paris-Sud, 91405 Orsay Cedex (France); Guerout, R. [Laboratoire Kastler-Brossel, CNRS, ENS, Univ Pierre et Marie Curie case 74, Campus Jussieu, F-75252 Paris Cedex 05 (France)

2011-08-14T23:59:59.000Z

109

Structure of the Alkali-metal-atom-Strontium molecular ions: towards photoassociation and formation of cold molecular ions  

E-Print Network [OSTI]

The potential energy curves, permanent and transition dipole moments, and the static dipolar polarizability, of molecular ions composed of one alkali-metal atom and a Strontium ion are determined with a quantum chemistry approach. The molecular ions are treated as effective two-electron systems and are treated using effective core potentials including core polarization, large gaussian basis sets, and full configuration interaction. In the perspective of upcoming experiments aiming at merging cold atom and cold ion traps, possible paths for radiative charge exchange, photoassociation of a cold Lithium or Rubidium atom and a Strontium ion are discussed, as well as the formation of stable molecular ions.

Aymar, Mireille; Dulieu, Olivier

2011-01-01T23:59:59.000Z

110

Twelfth Annual Report Interactive Graphics for Molecular Studies  

E-Print Network [OSTI]

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

North Carolina at Chapel Hill, University of

111

Molecular Interactions of Plutonium(VI) with Synthetic  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: VegetationEquipment SurfacesResource ProgramModification and Application ofof aEMSL

112

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

SciTech Connect (OSTI)

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

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

2014-10-16T23:59:59.000Z

113

Molecular gas and the dynamics of galaxies  

E-Print Network [OSTI]

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

F. Combes

1999-02-01T23:59:59.000Z

114

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

SciTech Connect (OSTI)

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.

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

2014-01-01T23:59:59.000Z

115

Molecular Dynamics Simulation of Damage Cascade Formation in Ion Bombarded Solids  

E-Print Network [OSTI]

/Molecular Massively Parallel Simulator). In one subtask, we studied damage cascade interactions caused by two 2 keV Si atoms simultaneously bombarding a crystalline Si substrate. We found that the enhanced displacement creation appears primarily in the thermal spike...

Chen, Di

2012-10-19T23:59:59.000Z

116

A co-axially configured submillimeter spectrometer and investigations of hydrogen bound molecular complexes  

E-Print Network [OSTI]

The development of a co-axially configured submillimeter spectrometer is reported. The spectrometer has been constructed to observe molecular complexes that exhibit non-covalent interactions with energies much less than that of a traditional...

McElmurry, Blake Anthony

2009-05-15T23:59:59.000Z

117

HNCO in molecular clouds  

SciTech Connect (OSTI)

In a survey of 18 molecular clouds, HNCO J/sub K/-1K1..-->..J'/sub K/'-1K'1 = 5/sub 05/..-->..4/sub 05/ and 4/sub 04/..-->..3/sub 03/ emission was etected in seven clouds, and possibly in one other. Emission in these transitions originates in high-density regions (n> or approx. =10/sup 6/ cm/sup -3/). The molecule's excitation requirements allow us to derive limits to excitation temperatures an optical depths. We discuss the possibility of clumping with respect to the beam and compare our results with data from other molecular species. The HNCO emission from Sgr A is an ordder of magnitude larger than the other detected sources as is the ratio ..delta..T +- /sub A/(HNCO 5/sub 05/..-->..4/sub 04/)/..delta..T +- /sub A/(C/sup 18/O 1..-->..0). HNCO is probably a constituent of most molecular clouds.

Jackson, J.M.; Armstrong, J.T.; Barrett, A.H.

1984-05-15T23:59:59.000Z

118

Substructured multibody molecular dynamics.  

SciTech Connect (OSTI)

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.

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

2006-11-01T23:59:59.000Z

119

The internal and translational energy dependence of molecular condensation coefficients: SF6 and CC&,  

E-Print Network [OSTI]

and the target surface since the gas-surface interaction potential is sampled by "single collision" scatteringThe internal and translational energy dependence of molecular condensation coefficients: SF6 and CC examine the internal and translational energy dependence of the molecular condensation probabilities

Mills, Allen P.

120

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

E-Print Network [OSTI]

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

Grant, Martin

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

Molecular dynamics simulation of Li surface erosion and bubble formation  

E-Print Network [OSTI]

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

Harilal, S. S.

122

Nano Research Kinetics of Molecular Recognition Mediated Nanoparticle  

E-Print Network [OSTI]

Nano Research Kinetics of Molecular Recognition Mediated Nanoparticle Self-Assembly Chinmay Soman1 the streptavidin-biotin interaction [9] 0078 Nano Res (2009) 2: 78 84 DOI 10.1007/s12274-009-9005-z Research Article #12;79Nano Res (2009) 2: 78 84 are incubated with specific antigens in a physiological buffer

123

Molecular Squares as Molecular Sieves: Size-Selective Transport Through  

E-Print Network [OSTI]

Molecular Squares as Molecular Sieves: Size-Selective Transport Through Porous-Membrane squaresº: cyclic structures typically featuring metal-ion cor- ners and difunctional bridging ligands processes: size-selective molecular transport from a guest-containing solution to one initially free

124

Molecular Gas in Early-type Galaxies  

E-Print Network [OSTI]

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

Alatalo, Katherine Anne

2012-01-01T23:59:59.000Z

125

Interactive portraiture : designing intimate interactive experiences  

E-Print Network [OSTI]

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

Zuckerman, Orit

2006-01-01T23:59:59.000Z

126

PDSF Interactive Batch Jobs  

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

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

127

Atomistic modeling of dislocation-interface interactions  

SciTech Connect (OSTI)

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

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

2011-01-31T23:59:59.000Z

128

Density functional study of molecular crystals: Polyethylene and a crystalline analog of bisphenol-A polycarbonate  

E-Print Network [OSTI]

Density functional study of molecular crystals: Polyethylene and a crystalline analog of bisphenol polyethylene comprising covalently bonded parallel chains with weak interchain interactions, and b reaction barriers.8 In a recent study of the interchain interactions in crystalline polyethylene PE ,9 we

129

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

E-Print Network [OSTI]

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

130

Molecular Science Computing | EMSL  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May Jun Jul(Summary)morphinanInformation Desert Southwest Regionat Cornell Batteries & Fuel CellsModels fromMolecular Science

131

Molecular Beam Epitaxy | EMSL  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recovery challenge fundProject8Mistakes to Avoid MistakesResponseModernMolecular

132

Molecular Beam Kinetics | EMSL  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recovery challenge fundProject8Mistakes to AvoidKinetics Molecular Beam Kinetics

133

Assessment of Molecular Modeling & Simulation  

SciTech Connect (OSTI)

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.

None

2002-01-03T23:59:59.000Z

134

Self-Assembly of Molecular Brick Wall and Molecular Honeycomb from Nickel(II) Macrocycle and 1,3,5-Benzenetricarboxylate  

E-Print Network [OSTI]

Self-Assembly of Molecular Brick Wall and Molecular Honeycomb from Nickel(II) Macrocycle and 130N6O2)]3[C6H3(COO)3]2,14H2O,2C5H5N (2), respec- tively, have been constructed by the self-assembly anti-ferromagnetic interactions between the S ) 1 Ni(II) paramagnetic centers. Introduction Self-assembled

Paik Suh, Myunghyun

135

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

DOE Patents [OSTI]

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.

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

1997-01-07T23:59:59.000Z

136

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

DOE Patents [OSTI]

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.

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

1997-01-01T23:59:59.000Z

137

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

E-Print Network [OSTI]

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

Ferreira, Márcia M. C.

138

Large-Scale Molecular Dynamics Simulations for Highly Parallel Infrastructures  

E-Print Network [OSTI]

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

Pazúriková, Jana

2014-01-01T23:59:59.000Z

139

REVIEW ARTICLE Taming molecular beams  

E-Print Network [OSTI]

REVIEW ARTICLE Taming molecular beams The motion of neutral molecules in a beam can be manipulated time-varying fields can be used to decelerate or accelerate beams of molecules to any desired velocity. We review the possibilities that this molecular-beam technology offers, ranging from ultrahigh

Loss, Daniel

140

Interaction networks: From protein functions to drug discovery. A review  

E-Print Network [OSTI]

-IMAG Laboratory, TIMB Team, faculté de médecine, 38706 La Tronche cedex, France Received 22 September 2008 on protein functions, signalling and metabolic pathways, and physiological processes, unraveled the molecular (interactome, transcriptome, phenome, localization) to switch from static to dynamic interaction networks

Thierry-Mieg, Nicolas

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

Interaction of Polycrystalline CVD  

E-Print Network [OSTI]

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

Adler, Joan

142

2011 Archaea: Ecology, Metabolism, & Molecular Biology  

SciTech Connect (OSTI)

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.

Keneth Stedman

2011-08-05T23:59:59.000Z

143

DISCOVERY OF THE PIGTAIL MOLECULAR CLOUD IN THE GALACTIC CENTER  

SciTech Connect (OSTI)

This paper reports the discovery of a helical molecular cloud in the central molecular zone (CMZ) of our Galaxy. This 'pigtail' molecular cloud appears at (l, b, V{sub LSR}) {approx_equal} (-0.{sup 0}7, + 0.{sup 0}0, - 70 to -30 km s{sup -1}), with a spatial size of {approx}20 Multiplication-Sign 20 pc{sup 2} and a mass of (2-6) Multiplication-Sign 10{sup 5} M{sub Sun }. This is the third helical gaseous nebula found in the Galactic center region to date. Line intensity ratios indicate that the pigtail molecular cloud has slightly higher temperature and/or density than the other normal clouds in the CMZ. We also found a high-velocity wing emission near the footpoint of this cloud. We propose a formation model of the pigtail molecular cloud. It might be associated with a magnetic tube that is twisted and coiled because of the interaction between clouds in the innermost x{sub 1} orbit and ones in the outermost x{sub 2} orbit.

Matsumura, Shinji; Oka, Tomoharu; Tanaka, Kunihiko [Institute of Science and Technology, Keio University, 3-14-1 Hiyoshi, Yokohama, Kanagawa 223-8522 (Japan); Nagai, Makoto [Institute of Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571 (Japan); Kamegai, Kazuhisa [Institute of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba (Japan); Hasegawa, Tetsuo [Joint ALMA Observatory, El Golf 40, Piso 18, Las Condes, Santiago (Chile)

2012-09-01T23:59:59.000Z

144

Coordinated Research Projects of the IAEA Atomic and Molecular Data Unit  

SciTech Connect (OSTI)

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

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

2011-05-11T23:59:59.000Z

145

Femtosecond Raman induced polarization spectroscopy studies of coherent rotational dynamics in molecular fluids  

SciTech Connect (OSTI)

We develop a polarization-sensitive femtosecond pump probe technique, Raman induced polarization spectroscopy (RIPS), to study coherent rotation in molecular fluids. By observing the collisional dephasing of the coherently prepared rotational states, we are able to extract information concerning the effects of molecular interactions on the rotational motion. The technique is quite sensitive because of the zero background detection method, and is also versatile due to its nonresonant nature.

Morgen, M.M. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; [Lawrence Berkeley National Lab., CA (United States)

1997-05-01T23:59:59.000Z

146

Accelerated Molecular Dynamics Simulation of Thermal Desorption.  

E-Print Network [OSTI]

??Desorption is a process ubiquitous in phenomena involving surfaces. However, it has rarely been simulated on the molecular level. Molecular dynamics simulation can provide the… (more)

Becker, Kelly

2008-01-01T23:59:59.000Z

147

Introduction to Accelerated Molecular Dynamics  

SciTech Connect (OSTI)

Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.

Perez, Danny [Los Alamos National Laboratory

2012-07-10T23:59:59.000Z

148

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

SciTech Connect (OSTI)

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

GUILFORD JONES

2005-09-14T23:59:59.000Z

149

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

E-Print Network [OSTI]

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

Ciobanu, Cristian

150

Steric effects in molecular adsorption  

SciTech Connect (OSTI)

The results of a molecular beam surface scattering experiment with preferentially orientated NO on Ag(111) are given. In adsorption molecules oriented with the O end towards the surface have a larger trapping probability.

Tenner, M.G.; Kuipers, E.W.; Kleyn, A.W.; Stolte, S.

1988-11-15T23:59:59.000Z

151

Size-exclusion chromatography system for macromolecular interaction analysis  

DOE Patents [OSTI]

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.

Stevens, Fred J. (Downers Grove, IL)

1988-01-01T23:59:59.000Z

152

Beam-Bem interactions  

SciTech Connect (OSTI)

In high energy storage-ring colliders, the nonlinear effect arising from beam-beam interactions is a major source that leads to the emittance growth, the reduction of beam life time, and limits the collider luminosity. In this paper, two models of beam-beam interactions are introduced, which are weak-strong and strong-strong beam-beam interactions. In addition, space-charge model is introduced.

Kim, Hyung Jin; /Fermilab

2011-12-01T23:59:59.000Z

153

Is Gravity an Interaction?  

E-Print Network [OSTI]

We consider a possibility that gravity is not an interaction but a manifestation of a symmetry based on a Galois field.

Felix M. Lev

2010-05-16T23:59:59.000Z

154

Nerve-pulse interactions  

SciTech Connect (OSTI)

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.

Scott, A.C.

1982-01-01T23:59:59.000Z

155

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

SciTech Connect (OSTI)

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

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

2012-01-01T23:59:59.000Z

156

Multiple time step integrators in ab initio molecular dynamics  

SciTech Connect (OSTI)

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

Luehr, Nathan; Martínez, Todd J. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States) [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); The PULSE Institute, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Markland, Thomas E. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)] [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

2014-02-28T23:59:59.000Z

157

Sandia National Laboratories: Molecular Geochemistry  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 -theErik Spoerke SSLS ExhibitIowaLosSandiaManagementMolecular Geochemistry Molecular

158

Can Protostellar Jets Drive Supersonic Turbulence in Molecular Clouds?  

E-Print Network [OSTI]

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

Robi Banerjee; Ralf S. Klessen; Christian Fendt

2007-06-25T23:59:59.000Z

159

Molecular weight and molecular weight distribution of kraft lignins  

SciTech Connect (OSTI)

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

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

1990-01-01T23:59:59.000Z

160

Molecular-level computational investigation of shock-wave mitigation capability of polyurea  

E-Print Network [OSTI]

.g., those generated as a result of blast-wave impact). By analyzing molecular- level interactions-level material models). Extension of these relations into the ``weak-shock'' regime of interest from the traumatic brain injury prevention point of view is also discussed. Introduction Within this study, advanced

Grujicic, Mica

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

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

E-Print Network [OSTI]

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

Gross, E.K.U.

162

Strongly interacting Fermi gases  

E-Print Network [OSTI]

Strongly interacting gases of ultracold fermions have become an amazingly rich test-bed for many-body theories of fermionic matter. Here we present our recent experiments on these systems. Firstly, we discuss high-precision ...

Bakr, W.

163

Human-machine interactions  

SciTech Connect (OSTI)

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.

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

2009-04-28T23:59:59.000Z

164

Quantum Theory of Chiral Interactions in Cholesteric Liquid Crystals  

E-Print Network [OSTI]

We study the effective chiral interaction between molecules arising from quantum dispersion interactions within a model in which a) the dominant excited states of a molecule form a band whose width is small compared to the average excitation energy and b) biaxial orientational correlation between adjacent molecules can be neglected. Previous treatments of quantum chiral interactions were based on a multipole expansion of the intermolecular interaction. However, because real liquid crystals are composed of elongated molecules, we utilize an expansion in terms of only coordinates transverse to the long molecular axes. We identify two distinct physical limits depending on whether one or both of the interacting molecules are excited in the virtual state. When both molecules are excited, our results are similar to those found previously by van der Meer et al. Previously unidentified terms in which only one molecule is excited involve the interactions of local dipole moments, which exist even when the global dipole moment of the molecule vanishes. We present analytic and numerical results for helical molecules. Our results do not indicate whether the dominant chiral interaction in cholesterics results from quantum or from steric interactions.

A. S. Issaenko; A. B. Harris; T. C. Lubensky

1998-10-15T23:59:59.000Z

165

Eighth international congress on nitrogen fixation  

SciTech Connect (OSTI)

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.

Not Available

1990-01-01T23:59:59.000Z

166

Eighth international congress on nitrogen fixation. Final program  

SciTech Connect (OSTI)

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.

Not Available

1990-12-31T23:59:59.000Z

167

Molecular Foundry, Berkeley, California (Revised)  

SciTech Connect (OSTI)

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

Carlisle, N.

2008-03-01T23:59:59.000Z

168

RMP Colloquia Modeling molecular motors  

E-Print Network [OSTI]

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

Jülicher, Frank

169

Nanoplasmonic molecular ruler for nuclease activity and DNA footprinting  

DOE Patents [OSTI]

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.

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

2013-10-29T23:59:59.000Z

170

Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite  

E-Print Network [OSTI]

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

A. Ito; H. Nakamura

2006-04-26T23:59:59.000Z

171

Chiral Interactions and Structures  

E-Print Network [OSTI]

The chiral structure of liquid crystalline phases arises due to the intrinsic chirality of the constituent mesogens. While it is seemingly straightforward to quantify the macroscopic chirality by using, for instance, the cholesteric pitch or the optical rotatory power, it is not as simple to quantify the chirality of a single molecule. I will discuss a systematic quantification of molecular chirality and show how the resulting chiral parameters may be used to predict macroscopic chiral structure.

Randall D. Kamien

1999-08-19T23:59:59.000Z

172

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

E-Print Network [OSTI]

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

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

2015-01-01T23:59:59.000Z

173

aluminophosphate molecular sieves: Topics by E-print Network  

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

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

174

aluminophosphate molecular sieve: Topics by E-print Network  

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

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

175

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

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

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

176

BE.442 Molecular Structure of Biological Materials, Fall 2005  

E-Print Network [OSTI]

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

Zhang, Shuguang, Dr.

177

Interacting With the Pharmaceutical Industry  

E-Print Network [OSTI]

INTERACTING WITH THE PHARMACEUTICAL INDUSTRY Stephen R.to interactions with the pharmaceutical industry! This is ancome from the pharmaceutical industry. It is also reality

Hayden, Stephen R

2003-01-01T23:59:59.000Z

178

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...

179

Master of Molecular and cellular biology  

E-Print Network [OSTI]

Master of Molecular and cellular biology From molecular developmental biology to biomedicine, evolution and systems biology ©UPMC-Directiondelacommunication-éditionF�VRIER2010-Imprimerie Biol, Development of marine organisms, Senior Lab practical Or Systems Biology -Barcelona: IEO Omics

Arleo, Angelo

180

Challenges for molecular neuroimaging with MRI  

E-Print Network [OSTI]

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

Lelyveld, Victor S.

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

How to Calculate Molecular Column Density  

E-Print Network [OSTI]

The calculation of the molecular column density from molecular spectral (rotational or ro-vibrational) transition measurements is one of the most basic quantities derived from molecular spectroscopy. Starting from first principles where we describe the basic physics behind the radiative and collisional excitation of molecules and the radiative transfer of their emission, we derive a general expression for the molecular column density. As the calculation of the molecular column density involves a knowledge of the molecular energy level degeneracies, rotational partition functions, dipole moment matrix elements, and line strengths, we include generalized derivations of these molecule-specific quantities. Given that approximations to the column density equation are often useful, we explore the optically thin, optically thick, and low-frequency limits to our derived general molecular column density relation. We also evaluate the limitations of the common assumption that the molecular excitation temperature is con...

Mangum, Jeffrey G

2015-01-01T23:59:59.000Z

182

Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps  

E-Print Network [OSTI]

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

Roie Volkovich; Uri Peskin

2010-12-01T23:59:59.000Z

183

Energy dissipation in bio molecular machines  

E-Print Network [OSTI]

Energy dissipation in bio molecular machines Thesis for the degree of Philosophiae Doctor Trondheim applied to molecular machines and energy trans- duction and dissipation in these. The main result to include heat effects. This framework is general and can be applied to other molecular machines as well

Kjelstrup, Signe

184

Dike/Drift Interactions  

SciTech Connect (OSTI)

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).

E. Gaffiney

2004-11-23T23:59:59.000Z

185

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

E-Print Network [OSTI]

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

186

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

E-Print Network [OSTI]

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

Ferreira, Márcia M. C.

187

Molecular engineering with bridged polysilsesquioxanes  

SciTech Connect (OSTI)

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.

LOY,DOUGLAS A.; SHEA,KENNETH J.

2000-05-09T23:59:59.000Z

188

Molecular gas and AGN fueling  

E-Print Network [OSTI]

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

F. Combes

2003-08-01T23:59:59.000Z

189

Molecular Science Computing: 2010 Greenbook  

SciTech Connect (OSTI)

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.

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

2010-04-02T23:59:59.000Z

190

Lattice cluster theory for polymer melts with specific interactions  

E-Print Network [OSTI]

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

Wen-Sheng Xu; Karl F. Freed

2014-07-12T23:59:59.000Z

191

Being Interactive Services and  

E-Print Network [OSTI]

for engineering software and more than sufficient justification for all the inter- est in services. AlthoughBeing Interactive Services and Situations 4 SEPTEMBER · OCTOBER 2001 http the Editor in Chief ... F orget objects. The killer buzzword of our era is now services. And who isn

192

Being Interactive Health Care  

E-Print Network [OSTI]

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

193

The Digital Interactive Video  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

194

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

E-Print Network [OSTI]

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

Ferreira, Márcia M. C.

195

Introduction to Molecular Dynamics and Accelerated Molecular Dynamics  

SciTech Connect (OSTI)

We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

Perez, Danny [Los Alamos National Laboratory

2012-06-25T23:59:59.000Z

196

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

SciTech Connect (OSTI)

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

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

2006-10-31T23:59:59.000Z

197

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

SciTech Connect (OSTI)

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

Anne McCoy

2012-02-03T23:59:59.000Z

198

Temperature inversion in long-range interacting systems  

E-Print Network [OSTI]

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

Teles, Tarcisio N; Casetti, Lapo

2015-01-01T23:59:59.000Z

199

Molecular Design of Branched and Binary Molecules at Ordered Interfaces  

SciTech Connect (OSTI)

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.

Kirsten Larson Genson

2005-12-27T23:59:59.000Z

200

Interactive design center.  

SciTech Connect (OSTI)

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

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

2005-07-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

MIXING OF CLUMPY SUPERNOVA EJECTA INTO MOLECULAR CLOUDS  

SciTech Connect (OSTI)

Several lines of evidence, from isotopic analyses of meteorites to studies of the Sun's elemental and isotopic composition, indicate that the solar system was contaminated early in its evolution by ejecta from a nearby supernova. Previous models have invoked supernova material being injected into an extant protoplanetary disk, or isotropically expanding ejecta sweeping over a distant (>10 pc) cloud core, simultaneously enriching it and triggering its collapse. Here, we consider a new astrophysical setting: the injection of clumpy supernova ejecta, as observed in the Cassiopeia A supernova remnant, into the molecular gas at the periphery of an H II region created by the supernova's progenitor star. To track these interactions, we have conducted a suite of high-resolution (1500{sup 3} effective) three-dimensional numerical hydrodynamic simulations that follow the evolution of individual clumps as they move into molecular gas. Even at these high resolutions, our simulations do not quite achieve numerical convergence, due to the challenge of properly resolving the small-scale mixing of ejecta and molecular gas, although they do allow some robust conclusions to be drawn. Isotropically exploding ejecta do not penetrate into the molecular cloud or mix with it, but, if cooling is properly accounted for, clumpy ejecta penetrate to distances {approx}10{sup 18} cm and mix effectively with large regions of star-forming molecular gas. In fact, the {approx}2 M{sub Sun} of high-metallicity ejecta from a single core-collapse supernova is likely to mix with {approx}2 Multiplication-Sign 10{sup 4} M{sub Sun} of molecular gas material as it is collapsing. Thus, all stars forming late ( Almost-Equal-To 5 Myr) in the evolution of an H II region may be contaminated by supernova ejecta at the level {approx}10{sup -4}. This level of contamination is consistent with the abundances of short-lived radionuclides and possibly some stable isotopic shifts in the early solar system and is potentially consistent with the observed variability in stellar elemental abundances. Supernova contamination of forming planetary systems may be a common, universal process.

Pan Liubin; Desch, Steven J.; Scannapieco, Evan; Timmes, F. X. [School of Earth and Space Exploration, Arizona State University, P.O. Box 871404, Tempe, AZ 85287-1404 (United States)

2012-09-01T23:59:59.000Z

202

Interactive Transportable Architecture  

E-Print Network [OSTI]

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

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

203

ELEMENTARY PARTICLE INTERACTIONS  

SciTech Connect (OSTI)

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.

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

2013-07-30T23:59:59.000Z

204

Molecular Design of Crosslinked Copolymers  

E-Print Network [OSTI]

is also shown to be an e ective optimization method. iii Acknowledgements This project was funded by NIH grants R13-DK069504-03 and NIH/NIDCR grant DE014392 (PI: Spencer). I would like to thank Dr. Spencer, Dr. Ye, and Dr. Park for helping me understand... polymer network makes devel- opment of quantitative structure property relations (QSPRs) di cult. Much of the current molecular design research focuses on relatively simple molecules, for which de- terministic optimization algorithms can be applied...

Eslick, John

2009-01-01T23:59:59.000Z

205

Molecular Science Computing Help | EMSL  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recovery challenge fundProject8Mistakes to AvoidKineticsMolecular Science

206

Molecular Science Computing Policies | EMSL  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recovery challenge fundProject8Mistakes to AvoidKineticsMolecular

207

The interactions of water and perfluorodiethyl ether on Ru(100)  

SciTech Connect (OSTI)

We have studied the interactions of water and perfluorodiethyl ether on Ru(100) in order to model the effects of surface structure and humidity on the bonding and decomposition of perfluoroalkyl ether lubricants with metal surfaces. In order to understand the interactions on Ru(100), we have first investigated the interactions of each of these adsorbates alone on the clean surface. The interactions of water with Ru(100) have been studied using both thermal desorption spectroscopy (TDS) and electron energy loss spectroscopy (EELS). From these studies we conclude that a small amount of water dissociates on this surface (5--10% of a monolayer), but water is adsorbed in a predominantly molecular form on this surface with an increasing degree of hydrogen-bonding with increasing coverage. The effects of hydrogen and oxygen coadsorption on the interactions of water with this surface have also been studied using TDS. Finally, the interactions of coadsorbed water and perfluorodiethyl ether on Ru(100) have been investigated using TDS.

Leavitt, P.

1990-09-21T23:59:59.000Z

208

Molecular Hydrogen in Infrared Cirrus  

E-Print Network [OSTI]

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

Kristen Gillmon; J. Michael Shull

2005-07-25T23:59:59.000Z

209

Turbulence-chemistry interactions in reacting flows  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

210

Molecular Characterization of Biomass Burning Aerosols Using...  

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

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

211

Iris Visoly-Fisher Molecular Optoelectronics  

E-Print Network [OSTI]

Iris Visoly-Fisher Molecular Optoelectronics Organic semiconductors are excellent candidates single molecules in order to develop better design criteria for photovoltaic energy conversion and opto-electronic

Vardi, Amichay

212

Molecular Characterization of Nitrogen Containing Organic Compounds...  

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

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

213

Molecular biology of signal transduction in plants  

SciTech Connect (OSTI)

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.

Not Available

1991-01-01T23:59:59.000Z

214

Molecular dynamics simulation of threshold displacement energies...  

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

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

215

Molecular Beam Epitaxy, Multi-source | EMSL  

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

beam epitaxy, is examined using a combination... Self-corrected Sensors Based On Atomic Absorption Spectroscopy For Atom Flux Measurements In Molecular Beam Epitaxy. A...

216

Molecular architecture and functionalization of graphene surface...  

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

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

217

Molecular dynamics simulation studies of electrolytes andelectrolyte...  

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

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

218

A Molecular Dynamics Investigation of Hydrolytic Polymerization...  

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

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

219

Molecular Designs Toward Improving Organic Photovoltaics.  

E-Print Network [OSTI]

??Organic photovoltaics (OPVs) that have been studied to date have poor power conversion efficiencies. This dissertation focuses on various molecular designs that could lead to… (more)

Nantalaksakul, Arpornrat

2009-01-01T23:59:59.000Z

220

Microbemetal interactions in marine hydrothermal environments James F Holden and Michael W W Adams  

E-Print Network [OSTI]

the scope of carbon cycling in hydrothermal environments. The advent of genome sequences and new molecularMicrobe­metal interactions in marine hydrothermal environments James F Holden and Michael W W Adams� Marine hydrothermal microorganisms respond rapidly to changes in the concentrations and availability

Holden, James F.

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

Microscopic models of quasicrystals J. Jdrzejewski and J. Mikisz, Devil's staircase for nonconvex interactions,  

E-Print Network [OSTI]

Microscopic models of quasicrystals J. Jdrzejewski and J. Mikisz, Devil's staircase for nonconvex-dimensional infinite-range lattice-gas interactions, molecules consisting of two particles form a molecular devil's staircase in the unique ground- state measure. The structure of the ground set is that of a Cantor set

Miekisz, Jacek

222

BNL | ATF Interaction Chambers  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to someone byDearTechnicalAwardssupportsBESElectron-plasma Interaction

223

PDSF Interactive Batch Jobs  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recoveryLaboratorySpeedingOptimizing I/OP-GlycoproteinInteractive Batch Jobs Running

224

PDSF Interactive Nodes  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas Conchas recoveryLaboratorySpeedingOptimizing I/OP-GlycoproteinInteractive Batch Jobs

225

Crystal and molecular structure of four adamantyl-substituted tetrazoles  

SciTech Connect (OSTI)

Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH{sub 2} groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

Polyakova, I. N., E-mail: polyakova@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Saraev, V. V.; Gavrilov, A. S.; Golod, E. L. [St. Petersburg State Technological Institute (Technical University) (Russian Federation)

2009-05-15T23:59:59.000Z

226

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

SciTech Connect (OSTI)

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.

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

2013-01-01T23:59:59.000Z

227

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

SciTech Connect (OSTI)

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.

Judith Berman

2012-06-22T23:59:59.000Z

228

Molecular Biology The molecular biology major at Stetson University is designed for  

E-Print Network [OSTI]

Molecular Biology The molecular biology major at Stetson University is designed for students interested in the interface between the life sciences and physical sciences. Molecular biology is an interdisciplinary science that uses the techniques of biology and chemistry to examine genetic inheritance

Miles, Will

229

Cotton and Protein Interactions  

SciTech Connect (OSTI)

The adsorbent properties of important wound fluid proteins and cotton cellulose are reviewed. This review focuses on the adsorption of albumin to cotton-based wound dressings and some chemically modified derivatives targeted for chronic wounds. Adsorption of elastase in the presence of albumin was examined as a model to understand the interactive properties of these wound fluid components with cotton fibers. In the chronic non-healing wound, elastase appears to be over-expressed, and it digests tissue and growth factors, interfering with the normal healing process. Albumin is the most prevalent protein in wound fluid, and in highly to moderately exudative wounds, it may bind significantly to the fibers of wound dressings. Thus, the relative binding properties of both elastase and albumin to wound dressing fibers are of interest in the design of more effective wound dressings. The present work examines the binding of albumin to two different derivatives of cotton, and quantifies the elastase binding to the same derivatives following exposure of albumin to the fiber surface. An HPLC adsorption technique was employed coupled with a colorimetric enzyme assay to quantify the relative binding properties of albumin and elastase to cotton. The results of wound protein binding are discussed in relation to the porosity and surface chemistry interactions of cotton and wound proteins. Studies are directed to understanding the implications of protein adsorption phenomena in terms of fiber-protein models that have implications for rationally designing dressings for chronic wounds.

Goheen, Steven C.; Edwards, J. V.; Rayburn, Alfred R.; Gaither, Kari A.; Castro, Nathan J.

2006-06-30T23:59:59.000Z

230

Optimal prediction in molecular dynamics  

E-Print Network [OSTI]

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

Benjamin Seibold

2008-08-22T23:59:59.000Z

231

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

E-Print Network [OSTI]

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

Richardson, David

232

Guided self-assembly of molecular dipoles on a substrate surface Y. F. Gao and Z. Suoa)  

E-Print Network [OSTI]

Guided self-assembly of molecular dipoles on a substrate surface Y. F. Gao and Z. Suoa) Department can self-assemble into a monolayer. This article models the process of self-assembly guided on the substrate surface, interact with one another through the intermolecular force, and self-assemble

Suo, Zhigang

233

Molecular Self-Assembly of Functionalized Fullerenes on a Metal Surface Bogdan Diaconescu,1,* Teng Yang,2  

E-Print Network [OSTI]

Molecular Self-Assembly of Functionalized Fullerenes on a Metal Surface Bogdan Diaconescu,1,* Teng and theoretical study of the self-assembly of C60 molecules functionalized with long alkane chains on the (111(111) and that the unit cell size in the self-assembled monolayer is determined by the interactions

Pohl, Karsten

234

Electron localization following attosecond molecular photoionization  

E-Print Network [OSTI]

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

Kling, Matthias

235

Molecular Computing with DNA Self-Assembly  

E-Print Network [OSTI]

Molecular Computing with DNA Self-Assembly Urmi Majumder #12;Self-Assembly in Nature #12;Key to DNA for Molecular Computing with DNA Self-Assembly Compact: Small library of assembly primitives Complex: Capable in Tiling Assembly: vitroation tural DNA self-assembly has powerful echanisms for error correction

Reif, John H.

236

MIDOS : Multimodal Interactive DialOgue System  

E-Print Network [OSTI]

Interactions between people are typically conversational, multimodal, and symmetric. In conversational interactions, information flows in both directions. In multimodal interactions, people use multiple channels. In symmetric ...

Adler, Aaron D. (Aaron Daniel), 1979-

2009-01-01T23:59:59.000Z

237

On statistics of molecular chaos  

E-Print Network [OSTI]

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

Yuriy Kuzovlev

2009-11-03T23:59:59.000Z

238

MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS  

SciTech Connect (OSTI)

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

Athanassios Z. Panagiotopoulos

2009-09-09T23:59:59.000Z

239

SLAC All Access: Atomic, Molecular and Optical Science Instrument  

ScienceCinema (OSTI)

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.

Bozek, John

2014-06-03T23:59:59.000Z

240

On the Computational Power of Molecular Heat Engines  

E-Print Network [OSTI]

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

Dominik Janzing

2005-02-02T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Molecular mechanisms of hydrogen loaded B-hydroquinone clathrate  

SciTech Connect (OSTI)

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

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

2006-09-07T23:59:59.000Z

242

Cold Water Vapor in the Barnard 5 Molecular Cloud  

E-Print Network [OSTI]

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

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

2014-01-01T23:59:59.000Z

243

Mass Spectral Molecular Networking of Living Microbial Colonies  

SciTech Connect (OSTI)

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

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

2012-06-26T23:59:59.000Z

244

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

E-Print Network [OSTI]

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

William T. Reach; Jeonghee Rho

1998-07-28T23:59:59.000Z

245

Molecular gas in nearby elliptical radio galaxies  

E-Print Network [OSTI]

Powerful radio-AGN are hosted by massive elliptical galaxies which are usually very poor in molecular gas. Nevertheless the central Black Hole (BH) needs molecular gas for the nuclear activity. Thus it is important to study the origin, the distribution and the kinematics of the molecular gas in such objects. We have performed at the IRAM-30m telescope a survey of the CO(1-0) and CO(2-1) emission in the most powerful radio galaxies of the Local Universe, selected only on the basis of their radio continuum fluxes. The main result of that survey is the low content in molecular gas of such galaxies compared to Seyfert galaxies. The median value of the molecular gas mass is 4x10^8 Msun. Moreover, the CO spectra indicate the presence of a central molecular gas disk in some of these radio galaxies. We complemented this survey with photometric data of SPITZER and IRAS fluxes with the purpose to study the dust and its relation with the molecular gas and AGN.

B. Ocana-Flaquer; S. Leon; J. Lim; F. Combes; Dinh-V-Trung

2008-03-31T23:59:59.000Z

246

Reactions of small molecular systems  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

247

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...

248

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

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

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

249

Minor Groove Deformability of DNA: A Molecular Dynamics Free...  

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

Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study. Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study. Abstract:...

250

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

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

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

251

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

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

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

252

Natural Oxidation of Black Carbon in Soils: Changes in Molecular...  

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

Carbon in Soils: Changes in Molecular Form and Surface Charge along a Climosequence. Abstract: The aim of this work was to investigate changes in molecular form and surface...

253

Probing Molecular Associations of Field-Collected and Laboratory...  

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

Molecular Associations of Field-Collected and Laboratory-Generated SOA with Nano-DESI High-Resolution Mass Spectrometry. Probing Molecular Associations of Field-Collected and...

254

Combined Quantum Mechanical and Molecular Mechanics Studies of...  

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

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

255

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

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

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

256

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

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

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

257

Comparative molecular dynamics analysis of tapasin-dependent...  

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

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

258

Functionalized Graphene Sheets as Molecular Templates for Controlled...  

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

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

259

ENERGETIC PHOTON AND ELECTRON INTERACTIONS WITH POSITIVE IONS  

SciTech Connect (OSTI)

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.

Phaneuf, Ronald A. [UNR

2013-07-01T23:59:59.000Z

260

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

E-Print Network [OSTI]

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

Bintu, Lacramioara

2010-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

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

E-Print Network [OSTI]

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

Yang, Sichun

262

Molecular Dynamics for Low Temperature Plasma-Surface Interaction David B. Graves a)  

E-Print Network [OSTI]

considerable problems as well. Controlled nuclear fusion devices employing highly energetic, hot, magnetized the current status of the technique for various applications of low temperature plasmas to material processing

Boyer, Edmond

263

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

E-Print Network [OSTI]

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

Hu, Yung-Jin

2011-01-01T23:59:59.000Z

264

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

E-Print Network [OSTI]

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

Peppas, Nicholas A.

265

Carbon Onion Films-Molecular Interactions of Multi-Layer Fullerenes Raed A. Alduhaileb,1  

E-Print Network [OSTI]

for wind power to a vacuum lubricant [1] for solar panel deployment in space. These uses of carbon onions were heated in inert ambience in infrared gold image furnace. A graphite holder filled with 10 mg of diamond nanoparticles was placed inside the furnace, which was evacuated to approximately 1.3 Pa

Ayres, Virginia

266

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

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

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

267

Ab initio molecular dynamics simulations of ion–solid interactions in  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc Documentation RUCProductstwrmrAre the Effects of GlobalASCR UserProgramICarbide.Ar-CF.

268

Understanding Molecular-scale Complexity and Interactions of Soil Organic Matter  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLasDelivered energy consumption by sectorlong version)Underground Natural Gas Storage byCenter

269

Dynamics in the presence of attractive patchy interactions  

E-Print Network [OSTI]

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

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

2005-11-04T23:59:59.000Z

270

Environmental Molecular Sciences Laboratory 2007 Annual Report  

SciTech Connect (OSTI)

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.

Showalter, Mary Ann; Foster, Nancy S.

2008-03-19T23:59:59.000Z

271

Optoelectronic switching of addressable molecular crossbar junctions  

E-Print Network [OSTI]

This letter reports on the observation of optoelectronic switching in addressable molecular crossbar junctions fabricated using polymer stamp-printing method. The active medium in the junction is a molecular self-assembled monolayer softly sandwiched between gold electrodes. The molecular junctions are investigated through currentvoltage measurements at varied temperature (from 95 to 300 K) in high vacuum condition. The junctions show reversible optoelectronic switching with the highest on/off ratio of 3 orders of magnitude at 95 K. The switching behavior is independent of both optical wavelength and molecular structure, while it strongly depends on the temperature. Initial analysis indicates that the distinct binding nature of the molecule/electrode interfaces play a dominant role in the switching performance.

J. C. Li

2006-11-22T23:59:59.000Z

272

12.458 Molecular Biogeochemistry, Fall 2006  

E-Print Network [OSTI]

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

Summons, Roger

273

Combinatorial molecular optimization of cement hydrates  

E-Print Network [OSTI]

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

Abdolhosseini Qomi, Mohammad

274

Molecular Simulation of Nanofluids Mark J. Biggs  

E-Print Network [OSTI]

Molecular Simulation of Nanofluids Mark J. Biggs School of Chemical Engineering, The University of Adelaide, South Australia, Australia, 5005. mark.biggs@adelaide.edu.au Models of nanofluid systems ­ which

Adler, Joan

275

Computational Molecular Design Using Tabu Search  

E-Print Network [OSTI]

The focus of this project is the use of computational molecular design (CMD) in the design of novel crosslinked polymers. A design example was completed for a dimethacrylate as part of a comonomer used in dental restoration, ...

Hacker, Joseph

2012-05-31T23:59:59.000Z

276

Novel molecular architectures from iptycene polymers  

E-Print Network [OSTI]

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

Tsui, Nicholas T. (Nicholas Tang)

2007-01-01T23:59:59.000Z

277

WANTED: Undergraduate Research Assistant Betelgeuse's Molecular Inventory  

E-Print Network [OSTI]

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

Harper, Graham

278

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

DOE Patents [OSTI]

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.

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

1983-01-01T23:59:59.000Z

279

Interactive Video Cubism Sidney Fels  

E-Print Network [OSTI]

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

Fels, Sidney S.

280

Mapping molecular dynamics computations to hypercubes  

E-Print Network [OSTI]

December 1993 Major Subject: ('omputer Science MAPPING MOLECULAR DYNAMICS COMPUTATIONS TO HYPERCUBES A Thesis by VAMSEE IvRISHNA LAIvAMSANI Submitted to Texas AX. 'M University in partial fnlfillment of the requirements for the degree of lv... for systematic modeling, mapping and perfornianrc analysis of a Grand Challenge application problein in computational biology called Moleru- lar Dynamics S&tnufat&un uj Proteins Molecular Dynamics (MD) is an important techn&que used m computational...

Lakamsani, Vamsee Krishna

1993-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Final Report - Molecular Mechanisms of Bacterial Mercury Transformation - UCSF  

SciTech Connect (OSTI)

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

Miller, Susan M. [UCSF

2014-04-24T23:59:59.000Z

282

Interaction of "rigid" quantum systems  

E-Print Network [OSTI]

We introduce the notion of a "rigid" quantum system as a system with constant relative positions of its nuclei and constant relative distribution of the electrons with respect to the nuclei. In accordance with this definition, a molecule which does not interact with other objects, is a "rigid" quantum system. Molecule is also "rigid" if it interacts with other objects, but the interaction does not change the intrinsic structure of the molecule (or this change can be neglected). Several "rigid" quantum systems interact one with another in the quantum manner. The interaction is ruled by the Schr{\\"o}dinger equation [1] written for all the particles of the systems under consideration. We consider the case when the external potential is zero.

A. A. Kolpakov; A. G. Kolpakov

2013-01-03T23:59:59.000Z

283

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

E-Print Network [OSTI]

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

Carla Goldman; Elisa T. Sena

2008-10-07T23:59:59.000Z

284

Interaction of acetonitrile with thin films of solid water  

SciTech Connect (OSTI)

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

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

2009-06-07T23:59:59.000Z

285

Molecular Biology Major www.biology.pitt.edu  

E-Print Network [OSTI]

Molecular Biology Major www.biology.pitt.edu Revised: 07/2012 Molecular biology emphasizes question, whether in biochemistry, cell biology, developmental biology, or some other biological discipline, applies molecular biology, often as the prime approach, in its solution. Biochemical and molecular

Jiang, Huiqiang

286

The Application of XML Languages for Integrating Molecular Resources  

E-Print Network [OSTI]

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

Rzepa, Henry S.

287

Perturbative gadgets without strong interactions  

E-Print Network [OSTI]

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

Yudong Cao; Daniel Nagaj

2014-08-25T23:59:59.000Z

288

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

SciTech Connect (OSTI)

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.

Dixon, David Adams [The University of Alabama

2013-06-27T23:59:59.000Z

289

Ernst Klenk Symposium in Molecular Medicine of the Center for Molecular Medicine Cologne (CMMC)  

E-Print Network [OSTI]

) DNA Damage Response and Repair Mechanisms in Aging and Disease Sept. 21 ­ 23, 2014 Program Scientific30th Ernst Klenk Symposium in Molecular Medicine of the Center for Molecular Medicine Cologne (CMMC Klenk Symposium Board 2014 Björn Schumacher (Chair) - Thomas Benzing - Michael Hallek - Thorsten Hoppe

Lübeck, Universität zu

290

Dynamics of a vesicle as a cell mimic: Effects of interior structure, cross-membrane transport, and interaction with filaments  

E-Print Network [OSTI]

Dynamics of a vesicle as a cell mimic: Effects of interior structure, cross-membrane transport, and interaction with filaments The biological membrane is, in essence, a thermodynamically-nonequilibrium lipid bilayer [6, 30, 34, 43, 47] with a variety of molecular motors, ion pumps, or channels residing within [19

Young, Yuan N.

291

Interactions between Copper(II) Complexes of Mono-, Bis-, and Tris(macrocyclic) Ligands and Inorganic or Organic Guests  

E-Print Network [OSTI]

FULL PAPER Interactions between Copper(II) Complexes of Mono-, Bis-, and Tris(macrocyclic) Ligands. Prikhod'ko,[b] and Hans Pritzkow[a] Keywords: Copper / Host-guest complexes / Macrocycles / Molecular recognition Template synthesis The copper(II)-assisted condensation of [Cu(2,3,2-tet)]2+ [2,3,2-tet = bis

Nazarenko, Alexander

292

Succinct non-Interactive arguments  

E-Print Network [OSTI]

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

Chiesa, Alessandro

2014-01-01T23:59:59.000Z

293

Interactive crayon rendering for animation  

E-Print Network [OSTI]

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

Halstead, Howard John IV

2006-04-12T23:59:59.000Z

294

Determining the Overpotential for a Molecular Electrocatalyst  

SciTech Connect (OSTI)

“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.

Appel, Aaron M.; Helm, Monte L.

2014-02-07T23:59:59.000Z

295

Non-standard Neutrino Interactions  

E-Print Network [OSTI]

Theories beyond the Standard Model must respect its gauge symmetry. This implies strict constraints on the possible models of Non-Standard Neutrino Interactions (NSIs). We review here the present status of NSIs from the point of view of effective field theory. Our recent work on the restrictions implied by Standard Model gauge invariance is provided along with some examples of possible gauge invariant models featuring non-standard interactions.

D. Hernandez

2009-11-25T23:59:59.000Z

296

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

SciTech Connect (OSTI)

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

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

1995-11-01T23:59:59.000Z

297

Technology Enhanced Interaction Framework Kewalin Angkananon  

E-Print Network [OSTI]

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

298

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

SciTech Connect (OSTI)

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.

Wang, Yusu

2013-03-25T23:59:59.000Z

299

On the emergence of molecular structure  

SciTech Connect (OSTI)

The structure of (a{sup {+-}},a{sup {+-}},b{sup {+-}})-type Coulombic systems is characterized by the effective ground-state density of the a-type particles, computed via nonrelativistic quantum mechanics without introduction of the Born-Oppenheimer approximation. A structural transition is observed when varying the relative mass of the a- and b-type particles, e.g., between atomic H{sup -} and molecular H{sub 2}{sup +}. The particle-density profile indicates a molecular-type behavior for the positronium ion, Ps{sup -}.

Matyus, Edit; Reiher, Markus [Laboratory of Physical Chemistry, ETH Zuerich, Wolfgang-Pauli-Strasse 10, CH-8093 Zuerich (Switzerland); Hutter, Juerg [Institute of Physical Chemistry, University of Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland); Mueller-Herold, Ulrich [Institute of Biogeochemistry and Pollutant Dynamics, ETH Zuerich, Universitaetstrasse 16, CH-8092 Zuerich (Switzerland)

2011-05-15T23:59:59.000Z

300

The Molecular Bond: October 2014 | EMSL  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2 andThe Molecular Bond: October 2014 The Molecular

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

Molecular Hydrogen Emission from Protoplanetary Disks  

E-Print Network [OSTI]

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

H. Nomura; T. J. Millar

2005-05-06T23:59:59.000Z

302

Prediction of flow rates through an orifice at pressures corresponding to the transition between molecular and isentropic flow  

SciTech Connect (OSTI)

A model of compressible flow through an orifice, in the region of transition from free molecular to isentropic expansion flow, has been developed and tested for accuracy. The transitional or slip regime is defined as the conditions where molecular interactions are too many for free molecular flow modeling, yet not great enough for isentropic expansion flow modeling. Due to a lack of literature establishing a well-accepted model for predicting transitional flow, it was felt such work would be beneficial. The model is nonlinear and cannot be satisfactorily linearized for a linear regression analysis. Consequently, a computer routine was developed which minimized the sum of the squares of the residual flow for the nonlinear model. The results indicate an average accuracy within 15% of the measured flow throughout the range of test conditions. Furthermore, the results of the regression analysis indicate that the transitional regime lies between Knudsen numbers of approximately 2 and 45. 4 refs., 3 figs., 1 tab.

DeMuth, S.F.; Watson, J.S.

1985-01-01T23:59:59.000Z

303

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

E-Print Network [OSTI]

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

Rubloff, Gary W.

304

The central focus of the graduate program in Biochemistry and Molecular Biophysics (BMB) is the relationship between biological form and function at a fundamental level. This  

E-Print Network [OSTI]

, such as sensory transduction, cell division, death and control of the cell cycle. · Determination of protein, RNA protein-protein interactions. · Molecular basis of energy transduction, including contractility and fluorescence microscopy · Nuclear magnetic and electron paramagnetic spectroscopy. · Optical and magnetic

Sharp, Kim

305

Hydrophobic force field as molecular alternative to surface-area models  

SciTech Connect (OSTI)

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.

Hummer, G.

1999-07-07T23:59:59.000Z

306

Reaction dynamics in polyatomic molecular systems  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

307

Molecular Dynamics Simulations of Supported Pt Nanoclusters  

E-Print Network [OSTI]

¤Introduction and Background ¤Constructing a Physical Model ¤Details of the Simulation ¤Results and Conclusions · Petroleum reformation · Gasification of biomass for biofuels #12;Previous Investigation of NanoclustersMolecular Dynamics Simulations of Supported Pt Nanoclusters Jeffrey Moore #12;A Brief Outline

Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group

308

Hypersonic Molecular Shocks in Star Forming Regions  

E-Print Network [OSTI]

Much emission from star forming regions is from shock-excited gas. Shocks in molecular clouds are still not fully understood, as magnetic fields, dust and chemistry all play significant roles. I review the history, physics and current work in understanding these shocks, and in their possible use as diagnostics of local conditions.

Brand, P W J L

2006-01-01T23:59:59.000Z

309

Hypersonic Molecular Shocks in Star Forming Regions  

E-Print Network [OSTI]

Much emission from star forming regions is from shock-excited gas. Shocks in molecular clouds are still not fully understood, as magnetic fields, dust and chemistry all play significant roles. I review the history, physics and current work in understanding these shocks, and in their possible use as diagnostics of local conditions.

Peter W. J. L. Brand

2006-09-08T23:59:59.000Z

310

Brownian Ratchets: Molecular Separations in Lipid Bilayers  

E-Print Network [OSTI]

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

Boxer, Steven G.

311

THERMODYNAMICS Molecular Simulation of Multicomponent Reaction  

E-Print Network [OSTI]

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

Lisal, Martin

312

Molecular gas in nearby powerful radio galaxies  

E-Print Network [OSTI]

We report the detection of CO(1-0) and CO(2-1) emission from the central region of nearby 3CR radio galaxies (z$gas content is below 10$^9$ \\msun. Their individual CO emission exhibit, for 5 cases, a double-horned line profile that is characteristic of an inclined rotating disk with a central depression at the rising part of its rotation curve. The inferred disk or ring distributions of the molecular gas is consistent with the observed presence of dust disks or rings detected optically in the cores of the galaxies. We reason that if their gas originates from the mergers of two gas-rich disk galaxies, as has been invoked to explain the molecular gas in other radio galaxies, then these galaxies must have merged a long time ago (few Gyr or more) but their remnant elliptical galaxies only recently (last 10$^7$ years or less) become active radio galaxies. Instead, we argue the the cannibalism of gas-rich galaxies provide a simpler explanation for the origin of molecular gas in the elliptical hosts of radio galaxies (Lim et al. 2000). Given the transient nature of their observed disturbances, these galaxies probably become active in radio soon after the accretion event when sufficient molecular gas agglomerates in their nuclei.

S. Leon; J. Lim; F. Combes; D. Van-Trung

2001-07-26T23:59:59.000Z

313

Molecular Cell Signaling Motifs and Weber's Law  

E-Print Network [OSTI]

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

314

Cellular/Molecular Separate Ca2  

E-Print Network [OSTI]

Cellular/Molecular Separate Ca2 Sources Are Buffered by Distinct Ca2 Handling Systems in Aplysia's University, Kingston, Ontario K7L 3N6, Canada AlthoughthecontributionofCa2 bufferingsystemscanvarybetweenneuronaltypesandcellularcompartments,itisunknownwhether distinct Ca2 sources within a neuron have different buffers. As individual Ca2

Blohm, Gunnar

315

High Performance Subgraph Mining in Molecular Compounds  

E-Print Network [OSTI]

High Performance Subgraph Mining in Molecular Compounds Giuseppe Di Fatta1,2 and Michael R data makes distributed graph mining techniques particularly relevant. In this paper, we present method has been evaluated on the well-known National Cancer Institute's HIV-screening dataset, where

Reiterer, Harald

316

Finding Discriminative Molecular Fragments Christian Borgelt1  

E-Print Network [OSTI]

a novel molecule will be active or inactive, so that future chemical tests can be focused on the most molecular fragments to discriminate between active and inactive molecules. In this paper we review classifiers that predict for a novel molecule whether it will be active or inactive, for example, w

Borgelt, Christian

317

Molecular Coordination of Hierarchical Self-Assembly  

E-Print Network [OSTI]

Molecular Coordination of Hierarchical Self-Assembly Technical Report UT-CS-10-662 Bruce J. Mac to self-assemble into multiscale complex hierarchical systems. Keywords: algorithmic assembly, embodied, nano communication, nanofabrication, nanotechnology, Moore's Law, self-assembly, self-organization. 1

MacLennan, Bruce

318

ScheduleDay 1: Molecular Evolution Introduction  

E-Print Network [OSTI]

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

Goldschmidt, Christina

319

Ernst Klenk Symposium in Molecular Medicine  

E-Print Network [OSTI]

30th Ernst Klenk Symposium in Molecular Medicine Sept. 21 - 23, 2014 DNA Damage Response and Repair Mechanisms in Aging and Disease Ernst Klenk Lecture - Jan H. J. Hoeijmakers - Rotterdam, NL Program and further information: www.zmmk.uni-koeln.de Participation is free of charge - free registration: klenk-symposium

Lübeck, Universität zu

320

Molecular Biology Basics Planning Restriction Enzyme Digests  

E-Print Network [OSTI]

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

Aris, John P.

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

Molecular sieving silica membrane fabrication process  

DOE Patents [OSTI]

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.

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

1999-01-01T23:59:59.000Z

322

Biogenic gas nanostructures as ultrasonic molecular reporters  

E-Print Network [OSTI]

Biogenic gas nanostructures as ultrasonic molecular reporters Mikhail G. Shapiro1,2,3 *, Patrick W on the nanoscale. Here, we introduce a new class of reporters for ultrasound based on genetically encoded gas nanostructures from microorganisms, including bacteria and archaea. Gas vesicles are gas-filled protein

Schaffer, David V.

323

CO J = 1-0 AND J = 2-1 LINE OBSERVATIONS OF THE MOLECULAR-CLOUD-BLOCKED SUPERNOVA REMNANT 3C434.1  

SciTech Connect (OSTI)

We present the results of CO emission line observations toward the semicircular Galactic supernova remnant (SNR) 3C434.1 (G94.0+1.0). We mapped an area covering the whole SNR in the {sup 12}CO J = 1-0 emission line using the Seoul Radio Astronomy Observatory 6 m telescope and found a large molecular cloud superposed on the faint western part of the SNR. The cloud was elongated along the north-south direction and showed a very good spatial correlation with the radio features of the SNR. We carried out {sup 12}CO J = 2-1 line observations of this cloud using the Koelner Observatorium fuer Sub-Millimeter Astronomie 3 m telescope and found a region in which the {sup 12}CO J = 2-1 to J = 1-0 ratio was high ({approx}1.6). This higher excitation, together with the morphological relation, strongly suggested that the molecular cloud was interacting with the SNR. The systemic velocity of the molecular cloud (-13 km s{sup -1}) gave a kinematic distance of 3.0 kpc to the SNR-molecular cloud system. We derived the physical parameters of the SNR based on this new distance. We examined the variation of the radio spectral index over the remnant and found that it was flatter in the western part, wherein the SNR was interacting with the molecular cloud. We therefore propose that 3C434.1 is the remnant of a supernova explosion that occurred just outside the boundary of a relatively thin, sheet-like molecular cloud. We present a hydrodynamic model showing that its asymmetric radio morphology can result from its interaction with this blocking molecular cloud.

Jeong, Il-Gyo; Koo, Bon-Chul; Cho, Wan-Kee [Astronomy Program, Department of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of); Kramer, Carsten [Instituto Radioastronomia Milimetrica (IRAM), Av. Divina Pastora 7, E-18012 Granada (Spain); Stutzki, Juergen [I. Physikalisches Institut, Universitaet zu Koeln, Zuelpicher Strasse 77, D-50937 Koeln (Germany); Byun, Do-Young, E-mail: igjeong@astro.snu.ac.kr, E-mail: koo@astro.snu.ac.kr [Korea Astronomy and Space Science Institute, Daejeon 305-348 (Korea, Republic of)

2013-06-20T23:59:59.000Z

324

Dynamical Properties of Interaction Data  

E-Print Network [OSTI]

Network dynamics are typically presented as a time series of network properties captured at each period. The current approach examines the dynamical properties of transmission via novel measures on an integrated, temporally extended network representation of interaction data across time. Because it encodes time and interactions as network connections, static network measures can be applied to this "temporal web" to reveal features of the dynamics themselves. Here we provide the technical details and apply it to agent-based implementations of the well-known SEIR and SEIS epidemiological models.

Bramson, Aaron

2015-01-01T23:59:59.000Z

325

Cosmology and the weak interaction  

SciTech Connect (OSTI)

The weak interaction plays a critical role in modern Big Bang cosmology. This review will emphasize two of its most publicized cosmological connections: Big Bang nucleosynthesis and Dark Matter. The first of these is connected to the cosmological prediction of Neutrino Flavours, N{sub {nu}} {approximately} 3 which is now being confirmed at SLC and LEP. The second is interrelated to the whole problem of galaxy and structure formation in the universe. This review will demonstrate the role of the weak interaction both for dark matter candidates and for the problem of generating seeds to form structure. 87 refs., 3 figs., 5 tabs.

Schramm, D.N. (Fermi National Accelerator Lab., Batavia, IL (USA)):(Chicago Univ., IL (USA))

1989-12-01T23:59:59.000Z

326

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

E-Print Network [OSTI]

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

Shujing Deng; Pengpeng Diao; Qianli Yu; Haibin Wu

2015-02-01T23:59:59.000Z

327

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

E-Print Network [OSTI]

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

Deng, Shujing; Yu, Qianli; Wu, Haibin

2015-01-01T23:59:59.000Z

328

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

E-Print Network [OSTI]

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

Y. Kanada-En'yo

2002-04-15T23:59:59.000Z

329

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

E-Print Network [OSTI]

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

Akinori Isshiki; Kenichi Naito; Akira Ohnishi

2005-07-13T23:59:59.000Z

330

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

E-Print Network [OSTI]

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

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

2015-01-01T23:59:59.000Z

331

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

SciTech Connect (OSTI)

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.

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

2013-12-16T23:59:59.000Z

332

UBIQUITOUS COMPUTING AND INTERACTION Kaj Grnbk, Professor,  

E-Print Network [OSTI]

actuator based interaction >"Gamification" of training >Performance measurement >In near future also focus

333

PHASE TRANSFORMATIONS, STABILITY AND MATERIALS INTERACTIONS  

E-Print Network [OSTI]

engine) Environmental Interactions Ceramic Membrane Development Research Opportunities: •Fundamentals of hydrogen-

Morris, Jr., J.W.

2010-01-01T23:59:59.000Z

334

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...

335

Princeton Diversity Programs in Molecular Biology and Quantitative & Computational Biology  

E-Print Network [OSTI]

CASE STUDY Princeton Diversity Programs in Molecular Biology and Quantitative & Computational Biology Author Princeton University Acknowledgments. Vides estius moluptaquis aut maxime vitin peroribus: Diversity Programs in Molecular Biology and Quantitative & Computational Biology Founded in 2007 in response

336

auf molecular imaging: Topics by E-print Network  

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

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

337

atherosclerosis molecular imaging: Topics by E-print Network  

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

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

338

OpenAtom -- Ab initio molecular dynamics package  

SciTech Connect (OSTI)

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

Roberto Car

2008-01-01T23:59:59.000Z

339

Optical activity of electronically delocalized molecular aggregates: Nonlocal response formulation  

E-Print Network [OSTI]

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

Mukamel, Shaul

340

Processing and thermal properties of molecularly oriented polymers  

E-Print Network [OSTI]

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

Skow, Erik (Erik Dean)

2007-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

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

E-Print Network [OSTI]

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

Ferreira, Márcia M. C.

342

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

E-Print Network [OSTI]

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

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

2002-08-15T23:59:59.000Z

343

Digital Soil Mapping: Interactions with  

E-Print Network [OSTI]

Chapter 21 Digital Soil Mapping: Interactions with and Applications for Hydropedology J.A. Thompson,1, * S. Roecker,2 S. Grunwald3 and P.R. Owens4 ABSTRACT Spatial information on soils, particularly hydrologic and hydromorphic soil properties, is used to understand and assess soil water retention, flooding

Grunwald, Sabine

344

Rotational ratchets with dipolar interactions  

E-Print Network [OSTI]

We report results from a computer simulation study on the rotational ratchet effect in systems of magnetic particles interacting via dipolar interactions. The ratchet effect consists of directed rotations of the particles in an oscillating magnetic field, which lacks a net rotating component. Our investigations are based on Brownian dynamics simulations of such many-particle systems. We investigate the influence of both, the random and deterministic contributions to the equations of motion on the ratchet effect. As a main result, we show that dipolar interactions can have an enhancing as well as a dampening effect on the ratchet behavior depending on the dipolar coupling strength of the system under consideration. The enhancement is shown to be caused by an increase in the effective field on a particle generated by neighboring magnetic particles, while the dampening is due to restricted rotational motion in the effective field. Moreover, we find a non-trivial influence of the short-range, repulsive interaction between the particles.

Sebastian Jäger; Sabine H. L. Klapp

2012-10-12T23:59:59.000Z

345

Interacting new generalized Chaplygin gas  

E-Print Network [OSTI]

We have presented a model in which the new generalized Chaplygin gas interacts with matter. We find that there exists a stable scaling solution at late times in the evolution of the universe. Moreover, the phantom crossing scenario is observed in this model.

Mubasher Jamil

2009-10-20T23:59:59.000Z

346

Mapping Interactions Within the Evolving  

E-Print Network [OSTI]

Laboratory School of Library and Information Science Indiana University, Bloomington, IN http://cns.iu.edu 13 #12;Research Questions · What interactions are made visible by analysis of formal communication messages over 2 years (Jan. `09 to Jan. `11) ­ Subscription lists, retrieved toward the middle and end

Menczer, Filippo

347

Numerical Modelling of Interaction between  

E-Print Network [OSTI]

plasma in arc furnace used in toxic waste destruction Plasma etching semiconductor High intensity arc lamp Electrode temperature after 1ms of arcing with power density of 3x109 W.m-2 Electrode temperatureNumerical Modelling of Interaction between the Electric Arc and Electrodes Principal researcher: W

Sóbester, András

348

Precision Tests of Electroweak Interactions  

SciTech Connect (OSTI)

The status of the precision tests of the electroweak interactions is reviewed in this paper. An emphasis is put on the Standard Model analysis based on measurements at LEP/SLC and the Tevatron. The results of the measurements of the electroweak mixing angle in the NuTeV experiment and the future prospects are discussed.

Akhundov, Arif [Institute of Physics, Azerbaijan Academy of Sciences, 370143 Baku (Azerbaijan); Departamento de Fisica Teorica and IFIC, Universidad de Valencia-CSIC, 46100 Valencia (Spain)

2008-04-21T23:59:59.000Z

349

www.cambridge.org/us/9780521194280 Molecular Machines in  

E-Print Network [OSTI]

www.cambridge.org/us/9780521194280 Molecular Machines in Biology Workshop of the Cell Joachim Frank Columbia University, New York About the Book The concept of molecular machines in biology has transformed, translation, protein folding, and protein degradation, are all carried out by molecular machines. This volume

Grishok, Alla

350

Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics  

E-Print Network [OSTI]

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

Zhao, Hongkai

351

Classical density functional theory to tackle solvation in molecular liquids  

E-Print Network [OSTI]

We present a brief review of the classical density functional theory of atomic and molecular fluids. We focus on the application of the theory to the determination of the solvation properties of arbitrary molecular solutes in arbitrary molecular solvent. This includes the prediction of the solvation free energies, as well as the characterization of the microscopic, three-dimensional solvent structure.

Jeanmairet, Guillaume; Sergiievskyi, Volodymyr; Borgis, Daniel

2015-01-01T23:59:59.000Z

352

Interaction between water cluster ions and mica surface  

SciTech Connect (OSTI)

Water cluster ion beams were irradiated on mica surfaces to investigate the interaction between molecular cluster ions and a mica surface. The contact angle of the mica surface increased with increasing dose of the water cluster ion beam, but the increase in the contact angle was smaller than that induced by an ethanol cluster ion beam. The surface roughness also increased with increasing dose of the water cluster ion beam, whereas the intensity of K 2p x-ray photoelectron spectroscopy peaks decreased with increasing dose of the water cluster ion beam. The decrease in the number of potassium atoms together with the increase in the surface roughness may be the causes of the increase in the contact angle.

Ryuto, Hiromichi, E-mail: ryuto@kuee.kyoto-u.ac.jp; Ohmura, Yuki; Nakagawa, Minoru; Takeuchi, Mitsuaki; Takaoka, Gikan H. [Photonics and Electronics Science and Engineering Center, Kyoto University, Nishikyo, Kyoto 615-8510 (Japan)

2014-03-15T23:59:59.000Z

353

Interactions of mobile helium clusters with surfaces and grain boundaries of plasma-exposed tungsten  

SciTech Connect (OSTI)

We report results of atomistic computations for the interactions of small mobile helium clusters (He{sub n}) with free surfaces and grain boundaries (GBs) in tungsten toward development of continuum drift-diffusion-reaction models for the dynamics of mobile helium clusters in plasma-exposed tungsten. Molecular-statics (MS) simulations based on reliable many-body interatomic potentials are carried out for He{sub n} (1???n???7) clusters near sinks to obtain the potential energy profiles of the He{sub n} clusters as a function of the clusters' center-of-mass distance from a sink. Sinks investigated include surfaces, GBs, and regions in the vicinity of junctions where GBs intersect free surfaces. Elastic interaction potentials based on elastic inclusion theory provide an excellent description of the MS results for the cluster-sink interactions. The key parameter in the elastic models is the sink segregation strength, which is found to increase with increasing cluster size. Such cluster-sink interactions are responsible for the migration of small helium clusters by drift and for helium segregation on surfaces and grain boundaries in tungsten. Such helium segregation on sinks is observed in large-scale molecular-dynamics simulations of helium aggregation in model polycrystalline tungsten at 933?K upon helium implantation.

Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu [Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003-9303 (United States); Hammond, Karl D.; Wirth, Brian D. [Department of Nuclear Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States)

2014-05-07T23:59:59.000Z

354

Dynamical Study of Guest-Host Orientational Interaction in LiquidCrystalline Materials  

SciTech Connect (OSTI)

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.

Truong, Thai Viet

2005-12-20T23:59:59.000Z

355

Dust Emission from the Perseus Molecular Cloud  

E-Print Network [OSTI]

Using far-infrared emission maps taken by IRAS and Spitzer and a near-infrared extinction map derived from 2MASS data, we have made dust temperature and column density maps of the Perseus molecular cloud. We show that the emission from transiently heated very small grains and the big grain dust emissivity vary as a function of extinction and dust temperature, with higher dust emissivities for colder grains. This variable emissivity can not be explained by temperature gradients along the line of sight or by noise in the emission maps, but is consistent with grain growth in the higher density and lower temperature regions. By accounting for the variations in the dust emissivity and VSG emission, we are able to map the temperature and column density of a nearby molecular cloud with better accuracy than has previously been possible.

S. Schnee; J. Li; A. A. Goodman; A. I. Sargent

2008-05-27T23:59:59.000Z

356

Counting molecular-beam grown graphene layers  

SciTech Connect (OSTI)

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.

Plaut, Annette S. [School of Physics, University of Exeter, Exeter EX4 4QL (United Kingdom)] [School of Physics, University of Exeter, Exeter EX4 4QL (United Kingdom); Wurstbauer, Ulrich [Department of Physics, Columbia University, New York, New York 10027 (United States)] [Department of Physics, Columbia University, New York, New York 10027 (United States); Pinczuk, Aron [Department of Physics, Columbia University, New York, New York 10027 (United States) [Department of Physics, Columbia University, New York, New York 10027 (United States); Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027 (United States); Garcia, Jorge M. [MBE Lab, IMM-Instituto de Microelectronica de Madrid (CNM-CSIC), Madrid, E-28760 (Spain)] [MBE Lab, IMM-Instituto de Microelectronica de Madrid (CNM-CSIC), Madrid, E-28760 (Spain); Pfeiffer, Loren N. [Electrical Engineering Department, Princeton University, New Jersey 08544 (United States)] [Electrical Engineering Department, Princeton University, New Jersey 08544 (United States)

2013-06-17T23:59:59.000Z

357

Atomic and Molecular Absorption at High Redshift  

E-Print Network [OSTI]

Strong constraints on possible variations in fundamental constants can be derived from HI 21-cm and molecular rotational absorption lines observed towards quasars. With the aim of forming a statistical sample of constraints we have begun a program of systematic searches for such absorption systems. Here we describe molecular rotational searches in 25 damped Lyman-alpha systems where, in many cases, we set optical depth limits an order of magnitude better than that required to detect the 4 known redshifted millimeter-wave absorbers. We also discuss the contributory factors in the detectability of HI 21-cm absorption, focusing on possible biases (e.g.low covering factors) in the currently known sample of absorbers and non-detections.

S. J. Curran; J. K. Webb; M. T. Murphy; Y. M. Pihlström

2004-05-14T23:59:59.000Z

358

Molecular Science Research Center, 1991 annual report  

SciTech Connect (OSTI)

During 1991, the Molecular Science Research Center (MSRC) experienced solid growth and accomplishment and the Environmental, and Molecular Sciences Laboratory (EMSL) construction project moved forward. We began with strong programs in chemical structure and dynamics and theory, modeling, and simulation, and both these programs continued to thrive. We also made significant advances in the development of programs in materials and interfaces and macromolecular structure and dynamics, largely as a result of the key staff recruited to lead these efforts. If there was one pervasive activity for the past year, however, it was to strengthen the role of the EMSL in the overall environmental restoration and waste management (ER/WM) mission at Hanford. These extended activities involved not only MSRC and EMSL staff but all PNL scientific and technical staff engaged in ER/WM programs.

Knotek, M.L.

1992-03-01T23:59:59.000Z

359

Self-doped molecular composite battery electrolytes  

DOE Patents [OSTI]

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.

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

2003-04-08T23:59:59.000Z

360

Institute for Molecular Medicine Research Program  

SciTech Connect (OSTI)

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.

Phelps, Michael E

2012-12-14T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

Free energy calculation of a molecule by removing VDW and Coulomb interactions in a transformation and treating the molecule as non interacting systems  

E-Print Network [OSTI]

Free energy calculations in molecular simulations have a variety of applications including determining the strength of molecular processes such as solvation and binding. It has been recently shown that when removing the VDW and Coulomb potential terms of a group of atoms in a molecule by performing a transformation, the molecule can be treated as non interacting systems in the free energy calculation. This treatment is applicable both when the molecule is in vacuum and in liquid and enables a very simple calculation of the free energies associated with the potentials that depend on the relative spherical coordinates of these atoms. Here we demonstrate the method in the free energy calculation of a Methanethiol molecule and compare the results to these obtained by MD simulations in vacuum and in water. The comparison of free energies associated with the potentials that depend on the relative spherical coordinates shows agreement between the results and faster computation when using the method by factors starti...

Farhi, Asaf

2015-01-01T23:59:59.000Z

362

Molecular Science Research Center 1992 annual report  

SciTech Connect (OSTI)

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.

Knotek, M.L.

1994-01-01T23:59:59.000Z

363

Stochastic heating of a molecular nanomagnet  

E-Print Network [OSTI]

We study the excitation dynamics of a single molecular nanomagnet by static and pulsed magnetic fields. Based on a stability analysis of the classical magnetization dynamics we identify analytically the fields parameters for which the energy is stochastically pumped into the system in which case the magnetization undergoes diffusively and irreversibly a large angle deflection. An approximate analytical expression for the diffusion constant in terms of the fields parameters is given and assessed by full numerical calculations.

L. Chotorlishvili; P. Schwab; Z. Toklikishvili; J. Berakdar

2010-07-02T23:59:59.000Z

364

Molecular Mechanism of Biological Proton Transport  

SciTech Connect (OSTI)

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.

Pomes, R.

1998-09-01T23:59:59.000Z

365

Frontiers of NMR in Molecular Biology  

SciTech Connect (OSTI)

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.

NONE

1999-08-25T23:59:59.000Z

366

Ultraviolet photoelectron spectroscopic study of the interaction of potassium with carbon monoxide and benzene on the Pt(111) surface  

SciTech Connect (OSTI)

The interaction of potassium with carbon monoxide and benezene has been studied on the Pt(111) crystal surface by ultraviolet photoelectron spectroscopy (UPS). The adsorptive changes reported in previous studies for carbon monoxide and benzene when potassium is coadsorbed are correlated with the UPS results presented here and are explained with the aid of a molecular orbital analysis. The authors find that the valence molecular orbitals increase their binding energy slightly when the potassium is coadsorbed, implying a model in which the adsorbates sense the potassium-induced changes in dipole field at the surface. 36 references, 11 figures.

Kudo, M.; Garfunkel, E.L.; Somorjai, G.A.

1985-07-18T23:59:59.000Z

367

Structure of the Alkali-metal-atom-Strontium molecular ions: towards photoassociation and formation of cold molecular ions  

E-Print Network [OSTI]

Structure of the Alkali-metal-atom-Strontium molecular ions: towards photoassociation and formation polarizability, of molecular ions composed of one alkali-metal atom and a Strontium ion are determined and a Strontium ion are discussed, as well as the formation of stable molecular ions. PACS numbers: 31.15.AR,31

368

Molecular graphics approach to bacterial AcrB proteinb-lactam antibiotic molecular recognition in drug efflux mechanism  

E-Print Network [OSTI]

Molecular graphics approach to bacterial AcrB protein­b-lactam antibiotic molecular recognition graphics study of the pump components AcrB and TolC, 16 b-lactam antibiotics and 7 other substrates; Multidrug resistance; Molecular graphics; Vestibules; Pore 1. Introduction Transmembrane solute transporters

Ferreira, Márcia M. C.

369

QSAR de alguns inibidores peptdicos da enzima HIV-1 protease utilizando "a priori" descritores moleculares e molecular graphics  

E-Print Network [OSTI]

moleculares e molecular graphics Rudolf Kiralj (PQ), Márcia Miguel Castro Ferreira (PQ) rudolf-calculator count/calculation using only 1D and 2D chemical formula). A work on COMBINE (COMparative BINding Energy of molecular graphics, are discussed in terms both of the a priori approach and of the HIV-1 protease inhibitor

Ferreira, Márcia M. C.

370

Molecular heat pump for rotational states  

E-Print Network [OSTI]

In this work we investigate the theory for three different uni-directional population transfer schemes in trapped multilevel systems which can be utilized to cool molecular ions. The approach we use exploits the laser-induced coupling between the internal and motional degrees of freedom so that the internal state of a molecule can be mapped onto the motion of that molecule in an external trapping potential. By sympathetically cooling the translational motion back into its ground state the mapping process can be employed as part of a cooling scheme for molecular rotational levels. This step is achieved through a common mode involving a laser-cooled atom trapped alongside the molecule. For the coherent mapping we will focus on adiabatic passage techniques which may be expected to provide robust and efficient population transfers. By applying far-detuned chirped adiabatic rapid passage pulses we are able to achieve an efficiency of better than 98% for realistic parameters and including spontaneous emission. Even though our main focus is on cooling molecular states, the analysis of the different adiabatic methods has general features which can be applied to atomic systems.

C. Lazarou; M. Keller; B. M. Garraway

2010-01-25T23:59:59.000Z

371

Molecular Selectivity of Brown Carbon Chromophores  

SciTech Connect (OSTI)

Complementary methods of high-resolution mass spectrometry and micro-spectroscopy were utilized for molecular analysis of secondary organic aerosol (SOA) generated from ozonolysis of two structural monoterpene isomers: D-limonene (LSOA) and a-pinene (PSOA). Laboratory simulated aging of LSOA and PSOA, through conversion of carbonyls into imines mediated by NH3 vapors in humid air, resulted in selective browning of the LSOA sample, while the PSOA sample remained white. Comparative analysis of the reaction products in the aged LSOA and PSOA samples provided insights into chemistry relevant to formation of brown carbon chromophores. A significant fraction of carbonyl-imine conversion products with identical molecular formulas were detected in both samples. This reflects the high level of similarity in the molecular composition of these two closely related SOA materials. Several highly conjugated products were detected exclusively in the brown LSOA sample and were identified as potential chromophores responsible for the observed color change. The majority of the unique products in the aged LSOA sample with the highest number of double bonds contain two nitrogen atoms. We conclude that chromophores characteristic of the carbonyl- imine chemistry in LSOA are highly conjugated oligomers of secondary imines (Schiff bases) present at relatively low concentrations. Formation of this type of conjugated compounds in PSOA is hindered by the structural rigidity of the a-pinene oxidation products. Our results suggest that the overall light-absorbing properties of SOA may be determined by trace amounts of strong brown carbon chromophores.

Laskin, Julia; Laskin, Alexander; Nizkorodov, Sergey; Roach, Patrick J.; Eckert, Peter A.; Gilles, Mary K.; Wang, Bingbing; Lee, Hyun Ji; Hu, Qichi

2014-09-18T23:59:59.000Z

372

Stochastic thermodynamics, fluctuation theorems, and molecular machines  

E-Print Network [OSTI]

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation-dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power, can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones like molecular motors, and heat engines like thermoelectric devices, using a common framework based on a cycle decomposition of entropy production.

Udo Seifert

2012-05-18T23:59:59.000Z

373

Molecular modeling gives insight into nonionic surfactants  

SciTech Connect (OSTI)

This paper describes the study of a nonionic surfactant through the use of molecular modeling software. The surfactant was decyl alcohol capped with 8 moles of ethylene oxide. This nonionic surfactant is a strong water-wetting agent as well as a good aqueous foaming agent. Four molecular dynamics studies of a single surfactant molecule were conducted under the following conditions: at a water surface at 80 F; in bulk water at 260 F; in bulk hexane at 80 F; at a hexane/water interface at 80 F. The conformations of the surfactant were observed and compared to known solubility data. The results from molecular modeling dynamics calculations will provide new insights into the behavior of surfactant molecules at surfaces and interfaces. This methodology was also extended to aggregates of surfactants to promote understanding of wetting behavior and non-emulsification behavior. In this paper, two studies were performed involving aggregates: one in bulk water at 80 F and another in bulk water at 260 F.

Gdanski, R.

1995-11-01T23:59:59.000Z

374

Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models  

E-Print Network [OSTI]

Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pair-wise interactions only, we have found 1) a significantly increased correlation with experimental phi-values and folding rates, 2) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ~ 20%, and 3) a considerably larger amount of 3-body energy present in Chymotripsin inhibitor than other proteins studied.

M. R. Ejtehadi; S. P. Avall; S. S. Plotkin

2004-07-14T23:59:59.000Z

375

Molecular-level Design of Heterogeneous Chiral Catalysts  

SciTech Connect (OSTI)

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.

Gellman, Andrew John [Carnegie Mellon University; Sholl, David S. [Georgia Institute of Technology; Tysoe, Wilfred T. [University of Wisconsin - Milwaukee; Zaera, Francisco [University of California at Riverside

2013-04-28T23:59:59.000Z

376

Dimuon production in hadronic interactions  

SciTech Connect (OSTI)

This report summarizes the new data submitted to the XXI International Conference on High Energy Physics on high mass dimuon production in ..pi../sup -/N and anti pN interactions by Fermilab Experiment E-537, CERN Experiment NA3 and Fermilab Experiment E-326. Successes and failures of the Drell-Yan model and low order QCD are reviewed. New results on the production of the J/psi from E-537, NA3 and CERN experiment WAll are also reported.

Cox, B.

1982-10-01T23:59:59.000Z

377

3 D interactive pictorial maps  

E-Print Network [OSTI]

of simplififcation and exaggeration.. . . . . . . . . . . . . . 21 8 3 D polygonal text in Maya. . . . . . . . . . . . . . . . . . . . . . . . 22 9 Final 3 D model of Italy with text. . . . . . . . . . . . . . . . . . . . 23 10 Top view of 3 D model of France... the files in a format that is suitable for web viewing. 15 CHAPTER IV METHODOLOGY There are three major steps to making an interactive pictorial map. The fifrst step is to build the 3 D model using a modeling software, Maya. The second step is to apply...

Naz, Asma

2005-02-17T23:59:59.000Z

378

Surprising Quasiparticle Interactions in Graphene  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security AdministrationcontrollerNanocrystalline GalliumSuppression ofSurprising Quasiparticle Interactions

379

Molecular Life Science | Daniel Loos | loos@mls.uni-luebeck.de IM FOCUS DAS LEBEN  

E-Print Network [OSTI]

Was ist Molecular Life Science? Hämoglobin. Protein Data Bank: 1HHO #12;Daniel Loos Molecular Life Science

Lübeck, Universität zu

380

An NMR (nuclear magnetic resonance) investigation of the chemical association and molecular dynamics in asphalt ridge tar sand ore and bitumen  

SciTech Connect (OSTI)

Preliminary studies on tar sand bitumen given in this report have shown that the reassociation of tar sand bitumen to its original molecular configuration after thermal stressing is a first-order process requiring nearly a week to establish equilibrium. Studies were also conducted on the dissolution of tar sand bitumen in solvents of varying polarity. At a high-weight fraction of solute to solvent the apparent molecular weight of the bitumen molecules was greater than that of the original bitumen when dissolved in chloroform-d/sub 1/ and benzene-d/sub 6/. This increase in the apparent molecular weight may be due to micellar formation or a weak solute-solvent molecular complex. Upon further dilution with any of the solvents studied, the apparent molecular weight of the tar sand bitumen decreased because of reduced van der Waals forces of interaction and/or hydrogen bonding. To define the exact nature of the interactions, it will be necessary to have viscosity measurements of the solutions. 30 refs., 3 figs., 3 tabs.

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

1987-09-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Molecular Environmental Science: An Assessment of Research Accomplishments, Available Synchrotron Radiation Facilities, and Needs  

SciTech Connect (OSTI)

Synchrotron-based techniques are fundamental to research in ''Molecular Environmental Science'' (MES), an emerging field that involves molecular-level studies of chemical and biological processes affecting the speciation, properties, and behavior of contaminants, pollutants, and nutrients in the ecosphere. These techniques enable the study of aqueous solute complexes, poorly crystalline materials, solid-liquid interfaces, mineral-aqueous solution interactions, microbial biofilm-heavy metal interactions, heavy metal-plant interactions, complex material microstructures, and nanomaterials, all of which are important components or processes in the environment. Basic understanding of environmental materials and processes at the molecular scale is essential for risk assessment and management, and reduction of environmental pollutants at field, landscape, and global scales. One of the main purposes of this report is to illustrate the role of synchrotron radiation (SR)-based studies in environmental science and related fields and their impact on environmental problems of importance to society. A major driving force for MES research is the need to characterize, treat, and/or dispose of vast quantities of contaminated materials, including groundwater, sediments, and soils, and to process wastes, at an estimated cost exceeding 150 billion dollars through 2070. A major component of this problem derives from high-level nuclear waste. Other significant components come from mining and industrial wastes, atmospheric pollutants derived from fossil fuel consumption, agricultural pesticides and fertilizers, and the pollution problems associated with animal waste run-off, all of which have major impacts on human health and welfare. Addressing these problems requires the development of new characterization and processing technologies--efforts that require information on the chemical speciation of heavy metals, radionuclides, and xenobiotic organic compounds and their reactions with environmental materials. To achieve this goal, both fundamental and targeted studies of complex environmental systems at a molecular level are needed, and examples of both types of studies are presented herein. These examples illustrate the fact that MES SR studies have led to a revolution in our understanding of the fundamental physical and chemical aspects of natural systems. The MES SR user community has continued to experience strong growth at U.S. SR laboratories, with MES researchers comprising up to 15% of the total user base. Further growth and development of the MES community is being hindered by insufficient resources, including support personnel, materials preparation facilities, and available beam time at U.S. SR laboratories. ''EnviroSync'' recommends the following actions, in cooperation with U.S. SR laboratory directors, to meet the MES community's needs.

Brown, G

2004-02-05T23:59:59.000Z

382

Molecular environmental science : an assessment of research accomplishments, available synchrotron radiation facilities, and needs.  

SciTech Connect (OSTI)

Synchrotron-based techniques are fundamental to research in ''Molecular Environmental Science'' (MES), an emerging field that involves molecular-level studies of chemical and biological processes affecting the speciation, properties, and behavior of contaminants, pollutants, and nutrients in the ecosphere. These techniques enable the study of aqueous solute complexes, poorly crystalline materials, solid-liquid interfaces, mineral-aqueous solution interactions, microbial biofilm-heavy metal interactions, heavy metal-plant interactions, complex material microstructures, and nanomaterials, all of which are important components or processes in the environment. Basic understanding of environmental materials and processes at the molecular scale is essential for risk assessment and management, and reduction of environmental pollutants at field, landscape, and global scales. One of the main purposes of this report is to illustrate the role of synchrotron radiation (SR)-based studies in environmental science and related fields and their impact on environmental problems of importance to society. A major driving force for MES research is the need to characterize, treat, and/or dispose of vast quantities of contaminated materials, including groundwater, sediments, and soils, and to process wastes, at an estimated cost exceeding 150 billion dollars through 2070. A major component of this problem derives from high-level nuclear waste. Other significant components come from mining and industrial wastes, atmospheric pollutants derived from fossil fuel consumption, agricultural pesticides and fertilizers, and the pollution problems associated with animal waste run-off, all of which have major impacts on human health and welfare. Addressing these problems requires the development of new characterization and processing technologies--efforts that require information on the chemical speciation of heavy metals, radionuclides, and xenobiotic organic compounds and their reactions with environmental materials. To achieve this goal, both fundamental and targeted studies of complex environmental systems at a molecular level are needed, and examples of both types of studies are presented herein. These examples illustrate the fact that MES SR studies have led to a revolution in our understanding of the fundamental physical and chemical aspects of natural systems. The MES SR user community has continued to experience strong growth at U.S. SR laboratories, with MES researchers comprising up to 15% of the total user base. Further growth and development of the MES community is being hindered by insufficient resources, including support personnel, materials preparation facilities, and available beam time at U.S. SR laboratories. EnviroSync* recommends the following actions, in cooperation with U.S. SR laboratory directors, to meet the MES community's needs.

Brown, G. E., Jr.; Sutton, S. R.; Bargar, J. R.; Shuh, D. K.; Fenter, P. A.; Kemner, K. M.

2004-10-20T23:59:59.000Z

383

Molecular dynamics of excited state intramolecular proton transfer: 3-hydroxyflavone in solution  

SciTech Connect (OSTI)

The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 3-hydroxyflavone is investigated using classical molecular dynamics in conjunction with empirical valence bond (EVB) potentials for the description of intramolecular interactions, and a molecular mechanics and variable partial charge model, dependent on transferring proton position, for the description of solute-solvent interactions. A parallel multi-level genetic program was used to accurately fit the EVB potential energy surfaces to high level ab initio data. We have studied the excited state intramolecular proton transfer (ESIPT) reaction in three different solvent environments: methylcyclohexane, acetonitrile, and methanol. The effects of the environment on the proton transfer time and the underlying mechanisms responsible for the varied time scales of the ESIPT reaction rates are analyzed. We find that simulations with our EVB potential energy surfaces accurately reproduce experimentally determined reaction rates, fluorescence spectra, and vibrational frequency spectra in all three solvents. Furthermore, we find that the ultrafast ESIPT process results from a combination of ballistic transfer, and intramolecular vibrational redistribution, which leads to the excitation of a set of low frequency promoting vibrational modes. From this set of promoting modes, we find that an O-O in plane bend and a C-H out of plane bend are present in all three solvents, indicating that they are fundamental to the ultrafast proton transfer. Analysis of the slow proton transfer trajectories reveals a solvent mediated proton transfer mechanism, which is diffusion limited.

Bellucci, Michael A.; Coker, David F. [Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215 (United States)

2012-05-21T23:59:59.000Z

384

Interaction blending equations enhance reformulated gasoline profitability  

SciTech Connect (OSTI)

The interaction approach to gasoline blending gives refiners an accurate, simple means of re-evaluating blending equations and increasing profitability. With reformulated gasoline specifications drawing near, a detailed description of this approach, in the context of reformulated gasoline is in order. Simple mathematics compute blending values from interaction equations and interaction coefficients between mixtures. A timely example of such interactions is: blending a mixture of catalytically cracked gasoline plus light straight run (LSR) from one tank with alkylate plus reformate from another. This paper discusses blending equations, using interactions, mixture interactions, other blending problems, and obtaining equations.

Snee, R.D. (Joiner Associates, Madison, WI (United States)); Morris, W.E.; Smith, W.E.

1994-01-17T23:59:59.000Z

385

Interaction of water with epoxy.  

SciTech Connect (OSTI)

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.

Powers, Dana Auburn

2009-07-01T23:59:59.000Z

386

Giant amplification of tunnel magnetoresistance in a molecular junction: Molecular spin-valve transistor  

SciTech Connect (OSTI)

Amplification of tunnel magnetoresistance by gate field in a molecular junction is the most important requirement for the development of a molecular spin valve transistor. Herein, we predict a giant amplification of tunnel magnetoresistance in a single molecular spin valve junction, which consists of Ru-bis-terpyridine molecule as a spacer between two ferromagnetic nickel contacts. Based on the first-principles quantum transport approach, we show that a modest change in the gate field that is experimentally accessible can lead to a substantial amplification (320%) of tunnel magnetoresistance. The origin of such large amplification is attributed to the spin dependent modification of orbitals at the molecule-lead interface and the resultant Stark effect induced shift in channel position with respect to the Fermi energy.

Dhungana, Kamal B.; Pati, Ranjit, E-mail: patir@mtu.edu [Department of Physics, Michigan Technological University, Houghton, Michigan 49931 (United States)

2014-04-21T23:59:59.000Z

387

Molecular Aspects of Transport in Thin Films of Controlled Architecture  

SciTech Connect (OSTI)

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.

Paul W. Bohn

2009-04-16T23:59:59.000Z

388

Measuring the Monitoring User Interactive Experiences on Franklin Interactive Nodes  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: VegetationEquipment Surfaces andMapping the Nanoscale LandscapeImportsBG4,Measurements+ CrossInteractive

389

Introduction Counterpropagating interactions Numerical methods Co-propagating interactions A result on energy transfer Solitary water wave interactions  

E-Print Network [OSTI]

on energy transfer Solitary water wave interactions Walter Craig Department of Mathematics & Statistics (energy loss) and S (amplitude change). Walter Craig McMaster University Solitary wave interactions #12 (energy loss) and S (amplitude change). Walter Craig McMaster University Solitary wave interactions #12

Craig, Walter

390

Molecular characterization and evolutionary plasticity of protein-protein interfaces  

E-Print Network [OSTI]

are the percentage of interfaces having non- zero values for this interaction type. Interaction types per unit area for the overall non-redundant set. . . . . . . . . . . . . . . . 99 3.11 Interaction types per unit area for obligate homodimers. . . . . . 100 3...

Bickerton, George Richard James

391

The Galactic Center: An Interacting System of Unusual Sources  

E-Print Network [OSTI]

The region bounded by the inner tens of light years at the center of the Milky Way contains five principal components that coexist within the central deep gravitational potential well. These constituents are a black hole candidate (Sgr~A*) with a mass equivalent to $2.6\\pm0.2\\times 10^6$ suns, a surrounding cluster of evolved stars, a complex of young stars, molecular and ionized gas clouds, and a powerful supernova-like remnant. The interaction of these components is responsible for many of the phenomena occurring in this complex and unique portion of the Galaxy. Developing a consistent picture of the primary interactions between the components at the Galactic Center will improve our understanding of the nature of galactic nuclei in general, and will provide with a better defined set of characteristics of black holes. For example, the accretion of stellar winds by Sgr A* appears to produce far less radiation than indicated by estimates based on models of galactic nuclei.

F. Yusef-Zade; F. Melia; M. Wardle

2000-01-11T23:59:59.000Z

392

Analytic energy gradients for constrained DFT-configuration interaction  

SciTech Connect (OSTI)

The constrained density functional theory-configuration interaction (CDFT-CI) method has previously been used to calculate ground-state energies and barrier heights, and to describe electronic excited states, in particular conical intersections. However, the method has been limited to evaluating the electronic energy at just a single nuclear configuration, with the gradient of the energy being available only via finite difference. In this paper, we present analytic gradients of the CDFT-CI energy with respect to nuclear coordinates, which gives the potential for accurate geometry optimization and molecular dynamics on both the ground and excited electronic states, a realm which is currently quite challenging for electronic structure theory. We report the performance of CDFT-CI geometry optimization for representative reaction transition states as well as molecules in an excited state. The overall accuracy of CDFT-CI for computing barrier heights is essentially unchanged whether the energies are evaluated at geometries obtained from quadratic configuration-interaction singles and doubles (QCISD) or CDFT-CI, indicating that CDFT-CI produces very good reaction transition states. These results open up tantalizing possibilities for future work on excited states.

Kaduk, Benjamin; Tsuchimochi, Takashi; Van Voorhis, Troy, E-mail: tvan@mit.edu [Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States)

2014-05-14T23:59:59.000Z

393

"deinewahl02" A Demonstrator for Interactive Television  

E-Print Network [OSTI]

"deinewahl02" A Demonstrator for Interactive Television Dr. Sepideh Chakaveh Olaf Geuer Fraunhofer Institute Media Communication Fraunhofer Institute Media Communication Competence Center Interactive innovation. In here we are considering to reverse this process, i.e. implementing internet type applications

Masthoff, Judith

394

Ultracold Fermi gas with repulsive interactions  

E-Print Network [OSTI]

This thesis presents results from experiments of ultracold atomic Fermi gases with repulsive interaction. Itinerant ferromagnetism was studied by simulating the Stoner model with a strongly interacting Fermi gas of ultracold ...

Lee, Ye-Ryoung

2012-01-01T23:59:59.000Z

395

Arm-Hand-Finger Video Game Interaction  

E-Print Network [OSTI]

Despite the growing popularity and expansion of video game interaction techniques and research in the area of hand gesture recognition, the application of hand gesture video game interaction using arm, hand, and finger motion has not been...

Logsdon, Drew Anthony

2012-02-14T23:59:59.000Z

396

Stability Index of Interaction forms Joseph Abdou  

E-Print Network [OSTI]

Stability Index of Interaction forms Joseph Abdou December 15, 2008 Abstract An interaction form, 106-112 boulevard de l'H^opital 75647 Paris Cedex 13 - France; email: abdou@univ-paris1.fr 1 halshs

Paris-Sud XI, Université de

397

Africa Infrastructure Country Diagnostic Documents: Interactive...  

Open Energy Info (EERE)

Not Available Website: infrastructureafrica.orgdocumentstoolslistinteractive-pdf-maps Transport Toolkit Region(s): Africa & Middle East Interactive infrastructure maps by...

398

Electron-electron and electron-phonon interactions in irradiated N-methyl pyridinium derivatives with TCNQ studied by optical spectroscopy  

E-Print Network [OSTI]

1417 Electron-electron and electron-phonon interactions in irradiated N-methyl pyridinium derivatives with TCNQ studied by optical spectroscopy A. Graja and R. Swietlik Institute of Molecular Physics le 13 mars 1985, accepti le ler avril 1985) Résumé. 2014 L'irradiation électronique des

Boyer, Edmond

399

Spectroscopic study of the interaction of U(VI) with transferrin and albumin for speciation of U(VI) under blood serum conditions  

E-Print Network [OSTI]

radiation in human tissue, TAT allows to selectively deliver a highly cytotoxic radiation dose to targeted ternary complexes with carbonate acting as a synergistic anion. Together with literature data describing the interaction of U(VI) with low molecular weight inorganic and organic serum components, the speciation of U

Boyer, Edmond

400

Molecular beam studies of reaction dynamics  

SciTech Connect (OSTI)

Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.

Lee, Y.T.

1987-03-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

Intrinsic Shapes of Molecular Cloud Cores  

E-Print Network [OSTI]

We conduct an analysis of the shapes of molecular cloud cores using recently compiled catalogs of observed axis ratios of individual cores mapped in ammonia or through optical selection. We apply both analytical and statistical techniques to deproject the observed axis ratios in order to determine the true distribution of cloud core shapes. We find that neither pure oblate nor pure prolate cores can account for the observed distribution of core shapes. Intrinsically triaxial cores produce distributions which agree with observations. The best-fit triaxial distribution contains cores which are more nearly oblate than prolate.

C. E. Jones; Shantanu Basu; John Dubinski

2001-01-08T23:59:59.000Z

402

Towards reproducible, scalable lateral molecular electronic devices  

E-Print Network [OSTI]

of a renaissance in recent years, due in part to the fact that silicon-based devices have continued to decrease in size towards molecular dimensions. Transistors have been fabricated with gate lengths as short as 3 nm [1], and a plethora of new... REFERENCES 1. Hyunjin Lee et al, 2006 Symposium on VLSI Technology, 58, 2006, DOI: 10.1109/VLSIT.2006.1705215 2. K. Tomioka, M. Yoshimura & T. Fukui, Nature, 488, 189 (2012) 3. G. Larrieu & X. –L. Han, Nanoscale, 5, 2437 (2013) 4. A. D. Franklin, S. O...

Durkan, Colm; Zhang, Qian

2014-08-26T23:59:59.000Z

403

Environmental Molecular Sciences Laboratory 2004 Annual Report  

SciTech Connect (OSTI)

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.

White, Julia C.

2005-04-17T23:59:59.000Z

404

Molecular Selectivity of Brown Carbon Chromophores. | EMSL  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: VegetationEquipment SurfacesResource ProgramModification and Application ofofMolecularSelectivity of

405

Accelerated Molecular Dynamics Methods | Department of Energy  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious Rank EERE:YearRound-Up fromDepartment of Energy 601Department ofEnergyDeploymentMolecular Dynamics

406

An Introduction to Wave-Current Interactions  

E-Print Network [OSTI]

-scale wave focusing across a storm can re-direct the wind-stress? #12;1. Adiabatic interaction StartAn Introduction to Wave-Current Interactions Jerry Smith, MPL-SIO-UCSD jasmith@ucsd.edu http just want to hold up your hand. #12;Some Questions in Wave-Current Interaction Physics 1. Adiabatic

Smith, Jerome A.

407

Multisurface Interaction in the WILD Room  

E-Print Network [OSTI]

- 1 - Multisurface Interaction in the WILD Room Michel Beaudouin-Lafon, Stéphane Huot, Mathieu University Abstract The WILD room (wall-sized interaction with large datasets) serves as a testbed. (2012), "Multisurface Interaction in the WILD Room", IEEE Computer, vol 45, nº 4, pp. 48-56. DOI

Paris-Sud XI, Université de

408

Turbulence transport with nonlocal interactions  

SciTech Connect (OSTI)

This preliminary report describes a variety of issues in turbulence transport analysis with particular emphasis on closure procedures that are nonlocal in wave-number and/or physical space. Anomalous behavior of the transport equations for large scale parts of the turbulence spectrum are resolved by including the physical space nonlocal interactions. Direct and reverse cascade processes in wave-number space are given a much richer potential for realistic description by the nonlocal formulations. The discussion also describes issues, many still not resolved, regarding new classes of self-similar form functions.

Linn, R.R.; Clark, T.T.; Harlow, F.H.; Turner, L.

1998-03-01T23:59:59.000Z

409

Stochastic pump of interacting particles  

E-Print Network [OSTI]

We consider the overdamped motion of Brownian particles, interacting via particle exclusion, in an external potential that varies with time and space. We show that periodic potentials that maintain specific position-dependent phase relations generate time-averaged directed current of particles. We obtain analytic results for a lattice version of the model using a recently developed perturbative approach. Many interesting features like particle-hole symmetry, current reversal with changing density, and system-size dependence of current are obtained. We propose possible experiments to test our predictions.

Chaudhuri, Debasish

2010-01-01T23:59:59.000Z

410

Stochastic pump of interacting particles  

E-Print Network [OSTI]

We consider the overdamped motion of Brownian particles, interacting via particle exclusion, in an external potential that varies with time and space. We show that periodic potentials that maintain specific position-dependent phase relations generate time-averaged directed current of particles. We obtain analytic results for a lattice version of the model using a recently developed perturbative approach. Many interesting features like particle-hole symmetry, current reversal with changing density, and system-size dependence of current are obtained. We propose possible experiments to test our predictions.

Debasish Chaudhuri; Abhishek Dhar

2010-12-28T23:59:59.000Z

411

Surprising Quasiparticle Interactions in Graphene  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security AdministrationcontrollerNanocrystalline GalliumSuppression ofSurprising Quasiparticle Interactions in

412

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

SciTech Connect (OSTI)

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.

Suwalsky, Mario, E-mail: msuwalsk@udec.cl [Faculty of Chemical Sciences, University of Concepcion, Concepcion (Chile)] [Faculty of Chemical Sciences, University of Concepcion, Concepcion (Chile); Zambrano, Pablo; Mennickent, Sigrid [Faculty of Pharmacy, University of Concepcion, Concepcion (Chile)] [Faculty of Pharmacy, University of Concepcion, Concepcion (Chile); Villena, Fernando [Faculty of Biological Sciences, University of Concepcion, Concepcion (Chile)] [Faculty of Biological Sciences, University of Concepcion, Concepcion (Chile); Sotomayor, Carlos P.; Aguilar, Luis F. [Instituto de Quimica, Pontificia Universidad Catolica de Valparaiso, Valparaiso (Chile)] [Instituto de Quimica, Pontificia Universidad Catolica de Valparaiso, Valparaiso (Chile); Bolognin, Silvia [CNR-Institute for Biomedical Technologies, University of Padova, Padova (Italy)] [CNR-Institute for Biomedical Technologies, University of Padova, Padova (Italy)

2011-03-18T23:59:59.000Z

413

PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small  

E-Print Network [OSTI]

113 2332988, E­mail bmb5dva@biovax.leeds.ac.uk 1 #12; Summary A software package is described this descriptor a plausible 3D structure can be regenerated using energy minimisation. Alternatively, an ensemble of structures can be generated using a distance geometry based algorithm. Keywords molecular dynamics, graph

van Aalten, Daan

414

Compact submanifolds supporting singular interactions  

SciTech Connect (OSTI)

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.

Kaynak, Burak Tevfik, E-mail: burak.kaynak@boun.edu.tr; Teoman Turgut, O., E-mail: turgutte@boun.edu.tr

2013-12-15T23:59:59.000Z

415

The ecology of coral-microbe interactions  

E-Print Network [OSTI]

algal symbioses. Molecular Ecology 18:1823-1833. Webster, N.F. Rohwer. 2008. Microbial ecology of four coral atolls inin Caribbean coral reefs. Ecology Letters 9:818-826. Porter,

Marhaver, Kristen Laura

2010-01-01T23:59:59.000Z

416

Quantum Walk of Two Interacting Bosons  

E-Print Network [OSTI]

We study the effect of interactions on the bosonic two-particle quantum walk and its corresponding spatial correlations. The combined effect of interactions and Hanbury-Brown Twiss interference results in unique spatial correlations which depend on the strength of the interaction, but not on its sign. The results are explained in light of the two-particle spectrum and the physics of attractively and repulsively bound pairs. We experimentally measure the weak interaction limit of these effects in nonlinear photonic lattices. Finally, we discuss an experimental approach to observe the strong interaction limit using single atoms in optical lattices.

Yoav Lahini; Mor Verbin; Sebastian D. Huber; Yaron Bromberg; Rami Pugatch; Yaron Silberberg

2011-05-11T23:59:59.000Z

417

Molecular heat pump for rotational states  

E-Print Network [OSTI]

In this work we investigate the theory for three different uni-directional population transfer schemes in trapped multilevel systems which can be utilized to cool molecular ions. The approach we use exploits the laser-induced coupling between the internal and motional degrees of freedom so that the internal state of a molecule can be mapped onto the motion of that molecule in an external trapping potential. By sympathetically cooling the translational motion back into its ground state the mapping process can be employed as part of a cooling scheme for molecular rotational levels. This step is achieved through a common mode involving a laser-cooled atom trapped alongside the molecule. For the coherent mapping we will focus on adiabatic passage techniques which may be expected to provide robust and efficient population transfers. By applying far-detuned chirped adiabatic rapid passage pulses we are able to achieve an efficiency of better than 98% for realistic parameters and including spontaneous emission. Even...

Lazarou, C; Garraway, B M

2010-01-01T23:59:59.000Z

418

Molecular basis for amyloid-[beta] polymorphism  

SciTech Connect (OSTI)

Amyloid-beta (A{beta}) aggregates are the main constituent of senile plaques, the histological hallmark of Alzheimer's disease. A{beta} molecules form {beta}-sheet containing structures that assemble into a variety of polymorphic oligomers, protofibers, and fibers that exhibit a range of lifetimes and cellular toxicities. This polymorphic nature of A{beta} has frustrated its biophysical characterization, its structural determination, and our understanding of its pathological mechanism. To elucidate A{beta} polymorphism in atomic detail, we determined eight new microcrystal structures of fiber-forming segments of A{beta}. These structures, all of short, self-complementing pairs of {beta}-sheets termed steric zippers, reveal a variety of modes of self-association of A{beta}. Combining these atomic structures with previous NMR studies allows us to propose several fiber models, offering molecular models for some of the repertoire of polydisperse structures accessible to A{beta}. These structures and molecular models contribute fundamental information for understanding A{beta} polymorphic nature and pathogenesis.

Colletier, Jacques-Philippe; Laganowsky, Arthur; Landau, Meytal; Zhao, Minglei; Soriaga, Angela B.; Goldschmidt, Lukasz; Flot, David; Cascio, Duilio; Sawaya, Michael R.; Eisenberga, David (UCLA); (ESRF)

2011-10-19T23:59:59.000Z

419

Nuclear molecular configurations in heavy ion collisions  

SciTech Connect (OSTI)

The possibilities of nuclear molecular configurations in symmetric and asymmetric heavy ion collisions are investigated by choosing a proper parametrization for the molecule-like compound state. We treat the nucleus as a rotating liquid drop in terms of the elliptic lemniscatoid parametrization suggested by Royer and Remaud which describes all deformed shapes that occur during the process of fusion of two nuclei, starting from two touching spheres to a single one with the intermediate formation of a deep neck. Only one parameter ({ital s} for the symmetric and {ital s}{sub 1} for the conditional asymmetric case) is needed to define all the shapes encountered in the process. The shape has a neck as long as {ital s} or {ital s}{sub 1} is less than 1/ {radical}2 . In this parametrization, analytical expressions can be obtained for volume, surface, and moment of inertia while the Coulomb energy has to be evaluated numerically. The total energy of the system is calculated as a function of the parameter {ital s} or {ital s}{sub 1}, for various spins and if the stable shape corresponding to minimum energy is one with a neck, then it is concluded that the molecular configuration is possible. Our model yields results which are in good agreement with the experimental findings.

Shanmugam, G.; Padmini, M.D. (Department of Physics, Presidency College, Madras 600005, India (IN))

1989-09-01T23:59:59.000Z

420

Magnetic Fields in Molecular Cloud Cores  

E-Print Network [OSTI]

Observations of magnetic field strengths imply that molecular cloud fragments are individually close to being in a magnetically critical state, even though both magnetic field and column density measurements range over two orders of magnitude. The turbulent pressure also approximately balances the self-gravitational pressure. These results together mean that the one-dimensional velocity dispersion $\\sigv$ is proportional to the mean \\Alf speed of a cloud $\\va$. Global models of MHD turbulence in a molecular cloud show that this correlation is naturally satisfied for a range of different driving strengths of the turbulence. For example, an increase of turbulent driving causes a cloud expansion which also increases $\\va$. Clouds are in a time averaged balance but exhibit large oscillatory motions, particularly in their outer rarefied regions. We also discuss models of gravitational fragmentation in a sheet-like region in which turbulence has already dissipated, including the effects of magnetic fields and ion-neutral friction. Clouds with near-critical mass-to-flux ratios lead to subsonic infall within cores, consistent with some recent observations of motions in starless cores. Conversely, significantly supercritical clouds are expected to produce extended supersonic infall.

Shantanu Basu

2004-10-22T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

Universal scaling of potential energy functions describing intermolecular interactions. II. The halide-water and alkali metal-water interactions  

SciTech Connect (OSTI)

The scaled forms of the newly introduced generalized potential energy functions (PEFs) describing intermolecular interactions [J. Chem. Phys. xx, yyyyy (2011)] have been used to fit the ab-initio minimum energy paths (MEPs) for the halide- and alkali metal-water systems X-(H2O), X=F, Cl, Br, I, and M+(H2O), M=Li, Na, K, Rb, Cs. These generalized forms produce fits to the ab-initio data that are between one and two orders of magnitude better in the ?2 than the original forms of the PEFs. They were found to describe both the long-range, minimum and repulsive wall of the potential energy surface quite well. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gB-e6) potentials were found to best fit the ab-initio data. Furthermore, a single set of parameters of the reduced form was found to describe all candidates within each class of interactions. The fact that in reduced coordinates a whole class of interactions can be represented by a single PEF, yields the simple relationship between the molecular parameters associated with energy (well depth, ?), structure (equilibrium distance, rm) and spectroscopy (anharmonic frequency, ?):€? = A? (? /?)1/ 2 /rm + B?? /rm 3 , where A and B are constants depending on the underlying PEF. This more general case of Badger’s rule has been validated using the experimentally measured frequencies of the hydrogen bonded OH stretching vibrations in the halide-water series.

Werhahn, Jasper C.; Akase, Dai; Xantheas, Sotiris S.

2014-08-14T23:59:59.000Z

422

Final Report for Integrated Multiscale Modeling of Molecular Computing Devices  

SciTech Connect (OSTI)

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.

Glotzer, Sharon C.

2013-08-28T23:59:59.000Z

423

Molecular Structure and Stability of Dissolved Lithium Polysulfide...  

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

Stability of Dissolved Lithium Polysulfide Species. Molecular Structure and Stability of Dissolved Lithium Polysulfide Species. Abstract: Ability to predict the solubility and...

424

Integrated Molecular Signature of Disease: Analysis of Influenza...  

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

of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected...

425

Molecular biology of signal transduction in plants. Abstracts  

SciTech Connect (OSTI)

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.

Not Available

1991-12-31T23:59:59.000Z

426

advanced molecular biology: Topics by E-print Network  

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

311 Biology and Medicine Websites Summary: Molecular Biology Biology 311 Fall 2013 Syllabus Instructor: Dr. Deborah Lycan Class: MWF 9@lclark.edu Website: http:...

427

MATERIALS AND MOLECULAR RESEARCH DIVISION Annual Report 1977.  

E-Print Network [OSTI]

ld Strength of Sialon-Type Materials . . High-Temperatureand Reports . . . . . . . . . . . C. Materials Chemistry 1.VIII. APPENDICES A. Materials and Molecular Research

Authors, Various

2011-01-01T23:59:59.000Z

428

Molecular simulations of the transport of molecules across the...  

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

simulations of the transport of molecules across the liquidvapor interface of water. Molecular simulations of the transport of molecules across the liquidvapor interface of...

429

Molecular movie of water oxidation | Center for Bio-Inspired...  

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

Center News Research Highlights Center Research News Media about Center Center Video Library Bisfuel Picture Gallery Molecular movie of water oxidation 22 Oct 2012 Shibom Basu,...

430

Neutron Powder Diffraction and Molecular Simulation Study of...  

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

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

431

amyloidogenic molecular structures: Topics by E-print Network  

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

the symmetry and phase space distribution of excited electronic states in bulk 10 Fractal Structure of Molecular Clouds Astrophysics (arXiv) Summary: Compelling evidence...

432

alkane molecular ions: Topics by E-print Network  

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

1977-01-01 25 Blackbody thermometry with cold molecular ions and application to ion-based frequency standards Physics Websites Summary: Blackbody thermometry with cold...

433

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

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

Precursor Transport Through the Hydrogen Electron-Stimulated Production of Molecular Oxygen in Amorphous Solid Water on Pt(111): Precursor Transport Through the Hydrogen...

434

Molecular Simulations of Electrolytes and Electrolyte/Electrode...  

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

"Mega" Merit Review 2008 on February 25, 2008 in Bethesda, Maryland. merit08smith.pdf More Documents & Publications Molecular dynamics simulation and ab intio studies...

435

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

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

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

436

A unified model of electroporation and molecular transport  

E-Print Network [OSTI]

Biological membranes form transient, conductive pores in response to elevated transmembrane voltage, a phenomenon termed electroporation. These pores facilitate electrical and molecular transport across cell membranes that ...

Smith, Kyle Christopher

2011-01-01T23:59:59.000Z

437

Condensed Phase and Interfacial Molecular Science | U.S. DOE...  

Office of Science (SC) Website

of theories on the molecular origins of surface-mediated catalysis and heterogeneous chemistry. Studies of model condensed-phase systems target first-principles understandings of...

438

Molecular Chemistry of Organic Aerosols Through the Application...  

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

Chemistry of Organic Aerosols Through the Application of High Resolution Mass Spectrometry. Molecular Chemistry of Organic Aerosols Through the Application of High Resolution Mass...

439

Molecular dynamics study of interfacial confinement effects of...  

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

Molecular dynamics study of interfacial confinement effects of aqueous NaCl brines in nanoporous carbon Re-direct Destination: In this paper, studies of aqueous electrolyte...

440

Molecular Dynamics Study of the Proposed Proton Transport Pathways...  

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

Dynamics Study of the Proposed Proton Transport Pathways in FeFe-Hydrogenase. Molecular Dynamics Study of the Proposed Proton Transport Pathways in FeFe-Hydrogenase. Abstract:...

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


441

Molecular Dynamics Investigation of Ferrous-Ferric Electron Transfer...  

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

Electron Transfer in a Hydrolyzing Aqueous Solution: Calculation of the pH Molecular Dynamics Investigation of Ferrous-Ferric Electron Transfer in a Hydrolyzing Aqueous Solution:...

442

Molecular Dynamics Simulation Studies of Electrolytes and Electrolyte...  

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

and is lower than the barrier for opening EC cyclic radical. ReaxFF molecular dynamics simulations show similar barriers in gas and condensed phases for these reactions....

443

Molecular dynamics simulations of ion range profiles for heavy...  

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

simulations of ion range profiles for heavy ions in light targets. Molecular dynamics simulations of ion range profiles for heavy ions in light targets. Abstract: The determination...

444

Effect of Solar Radiation on the Optical Properties and Molecular...  

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

Solar Radiation on the Optical Properties and Molecular Composition of Laboratory Proxies of Atmospheric Brown Carbon Effect of Solar Radiation on the Optical Properties and...

445

Molecular Dynamics Simulations of Uranyl and Uranyl Carbonate...  

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

Simulations of Uranyl and Uranyl Carbonate Adsorption at Alumino-silicate Surfaces. Molecular Dynamics Simulations of Uranyl and Uranyl Carbonate Adsorption at Alumino-silicate...

446

Activation of molecular catalysts using semiconductor quantum dots  

DOE Patents [OSTI]

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.

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

2011-10-04T23:59:59.000Z

447

Structural Consequences of Anionic Host-Cationic Guest Interactions in a Supramolecular Assembly  

SciTech Connect (OSTI)

The molecular structure of the self-assembled supramolecular assembly [M{sub 4}L{sub 6}]{sup 12-} has been explored with different metals (M = Ga{sup III}, Fe{sup III}, Ti{sup IV}) and different encapsulated guests (NEt{sub 4}{sup +}, BnNMe{sub 3}{sup +}, Cp{sub 2}Co{sup +}, Cp*{sub 2}Co{sup +}) by X-ray crystallography. While the identity of the metal ions at the vertices of the M{sub 4}L{sub 6} structure is found to have little effect on the assembly structure, encapsulated guests significantly distort the size and shape of the interior cavity of the assembly. Cations on the exterior of the assembly are found to interact with the assembly through either {pi}-{pi}, cation-{pi}, or CH-{pi} interactions. In some cases, the exterior guests interact with only one assembly, but cations with the ability to form multiple {pi}-{pi} interactions are able to interact with adjacent assemblies in the crystal lattice. The solvent accessible cavity of the assembly is modeled using the rolling probe method and found to range from 253-434 {angstrom}{sup 3}, depending on the encapsulated guest. Based on the volume of the guest and the volume of the cavity, the packing coefficient for each host-guest complex is found to range from 0.47-0.67.

Pluth, Michael D.; Johnson, Darren W.; Szigethy, Geza; Davis, Anna V.; Teat, Simon J.; Oliver, Allen G.; Bergman, Robert G.; Raymond, Kenneth N.

2008-07-09T23:59:59.000Z

448

Elastic free-energy of the edge of an open lipid bilayer based on the interactions of its constituent molecules  

E-Print Network [OSTI]

Lipid-bilayers are the fundamental constituents of the walls of most living cells and lipid vesicles, giving them shape and compartment. The formation and growing of pores in a lipid bilayer have attracted considerable attention from an energetic point of view in recent years. Such pores permit targeted delivery of drugs and genes to the cell, and regulate the concentration of various molecules within the cell. The formation of such pores is caused by various reasons such as changes in cell environment, mechanical stress or thermal fluctuations. Understanding the energy and elastic behaviour of a lipid-bilayer edge is crucial for controlling the formation and growth of such pores. In the present work, the interactions in the molecular level are used to obtain the free energy of the edge of an open lipid bilayer. The resulted free-energy density includes terms associated with flexural and torsional energies of the edge, in addition to a line-tension contribution. The line tension, elastic moduli, and spontaneous normal and geodesic curvatures of the edge are obtained as functions of molecular distribution, molecular dimensions, cutoff distance, and the interaction strength. These parameters are further analyzed by implementing a soft-core interaction potential in the microphysical model. The dependence of the elastic free-energy of the edge to the size of the pore is reinvestigated through an illustrative example, and the results are found to be in agreement with the previous observations.

Meisam Asgari; Aisa Biria

2015-02-17T23:59:59.000Z

449

Muon collider interaction region design  

SciTech Connect (OSTI)

Design of a muon collider interaction region (IR) presents a number of challenges arising from low {beta}* < 1 cm, correspondingly large beta-function values and beam sizes at IR magnets, as well as the necessity to protect superconducting magnets and collider detectors from muon decay products. As a consequence, the designs of the IR optics, magnets and machine-detector interface are strongly interlaced and iterative. A consistent solution for the 1.5 TeV c.o.m. muon collider IR is presented. It can provide an average luminosity of 10{sup 34} cm{sup -2}s{sup -1} with an adequate protection of magnet and detector components.

Alexahin, Y.I.; Gianfelice-Wendt, E.; Kashikhin, V.V.; Mokhov, N.V.; Zlobin, A.V.; /Fermilab; Alexakhin, V.Y.; /Dubna, JINR

2010-05-01T23:59:59.000Z

450

Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation  

SciTech Connect (OSTI)

Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

Carnevale, V. [Department of Chemistry, Center for Molecular Modeling, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6323 (United States); Raugei, S. [International School for Advanced Studies (SISSA) and CNR-INFM Democritos, Via Beirut 2, Trieste I-34014 Italy, Trieste (Italy)

2009-12-14T23:59:59.000Z

451

On supersymmetric Dirac delta interactions  

E-Print Network [OSTI]

In this paper we construct $\\mathcal{N}=2$ supersymmetric (SUSY) quantum mechanics over several configurations of Dirac-$\\delta$ potentials from one single delta to a Dirac " comb \\rq\\rq. We show in detail how the building of supersymmetry on potentials with delta interactions placed in two or more points on the real line requires the inclusion of quasi-square wells. Therefore, the basic ingredient of a supersymmetric Hamiltonian containing two or more Dirac-$\\delta$s is the singular potential formed by a Dirac-$\\delta$ plus a step ($\\theta$) at the same point. In this $\\delta/\\theta$ SUSY Hamiltonian there is only one singlet ground state of zero energy annihilated by the two supercharges or a doublet of ground states paired by supersymmetry of positive energy depending on the relation between the Dirac well strength and the height of the step potential. We find a scenario of either unbroken supersymmetry with Witten index one or supersymmetry breaking when there is one " bosonic\\rq\\rq and one " fermionic\\rq\\rq ground state such that the Witten index is zero. We explain next the different structure of the scattering waves produced by three $\\delta/\\theta$ potentials with respect to the eigenfunctions arising in the non-SUSY case. In particular, many more bound states paired by supersymmetry exist within the supersymmetric framework compared with the non-SUSY problem. An infinite array of equally spaced $\\delta$-interactions of the same strength but alternatively attractive and repulsive are susceptible of being promoted to a ${\\cal N}=2$ supersymmetric system...

J. Mateos Guilarte; J. M. Munoz Castaneda; A. Moreno Mosquera

2015-01-28T23:59:59.000Z

452

Henry's Law Constants of Methane, Nitrogen, Oxygen and Carbon Dioxide in Ethanol from 273 to 498 K: Prediction from Molecular Simulation  

E-Print Network [OSTI]

noindent Henry's law constants of the solutes methane, nitrogen, oxygen and carbon dioxide in the solvent ethanol are predicted by molecular simulation. The molecular models for the solutes are taken from previous work. For the solvent ethanol, a new rigid anisotropic united atom molecular model based on Lennard-Jones and Coulombic interactions is developed. It is adjusted to experimental pure component saturated liquid density and vapor pressure data. Henry's law constants are calculated by evaluating the infinite dilution residual chemical potentials of the solutes from 273 to 498K with Widom's test particle insertion. The prediction of Henry's Law constants without the use of binary experimental data on the basis of the Lorentz-Berthelot combining rule agree well with experimental data, deviations are 20%, except for carbon dioxide for which deviations of 70% are reached. Quantitative agreement is achieved by using the modified Lorentz-Berthelot combining rule which is adjusted to one experimental mixture ...

Schnabel, T; Hasse, H

2009-01-01T23:59:59.000Z

453

Molecular dynamics simulation of hydration in myoglobin  

SciTech Connect (OSTI)

This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After salvation of the protein, energy minimization and equilibration of the system, 50 pico seconds of Newtonian dynamics was performed. This data showed that only 4 water molecules are continously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water.

Gu, Wei [New Mexico Univ., Albuquerque, NM (United States). Dept. of Biochemistry; Schoenborn, B.P. [Los Alamos National Lab., NM (United States)

1995-09-01T23:59:59.000Z

454

Silicotitanate molecular sieve and condensed phases  

DOE Patents [OSTI]

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.

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

2002-01-01T23:59:59.000Z

455

Octahedral molecular sieve sorbents and catalysts  

DOE Patents [OSTI]

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.

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

2010-04-20T23:59:59.000Z

456

The study of colliding molecular clumps evolution  

E-Print Network [OSTI]

The results of study of the gravitational fragmentation in the interstellar medium (ISM) by clump-clump collisions are presented. We suggest, that collision of clumps, that are subparts of Giant Molecular Clouds (GMC) may be on of the basic mechanism, which result to ISM fragmentation and define the dynamical as well as statistical characteristics (e.g. the mass spectra) of protostellar condensation. In the present paper, we describe our 3D SPH-modeling, in isothermal approximation, of supersonic collisions of two identical clumps with a few variants of initial impact parameters ($\\beta$), that cover the wide range. Our results shown, that at all $\\beta$ in system began intensive fragmentation. The resulting fragments mass function depend from initial impact parameter. The obtained mass spectra have the slopes in a good enough agreement with observational data for our Galaxy -- especially for large impact parameters, which are more realistic as for large clumps ensembles.

S. B. Vinogradov; P. Berczik

2007-01-12T23:59:59.000Z

457

Fundamental hydrogen interactions with beryllium : a magnetic fusion perspective.  

SciTech Connect (OSTI)

Increasingly, basic models such as density functional theory and molecular dynamics are being used to simulate different aspects of hydrogen recycling from plasma facing materials. These models provide valuable insight into hydrogen diffusion, trapping, and recombination from surfaces, but their validation relies on knowledge of the detailed behavior of hydrogen at an atomic scale. Despite being the first wall material for ITER, basic single crystal beryllium surfaces have been studied only sparsely from an experimental standpoint. In prior cases researchers used electron spectroscopy to examine surface reconstruction or adsorption kinetics during exposure to a hydrogen atmosphere. While valuable, these approaches lack the ability to directly detect the positioning of hydrogen on the surface. Ion beam techniques, such as low energy ion scattering (LEIS) and direct recoil spectroscopy (DRS), are two of the only experimental approaches capable of providing this information. In this study, we applied both LEIS and DRS to examine how hydrogen binds to the Be(0001) surface. Our measurements were performed using an angle-resolved ion energy spectrometer (ARIES) to probe the surface with low energy ions (500 eV - 3 keV He{sup +} and Ne{sup +}). We were able to obtain a 'scattering maps' of the crystal surface, providing insight on how low energy ions are focused along open surface channels. Once we completed a characterization of the clean surface, we dosed the sample with atomic hydrogen using a heated tungsten capillary. A distinct signal associated with adsorbed hydrogen emerged that was consistent with hydrogen residing between atom rows. To aid in the interpretation of the experimental results, we developed a computational model to simulate ion scattering at grazing incidence. For this purpose, we incorporated a simplified surface model into the Kalypso molecular dynamics code. This approach allowed us to understand how the incident ions interacted with the surface hydrogen, providing confirmation of the preferred binding site.

Wampler, William R. (Sandia National Laboratories, Albuquerque, NM); Felter, Thomas E.; Whaley, Josh A.; Kolasinski, Robert D.; Bartelt, Norman Charles

2012-03-01T23:59:59.000Z

458

NONIDEAL MAGNETOHYDRODYNAMIC TURBULENT DECAY IN MOLECULAR CLOUDS  

SciTech Connect (OSTI)

It is well known that nonideal magnetohydrodynamic (MHD) effects are important in the dynamics of molecular clouds: both ambipolar diffusion and possibly the Hall effect have been identified as significant. We present the results of a suite of simulations with a resolution of 512{sup 3} of turbulent decay in molecular clouds, incorporating a simplified form of both ambipolar diffusion and the Hall effect simultaneously. The initial velocity field in the turbulence is varied from being super-Alfvenic and hypersonic, through to trans-Alfvenic but still supersonic. We find that ambipolar diffusion increases the rate of decay of the turbulence increasing the decay from t {sup -1.25} to t {sup -1.4}. The Hall effect has virtually no impact in this regard. The power spectra of density, velocity, and the magnetic field are all affected by the nonideal terms, being steepened significantly when compared with ideal MHD turbulence with exponents. The density power-spectra components change from {approx}1.4 to {approx}2.1 for the ideal and nonideal simulations respectively, and power spectra of the other variables all show similar modifications when nonideal effects are considered. Again, the dominant source of these changes is ambipolar diffusion rather than the Hall effect. There is also a decoupling between the velocity field and the magnetic field at short length scales. The Hall effect leads to enhanced magnetic reconnection, and hence less power, at short length scales. The dependence of the velocity dispersion on the characteristic length scale is studied and found not to be power law in nature.

Downes, T. P. [School of Cosmic Physics, Dublin Institute for Advanced Studies, 31 Fitzwilliam Place, Dublin 2 (Ireland); O'Sullivan, S. [National Centre for Plasma Science and Technology, Dublin City University, Glasnevin, Dublin 9 (Ireland)], E-mail: turlough.downes@dcu.ie

2009-08-20T23:59:59.000Z

459

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

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

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.

Plimpton, Steve; Thompson, Aidan; Crozier, Paul

460

Molecular Photodynamics in Rare Gas Solids V. A. Apkarian*  

E-Print Network [OSTI]

Molecular Photodynamics in Rare Gas Solids V. A. Apkarian* Department of Chemistry, University Processes 1490 III. Sample Preparation and Morphology 1492 IV. Photon-Induced Dissociation 1493 V. Perfect I. Introduction A molecular level understanding of dynamics in condensed media is one of the current

Apkarian, V. Ara

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


461

Molecular Gas Reservoir in low-z Powerful Radio Galaxies  

E-Print Network [OSTI]

We report a survey for molecular gas in 3C radio galaxies at redshifts z gas masses in the range 10^7--10^9 Msun. The remainder had typical upper limits in molecular gas masses of ~10^8 Msun.

Jeremy Lim; Stephane Leon; Francoise Combes; Dinh-V-Trung

2002-11-13T23:59:59.000Z

462

Current rectification, switching, polarons, and defects in molecular electronic devices  

E-Print Network [OSTI]

Devices for nano- and molecular size electronics are currently a focus of research aimed at an efficient current rectification and switching. A few generic molecular scale devices are reviewed here on the basis of first-principles and model approaches. Current rectification by (ballistic) molecular quantum dots can produce the rectification ratio ~100. Current switching due to conformational changes in the molecules is slow, on the order of a few kHz. Fast switching (~1THz) may be achieved, at least in principle, in a degenerate molecular quantum dot with strong coupling of electrons with vibrational excitations. We show that the mean-field approach fails to properly describe intrinsic molecular switching and present an exact solution to the problem. Defects in molecular films result in spurious peaks in conductance, apparent negative differential resistance, and may also lead to unusual temperature and bias dependence of current. The observed switching in many cases is_extrinsic_, caused by changes in molecule-electrode geometry, molecule reconfiguration, metallic filament formation through, and/or changing amount of disorder in a molecular film. We give experimental examples of telegraph "switching" and "hot spot" formation in the molecular films.

A. M. Bratkovsky

2006-11-06T23:59:59.000Z

463

SAFE WORKING ENVIRONMENT THE DEPARTMENT OF MOLECULAR BIOLOGY AND GENETICS  

E-Print Network [OSTI]

SAFE WORKING ENVIRONMENT THE DEPARTMENT OF MOLECULAR BIOLOGY AND GENETICS MAY 2013MAY 2013 #12;#12;SAFE WORKING ENVIRONMENT 1 The Working Environment Organisation at the Department The Working Environment organisation at the Department of Molecular Biology and Genetics (MBG) is divided into 11 working

464

Dynamic Load Balancing for the Distributed Mining of Molecular Structures  

E-Print Network [OSTI]

Dynamic Load Balancing for the Distributed Mining of Molecular Structures Giuseppe Di Fatta, Member the data mining community, where algorithms to find frequent graphs have received increasing attention over a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular

Berthold, Michael R.

465

Large Scale Mining of Molecular Fragments with Wildcards  

E-Print Network [OSTI]

Large Scale Mining of Molecular Fragments with Wildcards Heiko Hofer1 , Christian Borgelt2 a novel molecule will be active or inactive, so that future chemical tests can be focused on the most molecular fragments to discriminate between active and inactive molecules. In this paper we present two

Borgelt, Christian

466

Electrical Contacts to Molecular Layers by Nanotransfer Printing  

E-Print Network [OSTI]

Electrical Contacts to Molecular Layers by Nanotransfer Printing Yueh-Lin Loo, David V. Lang, John of electrical contact. Results show that the nTP method produces superior devices in which the electrical for making electrical contacts in molecular electronics. Organic molecules whose electronic properties can

Rogers, John A.

467

Minireview 501 Kinesin and myosin: molecular motors with similar engines  

E-Print Network [OSTI]

Minireview 501 Kinesin and myosin: molecular motors with similar engines Ivan Rayment Structure molecu- lar motors that fulfill many of these tasks. These fall into three general classes of molecular motor exhibits the same architecture as myosin and suggests that these microtubule- and actin

Rayment, Ivan

468

Reconstructing web evolution and spider diversification in the molecular era  

E-Print Network [OSTI]

Reconstructing web evolution and spider diversification in the molecular era Todd A. Blackledgea,1- catching webs. Here, we construct a broad higher-level phylogeny of spiders combining molecular data that the spider orb web evolved only once. We then examine spider diversification in relation to different web

Mathis, Wayne N.

469

animated molecular dynamics: Topics by E-print Network  

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

animated molecular dynamics First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Molecular dynamics of B DNA...

470

atom molecular dynamics: Topics by E-print Network  

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

atom molecular dynamics First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Billion Atom Molecular Dynamics...

471

Fabrication of a Molecular Self-Assembled Monolayer Diode Using  

E-Print Network [OSTI]

techniques are often incompatible with the conditions necessary to self-assemble single molecules. HenceFabrication of a Molecular Self-Assembled Monolayer Diode Using Nanoimprint Lithography Michael D the conductance characteristics of a molecular self-assembled monolayer (SAM) using nanoimprint lithography (NIL

472

Molecular Design Using Quantum Chemical Calculations for Property Estimation  

E-Print Network [OSTI]

techniques for molecular design. A simple hydrofluorocarbon refrigerant design example and a solvent design level information about any system can be predicted (e.g., molecular energies, electronic charge as the target property, motivated by an interest in chemically stable hydrofluorocarbon refrigerants. The second

Maranas, Costas

473

Electrochemical treatment of human waste coupled with molecular hydrogen production  

E-Print Network [OSTI]

in a hydrogen fuel cell. Herein, we report on the efficacy of a laboratory-scale wastewater electrolysis cell an electrolysis cell for on-site wastewater treatment coupled with molecular hydrogen production for useElectrochemical treatment of human waste coupled with molecular hydrogen production Kangwoo Cho

Heaton, Thomas H.

474

H I Self Absorption Toward Molecular Clouds: Theoretical Models  

E-Print Network [OSTI]

information and available data, visit the GRS web page at www.bu.eduwww.bu.edu/G/GRSRS References chemistry deep inside the molecular clouds. We study H I self- absorption toward molecular clouds is dominated by cold atomic hydrogen formed by cosmic ray chemistry deep in the interiors of clouds. If all

475

Interacting agegraphic tachyon model of dark energy  

E-Print Network [OSTI]

Scalar-field dark energy models like tachyon are often regarded as an effective description of an underlying theory of dark energy. In this Letter, we implement the interacting agegraphic dark energy models with tachyon field. We demonstrate that the interacting agegraphic evolution of the universe can be described completely by a single tachyon scalar field. We thus reconstruct the potential as well as the dynamics of the tachyon field according to the evolutionary behavior of interacting agegraphic dark energy.

A. Sheykhi

2009-11-16T23:59:59.000Z

476

Constraints on extra dimensions from precision molecular spectroscopy  

E-Print Network [OSTI]

Accurate investigations of quantum level energies in molecular systems are shown to provide a test ground to constrain the size of compactified extra dimensions. This is made possible by the recent progress in precision metrology with ultrastable lasers on energy levels in neutral molecular hydrogen (H$_2$, HD and D$_2$) and the molecular hydrogen ions (H$_2^+$, HD$^+$ and D$_2^+$). Comparisons between experiment and quantum electrodynamics calculations for these molecular systems can be interpreted in terms of probing large extra dimensions, under which conditions gravity will become much stronger. Molecules are a probe of space-time geometry at typical distances where chemical bonds are effective, i.e. at length scales of an \\AA. Constraints on compactification radii for extra dimensions are derived within the Arkani-Hamed-Dimopoulos-Dvali framework, while constraints for curvature or brane separation are derived within the Randall-Sundrum framework. Based on the molecular spectroscopy of D$_2$ molecules an...

Salumbides, E J; Gato-Rivera, B; Ubachs, W

2015-01-01T23:59:59.000Z

477

Quantifying turbidity current interactions with topography  

E-Print Network [OSTI]

This thesis advances our understanding of how transport properties of turbidity currents are mediated by interactions with seafloor topography, specifically channelized surfaces. Turbidity currents are responsible for ...

Straub, Kyle M

2007-01-01T23:59:59.000Z

478

Private Interactive Communication Across an Adversarial Channel  

E-Print Network [OSTI]

Private Interactive Communication Across an Adversarial Channel Ran Gelles, Amit Sahai, and Akshay Wadia Department of Computer Science, University of California, Los Angeles, CA, USA {gelles, sahai

479

Probing Higgs Boson Interactions At Future Colliders.  

E-Print Network [OSTI]

??We present in this thesis a detailed analysis of Higgs boson interactions at future colliders. In particular we examine, in a model independent way, the… (more)

Biswal, Sudhansu Sekhar

2009-01-01T23:59:59.000Z

480

Universality of conductivity in interacting graphene  

E-Print Network [OSTI]

The Hubbard model on the honeycomb lattice describes charge carriers in graphene with short range interactions. While the interaction modifies several physical quantities, like the value of the Fermi velocity or the wave function renormalization, the a.c. conductivity has a universal value independent of the microscopic details of the model: there are no interaction corrections, provided that the interaction is weak enough and that the system is at half filling. We give a rigorous proof of this fact, based on exact Ward Identities and on constructive Renormalization Group methods.

A. Giuliani; V. Mastropietro; M. Porta

2011-01-11T23:59:59.000Z

Note: This page contains sample records for the topic "molecular plant-microbe interactions" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


481

INTERACTIVE COMPUTER GRAPHICS DISPLAYS FOR HIERARCHICAL DATA STRUCTURES  

E-Print Network [OSTI]

INTERACTIVE COMPUTER GRAPHICS DISPLAYS FOR HIERARCHICAL DATAINTERACTIVE COMPUTER GRAPHICS DISPLAYS FOR HIERARCHICAL DATAtem. INTERACTIVE COMPUTER GRAPHICS DISPLAYS FOR HIERARCHICAL

Cahn, D.F.

2010-01-01T23:59:59.000Z

482

Simulations of the dissociation of small helium clusters with ab initio molecular dynamics in electronically excited states  

SciTech Connect (OSTI)

The dynamics resulting from electronic excitations of helium clusters were explored using ab initio molecular dynamics. The simulations were performed with configuration interaction singles and adiabatic classical dynamics coupled to a state-following algorithm. 100 different configurations of He{sub 7} were excited into the 2s and 2p manifold for a total of 2800 trajectories. While the most common outcome (90%) was complete fragmentation to 6 ground state atoms and 1 excited state atom, 3% of trajectories yielded bound, He {sub 2}{sup *}, and <0.5% yielded an excited helium trimer. The nature of the dynamics, kinetic energy release, and connections to experiments are discussed.

Closser, Kristina D.; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Department of Chemistry, University of California Berkeley, Berkeley, California 94720 (United States) [Department of Chemistry, University of California Berkeley, Berkeley, California 94720 (United States); Ultrafast X-Ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Gessner, Oliver [Ultrafast X-Ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)] [Ultrafast X-Ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

2014-04-07T23:59:59.000Z

483

Study of iron structure stability in high temperature molten lead-bismuth eutectic with oxygen injection using molecular dynamics simulation  

SciTech Connect (OSTI)

Corrosion of structural materials in high temperature molten lead-bismuth eutectic is a major problem for design of PbBi cooled reactor. One technique to inhibit corrosion process is to inject oxygen into coolant. In this paper we study and focus on a way of inhibiting the corrosion of iron using molecular dynamics method. For the simulation results we concluded that effective corrosion inhibition of iron may be achieved by injection 0.0532 wt% to 0.1156 wt% oxygen into liquid lead-bismuth. At this oxygen concentration the structure of iron material will be maintained at about 70% in bcc crystal structure during interaction with liquid metal.

Arkundato, Artoto [Physics Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Su'ud, Zaki [Physics Department, Faculty of Mathematical and Natural Sciences, Bandung Institute of Technology, Jl. Ganesha 10, Bandung (Indonesia); Sudarko [Chemistry Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Shafii, Mohammad Ali [Physics Department, Faculty of Mathematical and Natural Sciences, Andalas University, Padang (Indonesia); Celino, Massimo [ENEA, CR Casaccia, Via Anguillarese 301, Rome (Italy)

2014-09-30T23:59:59.000Z

484

How Soil Organic Matter Composition Controls Hexachlorobenzene-Soil-Interactions: Adsorption Isotherms and Quantum Chemical Modelling  

E-Print Network [OSTI]

Hazardous persistent organic pollutants (POPs) interact in soil with the soil organic matter (SOM) but this interaction is insufficiently understood at the molecular level. We investigated the adsorption of hexachlorobenzene (HCB) on soil samples with systematically modified SOM. These samples included the original soil, the soil modified by adding a hot water extract (HWE) fraction (soil+3 HWE and soil+6 HWE), and the pyrolyzed soil. The SOM contents increased in the order pyrolyzed soil soil soil+3 HWE soil+6 HWE. For the latter three samples this order was also valid for the HCB adsorption. The pyrolyzed soil adsorbed more HCB than the other samples at low initial concentrations, but at higher concentrations the HCB adsorption became weaker than in the samples with HWE addition. This adsorption behaviour combined with the differences in the chemical composition between the soil samples suggested that alkylated aromatic, phenol, and lignin monomer compounds contributed most to the HC...

Ahmed, Ashour; Kühn, Oliver

2013-01-01T23:59:59.000Z

485

Optimum laser intensity for the production of energetic deuterium ions from laser-cluster interaction  

SciTech Connect (OSTI)

We measured, using Petawatt-level pulses, the average ion energy and neutron yield in high-intensity laser interactions with molecular clusters as a function of laser intensity. The interaction volume over which fusion occurred (1–10 mm{sup 3}) was larger than previous investigations, owing to the high laser power. Possible effects of prepulses were examined by implementing a pair of plasma mirrors. Our results show an optimum laser intensity for the production of energetic deuterium ions both with and without the use of the plasma mirrors. We measured deuterium plasmas with 14 keV average ion energies, which produced 7.2 × 10{sup 6} and 1.6 × 10{sup 7} neutrons in a single shot with and without plasma mirrors, respectively. The measured neutron yields qualitatively matched the expected yields calculated using a cylindrical plasma model.

Bang, W.; Dyer, G.; Quevedo, H. J.; Bernstein, A. C.; Gaul, E.; Rougk, J.; Aymond, F.; Donovan, M. E.; Ditmire, T. [Department of Physics, Center for High Energy Density Science, C1510, University of Texas at Austin, Austin, Texas 78712 (United States)] [Department of Physics, Center for High Energy Density Science, C1510, University of Texas at Austin, Austin, Texas 78712 (United States)

2013-09-15T23:59:59.000Z

486

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

SciTech Connect (OSTI)

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.

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

2013-04-24T23:59:59.000Z

487

Energy or Mass and Interaction  

E-Print Network [OSTI]

A review. Problems: 1-Many empirical parameters and large dimension number; 2-Gravitation and Electrodynamics are challenged by dark matter and energy. Energy and nonlinear electrodynamics are fundamental in a unified nonlinear interaction. Nuclear energy appears as nonlinear SU(2) magnetic energy. Gravitation and electromagnetism are unified giving Einstein's equation and a geometric energy momentum tensor. A solution energy in the newtonian limit gives the gravitational constant G. Outside of this limit G is variable. May be interpreted as dark matter or energy. In vacuum, known gravitational solutions are obtained. Electromagnetism is an SU(2) subgroup. A U(1) limit gives Maxwell's equations. Geometric fields determine a generalized Dirac equation and are the germ of quantum physics. Planck's h and of Einstein's c are given by the potential and the metric. Excitations have quanta of charge, flux and spin determining the FQHE. There are only three stable 1/2 spin fermions. Mass is a form of energy. The rest energies of the fermions give the proton/electron mass ratio. Potential excitations have energies equal to the weak boson masses allowing a geometric interpretation of Weinberg's angle. SU(2) gives the anomalous magnetic moments of proton, electron, neutron and generates nuclear range attractive potentials strong enough to produce the binding energies of the deuteron and other nuclides. Lepton and meson masses are due to topological excitations. The geometric mass spectrum is satisfactory. The proton has a triple structure. The alpha constant is a geometric number.

Gustavo R Gonzalez-Martin

2010-07-19T23:59:59.000Z

488

VUV studies of molecular photofragmentation dynamics  

SciTech Connect (OSTI)

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.

White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)

1993-12-01T23:59:59.000Z

489

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

SciTech Connect (OSTI)

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.

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

2008-06-01T23:59:59.000Z

490

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

SciTech Connect (OSTI)

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.

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

2008-08-01T23:59:59.000Z

491

In Situ Molecular Spectroscopic Evidence for CO2 Intercalation into Montmorillonite in Supercritical Carbon Dioxide  

SciTech Connect (OSTI)

The interaction of anhydrous supercritical CO2 (scCO2) with both kaolinite and ~1W (i.e. close to but less than one layer of hydration) calcium-saturated montmorillonite was investigated under conditions relevant to geologic carbon sequestration (50 °C and 90 bar). The CO2 molecular environment was probed in situ using a combination of three novel high-pressure techniques: X-ray diffraction, magic angle spinning nuclear magnetic resonance spectroscopy and attenuated total reflection infrared spectroscopy. We report the first direct evidence that the expansion of montmorillonite under scCO2 conditions is due to CO2 migration into the interlayer. Intercalated CO2 molecules are rotationally constrained and do not appear to react with waters to form bicarbonate or carbonic acid. In contrast, CO2 does not intercalate into kaolinite. The findings show that predicting the seal integrity of caprock will have complex dependence on clay mineralogy and hydration state.

Loring, John S.; Schaef, Herbert T.; Turcu, Romulus VF; Thompson, Christopher J.; Miller, Quin RS; Martin, Paul F.; Hu, Jian Z.; Hoyt, David W.; Qafoku, Odeta; Ilton, Eugene S.; Felmy, Andrew R.; Rosso, Kevin M.

2012-04-25T23:59:59.000Z

492

Study of the interaction of C60 fullerene with human serum albumin in aqueous solution  

SciTech Connect (OSTI)

Concern about the toxicity of engineered nanoparticles, such as the prototypical nanomaterial C60 fullerene, continues to grow. While evidence continues to mount that C60 and its derivatives may pose health hazards, the specific molecular interactions of these particles with biological macromolecules require further investigation. To better understand the interaction of C60 with proteins, the protein human serum albumin (HSA) was studied in solution with C60 at C60:HSA molar ratios ranging from 1:2 to 4:1. HSA is the major protein component of blood plasma and plays a role in a variety of functions, such as the maintenance of blood pH and pressure. The C60-HSA interaction was probed by a combination of circular dichroism (CD) spectroscopy, small-angle neutron scattering (SANS) and atomistic molecular dynamics (MD) simulations to understand C60-driven changes in the structure of HSA in solution. The CD spectroscopy demonstrates that the secondary structure of the protein decreases in -helical content in response to the presence of C60. Similarly, C60 produces subtle changes in the solution conformation of HSA, as evidenced by the SANS data and MD. The data do not indicate that C60 is causing a change in the oligomerization state of the protein. Taken together results demonstrate that C60 interacts with HSA, but it does not strongly perturb the structure of the protein by unfolding it or inducing aggregation, suggesting a mechanism for transporting C60 throughout the body to accumulate in various tissues.

Li, Song [Vanderbilt University; Zhao, Xiongce [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Mo, Yiming [ORNL; Cummings, Peter T [ORNL; Heller, William T [ORNL

2013-01-01T23:59:59.000Z

493

HERSCHEL MEASUREMENTS OF MOLECULAR OXYGEN IN ORION  

SciTech Connect (OSTI)

We report observations of three rotational transitions of molecular oxygen (O{sub 2}) in emission from the H{sub 2} Peak 1 position of vibrationally excited molecular hydrogen in Orion. We observed the 487 GHz, 774 GHz, and 1121 GHz lines using the Heterodyne Instrument for the Far Infrared on the Herschel Space Observatory, having velocities of 11 km s{sup -1} to 12 km s{sup -1} and widths of 3 km s{sup -1}. The beam-averaged column density is N(O{sub 2}) = 6.5 x 10{sup 16} cm{sup -2}, and assuming that the source has an equal beam-filling factor for all transitions (beam widths 44, 28, and 19''), the relative line intensities imply a kinetic temperature between 65 K and 120 K. The fractional abundance of O{sub 2} relative to H{sub 2} is (0.3-7.3) x 10{sup -6}. The unusual velocity suggests an association with a {approx}5'' diameter source, denoted Peak A, the Western Clump, or MF4. The mass of this source is {approx}10 M{sub sun} and the dust temperature is {>=}150 K. Our preferred explanation of the enhanced O{sub 2} abundance is that dust grains in this region are sufficiently warm (T {>=} 100 K) to desorb water ice and thus keep a significant fraction of elemental oxygen in the gas phase, with a significant fraction as O{sub 2}. For this small source, the line ratios require a temperature {>=}180 K. The inferred O{sub 2} column density {approx_equal}5 x 10{sup 18} cm{sup -2} can be produced in Peak A, having N(H{sub 2}) {approx_equal} 4 x 10{sup 24} cm{sup -2}. An alternative mechanism is a low-velocity (10-15 km s{sup -1}) C-shock, which can produce N(O{sub 2}) up to 10{sup 17} cm{sup -2}.

Goldsmith, Paul F.; Chen, Jo-Hsin; Li Di [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Liseau, Rene; Black, John H. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-439 92 Onsala (Sweden); Bell, Tom A. [Centro de Astrobiologia, CSIC-INTA, 28850 Madrid (Spain); Hollenbach, David [SETI Institute, Mountain View, CA 94043 (United States); Kaufman, Michael J. [Department of Physics and Astronomy, San Jose State University, San Jose, CA 95192 (United States); Lis, Dariusz C. [California Institute of Technology, Cahill Center for Astronomy and Astrophysics 301-17, Pasadena, CA 91125 (United States); Melnick, Gary [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, MS 66, Cambridge, MA 02138 (United States); Neufeld, David [Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Pagani, Laurent; Encrenaz, Pierre [LERMA and UMR8112 du CNRS, Observatoire de Paris, 61 Av. de l'Observatoire, 75014 Paris (France); Snell, Ronald [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Benz, Arnold O.; Bruderer, Simon [Institute of Astronomy, ETH Zurich, Zurich (Switzerland); Bergin, Edwin [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States); Caselli, Paola [School of Physics and Astronomy, University of Leeds, Leeds (United Kingdom); Caux, Emmanuel [Universite de Toulouse, UPS-OMP, IRAP, Toulouse (France); Falgarone, Edith, E-mail: Paul.F.Goldsmith@jpl.nasa.gov [LRA/LERMA, CNRS, UMR8112, Observatoire de Paris and Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris Cedex 05 (France)

2011-08-20T23:59:59.000Z

494

Final Report, "Molecular Design of Hydrocarbon Oxidation Catalytic Processes"  

SciTech Connect (OSTI)

The main goal of this project had been to use model systems to correlate selectivities in partial oxidation catalysis with the presence of specific sites on the surface of the catalyst. Extensive work was performed this year on characterizing oxygen-treated nickel surfaces by chemical means. Specifically, the surface chemistry of ammonia coadsorbed with atomic oxygen on Ni(110) single-crystal surfaces was studied by temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). It was determined that at intermediate oxygen coverages direct ammonia adsorption on nickel sites is suppressed, but a new high-temperature reaction regime is generated at 400 K where NHx surface fragments are rehydrogenated concurrently with the production of water and molecular hydrogen. The extensive isotope scrambling and hydrogen transfer seen from nitrogen- to oxygen-containing surface intermediates, and the optimum yields seen for this 400 K state at intermediate oxygen coverages, strongly suggest the direct interaction of the adsorbed ammonia with oxygen atoms at the end of the –Ni–O- rows that form upon reconstruction of the surface. Hydrogen transfer between ammonia and oxygen appears to take place directly via hydrogen bonding, and to be reversible but biased towards water formation. An equilibrium is reached between the produced water and the reacting surface oxygen and hydrogen. The strong influence of the OH surface groups on the thermal chemistry of the adsorbed ammonia was interpreted in terms of the adsorbing geometry of the OH groups on the surface, and of hydrogen bonding between adsorbed OH and NH3 species. In terms of alcohol reactivity, the adsorption of 2-iodoethanol, a precursor for the preparation of 2-hydroxyethyl and oxametallacycle surface species, was found to lead to two configurations involving either just the iodine atom or both iodine and hydroxyl ends of the molecule. A complex chemical behavior starts around 140 K with the production of small amounts of ethylene and water, most likely via the concerted decomposition or disproportionation of the adsorbed molecular species. The bulk of the 2-iodoethanol decomposes at about 150 K via an initial carbon-iodine scission to form –O(H)CH2CH2– (~80%) and 2-hydroxyethyl (~20%) intermediates. Two competing reactions are involved with the subsequent conversion of the 2-hydroxyethyl species around 160 K, a reductive elimination with surface hydrogen to yield ethanol, and a ?-H elimination to surface vinyl alcohol. The –O(H)CH2CH2–, on the other hand, dehydrogenates to a –OCH2CH2– oxametallacycle species about the same temperature. Both 2-hydroxyethyl and oxametallacycle species tautomerize to acetaldehyde, around 210 K and above 250 K, respectively, and some of that acetaldehyde desorbs while the rest decomposes to hydrogen and carbon monoxide. We contend that a better understanding of the surface chemistry of oxygen-containing surfaces can lead to better selectivities in catalysis. This is arguably the most important issue in the field of catalysis in the near future, and one that impacts several technologies of interest to DOE such as the manufacturing of speciality chemicals and the control and removal of pollutants. Additional work was performed on the characterization of the chemistry of methyl and methylene adsorbed species on oxygen-treated nickel surfaces. Complex chemistry was observed involving not only hydrogenation and dehydrogenation steps, but also C-C couplings and methylene insertions to produce heavier hydrocarbons, and oxygen insertion reactions that yield oxygenates. Finally, a dual titration technique employing xenon and a chemically sensitive probe was developed to identify minority catalytic sites on oxide surfaces. In the case of oxygen-treated Ni(110) single crystals, it was found that both hydrogen transfer with adsorbed water or ammonia and certain hydrocarbon hydrogenation reactions take place at the end of the –Ni–O rows that form in this system. Carbon and nitrogen oxides, on the other hand, display no pre

Professor Francisco Zaera

2007-08-09T23:59:59.000Z

495

Molecular hydrogen uptake by soils in forest, desert, and marsh ecosystems in California  

E-Print Network [OSTI]

Elkins (1999), Molecular hydrogen in the troposphere: GlobalGlobal budget of molecular hydrogen and its deuterium con-and dD of molecular hydrogen in boreal forests: Ecosys- tem-

Smith-Downey, Nicole V; Randerson, James T; Eiler, John M

2008-01-01T23:59:59.000Z

496

Dramatically Improved Yields in Molecular Scale Electronic Devices Using Ultra-smooth Platinum Electrodes Prepared By  

E-Print Network [OSTI]

Dramatically Improved Yields in Molecular Scale Electronic Devices Using Ultra-smooth Platinum scale electronic devices by using ultra- smooth platinum (Pt) electrodes made with chemical mechanically Terms -- Molecular electronics, CMP, SAM, Langmuir-Blodgett, Device yields. I. INTRODUCTION Molecular

Islam, M. Saif

497

12/15/11 EBS AY11/12 Biochemistry and Molecular Biology  

E-Print Network [OSTI]

12/15/11 EBS AY11/12 Biochemistry and Molecular Biology Division of Environmental and Biomolecular and Molecular Biology ­ Master of Science ­ Nonthesis ............................2 Track: Biochemistry and Molecular Biology.................................................................................2

Chapman, Michael S.

498

10/13/08 DSE/BMB AY08/09 Biochemistry and Molecular Biology  

E-Print Network [OSTI]

10/13/08 DSE/BMB AY08/09 Biochemistry and Molecular Biology Division of Environmental-2009 Degree: Biochemistry and Molecular Biology ­ Master of Science ­ Nonthesis...........................2 Track: Biochemistry and Molecular Biology

Chapman, Michael S.

499

12/13/11 EBS AY10/11 Biochemistry and Molecular Biology  

E-Print Network [OSTI]

12/13/11 EBS AY10/11 Biochemistry and Molecular Biology Division of Environmental and Biomolecular and Molecular Biology ­ Master of Science ­ Nonthesis ............................2 Track: Biochemistry and Molecular Biology.................................................................................2

Chapman, Michael S.

500

10/29/12 EBS AY12/13 Biochemistry and Molecular Biology  

E-Print Network [OSTI]

10/29/12 EBS AY12/13 Biochemistry and Molecular Biology Division of Environmental and Biomolecular and Molecular Biology ­ Master of Science ­ Nonthesis ............................2 Track: Biochemistry and Molecular Biology.................................................................................2

Chapman, Michael S.