Powered by Deep Web Technologies
Note: This page contains sample records for the topic "molecular dynamics md" 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

Molecular dynamics (MD) calculation of the real zeta potential of neutral surfaces  

E-Print Network [OSTI]

Molecular dynamics (MD) simulations of the zeta potential are so poor that it has become common to term their predictions "apparent". Here we demonstrate how MD methods can predict zeta potentials accurate enough they can be termed "real". The critical new aspects of our method are: (1) integrating the net average charge in surface-parallel layers from the midpoint of the fluid layer (where the electrostatic potential is zero) to and then into two solid caps, (2) determining the position of slipping plane with separate Couette flow models, and (3) calculating the charge distribution and electrostatic potential under static conditions. The solids are charge neutral surfaces composed of atoms with zero charge or charge balanced monovalent or divalent ions. The zeta potentials calculated are within a few millivolts of measured values, and the measured values fall within the simulation error bars. The zeta potentials calculated with the Helmholtz and Smoluchowski equation following current practice are 10's of mi...

Liu, Hongyi

2013-01-01T23:59:59.000Z

2

Ad hoc continuum-atomistic thermostat for modeling heat flow in molecular dynamics simulations  

E-Print Network [OSTI]

Ad hoc continuum-atomistic thermostat for modeling heat flow in molecular dynamics simulations J 2004) An ad hoc thermostating procedure that couples a molecular dynamics (MD) simulation

Brenner, Donald W.

3

Lattice Boltzmann versus Molecular Dynamics Simulation of Nanoscale Hydrodynamic Flows  

SciTech Connect (OSTI)

A fluid flow in a simple dense liquid, passing an obstacle in a two-dimensional thin film geometry, is simulated by molecular dynamics (MD) computer simulation and compared to results of lattice Boltzmann (LB) simulations. By the appropriate mapping of length and time units from LB to MD, the velocity field as obtained from MD is quantitatively reproduced by LB. The implications of this finding for prospective LB-MD multiscale applications are discussed.

Horbach, Juergen [Institut fuer Physik, Johannes-Gutenberg-Universitaet Mainz, Staudinger Weg 7, D-55099 Mainz (Germany); Succi, Sauro [Istituto Applicazioni Calcolo, CNR, Via le del Policlinico 137, 00161, Rome (Italy)

2006-06-09T23:59:59.000Z

4

Molecular dynamics investigations of modulated phases in organic materials  

Science Journals Connector (OSTI)

Molecular dynamics (MD) has evolved into a reliable technique for simulating incommensurate modulated phases. The application of a compensating external pressure tensor to organic materials allows a better fit to the experimental measurements. An overview of the MD method and its applications is presented here.

Pan, Y.

2004-12-22T23:59:59.000Z

5

Accelerated Molecular Dynamics Methods  

Broader source: Energy.gov [DOE]

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

6

Effects of confinement on water structure and dynamics and on proton transport: a molecular simulation study  

E-Print Network [OSTI]

Classical molecular dynamics (MD) simulations are performed to study structural and dynamic properties of water confined within graphite surfaces. The surfaces are separated at distances varying between 7 and 14.5 Å and the water density is held...

Hirunsit, Pussana

2009-05-15T23:59:59.000Z

7

Coupling Lattice Boltzmann and Molecular Dynamics models for dense fluids  

E-Print Network [OSTI]

We propose a hybrid model, coupling Lattice Boltzmann and Molecular Dynamics models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with reference MD solutions demonstrate the validity of the present approach.

A. Dupuis; E. M. Kotsalis; P. Koumoutsakos

2006-10-27T23:59:59.000Z

8

Myoglobin-CO Conformational Substate Dynamics: 2D Vibrational Echoes and MD Simulations  

E-Print Network [OSTI]

Myoglobin-CO Conformational Substate Dynamics: 2D Vibrational Echoes and MD Simulations Kusai A over a range of temperatures. The A1 and A3 conformational substates of MbCO are found to have assignments for the MbCO conformational substates. INTRODUCTION Protein dynamics have been the focus of both

Fayer, Michael D.

9

Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins  

Science Journals Connector (OSTI)

There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for impro...

Jerome M. Karp; Ertan Erylimaz; David Cowburn

2014-11-01T23:59:59.000Z

10

Nanoparticle coalescence and sintering: molecular dynamics simulation  

Science Journals Connector (OSTI)

Molecular Dynamics (MD) simulations are employed to better understand coalescence and sintering processes of gold nanoparticles. During coalescence in the liquid phase, the initial neck growth can be well described by the viscous flow model. With initial temperature right below the single particle melting temperature, the initial neck growth is controlled by viscous flow at first and then, by grain boundary diffusion. At initial temperatures well below melting, the sintering process occurs very rapidly, which may be attributed to a formation of liquid-like neck regions. The sintering of two free Au nanoparticles irradiated by a femtosecond laser pulse is also simulated by combining the two-temperature and MD models. It is shown that by increasing laser input energy, nanoparticles can be melted forming a single larger nanoparticle. The effects of multinanoparticle melting, solidification and sintering are also investigated.

N. Wang; S.I. Rokhlin; D.F. Farson

2007-01-01T23:59:59.000Z

11

Molecular dynamics simulations of the nano-scale room-temperature oxidation of aluminum single crystals  

E-Print Network [OSTI]

Molecular dynamics simulations of the nano-scale room-temperature oxidation of aluminum single Abstract The oxidation of aluminum single crystals is studied using molecular dynamics (MD) simulations with dynamic charge transfer between atoms. The simulations are performed on three aluminum low-index surfaces

Southern California, University of

12

Why are MD simulated protein folding times wrong? Dmitry Nerukh  

E-Print Network [OSTI]

Why are MD simulated protein folding times wrong? Dmitry Nerukh Unilever Centre for Molecular.ac.uk The question of significant deviations of protein folding times simulated using molecular dynamics from

Nerukh, Dmitry

13

Molecular Dynamics Simulation of Nucleation of SWNT from a Metal Particle on a Substrate  

E-Print Network [OSTI]

a transition metal cluster on a substrate is studied using classical molecular dynamics (MD) simulations between pure metal and metal-carbide. Graphite structure gradually precipitates from the edgeMolecular Dynamics Simulation of Nucleation of SWNT from a Metal Particle on a Substrate Yasushi

Maruyama, Shigeo

14

Myoglobin-CO Substate Structures and Dynamics: Multidimensional Vibrational Echoes and Molecular Dynamics  

E-Print Network [OSTI]

Myoglobin-CO Substate Structures and Dynamics: Multidimensional Vibrational Echoes and Molecular) having its imidazole nitrogen protonated (N -H). The two conformational substate structures B and R observed in the MD simulations are assigned to the spectroscopic A1 and A3 conformational substates of Mb

Fayer, Michael D.

15

Molecular dynamics simulation of complex molecules at interfaces: dendritic surfactants in clay and amyloid peptides near lipid bilayers  

E-Print Network [OSTI]

We apply a molecular dynamics (MD) simulation technique to complex molecules at interfaces. Partitioning of dendritic surfactants into clay gallery and Ab protein behavior near hydrated lipids are chosen for the purpose. Using a full atomistic model...

Han, Kunwoo

2009-06-02T23:59:59.000Z

16

Transport coefficients of liquid CF4 and SF6 computed by molecular dynamics using polycenter Lennard-Jones potentials  

Science Journals Connector (OSTI)

For several liquid states of CF4 and SF4, the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-cent...

C. Hoheisel

1989-01-01T23:59:59.000Z

17

Molecular dynamics study of a polymeric reverse osmosis membrane.  

SciTech Connect (OSTI)

Molecular dynamics (MD) simulations are used to investigate the properties of an atomic model of an aromatic polyamide reverse osmosis membrane. The monomers forming the polymeric membrane are cross-linked progressively on the basis of a heuristic distance criterion during MD simulations until the system interconnectivity reaches completion. Equilibrium MD simulations of the hydrated membrane are then used to determine the density and diffusivity of water within the membrane. Given a 3 MPa pressure differential and a 0.125 {micro}m width membrane, the simulated water flux is calculated to be 1.4 x 10{sup -6} m/s, which is in fair agreement with an experimental flux measurement of 7.7 x 10{sup -6} m/s.

Harder, E.; Walters, D. E.; Bodnar, Y. D.; Faibish, R. S.; Roux, B. (Nuclear Engineering Division); (Univ. of Chicago); (Rosalind Franklin Univ. of Medicine and Science)

2009-07-30T23:59:59.000Z

18

Molecular dynamics simulation of chains mobility in polyethylene crystal  

E-Print Network [OSTI]

The mobility of polymer chains in perfect polyethylene (PE) crystal was calculated as a function of temperature and chain length through Molecular dynamics (MD) in united atom approximation. The results demonstrate that the chain mobility drastically increases in the vicinity of the phase transition from the orthorhombic to quasi-hexagonal phase. In the quasi-hexagonal phase, the chain mobility is almost independent on temperature and inversely proportional to the chain length.

V. I. Sultanov; V. V. Atrazhev; D. V. Dmitriev; S. F. Burlatsky

2014-01-17T23:59:59.000Z

19

Gas-Phase Molecular Dynamics  

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

Gas-Phase Molecular Dynamics Gas-Phase Molecular Dynamics The Gas-Phase Molecular Dynamics Group is dedicated to developing and applying spectroscopic and theoretical tools to challenging problems in chemical physics related to reactivity, structure, dynamics and kinetics of transient species. Recent theoretical work has included advances in exact variational solution of vibrational quantum dynamics, suitable for up to five atoms in systems where large amplitude motion or multiple strongly coupled modes make simpler approximations inadequate. Other theoretical work, illustrated below, applied direct dynamics, quantum force trajectory calculations to investigate a series of reactions of the HOCO radical. The potential energy surface for the OH + CO/ H + CO2 reaction, showing two barriers (TS1 and TS2) and the deep HOCO well along the minimum energy pathway. The inset figure shows the experimental and calculated reactivity of HOCO with selected collision partners. See J.S. Francisco, J.T. Muckerman and H.-G. Yu, "HOCO radical chemistry,"

20

Molecular Dynamics Simulations of Solutions at Constant Chemical Potential  

E-Print Network [OSTI]

Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, that range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, that influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the C$\\mu$MD method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$\\mu$MD method to the paradigmatic case of urea crystall...

Perego, Claudio; Parrinello, Michele

2015-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

X-AND W-BAND EPR SPECTROSCOPY COMBINED WITH MOLECULAR DYNAMICS SIMULATIONS UNRAVEL THE STRUCTURE AND STRUCTURAL  

E-Print Network [OSTI]

X- AND W-BAND EPR SPECTROSCOPY COMBINED WITH MOLECULAR DYNAMICS SIMULATIONS UNRAVEL THE STRUCTURE (EPR) spectroscopy is combined with molecular dynamics (MD) simulations to study the structure and thus the EPR spectral line shape contain direct information about the secondary and tertiary structure

Steinhoff, Heinz-Jürgen

22

A molecular dynamics study of polymer/graphene interfacial systems  

SciTech Connect (OSTI)

Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

Rissanou, Anastassia N.; Harmandaris, Vagelis [Department of Mathematics and Applied Mathematics, University of Crete, GR-71409, Heraklion, Crete, Greece and Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), GR-71110, Heraklion, Cret (Greece)

2014-05-15T23:59:59.000Z

23

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

24

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

25

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

26

Accelerated Molecular Dynamics Methods  

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

Dynamics Methods Dynamics Methods for Infrequent Events Arthur F. Voter Theoretical Division Los Alamos National Laboratory Los Alamos, New Mexico U.S. Department of Energy Theory Focus Session on Hydrogen Storage Materials Crystal City, VA May 18, 2006 Los Alamos Acknowledgments Blas P. Uberuaga (LANL, MST-8) Francesco Montalenti (U. Milano-Bicocca) Graeme Henkelman (U. Texas at Austin) Timothy C. Germann (LANL, X-7) James A. Sprague (NRL) Mads Sorensen (Novo Nordisk A/S, Copenhagen) Sriram Swaminarayan (LANL, MST-8) Steve Stuart (Clemson) David Sholl (Carnegie Mellon) John Hamilton (Sandia) Wolfgang Windl (Ohio State) Roger Smith (U. Loughborough) Robin Grimes (Imperial College) Kurt Sickafus (LANL, MST-8) Jacques Amar (U. Toledo) DOE Office of Basic Energy Sciences Motorola Intel Los Alamos Outline

27

Mapping molecular dynamics computations to hypercubes  

E-Print Network [OSTI]

What Is MD? 35 37 HI. C Mathematical Issues In MD 42 HI. D Why Is Protein MD a GC HI E EIIIcient MD Alger)thms 49 52 IV A GRAPH THEORETIC REPRESENTATION OF MD 53 IV A Parallel Link Cells Algorithm 54 IV B Algorithm make cube() IV. C Algorithm... What Is MD? 35 37 HI. C Mathematical Issues In MD 42 HI. D Why Is Protein MD a GC HI E EIIIcient MD Alger)thms 49 52 IV A GRAPH THEORETIC REPRESENTATION OF MD 53 IV A Parallel Link Cells Algorithm 54 IV B Algorithm make cube() IV. C Algorithm...

Lakamsani, Vamsee Krishna

2012-06-07T23:59:59.000Z

28

Radiation in molecular dynamic simulations  

SciTech Connect (OSTI)

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

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

2008-10-13T23:59:59.000Z

29

Molecular potentials and relaxation dynamics  

SciTech Connect (OSTI)

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X/sup 1/..sigma../sup +/ and a/sup 3/..sigma../sup +/ states of LiH, NaH, KH, RbH, and CsH and the X/sup 2/..sigma../sup +/ states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm/sup -1/ over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500/sup 0/K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy.

Karo, A.M.

1981-05-18T23:59:59.000Z

30

MOLECULAR DYNAMICS SIMULATIONS OF NANOPARTICLE INTERACTIONS.  

E-Print Network [OSTI]

??Molecular dynamics simulations using the Embedded Atom Method were performed to describe the interparticle behavior of two single crystal spherical nickel nanoparticles during compaction based… (more)

Stone, Tonya Williams

2006-01-01T23:59:59.000Z

31

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...

32

Hydrogen-Bonding Structure and Dynamics of Aqueous Carbonate Species from Car?Parrinello Molecular Dynamics Simulations  

Science Journals Connector (OSTI)

A comprehensive Car?Parrinello molecular dynamics (CP-MD) study of aqueous solutions of carbonic acid (H2CO3), bicarbonate (HCO3?), carbonate (CO32?), and carbon dioxide (CO2) provides new quantitative insight into the structural and dynamic aspects of the hydrogen-bonding environments for these important aqueous species and their effects on the structure, H-bonding, and dynamical behavior of the surrounding water molecules. ... The power spectra of the carbonate species were calculated as Fourier transforms of their velocity autocorrelation functions over the 14 ps production trajectories of the CP-MD simulations. ... The first solvation shell of the anion was found to contain between five and six hydrogen bonded water mols., compared to the six to seven waters found in analogous classical studies based on empirical potentials. ...

P. Padma Kumar; Andrey G. Kalinichev; R. James Kirkpatrick

2008-12-24T23:59:59.000Z

33

Simulation of shock-induced melting of Ni using molecular dynamics coupled to a two-temperature model  

E-Print Network [OSTI]

Department, University of Uppsala, Box 530, SE-751 21 Uppsala, Sweden 2Lawrence Livermore National Laboratory, Livermore, California 94550, USA 3National Centre for Laser Applications, Galway, Ireland 4Department at the National Ignition Facility NIF . Molecular dynamics MD simulations have been success- fully employed

Zhigilei, Leonid V.

34

Molecular dynamics simulation of hydrogen diffusion in titanium  

National Nuclear Security Administration (NNSA)

9: Computation Physics 9: Computation Physics Atomistic Simulation of Hydrogen Diffusion in Titanium. Alexandr S. Rokhmanenkov, Alexey Yu. Kuksin, and Vladimir V. Stegailov All-Russia Research Institute of Automatics, Moscow 125412, Russia rohmanenkov@gmail.com Summary Study of the behavior of hydrogen in metals and alloys. The study is based on classical molecular dynamics (MD) and density functional theory (DFT) calculations. Study of the behavior of hydrogen in metals and alloys is of great importance due to the practical uses of hydrogen-metal systems for absorption of nuclear radiation, in neutron sources, for storage of hydrogen, or as catalyzers. This work is devoted to atomistic simulation of hydrogen diffusion in titanium hydrides and the effect of stresses and lattice defects on diffusivity.

35

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:...

36

Molecular Dynamics Simulations of Protein Folding  

Science Journals Connector (OSTI)

I illustrate the use of the replica exchange molecular dynamics (REMD) algorithm to study the folding of a small (57 amino acids) protein that folds into a three-helix bundle, protein A. The REMD is a triviall...

Angel E. Garcia

2008-01-01T23:59:59.000Z

37

Non-Born?Oppenheimer Molecular Dynamics  

Science Journals Connector (OSTI)

Non-Born?Oppenheimer Molecular Dynamics ... Electronically nonadiabatic or non-Born?Oppenheimer (non-BO) chemical processes (photodissociation, charge-transfer, etc.) involve a nonradiative change in the electronic state of the system. ...

Ahren W. Jasper; Shikha Nangia; Chaoyuan Zhu; Donald G. Truhlar

2005-08-17T23:59:59.000Z

38

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis  

SciTech Connect (OSTI)

We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 ?s, and the obtained trajectory of C{sub ?} atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

Naritomi, Yusuke [Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)] [Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan); Fuchigami, Sotaro, E-mail: sotaro@tsurumi.yokohama-cu.ac.jp [Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)] [Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)

2013-12-07T23:59:59.000Z

39

Statistics of correlation functions from molecular dynamics  

Science Journals Connector (OSTI)

The statistical uncertainty in the calculation of velocity autocorrelation functions and self-diffusion coefficients from molecular dynamics is empirically determined from the spread of the molecular-dynamics results for an ensemble of macroscopically identical systems. The ‘‘experimental’’ uncertainties of the velocity-autocorrelation-function values at equilibrium and in the presence of flow agree well with theoretical predictions. The uncertainty of the self-diffusion coefficient is found to decrease as the inverse square root of the averaging time.

I. Bitsanis; M. Tirrell; H. Ted Davis

1987-07-15T23:59:59.000Z

40

A molecular dynamics investigation of the unusual concentration dependencies of Fick diffusivities in silica mesopores  

SciTech Connect (OSTI)

Molecular Dynamics (MD) simulations were carried out to determine the self-diffusivitiy, D{sub i,self}, the Maxwell–Stefan diffusivity, Ð{sub i}, and the Fick diffusivity, D{sub i}, for methane (C1), ethane (C2), propane (C3), n-butane (nC4), n-pentane (nC5), n-hexane (nC6), n-heptane (nC7), and cyclohexane (cC6) in cylindrical silica mesopores for a range of pore concentrations. The MD simulations show that zero-loading diffusivity Ð{sub i}(0) is consistently lower, by up to a factor of 20, than the values anticipated by the classical Knudsen formula. The concentration dependence of the Fick diffusivity, D{sub i} is found to be unusually complex, and displays a strong minimum in some cases; this characteristic can be traced to molecular clustering.

Krishna, Rajamani; van Baten, Jasper M

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Fermionic Molecular Dynamics for nuclear dynamics and thermodynamics  

E-Print Network [OSTI]

A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented

K. H. O. Hasnaoui; Ph. Chomaz; F. Gulminelli

2008-12-02T23:59:59.000Z

42

E-Print Network 3.0 - atomistic molecular simulation Sample Search...  

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

minimization and molecular dynamics (MD) simulations, is utilized... of Gas Mixtures and Fluids in Them. Nayong Kim, Muhammad Sahimi, and Theodore T. Tsotsis An ... Source:...

43

Test of the Gouy-Chapman Theory for a Charged Lipid Membrane against Explicit-Solvent Molecular Dynamics Simulations  

Science Journals Connector (OSTI)

A wealth of experimental data has verified the applicability of the Gouy-Chapman (GC) theory to charged lipid membranes. Surprisingly, a validation of GC by molecular dynamics (MD) simulations has been elusive. Here, we report a test of GC against extensive MD simulations of an anionic lipid bilayer solvated by water at different concentrations of NaCl or KCl. We demonstrate that the ion distributions from the simulations agree remarkably well with GC predictions when information on the adsorption of counterions to the bilayer is incorporated.

Myunggi Yi; Hugh Nymeyer; Huan-Xiang Zhou

2008-07-18T23:59:59.000Z

44

Induced crystallization of single-chain polyethylene on a graphite surface: Molecular dynamics simulation  

Science Journals Connector (OSTI)

Molecular dynamics (MD) simulations have been carried out on the crystallization of single-chain polyethylene (PE) which was adsorbed on a graphite (001) surface on one side and exposed to vacuum on the other at different temperatures. The MD simulation data have been analyzed to provide information about the crystallization process of polymer adsorbed on the solid substrate. The isothermal crystallization of PE proceeds in two steps: (1) adsorption and (2) orientation. The results detail the radial density distribution function, ordered parameters, local bond-orientational order parameters, and the local properties displayed in layers of the polymer parallel to the graphite and vacuum interfaces. It was also shown that the film thickness affected the critical crystallization temperature of the adsorbed polymer on the substrate surface. Furthermore, the influence of the graphite surface area on the crystallization of PE is discussed by comparing the crystallinity evolution of PE on graphite with different coverage.

Hua Yang (??); Xiao Jun Zhao (???); Miao Sun (??)

2011-07-14T23:59:59.000Z

45

Temperature-dependent mechanical properties of single-layer molybdenum disulphide: Molecular dynamics nanoindentation simulations  

SciTech Connect (OSTI)

The temperature-dependent mechanical properties of single-layer molybdenum disulphide (MoS{sub 2}) are obtained using molecular dynamics (MD) nanoindentation simulations. The Young's moduli, maximum load stress, and maximum loading strain decrease with increasing temperature from 4.2?K to 500?K. The obtained Young's moduli are in good agreement with those using our MD uniaxial tension simulations and the available experimental results. The tendency of maximum loading strain with different temperature is opposite with that of metal materials due to the short range Stillinger-Weber potentials in MoS{sub 2}. Furthermore, the indenter tip radius and fitting strain effect on the mechanical properties are also discussed.

Zhao, Junhua, E-mail: junhua.zhao@uni-weimar.de [Jiangsu Province Key Laboratory of Advanced Manufacturing Equipment and Technology of Food, Jiangnan University, 214122 Wuxi (China) [Jiangsu Province Key Laboratory of Advanced Manufacturing Equipment and Technology of Food, Jiangnan University, 214122 Wuxi (China); Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); Jiang, Jin-Wu, E-mail: jwjiang5918@hotmail.com [Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany)] [Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); Rabczuk, Timon, E-mail: timon.rabczuk@uni-weimar.de [Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany) [Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); School of Civil, Environmental and Architectural Engineering, Korea University, 136-701 Seoul (Korea, Republic of)

2013-12-02T23:59:59.000Z

46

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

47

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

48

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

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

Molecular dynamics simulations: Properties of bulk electrolytes (structure, thermodynamics, transport), interfacial properties of electrolyte at electroactive interfaces,...

49

Molecular dynamics of LiF melting  

Science Journals Connector (OSTI)

We performed molecular-dynamics simulations of the melting and/or freezing of LiF. The simulations were done using the Tosi-Fumi model and our own model of interatomic interactions. The latter was verified by ab initio calculations of the equation of state for LiF. We show that the recent molecular-dynamics calculations by Boehler and co-workers are not adequate and their model for the interactions is not capable of providing melting temperatures in agreement with experiment. Our calculated pressure dependence of the melting temperatures gives valuable information. We found that the B1-B2 transition in LiF at around 1 Mbar removes the discrepancy between the diamond-anvil cell and shockwave melting temperatures. An explanation of the controversy between “low” and “high” melting temperatures obtained from diamond-anvil cell experiments is suggested.

A. B. Belonoshko; R. Ahuja; B. Johansson

2000-05-01T23:59:59.000Z

50

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

51

Anharmonic lattice dynamics of Ag2O studied by inelastic neutron scattering and first-principles molecular dynamics simulations  

SciTech Connect (OSTI)

Inelastic neutron scattering measurements on silver oxide (Ag2O) with the cuprite structure were performed at temperatures from 40 to 400 K, and Fourier transform far-infrared spectra were measured from 100 to 300 K. The measured phonon densities of states and the infrared spectra showed unusually large energy shifts with temperature, and large linewidth broadenings. First principles molecular dynamics (MD) calculations were performed at various temperatures, successfully accounting for the negative thermal expansion (NTE) and local dynamics. Using the Fourier-transformed velocity autocorrelation method, the MD calculations reproduced the large anharmonic effects of Ag2O, and were in excellent agreement with the neutron scattering data. The quasiharmonic approximation (QHA) was less successful in accounting for much of the phonon behavior. The QHA could account for some of the NTE below 250 K, although not at higher temperatures. Strong anharmonic effects were found for both phonons and for the NTE. The lifetime broadenings of Ag2O were explained by anharmonic perturbation theory, which showed rich interactions between the Ag-dominated modes and the O-dominated modes in both up- and down-conversion processes.

Lan, Tian [California Institute of Technology, Pasadena] [California Institute of Technology, Pasadena; Li, Chen [ORNL] [ORNL; Niedziela, Jennifer L [ORNL] [ORNL; Smith, Hillary [California Institute of Technology, Pasadena] [California Institute of Technology, Pasadena; Abernathy, Douglas L [ORNL] [ORNL; Rossman, George [California Institute of Technology, Pasadena] [California Institute of Technology, Pasadena; Fultz, B. [California Institute of Technology, Pasadena] [California Institute of Technology, Pasadena

2014-01-01T23:59:59.000Z

52

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

53

Molecular Dynamics Study of the Electrical Double Layer at Silver...  

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

Electrical Double Layer at Silver Chloride Electrolyte Interfaces. Molecular Dynamics Study of the Electrical Double Layer at Silver Chloride Electrolyte Interfaces. Abstract:...

54

Molecular dynamics simulations of osmosis and reverse osmosis in solutions  

Science Journals Connector (OSTI)

Computer simulation studies using the method of molecular dynamics have been carried out to investigate osmosis and reverse osmosis in solutions separated by semi-permeable membranes....

S. Murad

1996-01-01T23:59:59.000Z

55

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...

56

Water adsorption on stepped ZnO surfaces from MD simulation David Raymand a  

E-Print Network [OSTI]

Water adsorption on stepped ZnO surfaces from MD simulation David Raymand a , Adri C.T. van Duin b Keywords: Zinc oxide Water Solid­gas interfaces Construction and use of effective interatomic interactions force-field for use in molecular dynamics simulations of the ZnO­ water system. The force

Goddard III, William A.

57

Charge constrained density functional molecular dynamics for simulation of condensed phase electron transfer reactions  

SciTech Connect (OSTI)

We present a plane-wave basis set implementation of charge constrained density functional molecular dynamics (CDFT-MD) for simulation of electron transfer reactions in condensed phase systems. Following the earlier work of Wu and Van Voorhis [Phys. Rev. A 72, 024502 (2005)], the density functional is minimized under the constraint that the charge difference between donor and acceptor is equal to a given value. The classical ion dynamics is propagated on the Born-Oppenheimer surface of the charge constrained state. We investigate the dependence of the constrained energy and of the energy gap on the definition of the charge and present expressions for the constraint forces. The method is applied to the Ru{sup 2+}-Ru{sup 3+} electron self-exchange reaction in aqueous solution. Sampling the vertical energy gap along CDFT-MD trajectories and correcting for finite size effects, a reorganization free energy of 1.6 eV is obtained. This is 0.1-0.2 eV lower than a previous estimate based on a continuum model for solvation. The smaller value for the reorganization free energy can be explained by the fact that the Ru-O distances of the divalent and trivalent Ru hexahydrates are predicted to be more similar in the electron transfer complex than for the separated aqua ions.

Oberhofer, Harald; Blumberger, Jochen [Department of Chemistry, University of Cambridge, Cambridge CB2 1EW (United Kingdom)

2009-08-14T23:59:59.000Z

58

Molecular beam studies of reaction dynamics  

SciTech Connect (OSTI)

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

Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01T23:59:59.000Z

59

Molecular beam studies of reaction dynamics  

SciTech Connect (OSTI)

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

Lee, Yuan T.

1991-03-01T23:59:59.000Z

60

A study of local and extended migration of H and defects in a-Si by molecular dynamics simulations  

SciTech Connect (OSTI)

The author reports on extensive molecular dynamics (MD) simulations on a-Si:H for up to 5 Ps using the ab initio code of Sankey and Drabold. The supercells contain about 70 atoms and only one defect in order to minimize defect-defect interaction. Simulations on supercell samples that originally contain one bond centered (BC) H in an otherwise defect free sample exhibit BC to BC diffusion as in c-Si. However, the author also observed localized motion of defects and H atoms on a very fast time scale that probably has been observed in several experiments.

Fedders, P.A. [Washington Univ., St. Louis, MO (United States). Dept. of Physics

1996-12-31T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Where to find the mind: Identifying the scale of cognitive dynamics Luke Conlin, Department of Curriculum & Instruction,Benjamin Building, College Park, MD 20742 USA,  

E-Print Network [OSTI]

of Curriculum & Instruction,Benjamin Building, College Park, MD 20742 USA, luke.conlin@gmail.com Ayush Gupta, Department of Physics, Toll Building, College Park, MD 20742 USA, ayush@umd.edu David Hammer, Departments of Physics and Curriculum & Instruction, , Toll Building, College Park, MD 20742 USA, davidham

Hammer, David

62

Trends in Ln(III) Sorption to Quartz Assessed by Molecular Dynamics...  

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

Ln(III) Sorption to Quartz Assessed by Molecular Dynamics Simulations and Laser Induced Flourescence Studies. Trends in Ln(III) Sorption to Quartz Assessed by Molecular Dynamics...

63

Path integral Monte Carlo and density functional molecular dynamics simulations of hot, dense helium  

Science Journals Connector (OSTI)

Two first-principles simulation techniques, path integral Monte Carlo (PIMC) and density functional molecular dynamics (DFT-MD), are applied to study hot, dense helium in the density-temperature range of 0.387–5.35?g?cm?3 and 500?K–1.28×108?K. One coherent equation of state is derived by combining DFT-MD data at lower temperatures with PIMC results at higher temperatures. Good agreement between both techniques is found in an intermediate-temperature range. For the highest temperatures, the PIMC results converge to the Debye-Hückel limiting law. In order to derive the entropy, a thermodynamically consistent free-energy fit is used that reproduces the internal energies and pressure derived from the first-principles simulations. The equation of state is presented in the form of a table as well as a fit and is compared with different free-energy models. Pair-correlation functions and the electronic density of states are discussed. Shock Hugoniot curves are compared with recent laser shock-wave experiments.

B. Militzer

2009-04-08T23:59:59.000Z

64

Considerations and Recent Advances in Molecular Dynamics Introduction  

E-Print Network [OSTI]

numbers of computers like Folding@Home, or utilizing extremely specialized hardware such as Anton, MD

65

Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene  

E-Print Network [OSTI]

Using a realistic united-atom force field, molecular dynamics simulations were performed to study homogeneous nucleation of the crystal phase at about 30% supercooling from the melts of n-pentacontahectane (C150) and a ...

Yi, Peng

66

Structural models of bioactive glasses from molecular dynamics simulations  

Science Journals Connector (OSTI)

...to adsorb and dissociate a water molecule (Tilocca Cormack 2008...the available computational power steadily grows, it will become...surface of bioactive glasses: water adsorption and reactivity...soda-lime silicate glasses by Car-Parrinello molecular dynamics...

2009-01-01T23:59:59.000Z

67

Molecular Dynamics Simulation Studies of Electrolytes andElectrolyte...  

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

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

68

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

69

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.

70

Vacancy profile in reverse osmosis membranes studied by positron annihilation lifetime measurements and molecular dynamics simulations  

Science Journals Connector (OSTI)

The positron annihilation technique using a slow positron beam can be used for the study of the vacancy profiles in typical reverse osmosis (RO) membranes. In this study, the vacancy profile in the polyamide membrane that exhibits a high permselectivity between ions and water was studied using the positron annihilation technique and molecular dynamics simulations. Ortho-positronium (o-Ps) lifetimes in the surface region of the membranes were evaluated by using a slow positron beam. The diffusion behavior of Na+ and water in the polyamides was simulated by molecular dynamics (MD) methods using the TSUBAME2 supercomputer at the Tokyo Institute of Technology and discussed with the vacancy profile probed by the o-Ps. The results suggested that the large hydration size of Na+ compared to the vacancy size in the polyamides contributes to the increased diffusivity selectivity of water/Na+ that is related to the NaCl desalination performance of the membrane. Both the hydration size of the ions and the vacancy size appeared to be significant parameters to discuss the diffusivity selectivity of water/ions in typical polyamide membranes.

A Shimazu; H Goto; T Shintani; M Hirose; R Suzuki; Y Kobayashi

2013-01-01T23:59:59.000Z

71

Symmetry and dynamics of molecular rotors in amphidynamic molecular crystals  

Science Journals Connector (OSTI)

...axial symmetry order Cn represented with a heavy line with the enclosure formed by their close...Nano & Molecular Medicine, University of Missouri-Columbia...20 g of a 60% dispersion in mineral oil) in 500 mL of 1,2-dimethoxyethane...

Steven D. Karlen; Horacio Reyes; R. E. Taylor; Saeed I. Khan; M. Frederick Hawthorne; Miguel A. Garcia-Garibay

2010-01-01T23:59:59.000Z

72

Conformational statistics of poly(dimethylsiloxane). 1. Probability distribution of rotational isomers from molecular dynamics simulations  

Science Journals Connector (OSTI)

Conformational statistics of poly(dimethylsiloxane). 1. Probability distribution of rotational isomers from molecular dynamics simulations ...

Ivet Bahar; Ignacio Zuniga; Robert Dodge; Wayne L. Mattice

1991-05-01T23:59:59.000Z

73

Molecular dynamics simulation of phosphorylation-induced conformational transitions in the mycobacterium tuberculosis response regulator PrrA  

SciTech Connect (OSTI)

Phosphorylation-activated modulation of response regulators (RR) is predominantly used by bacteria as a strategy in regulating their two-component signaling (TCS) systems, the underlying molecular mechanisms are however far from fully understood. In this work we have conducted a molecular dynamics (MD) simulation of the phosphorylation-induced conformational transitions of RRs with the Mycobacterium Tuberculosis PrrA as a particular example. Starting from the full-length inactive structure of PrrA we introduced a local disturbance by phosphorylating the conserved aspartic acid residue, Asp-58, in the regulatory domain. A Go-model-type algorithm packaged with AMBER force fields was then applied to simulate the dynamics upon phosphorylation. The MD simulation shows that the phosphorylation of Asp-58 facilitates PrrA, whose inactive state has a compact conformation with a closed interdomain interface, to open up with its interdomain separation being increased by an average of about 1.5 {angstrom} for a simulation of 20 ns. The trans-activation loop, which is completely buried within the interdomain interface in the inactive PrrA, is found to become more exposed with the phosphorylated structure as well. These results provide more structural details of how the phosphorylation of a local aspartate activates PrrA to undergo a global conformational rearrangement toward its extended active state. This work also indicates that MD simulations can serve as a fast tool to unravel the regulation mechanisms of all RRs, which is especially valuable when the structures of full-length active RRs are currently unavailable.

Chen, Guo [Los Alamos National Laboratory; Mcmahon, Benjamin H [Los Alamos National Laboratory; Tung, Chang - Shung [Los Alamos National Laboratory

2008-01-01T23:59:59.000Z

74

Dynamical analysis of highly excited molecular spectra  

SciTech Connect (OSTI)

The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

Kellman, M.E. [Univ. of Oregon, Eugene (United States)

1993-12-01T23:59:59.000Z

75

First principles molecular dynamics without self-consistent field optimization  

SciTech Connect (OSTI)

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.

Souvatzis, Petros, E-mail: petros.souvatsiz@fysik.uu.se [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden)] [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); Niklasson, Anders M. N., E-mail: amn@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2014-01-28T23:59:59.000Z

76

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

77

Diffusion of the Cu monomer and dimer on Ag(111): Molecular dynamics simulations and density functional theory calculations  

Science Journals Connector (OSTI)

We present results of molecular dynamics (MD) simulations and density functional theory (DFT) calculations of the diffusion of Cu adatom and dimer on Ag(111). We have used potentials generated by the embedded-atom method for the MD simulations and pseudopotentials derived from the projected-augmented-wave method for the DFT calculations. The MD simulations (at three different temperatures: 300, 500, and 700 K) show that the diffusivity has an Arrhenius behavior. The effective energy barriers obtained from the Arrhenius plots are in excellent agreement with those extracted from scanning tunneling microscopy experiments. While the diffusion barrier for Cu monomers on Ag(111) is higher than that reported (both in experiment and theory) for Cu(111), the reverse holds for dimers [which, for Cu(111), has so far only been theoretically assessed]. In comparing our MD result with those for Cu islets on Cu(111), we conclude that the higher barriers for Cu monomers on Ag(111) results from the comparatively large Ag-Ag bond length, whereas for Cu dimers on Ag(111) the diffusivity is taken over and boosted by the competition in optimization of the Cu-Cu dimer bond and the five nearest-neighbor Cu-Ag bonds. Our DFT calculations confirm the relatively large barriers for the Cu monomer on Ag(111)—69 and 75 meV—compared to those on Cu(111) and hint a rationale for them. In the case of the Cu dimer, the relatively long Ag-Ag bond length makes available a diffusion route whose highest relevant energy barrier is only 72 meV and which is not favorable on Cu(111). This process, together with another involving an energy barrier of 83 meV, establishes the possibility of low-barrier intercell diffusion by purely zigzag mechanisms.

Sardar Sikandar Hayat; Marisol Alcántara Ortigoza; Muhammad A. Choudhry; Talat S. Rahman

2010-08-03T23:59:59.000Z

78

Modeling of interface cracking in copper–graphite composites by MD and CFE method  

Science Journals Connector (OSTI)

Abstract Molecular dynamics (MD) method was used to study mechanical properties of copper–graphite composite interface. Mode I fracture of the interface of copper–graphite composite was modeled by considering fixed and free boundary conditions, which means slipping constraint conditions for atomic layers in the composite. The stress near crack tip and the energy changes of the system are obtained. Then a cohesive traction–separation law of copper–graphite interface can also be obtained by using the MD simulation. For the purpose of comparisons, a modeling of interfacial fracture of the composite by using a zero-thickness cohesive finite element (CFE) was carried out. It is found that there is a stress concentration but no singularity for the normal stress at the crack tip in interface obtained by using the present MD simulation and CFE method. While in the interface away from the crack tip, the obtained stress is consistent with the solution of classical interfacial fracture mechanics.

Shi-Jun Guo; Qing-Sheng Yang; X.Q. He; K.M. Liew

2014-01-01T23:59:59.000Z

79

Last Name First Name Degree Abookire Susan MD, MPH  

E-Print Network [OSTI]

Frey-Vogel Ariel MD, MAT Garfield Joseph M.D. Gaufberg Elizabeth MD MPH Ghosh Arundhati MBBS, FRCS MD Miller Katherine MD Minehart Rebecca M.D. Mitchell John MD Monaghan Colleen MD Muto Michael MD-Vernaglia Shannon MD Shapiro Jo MD Sharma Niraj MD, MPH Sharp John MD Shields Helen MD Ship Amy MD Simone

Paulsson, Johan

80

State-to-state dynamics of molecular energy transfer  

SciTech Connect (OSTI)

The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

1993-12-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

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

82

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

83

Structural transformation in densified silica glass: A molecular-dynamics study  

Science Journals Connector (OSTI)

Pressure-induced structural transformation and the concomitant loss of intermediate-range order (IRO) in high-density SiO2 glass are investigated with the molecular-dynamics (MD) approach. The MD simulations cover a wide range of mass densities—from normal density (2.20 g/cm3) to the density corresponding to stishovite (4.28 g/cm3). This twofold increase in the density produces significant changes in the short-range order and intermediate-range order. As the density increases from 2.20 to 4.28 g/cm3, the Si-O bond length increases from 1.61 to 1.67 Å, the Si-O and O-O coordinations change from 4 to 5.8 and from 6 to 12, respectively, and the O-Si-O bond angle changes from 109° to 90°. These results provide firm evidence of structural transition from a corner-sharing Si(O1/2)4 tetrahedral network to a network of Si(O1/3)6 octahedra jointed at corners and edges. At normal density, the first sharp diffraction peak (FSDP) in the static structure factor S(q) is at 1.6 A?-1 whereas under pressure the height of the FSDP is considerably diminished and its position shifts to larger q values. At a density of 2.64 g/cm3, a peak in S(q) appears at 2.85 A?-1. The height of this peak grows as the density increases. All of these results are in agreement with the recent high-pressure x-ray measurements on SiO2 glass.

Wei Jin; Rajiv K. Kalia; Priya Vashishta; José P. Rino

1994-07-01T23:59:59.000Z

84

Metascalable quantum molecular dynamics simulations of hydrogen-on-demand  

Science Journals Connector (OSTI)

We enabled an unprecedented scale of quantum molecular dynamics simulations through algorithmic innovations. A new lean divide-and-conquer density functional theory algorithm significantly reduces the prefactor of the O(N) computational ... Keywords: density functional theory, divide-and-conquer, on-demand hydrogen production

Ken-ichi Nomura, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta, Kohei Shimamura, Fuyuki Shimojo, Manaschai Kunaseth, Paul C. Messina, Nichols A. Romero

2014-11-01T23:59:59.000Z

85

Molecular dynamics simulations of boronnitride nanotubes embedded in  

E-Print Network [OSTI]

, theoretical studies suggest that BN nanotubes exhibit an energy gap of about 4--5 eV independent of chiralityMolecular dynamics simulations of boron­nitride nanotubes embedded in amorphous Si­B­N Michael In this article, we examine the elastic properties of boron­nitride nanotubes, which are embedded in amorphous

Ferrari, Patrik L.

86

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine  

E-Print Network [OSTI]

centuries ago and an early competitor of the steam engine, continues to attract interest owing to itsSimulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine D 2009; published 30 April 2009 A nanoscale-sized Stirling engine with an atomistic working fluid has

Rapaport, Dennis C.

87

A Molecular Dynamics Simulation of Hydrogen Storage with SWNTs  

E-Print Network [OSTI]

A Molecular Dynamics Simulation of Hydrogen Storage with SWNTs S. Maruyama and T. Kimura, Bunkyo-ku, Tokyo 113-8656, Japan The mechanism of efficient hydrogen storage (1) with SWNTs (2, and the storage amount became about 5 wt % regardless of the tube radius. The number of absorbed hydrogen

Maruyama, Shigeo

88

Molecular Dynamics of Methanol Monocation (CH3OH+ ) in Strong  

E-Print Network [OSTI]

ultrafast hydrogen migration.7,8 The 38 fs 800 nm pump pulse produced methanol monocation, and a probe pulseMolecular Dynamics of Methanol Monocation (CH3OH+ ) in Strong Laser Fields Bishnu Thapa and H surfaces of methanol neutral, monocation, and singlet and triplet dication were explored using the CBS

Schlegel, H. Bernhard

89

Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation  

E-Print Network [OSTI]

Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation S.J.V. Frankland *, D hydrogen in individual single-shell carbon nanotubes and nanotube ropes using a semiclassical model. The calculations predict that isolated hydrogen molecules inside of nanotubes have a Raman frequency that increases

Brenner, Donald W.

90

Molecular Determinants and Dynamics of Hepatitis C Virus Secretion  

E-Print Network [OSTI]

Molecular Determinants and Dynamics of Hepatitis C Virus Secretion Kelly E. Coller, Nicholas S virus (HCV) production involves the assembly of virions on or near the surface of lipid droplets. However, the cellular requirements for and a mechanistic understanding of HCV secretion are incomplete

91

Observing molecular dynamics with timed Coulomb explosion imaging  

Science Journals Connector (OSTI)

...femtosecond pulses can replace accelerators as a means of initiating...through a nozzle into a vacuum chamber maintained at...Ellert and others nuclear axis aligned to the...oriented with inter- nuclear axis perpendicular to...dynamics of molecular nuclear wave packets. Preprint...

1998-01-01T23:59:59.000Z

92

Correlation Effects in Diffusion of CH4/CF4 Mixtures in MFI Zeolite. A Study Linking MD Simulations with the Maxwell?Stefan Formulation  

Science Journals Connector (OSTI)

Correlation effects in diffusion of CH4 and CF4 in MFI zeolite have been investigated with the help of molecular dynamics (MD) simulations and the Maxwell?Stefan (M?S) formulation. For single-component diffusion, the correlations are captured by the self-...

Anastasios I. Skoulidas; David S. Sholl; Rajamani Krishna

2003-08-08T23:59:59.000Z

93

E-Print Network 3.0 - anharmonic vibrational dynamics Sample...  

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

of Coupled Anharmonic Systems Towards the 2D IR Spectrum of H2O A... -stretching vibration in pure water. We use molecular dynamics (MD) simulations in combination with an ab...

94

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics  

E-Print Network [OSTI]

such as Folding@Home.1 After generating large ensembles of molecular dynamics simulations, we wish to analyze

Hinrichs, Nina Singhal

95

NAMD - The Engine for Large-Scale Classical MD Simulations of Biomolecular  

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

NAMD NAMD NAMD - The Engine for Large-Scale Classical MD Simulations of Biomolecular Systems Based on a Polarizable Force Field PI Name: Benoit Roux PI Email: roux@uchicago.edu Institution: Argonne National Laboratory & University of Chicago Allocation Program: ESP Allocation Hours at ALCF: 80 Million Year: 2010 to 2013 Research Domain: Biological Sciences Biology, at the atomic and molecular level, is governed by complex interactions involving a large number of key constituents, including water, ions, proteins, nucleic acids, and lipid membranes. The goal of this project is to develop new technologies to simulate virtual models of biomolecular systems with an unprecedented accuracy. Large-scale molecular dynamics (MD) simulations based on atomic models play an increasingly

96

Born?Oppenheimer Molecular Dynamics of the Hydration of Na+ in a Water Cluster  

Science Journals Connector (OSTI)

Born?Oppenheimer Molecular Dynamics of the Hydration of Na+ in a Water Cluster ... The hydration of Na+ in a water cluster is studied through all-electron Born?Oppenheimer molecular dynamics. ... The method chosen in the present study was all-electron, density functional theory based, Born?Oppenheimer molecular dynamics (BOMD). ...

N. Galamba; B. J. Costa Cabral

2009-11-23T23:59:59.000Z

97

Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes Shigeo MARUYAMA1,2  

E-Print Network [OSTI]

Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes * Shigeo-8656 The hydrogen storage mechanism of SWNTs was studied through molecular dynamics simulations. Assuming the simple : Molecular Dynamics Method, Hydrogen Storage, Single Walled Carbon Nanotubes, Lennard-Jones, Adsorption

Maruyama, Shigeo

98

Molecular Dynamics Study of Freezing Point and Solid-Liquid Interfacial Free Energy of Stockmayer Fluids  

SciTech Connect (OSTI)

Freezing temperatures of Stockmayer fluids with different dipolar strength at zero pressure are estimated and computed using three independent molecular-dynamics (MD) simulation methods, namely, the superheating-undercooling method, the constant-pressure and constant-temperature (NPT) two phase coexistence method, and the constant-pressure and constant-enthalpy (NPH) coexistence method. The best estimate of the freezing temperature (in reduced unit) for the Stockmayer (SM) fluid with a reduced dipole moment is 0.656 0.001, 0.726 0.002 and 0.835 0.005, respectively. The freezing temperature increases with the dipolar strength. The solid-liquid interfacial free energies of the (111), (110) and (100) interface are calculated for the first time using two independent methods, namely, the cleaving-wall method and the interfacial fluctuation method. Both methods predict that the interfacial free energy increases with the dipole moment. Although the interfacial fluctuation method suggests a weaker interfacial anisotropy, particularly for strongly dipolar SM fluids, both methods predicted the same trend of interfacial anisotropy, that is, .

Wang, J. [University of Nebraska, Lincoln; Apte, Pankaj [Indian Institute of Technology, Kanpur; Morris, James R [ORNL; Zeng, X.C. [University of Nebraska, Lincoln

2013-01-01T23:59:59.000Z

99

Molecular dynamics studies of the size and temperature dependence of the kinetics of freezing of Fe nanoparticles  

SciTech Connect (OSTI)

Molecular dynamics (MD) computer simulations have been carried out and a novel modified technique of Voronoi polyhedra has been performed to identify solid-like particles in a molten nanoparticle. This technique works quite well in analyzing the effects of particle size on nucleation rates of iron nanoparticles in the temperature range of 750–1160 K. Nanoparticles with 1436 and 2133 Fe atoms have been examined and the results are compared with those obtained earlier with Fe{sub 331} nanoparticles. Nucleation rates for freezing obtained from MD simulations for Fe{sub 2133} vary from 8.8×10{sup 34} m{sup 3}/s to 4.1×10{sup 35} m{sup 3}/s at over a temperature range from 1160 K to 900 K, Rates for. Fe{sub 1436} and Fe{sub 331} are somewhat higher. Nucleation rates increase as supercooling deepens until the viscosity of the liquid increases sharply enough to slow down the rate. Bt applying classical nucleation theory, the interfacial free energy between solid and liquid cab be estimated From this and other thermodynamic information can be derived a theoretical expression for the size-dependence of the heat of fusion of nanoparticles. Results agreed quite well with those observed in our MD observations. An earlier expression in the literature for this size-dependence was shown to be incorrect. The size dependence of melting point is discussed. - Graphical abstract: Critical nuclei of crystallization. Display Omitted - Highlights: • Solid state material synthesis. • Material structure. • Experimental study of nucleation in condensed materials. • Computation study of nucleation in condensed materials.

Zhao, Bo; Huang, Jinfan, E-mail: jinfanh@umich.edu; Bartell, Lawrence S.

2013-11-15T23:59:59.000Z

100

Molecular dynamics studies on the NMR structures of rabbit prion protein wild-type and mutants: surface electrostatic charge distributions  

E-Print Network [OSTI]

Prion is a misfolded protein found in mammals that causes infectious diseases of the nervous system in humans and animals. Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and goats, cattle, deer, elk and humans etc. Recent studies have shown that rabbits have a low susceptibility to be infected by prion diseases with respect to other animals including humans. The present study employs molecular dynamics (MD) means to unravel the mechanism of rabbit prion proteins (RaPrPC) based on the recently available rabbit NMR structures (of the wild-type and its two mutants of two surface residues). The electrostatic charge distributions on the protein surface are the focus when analysing the MD trajectories. It is found that we can conclude that surface electrostatic charge distributions indeed contribute to the structural stability of wild-type RaPrPC; this may be useful for the medicinal treatment of prion diseases.

Zhang, Jiapu

2014-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Transient dynamics of molecular devices under a steplike pulse bias  

Science Journals Connector (OSTI)

We report first-principles investigation of time-dependent current of molecular devices under a steplike pulse. Our results show that although the switch-on time of the molecular device is comparable to the transit time, much longer time is needed to reach the steady state. In reaching the steady state the current is dominated by resonant states below Fermi level. The contribution of each resonant state to the current shows the damped oscillatory behavior with frequency approximately equal to half of the bias of steplike pulse and decay rate determined by the life time of the corresponding resonant state. We found that all the resonant states below Fermi level have to be included for accurate results. This indicates that going beyond wideband limit is essential for a quantitative analysis of transient dynamics of molecular devices.

Bin Wang; Yanxia Xing; Lei Zhang; Jian Wang

2010-03-17T23:59:59.000Z

102

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine  

Science Journals Connector (OSTI)

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

D. C. Rapaport

2009-04-30T23:59:59.000Z

103

Multiscale simulation of polymer nano-composites (PNC) using molecular dynamics (MD) and generalized interpolation material point method (GIMP).  

E-Print Network [OSTI]

??Recent mechanical characterization experiments with pultruded E-Glass / polypropylene (PP) and compression molded E-Glass/Nylon-6 composite samples with 3-4 weight% nanoclay and baseline polymer (polymer without… (more)

Nair, Abilash Rajendran

2010-01-01T23:59:59.000Z

104

Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species  

SciTech Connect (OSTI)

This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

Hall, G.E.

2011-05-31T23:59:59.000Z

105

Enhanced heat transfer through filler-polymer interface by surface-coupling agent in heat-dissipation material: A non-equilibrium molecular dynamics study  

SciTech Connect (OSTI)

Developing a composite material of polymers and micrometer-sized fillers with higher heat conductance is crucial to realize modular packaging of electronic components at higher densities. Enhancement mechanisms of the heat conductance of the polymer-filler interfaces by adding the surface-coupling agent in such a polymer composite material are investigated through the non-equilibrium molecular dynamics (MD) simulation. A simulation system is composed of ?-alumina as the filler, bisphenol-A epoxy molecules as the polymers, and model molecules for the surface-coupling agent. The inter-atomic potential between the ?-alumina and surface-coupling molecule, which is essential in the present MD simulation, is constructed to reproduce the calculated energies with the electronic density-functional theory. Through the non-equilibrium MD simulation runs, we find that the thermal resistance at the interface decreases significantly by increasing either number or lengths of the surface-coupling molecules and that the effective thermal conductivity of the system approaches to the theoretical value corresponding to zero thermal-resistance at the interface. Detailed analyses about the atomic configurations and local temperatures around the interface are performed to identify heat-transfer routes through the interface.

Tanaka, Kouichi [DENSO CORPORATION, Kariya, Aichi 448-8661 (Japan); Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Ogata, Shuji; Kobayashi, Ryo; Tamura, Tomoyuki [Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Kitsunezuka, Masashi; Shinma, Atsushi [DENSO CORPORATION, Kariya, Aichi 448-8661 (Japan)

2013-11-21T23:59:59.000Z

106

Generalized Extended Lagrangian Born-Oppenheimer Molecular Dynamics  

E-Print Network [OSTI]

Extended Lagrangian Born-Oppenheimer molecular dynamics based on Kohn-Sham density functional theory is generalized in the limit of vanishing self-consistent field optimization prior to the force evaluations. The equations of motion are derived directly from the extended Lagrangian under the condition of an adiabatic separation between the nuclear and the electronic degrees of freedom. We show how this separation is automatically fulfilled and system independent. The generalized equations of motion require only one diagonalization per time step and are applicable to a broader range of materials with improved accuracy and stability compared to previous formulations.

Niklasson, Anders M N

2014-01-01T23:59:59.000Z

107

Higher-order symplectic Born-Oppenheimer molecular dynamics  

SciTech Connect (OSTI)

The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics (TR-BOMD) enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the 6th order have been adapted and optimized to TR-BOMD in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements.

Niklasson, Anders [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, Matt [Los Alamos National Laboratory; Odell, Anders [RIT; Delin, Anna [RIT; Johansson, Borje [RIT

2009-01-01T23:59:59.000Z

108

Large scale molecular dynamics modeling of materials fabrication processes  

SciTech Connect (OSTI)

An atomistic molecular dynamics model of materials fabrication processes is presented. Several material removal processes are shown to be within the domain of this simulation method. Results are presented for orthogonal cutting of copper and silicon and for crack propagation in silica glass. Both copper and silicon show ductile behavior, but the atomistic mechanisms that allow this behavior are significantly different in the two cases. The copper chip remains crystalline while the silicon chip transforms into an amorphous state. The critical stress for crack propagation in silica glass was found to be in reasonable agreement with experiment and a novel stick-slip phenomenon was observed.

Belak, J.; Glosli, J.N.; Boercker, D.B.; Stowers, I.F.

1994-02-01T23:59:59.000Z

109

Molecular nonlinear dynamics and protein thermal uncertainty quantification  

SciTech Connect (OSTI)

This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction.

Xia, Kelin [Department of Mathematics, Michigan State University, Michigan 48824 (United States)] [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, Michigan 48824 (United States) [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States)

2014-03-15T23:59:59.000Z

110

High temperature phonon dispersion in graphene using classical molecular dynamics  

SciTech Connect (OSTI)

Phonon dispersion and phonon density of states of graphene are calculated using classical molecular dynamics simulations. In this method, the dynamical matrix is constructed based on linear response theory by computing the displacement of atoms during the simulations. The computed phonon dispersions show excellent agreement with experiments. The simulations are done in both NVT and NPT ensembles at 300 K and found that the LO/TO modes are getting hardened at the ? point. The NPT ensemble simulations capture the anharmonicity of the crystal accurately and the hardening of LO/TO modes is more pronounced. We also found that at 300 K the C-C bond length reduces below the equilibrium value and the ZA bending mode frequency becomes imaginary close to ? along K-? direction, which indicates instability of the flat 2D graphene sheets.

Anees, P., E-mail: anees@igcar.gov.in; Panigrahi, B. K. [Materials Physics Division, Indira Gandhi Centre for Atomic Research, Kalpakkam-603102 (India); Valsakumar, M. C., E-mail: anees@igcar.gov.in [School of Engineering Sciences and Technology, University of Hyderabad, Hyderabad-500046 (India)

2014-04-24T23:59:59.000Z

111

Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations  

SciTech Connect (OSTI)

We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation.

Bresme, F., E-mail: f.bresme@imperial.ac.uk [Department of Chemistry, Chemical Physics Section, Imperial College London, London SW7 2AZ (United Kingdom); Department of Chemistry, Norwegian University of Science and Technology, Trondheim (Norway); Armstrong, J., E-mail: j.armstrong@imperial.ac.uk [Department of Chemistry, Chemical Physics Section, Imperial College London, London SW7 2AZ (United Kingdom)

2014-01-07T23:59:59.000Z

112

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

113

Investigation of Protein Folding by Using Combined Method of Molecular Dynamics and Monte Carlo Simulations.  

E-Print Network [OSTI]

??We used the combination of molecular dynamics and Monte Carlo method to investigate protein folding problems. The environments of proteins are very big, and often… (more)

Liao, Jun-min

2006-01-01T23:59:59.000Z

114

E-Print Network 3.0 - all-atom molecular dynamics Sample Search...  

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

the presence of biological... of Protein Dynamics The self-assembly of proteins ("protein folding") is one of the key steps in the function... - standing question in molecular...

115

Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?  

SciTech Connect (OSTI)

The ring polymer molecular dynamics (RPMD) method has gained popularity in recent years as a simple approximation for calculating real time quantum correlation functions in condensed media. However, the extent to which RPMD captures real dynamical quantum effects and why it fails under certain situations have not been clearly understood. Addressing this issue has been difficult in the absence of a genuine justification for the RPMD algorithm starting from the quantum Liouville equation. To this end, a new and exact path integral formalism for the calculation of real time quantum correlation functions is presented in this work, which can serve as a rigorous foundation for the analysis of the RPMD method as well as providing an alternative derivation of the well established centroid molecular dynamics method. The new formalism utilizes the cyclic symmetry of the imaginary time path integral in the most general sense and enables the expression of Kubo-transformed quantum time correlation functions as that of physical observables pre-averaged over the imaginary time path. Upon filtering with a centroid constraint function, the formulation results in the centroid dynamics formalism. Upon filtering with the position representation of the imaginary time path integral, we obtain an exact quantum dynamics formalism involving the same variables as the RPMD method. The analysis of the RPMD approximation based on this approach clarifies that an explicit quantum dynamical justification does not exist for the use of the ring polymer harmonic potential term (imaginary time kinetic energy) as implemented in the RPMD method. It is analyzed why this can cause substantial errors in nonlinear correlation functions of harmonic oscillators. Such errors can be significant for general correlation functions of anharmonic systems. We also demonstrate that the short time accuracy of the exact path integral limit of RPMD is of lower order than those for finite discretization of path. The present quantum dynamics formulation also serves as the basis for developing new quantum dynamical methods that utilize the cyclic nature of the imaginary time path integral.

Jang, Seogjoo, E-mail: sjang@qc.cuny.edu [Department of Chemistry and Biochemistry, Queens College and the Graduate Center, City University of New York, 65-30 Kissena Boulevard, Flushing, New York 11367 (United States)] [Department of Chemistry and Biochemistry, Queens College and the Graduate Center, City University of New York, 65-30 Kissena Boulevard, Flushing, New York 11367 (United States); Sinitskiy, Anton V.; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics and Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637 (United States)

2014-04-21T23:59:59.000Z

116

Mechanical unfolding of a beta-hairpin using molecular dynamics  

SciTech Connect (OSTI)

Single molecule mechanical unfolding experiments have the potential to provide insights into the details of protein folding pathways. To investigate the relationship between force-extension unfolding curves and microscopic events, we performed molecular dynamics simulations of the mechanical unfolding of the C-terminal hairpin of protein G. We have studied the dependence of the unfolding pathway on pulling speed, cantilever stiffness, and attachment points. Under conditions which generate low forces, the unfolding trajectory mimics the untethered, thermally accessible pathway previously proposed based on high temperature studies. In this stepwise pathway, complete breakdown of backbone hydrogen bonds precedes dissociation of the hydrophobic cluster. Under more extreme conditions, the cluster and hydrogen bonds break simultaneously. Transitions between folding intermediates can be identified in our simulations as features of the calculated force-extension curves.

Bryant, Zev; Pande, Vijay S.; Rokhsar, Daniel S.

1999-10-16T23:59:59.000Z

117

Molecular dynamics simulations of optical conductivity of dense plasmas  

Science Journals Connector (OSTI)

The optical conductivity ?(?) for dense Coulomb systems is investigated using molecular dynamics simulations on the basis of pseudopotentials to mimic quantum effects. Starting from linear response theory, the response in the long-wavelength limit k=0 can be expressed by different types of autocorrelation functions (ACF’s) such as the current ACF, the force ACF, or the charge density ACF. Consistent simulation data for transverse as well as longitudinal ACF’s are shown which are based on calculations with high numerical accuracy. Results are compared with perturbation expansions which are restricted to small values of the plasma parameter. The relevance with respect to a quantum Coulomb plasma is discussed. Finally, results are presented showing a consistent description of these model plasmas in comparison to quantum statistical approaches and to experimental data.

I. Morozov, H. Reinholz, G. Röpke, A. Wierling, and G. Zwicknagel

2005-06-22T23:59:59.000Z

118

Polarization effects in molecular dynamics simulations of glass-formers Ca ( NO 3 ) 2 ? n H 2 O , n = 4 , 6, and 8  

Science Journals Connector (OSTI)

Thermodynamics equilibrium structure and dynamics of glass-forming liquids Ca ( NO 3 ) 2 ? n H 2 O n = 4 6 and 8 have been investigated by molecular dynamics (MD) simulations. A polarizable model was considered for H 2 O and NO 3 ? on the basis of previous fluctuating charge models for pure water and the molten salt 2 Ca ( NO 3 ) 2 ? 3 KNO 3 . Similar thermodynamic properties have been obtained with nonpolarizable and polarizable models. The glass transition temperature T g estimated from MD simulations was dependent on polarization in particular the dependence of T g with electrolyte concentration. Significant polarization effects on equilibrium structure were observed in cation-cation cation-anion and water-water structures. Polarization increases the diffusion coefficient of H 2 O but does not change significantly the diffusion coefficients of ions. Viscosity decreases upon inclusion of polarization but the conductivity calculated with the polarizable model is smaller than the nonpolarizable model because polarization enhances anion-cation interactions.

Mauro C. C. Ribeiro

2010-01-01T23:59:59.000Z

119

Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements  

SciTech Connect (OSTI)

The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15T23:59:59.000Z

120

Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes  

E-Print Network [OSTI]

Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes Shigeo MARUYAMA #12;The hydrogen storage mechanism of SWNTs was studied through molecular dynamics simulations,12) Fig. 6 Hydrogen storage inside each SWNT #12;Table 1 Potential parameters between SWNTs Tube d0 [Ã?

Maruyama, Shigeo

Note: This page contains sample records for the topic "molecular dynamics md" 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

A Molecular Dynamics Simulation of Hydrogen Storage by SWNTs Tatsuto Kimuraa  

E-Print Network [OSTI]

A Molecular Dynamics Simulation of Hydrogen Storage by SWNTs Tatsuto Kimuraa and Shigeo Maruyamab of efficient hydrogen storage [1] with SWNTs [2,3] was studied through classical molecular dynamics simulations adsorbed hydrogen molecules was almost proportional to the number of carbon atoms, and the storage amount

Maruyama, Shigeo

122

Molecular Dynamics Simulations of Laser Induced Incandescence Dr. Adri van Duin  

E-Print Network [OSTI]

Molecular Dynamics Simulations of Laser Induced Incandescence (LII) Dr. Adri van Duin Associate of Engineering. Laser Induced Incandescence (LII) is a popular method to estimate the properties of soot. Molecular Dynamics Simulations of Laser-Induced Incandescence of Soot Using an Extended ReaxFF Reactive

Bjørnstad, Ottar Nordal

123

Rapid hydrogen production from water using aluminum nanoclusters: A quantum molecular dynamics simulation study  

E-Print Network [OSTI]

Rapid hydrogen production from water using aluminum nanoclusters: A quantum molecular dynamics Available online 31 December 2013 Keywords: Hydrogen production Water Aluminum nanoclusters Quantum molecular dynamics simulation It is hoped that a hydrogen-on-demand generator may one day start with just

Southern California, University of

124

Electron-nuclear correlations for photo-induced dynamics in molecular dimers  

E-Print Network [OSTI]

processes are accompanied by a noticeable growth of the nuclear coordinate dispersion associatedElectron-nuclear correlations for photo-induced dynamics in molecular dimers Dmitri S. Kilin, Yuri dimers is drastically affected by the dynamic reorganization of inter- and intra- molecular nuclear

125

Fluorescence of PRODAN in Water: a Computational QM/MM MD Study  

SciTech Connect (OSTI)

Fluorescent properties of PRODAN (6-propionyl-2-dimethylaminonaphthalene) in water were studied by means of excited state molecular dynamics simulations employing a combined quantum mechanical and molecular mechanical approach with the time-dependent density functional theory (TD-DFT QM/MM MD). The state of the art coupled cluster method was used to benchmark density functional theory calculations. The influence of the water environment on PRODAN emission was investigated by employing several computational schemes with varying description of the solvent. The issue of the molecular geometry of the excited state PRODAN molecule in water was addressed. The experimental emission spectrum was reproduced for the planar excited state conformer of PRODAN in the extended environment of 300 explicit water molecules. The planar conformer was shown to be predominantly responsible for fluorescence. The twisted isomer is strongly stabilized in water, but rapidly evolve towards a conical intersection, and hence the twisted conformer is fluorescently inactive.

Pederzoli, Marek; Sobek, Lukas; Brabec, Jiri; Kowalski, Karol; Cwiklik, Lukasz; Pittner, Jiri

2014-03-28T23:59:59.000Z

126

Extended Lagrangian quantum molecular dynamics simulations of shock-induced chemistry in hydrocarbons  

SciTech Connect (OSTI)

A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.

Sanville, Edward J [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, William M [Los Alamos National Laboratory; Cawkwell, Marc J [Los Alamos National Laboratory; Niklasson, Anders M N [Los Alamos National Laboratory; Dattelbaum, Dana M [Los Alamos National Laboratory; Sheffield, Stephen [Los Alamos National Laboratory; Sewell, Thomas D [UNIV OF MISSOURI

2010-01-01T23:59:59.000Z

127

Dynamics of Different Hydrogen Classes in -lactoglobulin: A Quasielastic Neutron Scattering Investigation  

E-Print Network [OSTI]

Dynamics of Different Hydrogen Classes in -lactoglobulin: A Quasielastic Neutron Scattering investigated by means of quasielastic neutron scattering. To discriminate the possibly different dynamical- thods,11-13 molecular dynamics (MD) simulations,14 X-ray crys- tallography,15 and neutron scattering.6

Tuscia, Università Degli Studi Della

128

Molecular dynamics simulation: a tool for exploration and discovery using simple models  

E-Print Network [OSTI]

Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome is not always a foregone conclusion. The present survey focuses on several simple model systems that exhibit surprisingly rich emergent behavior, all studied by MD simulation. The examples are taken from the disparate fields of fluid dynamics, granular matter and supramolecular self-assembly. In studies of fluids modeled at the detailed microscopic level using discrete particles, the simulations demonstrate that complex hydrodynamic phenomena in rotating and convecting fluids, the Taylor-Couette and Rayleigh-B\\'enard instabilities, can not only be observed within the limited length and time scales accessible to MD, but even quantitative agreement can be achieved. Simulation of highly counterintuitive segregation phenomena in granular mixtures, again using MD methods, but now augmented by forces producing damping and friction, leads to results that resemble experimentally observed axial and radial segregation in the case of a rotating cylinder, and to a novel form of horizontal segregation in a vertically vibrated layer. Finally, when modeling self-assembly processes analogous to the formation of the polyhedral shells that package spherical viruses, simulation of suitably shaped particles reveals the ability to produce complete, error-free assembly, and leads to the important general observation that reversible growth steps contribute to the high yield. While there are limitations to the MD approach, both computational and conceptual, the results offer a tantalizing hint of the kinds of phenomena that can be explored, and what might be discovered when sufficient resources are brought to bear on a problem.

D. C. Rapaport

2014-11-13T23:59:59.000Z

129

MOLECULAR DYNAMICS SIMULATIONS OF DISPLACEMENT CASCADES IN MOLYBDENUM  

SciTech Connect (OSTI)

Molecular dynamics calculations have been employed to simulate displacement cascades in neutron irradiated Mo. A total of 90 simulations were conducted for PKA energies between 1 and 40 keV and temperatures from 298 to 923K. The results suggest very little effect of temperature on final defect count and configuration, but do display a temperature effect on peak defect generation prior to cascade collapse. Cascade efficiency, relative to the NRT model, is computed to lie between 1/4 and 1/3 in agreement with simulations performed on previous systems. There is a tendency for both interstitials and vacancies to cluster together following cascade collapse producing vacancy rich regions surrounded by interstitials. Although coming to rest in close proximity, the point defects comprising the clusters generally do not lie within the nearest neighbor positions of one another, except for the formation of dumbbell di-interstitials. Cascades produced at higher PKA energies (20 or 40 keV) exhibit the formation of subcascades.

Smith, Richard Whiting

2003-09-08T23:59:59.000Z

130

Molecular Dynamics Simulations of the Nucleation of Water: Determining the Sticking Probability and Formation Energy of a Cluster  

E-Print Network [OSTI]

We performed molecular dynamics (MD) simulations of the nucleation of water vapor in order to test nucleation theories. Simulations were performed for a wide range of supersaturation ratios (S = 3-25) and water temperatures (Tw=300-390K). We obtained the nucleation rates and the formation free energies of a subcritical cluster from the cluster size distribution. The classical nucleation theory (CNT) and the modified classical nucleation theory (MCNT) overestimate the nucleation rates in all cases. The semi-phenomenological (SP) model, which corrects the MCNT prediction using the second virial coefficient of a vapor, reproduces the formation free energy of a cluster with the size < 20 to within 10 % and the nucleation rate and cluster size distributions to within one order of magnitude. The sticking probability of the vapor molecules to the clusters was also determined from the growth rates of the clusters. The sticking probability rapidly increases with the supersaturation ratio S, which is similar to the Lennard-Jones system.

Kyoko K. Tanaka; Akio Kawano; Hidekazu Tanaka

2014-02-26T23:59:59.000Z

131

X-ray Diffraction and Molecular Dynamics Study of Medium-range Order in Ambient and Hot Water  

E-Print Network [OSTI]

We have developed x-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 C) under normal pressure. Using a spherically curved Ge crystal an energy resolution better than 15 eV has been achieved which eliminates influence from Compton scattering. The high quality of the data allows a precise oxygen-oxygen pair correlation function (PCF) to be directly derived from the Fourier transform of the experimental data resolving shell structure out to ~12 {\\AA}, i.e. 5 hydration shells. Large-scale molecular dynamics (MD) simulations using the TIP4P/2005 force-field reproduce excellently the experimental shell-structure in the range 4-12 {\\AA} although less agreement is seen for the first peak in the PCF. The Local Structure Index [J. Chem. Phys. 104, 7671 (1996)] identifies a tetrahedral minority giving the intermediate-range oscillations in the PCF and a disordered majority providing a more featureless background in this range. The current study supports the proposal that the structure of liquid water, even at high temperatures, can be described in terms of a two-state fluctuation model involving local structures related to the high-density and low-density forms of liquid water postulated in the liquid-liquid phase transition hypothesis.

Congcong Huang; K. T. Wikfeldt; D. Nordlund; U. Bergmann; T. McQueen; J. Sellberg; L. G. M. Pettersson; A. Nilsson

2011-07-24T23:59:59.000Z

132

Brittle dynamic fracture of crystalline cubic silicon carbide ,,3C-SiC... via molecular dynamics simulation  

E-Print Network [OSTI]

Brittle dynamic fracture of crystalline cubic silicon carbide ,,3C-SiC... via molecular dynamics for three low-index crack surfaces, i.e., 110 , 111 , and 100 , in crystalline cubic silicon carbide 3C Institute of Physics. DOI: 10.1063/1.2135896 I. INTRODUCTION Potential applications of silicon carbide Si

Southern California, University of

133

Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solution: Car–Parrinello Molecular Dynamics and Vibrational Spectroscopy Study  

Science Journals Connector (OSTI)

Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solution: Car–Parrinello Molecular Dynamics and Vibrational Spectroscopy Study ... Our focus was on the part of vibrational spectra that corresponds to histamine N–H stretching, since these degrees of freedom are essential for its interactions with either water molecules or transporters and receptors. ... The resulting vibrational power spectrum is presented in Figure 9. ...

Jernej Stare; Janez Mavri; Jože Grdadolnik; Jernej Zidar; Zvonimir B. Maksi?; Robert Vianello

2011-04-25T23:59:59.000Z

134

Short-Range Order and Collective Dynamics of DMPC Bilayers: A Comparison between Molecular Dynamics Simulations, X-Ray,  

E-Print Network [OSTI]

Simulations, X-Ray, and Neutron Scattering Experiments Jochen S. Hub,* Tim Salditt,y Maikel C. Rheinsta derived by molecular dynamics simulations, elastic x-ray, and inelastic neutron scattering experiments dynamics obtained from the simulations and from inelastic neutron scattering are analyzed and compared

de Groot, Bert

135

Ab Initio Molecular Dynamics Studies on Substitution vs. Electron Transfer Reactions of Substituted Ketyl Radical Anions with Chloroalkanes: How Do the Two Products Form in a Borderline Mechanism?  

SciTech Connect (OSTI)

We present a qualitative analysis, based on ab initio molecular dynamics (MD) calculations, of the SN2/ET mechanistic spectrum for three reactions: (1) HC(CN)=O.- + CH3Cl, (2) HC(CN)=O.- + (CH3)2CHCl, and (3) H2C=O.- + CH3Cl, passing through their SN2-like transition states. The finite temperature (298 K) direct-MD simulations indicate that the trajectories for reaction 1 appear to have a propensity towards SN2 products, the propensity for trajectories for reaction 2 seems to be towards ET products, whereas trajectories for reaction 3 appear to show no particular propensity towards either ET or SN2 products. The mechanistic diversity is consistent with the electron donating ability of the ketyl species and steric bulkiness of chloroalkanes. We find that the trajectories have characteristics that reflect strongly the types of process (SN2 trajectories in reactions 1 and 3 vs. ET trajectories in reactions 2 and 3). Trajectories that lead to SN2 products are simple with C-C bond formation and C-Cl bond breaking essentially completed within 50 fs. By contrast, trajectories leading to ET products are more complex with a sudden electron reorganization taking place within 15 - 30 fs and the major bonding changes and electron and spin reorganizations completed after 250 fs.

Yamataka, H.; Aida, Misako; Dupuis, Michel

2003-08-06T23:59:59.000Z

136

Direct ab initio molecular dynamics study on a SN2 reaction OH? + CH3Cl ? CH3OH + Cl?: Effect of non-zero impact parameter on the reaction dynamics  

Science Journals Connector (OSTI)

Direct ab initio molecular dynamics (MD) calculations have been applied to a SN2 reaction OH? + CH3Cl ? CH3OH + Cl?. The collision dynamics with non-zero impact parameters were treated in the present study, and the results are compared with the near collinear collision dynamics previously reported by us [H. Tachikawa, M. Igarashi, T. Ishibashi, J. Phys. Chem. A 106 (2002) 10977]. The collision energy was fixed to 25 kcal/mol. The product state distribution obtained for the non-zero impact parameter collision dynamics was slightly different from that of the collinear collision. The distribution of relative translational energy between products Cl? and CH3OH in the non-zero impact parameter collision dynamics was shifted to higher energy region from that of collinear collision. Also, it was found that the mean translational energy of the product has a maximum at non-zero impact parameter (b = 0.6–1.2 Å). The reaction mechanism is discussed on the basis of theoretical results.

Hiroto Tachikawa; Manabu Igarashi

2006-01-01T23:59:59.000Z

137

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study  

SciTech Connect (OSTI)

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21T23:59:59.000Z

138

Time-Resolved Molecular Frame Dynamics of Fixed-in-Space CS2 Molecules  

SciTech Connect (OSTI)

Random orientation of molecules within a sample leads to blurred observationsof chemical reactions studied from the laboratory perspective. Methodsdeveloped for the dynamic imaging of molecular structures and processesstruggle with this, as measurements are optimally made in the molecular frame.Here we uselaser alignment to transiently fix CS2 molecules in space longenough to elucidate, in the molecular reference frame, details of ultrafast electronic vibrationaldynamics during a photochemical reaction. These three-dimensional photoelectron imaging results, combined with ongoing efforts in molecular alignment and orientation, presage a wide range of insights obtainable fromtime-resolved studies in the molecular frame.

Bisgaard, Christer; Clarkin, Owen; Wu, Guorong; Lee, Anthony; Gessner, Oliver; Hayden, Carl; Stolow, Albert

2009-04-02T23:59:59.000Z

139

Molecular Dynamics by Light Scattering in the Condensed Phases of Ar, Kr, and Xe  

Science Journals Connector (OSTI)

Temperature dependence of molecular dynamics as revealed by intermolecular and second-order Raman scattering in the condensed rare gases are reported with special emphasis on the behavior near the melting transition.

P. A. Fleury; J. M. Worlock; H. L. Carter

1973-03-26T23:59:59.000Z

140

ls1 mardyn: The massively parallel molecular dynamics code for large systems  

E-Print Network [OSTI]

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales which were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multi-center rigid potential models based on Lennard-Jones sites, point charges and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, e.g. for fluids at interfaces, as well as non-equilibrium molecular dynamics simulation of heat and mass transfer.

Christoph Niethammer; Stefan Becker; Martin Bernreuther; Martin Buchholz; Wolfgang Eckhardt; Alexander Heinecke; Stephan Werth; Hans-Joachim Bungartz; Colin W. Glass; Hans Hasse; Jadran Vrabec; Martin Horsch

2014-08-20T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Finite Element Modelling and Molecular Dynamic Simulations of Carbon nanotubes/ Polymer Composites  

E-Print Network [OSTI]

Modeling of single-walled carbon nanotubes, multi-walled nanotubes and nanotube reinforced polymer composites using both the Finite Element method and the Molecular Dynamic simulation technique is presented. Nanotubes subjected to mechanical loading...

Gaddamanugu, Dhatri

2010-07-14T23:59:59.000Z

142

Dynamic molecular recognition on the surface of vesicle membranes{ Hua Jiang and Bradley D. Smith*  

E-Print Network [OSTI]

Dynamic molecular recognition on the surface of vesicle membranes{ Hua Jiang and Bradley D. Smith-mail: smith.115@nd.edu; Fax: 1 574 631 6652; Tel: 1 574 631 8632 { Electronic supplementary information (ESI

Smith, Bradley D.

143

Nonequilibrium molecular dynamics simulations of confined fluids in contact with the bulk  

E-Print Network [OSTI]

Nonequilibrium molecular dynamics simulations of confined fluids in contact with the bulk Luzheng Zhang, Ramkumar Balasundaram,a) and Stevin H. Gehrke Department of Chemical Engineering, Kansas State University, Manhattan, Kansas 66506 Shaoyi Jiangb) Department of Chemical Engineering, University

Zhang, Luzheng

144

Diffusive Dynamics of Water inside Hydrophobic Carbon Micropores Studied by Neutron Spectroscopy and Molecular Dynamics Simulation  

E-Print Network [OSTI]

When water molecules are confined to nanoscale spacings, such as in the nanometer size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures ($\\sim$ 150 K), leading to a metastable liquid state with remarkable physical properties. We have investigated the ambient pressure diffusive dynamics of water in microporous Kynol\\texttrademark ACF-10 (average pore size $\\sim$11.6 {\\AA}, with primarily slit-like pores) from temperature $T=$ 280 K in its stable liquid state down to $T=$ 230 K into the metastable supercooled phase. The observed characteristic relaxation times and diffusion coefficients are found to be respectively higher and lower than those in bulk water, indicating a slowing down of the water mobility with decreasing temperature. The observed temperature-dependent average relaxation time $$ when compared to previous findings indicate that it is the size of the confining pores - not their shape - that primarily affects the dynamics of water for pore sizes larger than 10 {\\AA}. The experimental observations are compared to complementary molecular dynamics simulations of a model system, in which we studied the diffusion of water within the 11.6 {\\AA} gap of two parallel graphene sheets. We find generally a reasonable agreement between the observed and calculated relaxation times at the low momentum transfer $Q$ ($Q\\le 0.9$ \\AA${^{-1}}$). At high $Q$ however, where localized dynamics becomes relevant, this ideal system does not satisfactorily reproduce the measurements. The best agreement is obtained for the diffusion parameter $D$ associated with the hydrogen-site when a representative stretched exponential function, rather than the standard bi-modal exponential model, is used to parameterize the self-correlation function $I(Q,t)$.

S. O. Diallo; L. Vlcek; E. Mamontov; J. K. Keum; Jihua Chen; J. S. Hayes Jr.; A. A. Chialvo

2014-12-15T23:59:59.000Z

145

Effect of the sliding orientation on the tribological properties of polyethylene in molecular dynamics simulations  

E-Print Network [OSTI]

Effect of the sliding orientation on the tribological properties of polyethylene in molecular properties of polyethylene PE is investigated by using classical molecular dynamics simulations. Cross: 10.1063/1.2900884 I. INTRODUCTION Polyethylene PE is one of the most widely used poly- mers because

Sawyer, Wallace

146

Dynamical mechanism for the conversion of energy at a molecular scale Naoko Nakagawa  

E-Print Network [OSTI]

Dynamical mechanism for the conversion of energy at a molecular scale Naoko Nakagawa Department mechanism of a molecular machine for energy conversion, by considering a simple model describing is thermal ratchet 4­7 , which gives one plausible mechanism for the conversion of energy to mechanical work

Kaneko, Kunihiko

147

Understanding the Dynamics Behind the Photoisomerization of a Light-Driven Fluorene Molecular Rotary Motor  

Science Journals Connector (OSTI)

In the present contribution we report a combined quantum chemical and molecular dynamics study of the mechanism of the rotational cycle of the fluorene-based molecular rotary motor 9-(2,4,7-trimethyl-2,3-dihydro-1H-inden-1-ylidene)-9H-fluorene (1). ... (41) The theoretical results obtained hold considerable implications in achieving a rational synthetic design of future molecular motors with application defined functionality. ...

Andranik Kazaryan; Jos C. M. Kistemaker; Lars V. Scha?fer; Wesley R. Browne; Ben L. Feringa; Michael Filatov

2010-03-29T23:59:59.000Z

148

Category:Baltimore, MD | Open Energy Information  

Open Energy Info (EERE)

MD MD Jump to: navigation, search Go Back to PV Economics By Location Media in category "Baltimore, MD" The following 16 files are in this category, out of 16 total. SVFullServiceRestaurant Baltimore MD Baltimore Gas & Electric Co.png SVFullServiceRestauran... 69 KB SVQuickServiceRestaurant Baltimore MD Baltimore Gas & Electric Co.png SVQuickServiceRestaura... 67 KB SVHospital Baltimore MD Baltimore Gas & Electric Co.png SVHospital Baltimore M... 69 KB SVLargeHotel Baltimore MD Baltimore Gas & Electric Co.png SVLargeHotel Baltimore... 69 KB SVLargeOffice Baltimore MD Baltimore Gas & Electric Co.png SVLargeOffice Baltimor... 69 KB SVMediumOffice Baltimore MD Baltimore Gas & Electric Co.png SVMediumOffice Baltimo... 68 KB SVMidriseApartment Baltimore MD Baltimore Gas & Electric Co.png

149

A molecular dynamics investigation of the diffusion characteristics of cavity-type zeolites with 8-ring windows  

SciTech Connect (OSTI)

Molecular dynamics (MD) simulations are used to investigate the diffusion characteristics in DDR, CHA, LTA, ITQ-29, and TSC zeolites that have cavities separated by 8-member ring windows of dimensions in the 3.4–4.6 Å range. These zeolites have potential usage for separation of a variety of mixtures, such as CO{sub 2}/CH{sub 4}, CO{sub 2}/H{sub 2}, H{sub 2}/CH{sub 4}, and propane/propene, relying on a combination of adsorption and diffusion selectivities. The magnitude of self-diffusivities, D{sub i,self}, of the CH{sub 4} is found to have a direct correlation with the size of the window opening, increasing by about two orders of magnitude for a 0.5 Å increase in the window aperture. The diffusion selectivities of CO{sub 2}/CH{sub 4}, and H{sub 2}/CH{sub 4} mixtures were also found to have direct, and strong, correlation, with the window aperture. This opens up the possibility of tuning diffusion selectivities by appropriate choice of the framework structure. Framework flexibility dynamics have also been investigated with the aid of two published force fields for all-silica zeolites. Due to the lattice vibrations there is a distribution of window sizes that varies with time. The diffusivity of CH4 for a flexible lattice was found to correlate with aperture size of the time-averaged window, in precisely the same manner as for fixed framework lattices. This leads to the conclusion that lattice flexibility, per se, has no influence on the magnitude of the diffusivity or diffusion selectivity.

Krishna, Rajamani; van Baten, Jasper M.

2011-01-01T23:59:59.000Z

150

Crossed molecular beam studies of atmospheric chemical reaction dynamics  

SciTech Connect (OSTI)

The dynamics of several elementary chemical reactions that are important in atmospheric chemistry are investigated. The reactive scattering of ground state chlorine or bromine atoms with ozone molecules and ground state chlorine atoms with nitrogen dioxide molecules is studied using a crossed molecular beams apparatus with a rotatable mass spectrometer detector. The Cl + O{sub 3} {yields} ClO + O{sub 2} reaction has been studied at four collision energies ranging from 6 kcal/mole to 32 kcal/mole. The derived product center-of-mass angular and translational energy distributions show that the reaction has a direct reaction mechanism and that there is a strong repulsion on the exit channel. The ClO product is sideways and forward scattered with respect to the Cl atom, and the translational energy release is large. The Cl atom is most likely to attack the terminal oxygen atom of the ozone molecule. The Br + O{sub 3} {yields} ClO + O{sub 2} reaction has been studied at five collision energies ranging from 5 kcal/mole to 26 kcal/mole. The derived product center-of-mass angular and translational energy distributions are quite similar to those in the Cl + O{sub 3} reaction. The Br + O{sub 3} reaction has a direct reaction mechanism similar to that of the Cl + O{sub 3} reaction. The electronic structure of the ozone molecule seems to play the central role in determining the reaction mechanism in atomic radical reactions with the ozone molecule. The Cl + NO{sub 2} {yields} ClO + NO reaction has been studied at three collision energies ranging from 10.6 kcal/mole to 22.4 kcal/mole. The center-of-mass angular distribution has some forward-backward symmetry, and the product translational energy release is quite large. The reaction proceeds through a short-lived complex whose lifetime is less than one rotational period. The experimental results seem to show that the Cl atom mainly attacks the oxygen atom instead of the nitrogen atom of the NO{sub 2} molecule.

Zhang, Jingsong

1993-04-01T23:59:59.000Z

151

Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer  

E-Print Network [OSTI]

Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics January 2001 A hybrid approach for simulating proton and hydride transfer reactions in enzymes coefficient and to investigate the real-time dynamics of reactive trajectories. This hybrid approach includes

Hammes-Schiffer, Sharon

152

Nonadiabatic Molecular Dynamics Simulations of the Energy Transfer between Building Blocks in a Phenylene Ethynylene Dendrimer  

E-Print Network [OSTI]

Nonadiabatic Molecular Dynamics Simulations of the Energy Transfer between Building Blocks E. Roitberg*, UniVersidad Nacional de Quilmes, Roque Saenz Pen~a 352, B1876BXD Bernal, Argentina, 2009 The ultrafast dynamics of electronic and vibrational energy transfer between two- and three

Tretiak, Sergei

153

Self-assembly of polyhedral shells: A molecular dynamics study D. C. Rapaport*  

E-Print Network [OSTI]

Self-assembly of polyhedral shells: A molecular dynamics study D. C. Rapaport* Physics Department) The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures

Rapaport, Dennis C.

154

Crossed Molecular Beam Studies and Dynamics of Decomposition of Chemically Activated Radicals  

DOE R&D Accomplishments [OSTI]

The power of the crossed molecular beams method in the investigation of the dynamics of chemical reactions lies mainly in the direct observation of the consequences of single collisions of well controlled reactant molecules. The primary experimental observations which provide information on reaction dynamics are the measurements of angular and velocity distributions of reaction products.

Lee, Y. T.

1973-09-00T23:59:59.000Z

155

subm. to Surf. Sci. Ab initio molecular dynamics study of H2 adsorption on sulfur-and chlorine-covered  

E-Print Network [OSTI]

subm. to Surf. Sci. Ab initio molecular dynamics study of H2 adsorption on sulfur- and chlorine/Germany The adsorption of molecular hydrogen on sulfur- and chlorine-covered Pd(100) in a (2Ã?2) geometry is studied by ab initio molecular dynamics simulations. The potential energy surfaces of H2/S(2 Ã? 2)/Pd(100) and H2/Cl(2

Ulm, Universität

156

Cooling rate and size effects on the medium-range structure of multicomponent oxide glasses simulated by molecular dynamics  

SciTech Connect (OSTI)

A set of molecular dynamics simulations were performed to investigate the effect of cooling rate and system size on the medium-range structure of melt-derived multicomponent silicate glasses, represented by the quaternary 45S5 Bioglass composition. Given the significant impact of the glass degradation on applications of these materials in biomedicine and nuclear waste disposal, bulk structural features which directly affect the glass dissolution process are of particular interest. Connectivity of the silicate matrix, ion clustering and nanosegregation, distribution of ring and chain structural patterns represent critical features in this context, which can be directly extracted from the models. A key issue is represented by the effect of the computational approach on the corresponding glass models, especially in light of recent indications questioning the suitability of conventional MD approaches (that is, involving melt-and-quench of systems containing ?10{sup 3} atoms at cooling rates of 5-10 K/ps) when applied to model these glasses. The analysis presented here compares MD models obtained with conventional and nonconventional cooling rates and system sizes, highlighting the trend and range of convergence of specific structural features in the medium range. The present results show that time-consuming computational approaches involving much lower cooling rates and/or significantly larger system sizes are in most cases not necessary in order to obtain a reliable description of the medium-range structure of multicomponent glasses. We identify the convergence range for specific properties and use them to discuss models of several glass compositions for which a possible influence of cooling-rate or size effects had been previously hypothesized. The trends highlighted here represent an important reference to obtain reliable models of multicomponent glasses and extract converged medium-range structural features which affect the glass degradation and thus their application in different fields. In addition, as a first application of the present findings, the fully converged structure of the 45S5 glass was further analyzed to shed new light on several dissolution-related features whose interpretation has been rather controversial in the past.

Tilocca, Antonio [Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom)] [Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom)

2013-09-21T23:59:59.000Z

157

A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon  

SciTech Connect (OSTI)

This report describes the use of shared memory emulation with DOLIB (Distributed Object Library) to simplify parallel programming on the Intel Paragon. A molecular dynamics application is used as an example to illustrate the use of the DOLIB shared memory library. SOTON-PAR, a parallel molecular dynamics code with explicit message-passing using a Lennard-Jones 6-12 potential, is rewritten using DOLIB primitives. The resulting code has no explicit message primitives and resembles a serial code. The new code can perform dynamic load balancing and achieves better performance than the original parallel code with explicit message-passing.

D`Azevedo, E.F.; Romine, C.H.

1994-12-01T23:59:59.000Z

158

Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture  

E-Print Network [OSTI]

Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.

Wei Feng; Luting Xu; Xin-Qi Li; Weihai Fang; YiJing Yan

2013-12-17T23:59:59.000Z

159

An Efficient and Accurate Car-Parrinello-like Approach to Born-Oppenheimer Molecular Dynamics  

E-Print Network [OSTI]

We present a new method which combines Car-Parrinello and Born-Oppenheimer molecular dynamics in order to accelerate density functional theory based ab-initio simulations. Depending on the system a gain in efficiency of one to two orders of magnitude has been observed, which allows ab-initio molecular dynamics of much larger time and length scales than previously thought feasible. It will be demonstrated that the dynamics is correctly reproduced and that high accuracy can be maintained throughout for systems ranging from insulators to semiconductors and even to metals in condensed phases. This development considerably extends the scope of ab-initio simulations.

Thomas D. Kühne; Matthias Krack; Fawzi R. Mohamed; Michele Parrinello

2006-12-20T23:59:59.000Z

160

Car?Parrinello Molecular Dynamics Study of Anharmonic Systems:? A Mannich Base in Solution  

Science Journals Connector (OSTI)

Car?Parrinello Molecular Dynamics Study of Anharmonic Systems:? A Mannich Base in Solution ... Proton dynamics play a crucial role in many chemical, biochemical, and industrial processes1-4 because most of the properties of the water, which is the solvent in these systems, can be traced to intermolecular hydrogen bonds. ... However, there is also a fundamental reason for our choice of the atomic velocity power spectrum method; only in this way can we capture the dynamic nature of processes at the molecular level. ...

Aneta Jezierska; Jaros?aw Panek; Urban Borštnik; Janez Mavri; Dušanka Janeži?

2007-04-21T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Dynamical Host/Guest Interactions in Zeolites:? Framework Isotope Effects on Proton Transfer Studied by Car?Parrinello Molecular Dynamics  

Science Journals Connector (OSTI)

Dynamical Host/Guest Interactions in Zeolites:? Framework Isotope Effects on Proton Transfer Studied by Car?Parrinello Molecular Dynamics ... While in liquids the proper relaxation mechanisms can be described in terms of the orientational correlation functions of solvent molecules,8 in solids and in zeolites in particular, velocity or dipole autocorrelation functions (or their Fourier Transform giving the power or IR spectra) are good candidates to describe this phenomenon. ... A single band in the stretching region indicates the absence of water molecules. ...

Ettore Fois; Aldo Gamba

1999-03-02T23:59:59.000Z

162

Ab Initio Molecular Dynamics Simulations of Low-Energy Recoil...  

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

A variety of different defect configurations are created, consisting mainly of vacancies and interstitials. Charge transfer occurs during the dynamic displacement process....

163

Extended Lagrangian Born-Oppenheimer molecular dynamics in the limit of vanishing self-consistent field optimization  

SciTech Connect (OSTI)

We present an efficient general approach to first principles molecular dynamics simulations based on extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The reduction of the optimization requirement reduces the computational cost to a minimum, but without causing any significant loss of accuracy or long-term energy drift. The optimization-free first principles molecular dynamics requires only one single diagonalization per time step, but is still able to provide trajectories at the same level of accuracy as “exact,” fully converged, Born-Oppenheimer molecular dynamics simulations. The optimization-free limit of extended Lagrangian Born-Oppenheimer molecular dynamics therefore represents an ideal starting point for robust and efficient first principles quantum mechanical molecular dynamics simulations.

Souvatzis, Petros, E-mail: petros.souvatsiz@fysik.uu.se [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120, Uppsala (Sweden)] [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120, Uppsala (Sweden); Niklasson, Anders M. N., E-mail: amn@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2013-12-07T23:59:59.000Z

164

Molecular Simulations of Aqueous Electrolyte Solubility: 1. The Expanded-Ensemble Osmotic Molecular Dynamics Method for the Solution Phase  

E-Print Network [OSTI]

+, and Cl-); undissociated molecular units (HgCl2) are the predominant solution solute species.1 such as mercury(II) chloride (HgCl2), only a small fraction of the atoms dissociate into free ions (HgCl+, Hg2 Dynamics Method for the Solution Phase Martin Li´sal,*,, William R. Smith,§ and Jiri´ Kolafa| E. Ha

Lisal, Martin

165

Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution  

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

Molecular dynamics simulations of the interaction of glucose with imidazole in Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution Mo Chen, Yannick J. Bomble, Michael E. Himmel, John W. Brady PII: S0008-6215(11)00592-1 DOI: 10.1016/j.carres.2011.12.008 Reference: CAR 6026 To appear in: Carbohydrate Research Received Date: 15 June 2011 Revised Date: 22 November 2011 Accepted Date: 8 December 2011 Please cite this article as: Chen, M., Bomble, Y.J., Himmel, M.E., Brady, J.W., Molecular dynamics simulations of the interaction of glucose with imidazole in aqueous solution, Carbohydrate Research (2011), doi: 10.1016/j.carres. 2011.12.008 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and

166

Free energy calculations using dual-level Born-Oppenheimer molecular dynamics  

SciTech Connect (OSTI)

We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.

Retegan, Marius; Martins-Costa, Marilia; Ruiz-Lopez, Manuel F. [Theoretical Chemistry and Biochemistry Group, SRSMC, CNRS, Nancy-University, BP 70239, 54506 Vandoeuvre-les-Nancy (France)

2010-08-14T23:59:59.000Z

167

How accurate is Born-Oppenheimer molecular dynamics for crossings of potential surfaces ?  

E-Print Network [OSTI]

The difference of the value of observables for the time-independent Schr\\"odinger equation, with matrix valued potentials, and the values of observables for ab initio Born-Oppenheimer molecular dynamics, of the ground state, depends on the probability to be in excited states and the electron/nuclei mass ratio. The paper first proves an error estimate (depending on the electron/nuclei mass ratio and the probability to be in excited states) for this difference of observables, assuming that molecular dynamics space-time averages converge, with a rate related to the maximal Lyapunov exponent. The analysis does not assume a uniform lower bound on the spectral gap and consequently the probability to be in excited states can be large. A numerical method to determine the probability to be in excited states is then presented, based on Ehrenfest molecular dynamics and stability analysis of a perturbed eigenvalue problem.

Hakon Hoel; Ashraful Kadir; Petr Plechac; Mattias Sandberg; Anders Szepessy

2014-06-13T23:59:59.000Z

168

Origin of the Difference in Structural Behavior of Poly(acrylic acid) and Poly(methacrylic acid) in Aqueous Solution Discerned by Explicit-Solvent Explicit-Ion MD Simulations  

Science Journals Connector (OSTI)

Origin of the Difference in Structural Behavior of Poly(acrylic acid) and Poly(methacrylic acid) in Aqueous Solution Discerned by Explicit-Solvent Explicit-Ion MD Simulations ... Polyelectrolytes such as sodium polyacrylate (Na-PAA) are widely used as adhesives, dispersants, wetting agents, and additives in coatings. ... Levitt, M.; Hirshberg, M.; Sharon, R.; Daggett, V.Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution Comput. ...

Muralidharan S. Sulatha; Upendra Natarajan

2011-10-10T23:59:59.000Z

169

Time-Dependent Properties of Liquid Water:? A Comparison of Car?Parrinello and Born?Oppenheimer Molecular Dynamics Simulations  

Science Journals Connector (OSTI)

Time-Dependent Properties of Liquid Water:? A Comparison of Car?Parrinello and Born?Oppenheimer Molecular Dynamics Simulations ... Dynamical information of water interacting with its local environment can be gleaned from the vibrational power spectrum. ...

I-Feng W. Kuo; Christopher J. Mundy; Matthew J. McGrath; J. Ilja Siepmann

2006-07-27T23:59:59.000Z

170

Theoretical aspects of gas-phase molecular dynamics  

SciTech Connect (OSTI)

Research in this program is focused on the development and application of time-dependent quantum mechanical and semiclassical methods for treating inelastic and reactive molecular collisions, and the photochemistry and photophysics of atoms and molecules in laser fields. Particular emphasis is placed on the development and application of grid methods based on discrete variable representations, on time-propagation methods, and, in systems with more that a few degrees of freedom, on the combined use of quantal wavepackets and classical trajectories.

Muckerman, J.T. [Brookhaven National Laboratory, Upton, NY (United States)

1993-12-01T23:59:59.000Z

171

Resonant behavior in heat transfer across weak molecular interfaces  

SciTech Connect (OSTI)

Molecular dynamics (MD) simulations are used to study, in detail, the transfer of thermal (vibrational) energy between objects with discrete vibrational spectra to those with a semi-continuum of spectra. The transfer of energy is stochastic and strongly dependent on the instantaneous separation between the bodies. The insight from the MD simulations can be captured with a simple classical model that agrees well with quantum models. This model can be used to optimize systems for efficient frequency selective energy transfer, which can be used in designing a chemical sensor through nanomechanical resonance spectroscopy.

Sklan, Sophia R. [Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Alex Greaney, P. [Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); School of Mechanical, Industrial, and Manufacturing Engineering, Oregon State University, Corvalis, Oregon 97331 (United States); Grossman, Jeffrey C., E-mail: jcg@mit.edu [Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

2013-12-21T23:59:59.000Z

172

Thermophysical properties of warm dense hydrogen using quantum molecular dynamics simulations  

Science Journals Connector (OSTI)

We study the thermophysical properties of warm dense hydrogen by using quantum molecular dynamics simulations. Results are presented for the pair distribution functions, the equation of state, and the Hugoniot curve. From the dynamic conductivity, we derive the dc electrical conductivity and the reflectivity. We compare with available experimental data and predictions of the chemical picture. In particular, we discuss the nonmetal-to-metal transition, which occurs at about 40 GPa in the dense fluid.

Bastian Holst, Ronald Redmer, and Michael P. Desjarlais

2008-05-09T23:59:59.000Z

173

Electron Transfer Dynamics in Efficient Molecular Solar Cells  

SciTech Connect (OSTI)

This research provided new mechanistic insights into surface mediated photochemical processes relevant to solar energy conversion. In this past three years our research has focused on oxidation photo-redox chemistry and on the role surface electric fields play on basic spectroscopic properties of molecular-semiconductor interfaces. Although this research as purely fundamental science, the results and their interpretation have relevance to applications in dye sensitized and photogalvanic solar cells as well as in the storage of solar energy in the form of chemical bonds.

Meyer, Gerald John

2014-10-01T23:59:59.000Z

174

Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature  

E-Print Network [OSTI]

Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature Simone film crystal growth of silicon carbide (SiC), a semiconductor syn- thesized to replace silicon in harsh

Alfè, Dario

175

Heat conduction of single-walled carbon nanotube isotope-superlattice structures: A molecular dynamics study  

E-Print Network [OSTI]

-folding effect to thermal boundary resistance of lattice interface. The crossover mechanism is explained-dimensional materials. In our previous molecular dynamics study, isotope-effects on the thermal conduction were of heat conduction of SWNTs subjected to nanoscale intrinsic thermal resistances. Here, in order to reduce

Maruyama, Shigeo

176

MOLECULAR PHYSICS, 1999, VOL. 97, NO. 7, 897 905 Dynamics and hydrogen bonding in liquid ethanol  

E-Print Network [OSTI]

MOLECULAR PHYSICS, 1999, VOL. 97, NO. 7, 897± 905 Dynamics and hydrogen bonding in liquid ethanol L of liquid ethanol at three temperatures have been carried out. The hydrogen bonding states of ethanol measurements of the frequency-dependent dielectric permittivity of liquid ethanol. 1. Introduction A detailed

Saiz, Leonor

177

SELECTED RECENT PUBLICATIONS: Nanoindentation of Silicon Nitride: A Multi-million Atom Molecular Dynamics Study, P.  

E-Print Network [OSTI]

, and G. Z. Voyiadjis, Phys. Rev. Lett. 87, 086104 (2001). · Linear-scaling Density-functional-theory). · Hybrid Finite-element/Molecular-dynamics/Electronic-density-functional Approach to Materials Simulations). SELECTED BOOKS: · High Performance Computing and its Applications in the Physical Sciences, (1993), World

Southern California, University of

178

Non-Born-Oppenheimer molecular dynamics of NaFH photodissociation Ahren W. Jaspera  

E-Print Network [OSTI]

Non-Born-Oppenheimer molecular dynamics of Na¯FH photodissociation Ahren W. Jaspera Combustion 20 November 2007 The accuracy of non-Born-Oppenheimer electronically nonadiabatic semiclassical are re- stricted to a single Born-Oppenheimer electronic state typi- cally, the ground electronic state

Truhlar, Donald G

179

Solvation Structure of Hydroxyl Radical by Car?Parrinello Molecular Dynamics  

Science Journals Connector (OSTI)

Car?Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. ... A hydrogen bond between the two waters is formed and the first water molecule is pushed toward the hydroxyl. ... The resulting velocity autocorrelation power spectra calculated separately for the atomic species from the hydroxyl and from the water molecules are shown in Figure 12. ...

Julia M. Khalack; Alexander P. Lyubartsev

2004-12-07T23:59:59.000Z

180

Creeping Friction Dynamics and Molecular Dissipation Mechanisms in Glassy Polymers Scott Sills and Rene M. Overney  

E-Print Network [OSTI]

Creeping Friction Dynamics and Molecular Dissipation Mechanisms in Glassy Polymers Scott Sills kinetic friction between an atomic force microscopy tip and a surface of amorphous glassy polystyrene has of the friction results using the method of reduced variables revealed the dissipative behavior as an activated

Note: This page contains sample records for the topic "molecular dynamics md" 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

Understanding graphene production by ionic surfactant exfoliation: A molecular dynamics simulation study  

E-Print Network [OSTI]

Understanding graphene production by ionic surfactant exfoliation: A molecular dynamics simulation simulated sodium dodecyl sulfate (SDS) surfactant/water þ bilayer graphene mixture system to investigate two mechanisms of graphene exfoliation: changing the interlayer distance and sliding away the relative distance

Simons, Jack

182

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

183

Mechanical Unfolding of a -Hairpin Using Molecular Dynamics Zev Bryant,* Vijay S. Pande,  

E-Print Network [OSTI]

Mechanical Unfolding of a -Hairpin Using Molecular Dynamics Zev Bryant,* Vijay S. Pande, and Daniel Laboratory, Berkeley, California 94720, USA ABSTRACT Single-molecule mechanical unfolding experiments have simulations of the mechanical unfolding of the C-terminal hairpin of protein G. We have studied the dependence

Bryant, Zev

184

Molecular dynamics of gas phase hydrogen-bonded complexes  

E-Print Network [OSTI]

---HF are compared with previously determined values using microwave absolute intensity measurements and ab-initio molecular orbital calculations. Current work D /kJ mole -1 20. 77(22) De/kJ mole 28. 77(45) Rovibrational band information available for HCN... ? -RF 2 ?1 4 5 6 7 1 -116. 9(1) 8. 025(7) 4. 216&5) -51. 26&1) -14. 61(22) -D. lgl(1) -18. 98(2) -0. 408&2& -10. 45(38) -3. 61(22) -0. 61(2& -2. 01(1) 2. 61(5) -21. 61&18& 1. 00(5) Ixlgl, I lgl, I 15I, lxggl assam IX341, IX361 assumed 63 cm ' Ix...

Wofford, Billy Alan

2012-06-07T23:59:59.000Z

185

Graphics processing units accelerated semiclassical initial value representation molecular dynamics  

SciTech Connect (OSTI)

This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the benchmark values. The computational time scaling of two GPUs (NVIDIA Tesla C2075 and Kepler K20), respectively, versus two CPUs (Intel Core i5 and Intel Xeon E5-2687W) and the critical issues related to the GPU implementation are discussed. The resulting reduction in computational time and power consumption is significant and semiclassical GPU calculations are shown to be environment friendly.

Tamascelli, Dario; Dambrosio, Francesco Saverio [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy)] [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy); Conte, Riccardo [Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States)] [Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States); Ceotto, Michele, E-mail: michele.ceotto@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano (Italy)] [Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano (Italy)

2014-05-07T23:59:59.000Z

186

Car?Parrinello Molecular Dynamics in a Finite Homogeneous Electric Field  

Science Journals Connector (OSTI)

We introduce a variational total?energy functional to treat finite homogeneous electric fields with periodic boundary conditions and show that this functional can be implemented within a Car?Parrinello molecular dynamics scheme. The coupling to an electric field is achieved through the Berry?phase expression of the polarization. The minimization of this extended functional gives a ground state which describes the polarized state in an electric field. For a crystalline system the ground state of this extended functional preserves the Bloch symmetry. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges and the high? and low?frequency dielectric constants. In the latter case we evaluated the static dielectric constant by performing a damped molecular dynamics in the presence of a finite electric field completely avoiding the calculation of the dynamical matrix.

P. Umari; Alfredo Pasquarello

2003-01-01T23:59:59.000Z

187

Pseudorandom number generator for massively parallel molecular-dynamics simulations  

Science Journals Connector (OSTI)

A class of uniform pseudorandom number generators is proposed for modeling and simulations on massively parallel computers. The algorithm is simple, nonrecursive, and is easily transported to serial or vector computers. We have tested the procedure for uniformity, independence, and correlations by several methods. Related, less complex sequences passed some of these tests well enough; however, inadequacies were revealed by tests for correlations and in an interesting application, namely, annealing from an initial lattice that is mechanically unstable. In the latter case, initial velocities chosen by a random number generator that is not sufficiently random lead quickly to unphysical regularity in grain structure. The new class of generators passes this dynamical diagnostic for unwanted correlations.

Brad Lee Holian; Ora E. Percus; Tony T. Warnock; Paula A. Whitlock

1994-08-01T23:59:59.000Z

188

Car–Parrinello Molecular Dynamics Simulations of CaCl2 Aqueous Solutions  

Science Journals Connector (OSTI)

(24, 25) Such ab initio molecular orbital calculations, performed at the restricted Hartree–Fock (HF) and second-order M?ller–Plesset perturbation (MP2) levels of theory and followed by natural energy decomposition analysis, emphasized the importance of polarization effects in the binding energies of M2+(H2O)n clusters. ... It shows a maximum at 3.35 D, due to the electron polarization caused by the strong electric field of the ion. ... Solution Structure of Energy Stored System I: Aqua-B(OH)4–: A DFT, Car–Parrinello Molecular Dynamics, and Raman Study ...

Teodora Todorova; Philippe H. Hünenberger; Jürg Hutter

2008-04-15T23:59:59.000Z

189

Atomic Level Green-Kubo Stress Correlation Function for a Model Crystal: An Insight into Molecular Dynamics Results on a Model Liquid  

E-Print Network [OSTI]

In order to get insight into the connection between the vibrational dynamics and the atomic level Green-Kubo stress correlation function in liquids we consider this connection in a model crystal instead. Of course, vibrational dynamics in liquids and crystals are quite different and it is not expected that the results obtained on a model crystal should be valid for liquids. However, these considerations provide a benchmark to which the results of the previous molecular dynamics simulations can be compared. Thus, assuming that vibrations are plane waves, we derive analytical expressions for the atomic level stress correlation functions in the classical limit and analyze them. These results provide, in particular, a recipe for analysis of the atomic level stress correlation functions in Fourier space and extraction of the wavevector and frequency dependent information. We also evaluate the energies of the atomic level stresses. Obtained energies are significantly smaller than the energies that were obtained in MD simulations of liquids previously. This result suggests that the average energies of the atomic level stresses in liquids and glasses are largely determined by the structural disorder. We discuss this result in the context of equipartition of the atomic level stress energies. Analysis of the previously published data suggests that it is possible to speak about configurational and vibrational contributions to the average energies of the atomic level stresses in a glass state. However, this separation in a liquid state is problematic. We also consider peak broadening in the pair distribution function with increase of distance. We find that peak broadening (by ~40%) occurs due to the transverse vibrational modes, while contribution from the longitudinal modes does not change with distance. Finally, we introduce and consider atomic level transverse current correlation function.

V. A. Levashov

2014-03-25T23:59:59.000Z

190

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

191

Self-consistent field theory based molecular dynamics with linear system-size scaling  

SciTech Connect (OSTI)

We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany)] [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)

2014-04-07T23:59:59.000Z

192

Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.  

SciTech Connect (OSTI)

Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.

Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (Oak Ridge National Laboratories, Oak Ridge, TN); Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl

2011-09-01T23:59:59.000Z

193

Quantum molecular dynamics simulation of shock-wave experiments in aluminum  

SciTech Connect (OSTI)

We present quantum molecular dynamics calculations of principal, porous, and double shock Hugoniots, release isentropes, and sound velocity behind the shock front for aluminum. A comprehensive analysis of available shock-wave data is performed; the agreement and discrepancies of simulation results with measurements are discussed. Special attention is paid to the melting region of aluminum along the principal Hugoniot; the boundaries of the melting zone are estimated using the self-diffusion coefficient. Also, we make a comparison with a high-quality multiphase equation of state for aluminum. Independent semiempirical and first-principle models are very close to each other in caloric variables (pressure, density, particle velocity, etc.) but the equation of state gives higher temperature on the principal Hugoniot and release isentropes than ab initio calculations. Thus, the quantum molecular dynamics method can be used for calibration of semiempirical equations of state in case of lack of experimental data.

Minakov, D. V.; Khishchenko, K. V.; Fortov, V. E. [Joint Institute for High Temperatures RAS, Izhorskaya 13 Bldg 2, Moscow 125412 (Russian Federation); Moscow Institute of Physics and Technology, Institutskii per. 9, Dolgoprudny, Moscow Region 141700 (Russian Federation); Levashov, P. R. [Joint Institute for High Temperatures RAS, Izhorskaya 13 Bldg 2, Moscow 125412 (Russian Federation); Tomsk State University, 36 Lenin Prospekt, Tomsk 634050 (Russian Federation)

2014-06-14T23:59:59.000Z

194

Connecting the Molecular and the Continuum Scales  

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

Connecting the Connecting the Molecular and the Continuum Scales Connecting the Molecular and the Continuum Scales Key Challenges: A molecular-scale understanding of structure and surface chemistry of clay mineral surface nanoparticles. Why it Matters: With a ubiquitous presence in natural materials and strong surface reactions, nanoparticles figure importantly in a broad range of phenomena, from climate change to contaminant remediation. Accomplishments: Used molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients of water tracers and representative cations (Na+,Cs+,Sr2+) in Smectite and found a simple way to accurately relate this to bulk, pore-scale diffusion. The result is that a remarkably simple expression relates Dinterlayer to the pore-scale

195

Estimate of nuclear fusion rates arising from a molecular-dynamics model of PdDx  

Science Journals Connector (OSTI)

We describe an estimate of the fusion rate of deuterium in palladium metal based on molecular-dynamics simulation. Quantum effects on the motion of the deuterium are treated semiclassically and the effects of electronic screening of the interactions are studied by varying a screening parameter in the potentials. We find very low fusion rates of the order of 10-150 s-1 per deuteron, consistent with bounds suggested by Leggett and Baym.

J. W. Halley and J. L. Vallés

1990-03-15T23:59:59.000Z

196

Detonation Initiation from Spontaneous Hotspots Formed During Cook-Off Observed in Molecular Dynamics Simulations  

Science Journals Connector (OSTI)

Detonation Initiation from Spontaneous Hotspots Formed During Cook-Off Observed in Molecular Dynamics Simulations ... New equations based on Johnson?Mehl?Avrami?Kolmogorov kinetics are proposed for describing the extent of detonated material that could provide new insight into mechanisms of critical hotspot nucleation. ... Depending on the chemical and thermal properties of the energetic material as well as the size and containment of the material during cook-off, a supersonic reaction front can form; that is, the material can detonate. ...

Yanhong Hu; Donald W. Brenner; Yunfeng Shi

2011-01-06T23:59:59.000Z

197

Proton Transport in Triflic Acid Hydrates Studied via Path Integral Car?Parrinello Molecular Dynamics  

Science Journals Connector (OSTI)

Proton Transport in Triflic Acid Hydrates Studied via Path Integral Car?Parrinello Molecular Dynamics ... The mono-, di-, and tetrahydrates of trifluoromethanesulfonic acid, which contain characteristic H3O+, H5O2+, and H9O4+ structures, provide model systems for understanding proton transport in materials with high perfluorosulfonic acid density such as perfluorosulfonic acid membranes commonly employed in hydrogen fuel cells. ... Hydrogen is described as a promising future fuel if the fuel cell technol. ...

Robin L. Hayes; Stephen J. Paddison; Mark E. Tuckerman

2009-12-07T23:59:59.000Z

198

FT-ICR Reaction Experiments and Molecular Dynamics Simulations of Precursor Clusters for  

E-Print Network [OSTI]

. J. D, 9, 1-4, 385 (1999). 30 40 50 60 70 Number of Carbon Atoms Intensity(arbitrary) Noise (a carbon sample. 520 530 540 43 44 45 Number of Carbon Atoms Intensity(arbitrary) NiC38 ­ CoC38 ­ NiC38(NO mechanism of single walled carbon nanotubes is investigated through experimental and molecular dynamics

Maruyama, Shigeo

199

Predicting anisotropic displacement parameters using molecular dynamics: density functional theory plus dispersion modelling of thermal motion in benzophenone  

Science Journals Connector (OSTI)

The potential for first-princples molecular dynamics simulations to predict thermal-motion parameters has been illustrated by good agreement between theoretical and neutron-diffraction-determined anisotropic displacement parameters of benzophenone.

Reilly, A.M.

2013-04-18T23:59:59.000Z

200

Quantized Hamiltonian dynamics captures the low-temperature regime of charge transport in molecular crystals  

SciTech Connect (OSTI)

The quantized Hamiltonian dynamics (QHD) theory provides a hierarchy of approximations to quantum dynamics in the Heisenberg representation. We apply the first-order QHD to study charge transport in molecular crystals and find that the obtained equations of motion coincide with the Ehrenfest theory, which is the most widely used mixed quantum-classical approach. Quantum initial conditions required for the QHD variables make the dynamics surpass Ehrenfest. Most importantly, the first-order QHD already captures the low-temperature regime of charge transport, as observed experimentally. We expect that simple extensions to higher-order QHDs can efficiently represent other quantum effects, such as phonon zero-point energy and loss of coherence in the electronic subsystem caused by phonons.

Wang, Linjun, E-mail: linjun.wang@rochester.edu, E-mail: oleg.prezhdo@rochester.edu; Chen, Liping; Prezhdo, Oleg V., E-mail: linjun.wang@rochester.edu, E-mail: oleg.prezhdo@rochester.edu [Department of Chemistry, University of Rochester, Rochester, New York 14627 (United States); Akimov, Alexey V. [Department of Chemistry, University of Rochester, Rochester, New York 14627 (United States) [Department of Chemistry, University of Rochester, Rochester, New York 14627 (United States); Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973-5000 (United States)

2013-11-07T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

2.13 HEAT TRANSFER & FLUID FLOW IN MICROCHANNELS 2.13.7-1 Molecular dynamics methods in  

E-Print Network [OSTI]

2.13 HEAT TRANSFER & FLUID FLOW IN MICROCHANNELS 2.13.7-1 2.13.7 Molecular dynamics methods in microscale heat transfer Shigeo Maruyama A. Introduction In normal heat transfer and fluid flow calculations of molecules. This situation is approached in microscale heat transfer and fluid flow. Molecular level

Maruyama, Shigeo

202

A Combined 6,7Li NMR and Molecular Dynamics Study of Li Diffusion...  

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

MD simulations predict that lithium can occupy a tetrahedral site if two or more vacancies exist in the vicinity, which may result, for example, from the presence of a Ti...

203

Near quantitative agreement of model free DFT- MD predictions...  

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

Near quantitative agreement of model free DFT- MD predictions with XAFS observations of the hydration structure of highly Near quantitative agreement of model free DFT- MD...

204

Editorial John Hickner, MD, MSc Editor-in-Chief  

E-Print Network [OSTI]

Health Care, Overland Park, Kan kEVin PEtErSon, MD, MPH University of Minnesota, St. Paul goutHAM rAo, MD

Alford, Simon

205

Calculation of Cauchy stress tensor in molecular dynamics system with a generalized Irving-Kirkwood formulism  

E-Print Network [OSTI]

Irving and Kirkwood formulism (IK formulism) provides a way to compute continuum mechanics quantities at certain location in terms of molecular variables. To make the approach more practical in computer simulation, Hardy proposed to use a spacial kernel function that couples continuum quantities with atomistic information. To reduce irrational fluctuations, Murdoch proposed to use a temporal kernel function to smooth the physical quantities obtained in Hardy's approach. In this paper, we generalize the original IK formulism to systematically incorporate both spacial and temporal average. The Cauchy stress tensor is derived in this generalized IK formulism (g-IK formulism). Analysis is given to illuminate the connection and difference between g-IK formulism and traditional temporal post-process approach. The relationship between Cauchy stress and first Piola-Kirchhoff stress is restudied in the framework of g-IK formulism. Numerical experiments using molecular dynamics are conducted to examine the analysis res...

Yang, Jerry Zhijian

2014-01-01T23:59:59.000Z

206

DOCTOR'S HEART George Stetten, M.D.  

E-Print Network [OSTI]

1 DOCTOR'S HEART George Stetten, M.D. "Resident Forum," Journal of the American Medical Association War --- soldier's heart. We should not be surprised or ashamed to find such reactions in ourselves

Stetten, George

207

David Brick, MD, FAAP, FACC Image credit  

E-Print Network [OSTI]

#12;David Brick, MD, FAAP, FACC #12;Image credit: www.imagewisely.org #12;1) Understand why Adolescent medicine 12-24 years Brain scans show unique features. Adult congenital Brand new natural

208

Ab initio molecular-dynamical relaxation applied to the silicon(111)-5×5 surface reconstruction  

Science Journals Connector (OSTI)

We have applied first-principles molecular-dynamic relaxation to the Si(111) surface in the 5×5 dimer–adatom–stacking-fault structure. We have determined the relaxed atomic surface geometry and the corresponding electronic structure. We find that the filled adatom dangling-bond states are segregated, with the charge density residing on the faulted side of the unit cell, and that the adatoms on the faulted side are higher than the adatoms on the unfaulted side. Surprisingly, we find that, at low temperature, the adatoms on each side of the unit cell are corrugated in a variety of patterns.

Gary B. Adams and Otto F. Sankey

1991-08-12T23:59:59.000Z

209

Molecular dynamics simulation of anhydrous lithium acetate: crystalline and molten phases  

Science Journals Connector (OSTI)

The results of molecular dynamics simulations of the crystalline and molten phase of anhydrous lithium acetate are presented. The potential parameters were obtained from empirical fitting to the crystalline phases of the material. The simulations were carried out for 216 molecules in an NPT ensemble using the DLPOLY program. A structural model is proposed for both the crystalline and molten phases of lithium acetate. Calculated values of the melting point, diffusion coefficient and structural parameters of lithium acetate are in reasonable agreement with experimental results.

L.S. Barreto; K.A. Mort; R.A. Jackson; O.L. Alves

2002-01-01T23:59:59.000Z

210

Ion-beam-induced epitaxial vapor-phase growth: A molecular-dynamics study  

Science Journals Connector (OSTI)

Low-energy ions which bombard a vapor-deposited film of low adatom mobility during growth mobilize surface atoms in the vicinity of the ion impact, causing a modification in the evolving microstructure. In a two-dimensional molecular-dynamics simulation where inert-gas ions strike a growing film of Lennard-Jones particles, it is demonstrated that ion bombardment during growth causes the filling of voids quenched in during vapor condensation and induces homoepitaxial growth. The dependence of film density and degree of homoepitaxial growth on the ion-to-vapor arrival rate ratio and ion energy is studied in detail.

Karl-Heinz Müller

1987-05-15T23:59:59.000Z

211

Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments  

SciTech Connect (OSTI)

Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at T{sub d} from the collective (?) structural relaxation rates of the solvation shell as input. By contrast, the secondary (?) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature T{sub g}. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature T{sub d}.

Doster, W. [Physik-Department, Technische Universität München, D-85748 Garching (Germany)] [Physik-Department, Technische Universität München, D-85748 Garching (Germany); Nakagawa, H. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany) [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany); Japan Atomic Energy Agency, Quantum Beam Science Directorate, Tokai, Ibaraki 319-1195 (Japan); Appavou, M. S. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany)] [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany)

2013-07-28T23:59:59.000Z

212

Water dynamical anomalies evidenced by molecular-dynamics simulations at the solvent-protein interface  

Science Journals Connector (OSTI)

We present a computer simulation picture of the dynamical behavior, at room temperature, of water in the region close to a protein surface. We analyzed the probability distribution of water molecules diffusing near the surface, and we found that it deviates from a Gaussian, which is predicted for Brownian particles. Consistently, the mean square displacements of water oxygens show a sublinear trend with time. Moreover, the relaxation of hydration layers around the whole protein is found to follow a stretched exponential decay, typical of complex systems, which could as well be ascribed to the non-Gaussian shape of the propagator. In agreement with such findings, the analysis of water translational and reorientational diffusion showed that not only are the solvent molecule motions hindered in the region close to the protein surface, but also the very nature of the particle diffusive processes, both translational and rotational, is affected. The deviations from the bulk water properties, which put into evidence a deep influence exerted by the protein on the solvent molecule motion, are discussed in connection with the presence of spatial (protein surface roughness) and temporal (distribution of water residence times) disorder inherent in the system.

Claudia Rocchi; Anna Rita Bizzarri; Salvatore Cannistraro

1998-03-01T23:59:59.000Z

213

A molecular dynamics simulation of DNA damage induction by ionizing radiation  

E-Print Network [OSTI]

We present a multi-scale simulation of early stage of DNA damages by the indirect action of hydroxyl ($^\\bullet$OH) free radicals generated by electrons and protons. The computational method comprises of interfacing the Geant4-DNA Monte Carlo with the ReaxFF molecular dynamics software. A clustering method was employed to map the coordinates of $^\\bullet$OH-radicals extracted from the ionization track-structures onto nano-meter simulation voxels filled with DNA and water molecules. The molecular dynamics simulation provides the time evolution and chemical reactions in individual simulation voxels as well as the energy-landscape accounted for the DNA-$^\\bullet$OH chemical reaction that is essential for the first principle enumeration of hydrogen abstractions, chemical bond breaks, and DNA-lesions induced by collection of ions in clusters less than the critical dimension which is approximately 2-3 \\AA. We show that the formation of broken bonds leads to DNA base and backbone damages that collectively propagate ...

Abolfath, Ramin M; Chen, Zhe J; Nath, Ravinder

2013-01-01T23:59:59.000Z

214

The peptide-receptive transition state of MHC-1 molecules: Insight from structure and molecular dynamics  

SciTech Connect (OSTI)

MHC class I (MHC-I) proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8(+) T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. In this study, we show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 3(10) helix that flips from an exposed 'open' position in the PR transition state to a 'closed' position with buried hydrophobic side chains in the peptide-loaded mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2L(d) MHC-I H chain, complexed with mAb 64-3-7, demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature peptide-loaded conformation, chaperone dissociation, and Ag presentation.

Robinson H.; Mage, M.; Dolan, M.; Wang, R.; Boyd, L.; Revilleza, M.; Natarajan, K.; Myers, N.; Hansen, T.; Margulies, D.

2012-05-01T23:59:59.000Z

215

E-Print Network 3.0 - allen byrnes md Sample Search Results  

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

, M.D., 1975 Sue K. Anderson, M.D., 1977 Terry Allen Boulware, M.D., 1977 William E. Stricker, M.D... BAMD program. We also accept students into MD-only and MDoral surgery...

216

Surface Hopping Excited-State Dynamics Study of the Photoisomerization of a Light-Driven Fluorene Molecular Rotary Motor  

Science Journals Connector (OSTI)

Surface Hopping Excited-State Dynamics Study of the Photoisomerization of a Light-Driven Fluorene Molecular Rotary Motor ... The potential energy surfaces of the ground electronic state (S0) and the first singlet excited state (S1) are explored by semiempirical quantum-chemical calculations using the orthogonalization-corrected OM2 Hamiltonian in combination with a multireference configuration interaction (MRCI) treatment. ... Photoswitching of simple photochromic molecules attracts substantial attention because of its possible role in future photon-driven molecular electronics. ...

Andranik Kazaryan; Zhenggang Lan; Lars V. Schäfer; Walter Thiel; Michael Filatov

2011-05-24T23:59:59.000Z

217

Molecular-dynamics simulation of compressible fluid flow in two-dimensional channels  

Science Journals Connector (OSTI)

We study compressible fluid flow in narrow two-dimensional channels using a molecular-dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream reservoir is kept at vacuum. The channel is sufficiently long in the direction of the flow that the finite length has little effect on the properties of the fluid in the central region. The simulated system is represented by an efficient data structure, whose internal elements are created and manipulated dynamically in a layered fashion. Consequently the computer code is highly efficient and manifests completely linear performance in simulations of large systems. We obtain the steady-state velocity, temperature, and density distributions in the system. The velocity distribution across the channel is very nearly a quadratic function of the distance from the center of the channel and reveals velocity slip at the boundaries; the temperature distribution is only approximately a quartic function of this distance from the center to the channel. The density distribution across the channel is nonuniform. We attribute this nonuniformity to the relatively high Mach number, approximately 0.5, in the fluid flow. An equation for the density distribution based on simple compressibility arguments is proposed; its predictions agree well with the simulation results. The validity of the concept of local dynamic temperature and the variation of the temperature along the channel are discussed.

M. Sun and C. Ebner

1992-10-15T23:59:59.000Z

218

Fast molecular-dynamics simulation for ferroelectric thin-film capacitors using a first-principles effective Hamiltonian  

Science Journals Connector (OSTI)

A newly developed fast molecular dynamics method is applied to BaTiO3 ferroelectric thin-film capacitors with short-circuited electrodes or under applied voltage. The molecular dynamics simulations based on a first-principles effective Hamiltonian clarify that dead layers (or passive layers) between ferroelectrics and electrodes markedly affect the properties of capacitors, and predict that the system is unable to hop between a uniformly polarized ferroelectric structure and a striped ferroelectric domain structure at low temperatures. Simulations of hysteresis loops of thin-film capacitors are also performed, and their dependence on film thickness, epitaxial constraints, and electrodes are discussed.

Takeshi Nishimatsu; Umesh V. Waghmare; Yoshiyuki Kawazoe; David Vanderbilt

2008-09-04T23:59:59.000Z

219

Interaction potential for SiO2: A molecular-dynamics study of structural correlations  

Science Journals Connector (OSTI)

An interaction potential consisting of two-body and three-body covalent interactions is proposed for SiO2. The interaction potential is used in molecular-dynamics studies of structural and dynamical correlations of crystalline, molten, and vitreous states under various conditions of densities and temperatures. The two-body contribution to the interaction potential consists of steric repulsion due to atomic sizes, Coulomb interactions resulting from charge transfer, and charge-dipole interaction to include the effects of large electronic polarizability of anions. The three-body covalent contributions include O-Si-O and Si-O-Si interactions which are angle dependent and functions of Si-O distance. In lattice-structure calculations with the total potential function, ?-cristobalite and ?-quartz are found to have the lowest and almost degenerate energies, in agreement with experiments. The energies for ?-cristobalite, ?-quartz, and keatite are found to be higher than those for ?-cristobalite and ?-quartz. Molecular-dynamics calculations with this potential function correctly describe the short- and intermediate-range order in molten and vitreous states.In the latter, partial pair-distribution functions give Si-O, O-O, and Si-Si bond lengths of 1.62, 2.65, and 3.05 Å, respectively. The vitreous state consists of nearly ideal Si(O1/2)4 tetrahedra in corner-sharing configurations. The Si-O-Si bond-angle distribution has a peak at 142° and a full width at half maximum (FWHM) of 25° in good agreement with nuclear magnetic resonance experiments. The calculated static structure factor is also in agreement with neutron-diffraction experiments. Partial static structure factors reveal that intermediate-range Si-Si, O-O, and Si-O correlations between 4 and 8 Å give rise to the first sharp diffraction peak (FSDP). The FSDP is absent in charge-charge structure factor, which indicates that charge neutrality prevails over length scales between 4 and 8 Å. Dynamical correlations in vitreous and molten states, phonon densities of states of crystalline and vitreous SiO2, infrared spectra of crystalline, vitreous and molten states, isotope effect, distribution of rings and their structure in molten and vitreous states, and structural transformations at high pressures will be discussed in subsequent papers.

P. Vashishta; Rajiv K. Kalia; José P. Rino; Ingvar Ebbsjö

1990-06-15T23:59:59.000Z

220

An Evaluation of Molecular Dynamics Performance on the Hybrid Cray XK6 Supercomputer  

SciTech Connect (OSTI)

For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little modification to existing codes. Engineering and electrical power constraints have disrupted this trend, requiring more drastic changes to both hardware and software solutions. Here, we present details of the Cray XK6 architecture that achieves increased performance with the use of GPU accelerators. We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers. We present benchmark results for solid-state, biological, and mesoscopic systems and discuss some challenges for utilizing hybrid systems. We present some early work in improving application performance on the XK6 and performance results for the simulation of liquid copper nanostructures with the embedded atom method.

Brown, W Michael [ORNL] [ORNL; Nguyen, Trung D [ORNL] [ORNL; Fuentes-Cabrera, Miguel A [ORNL] [ORNL; Fowlkes, Jason Davidson [ORNL] [ORNL; Rack, Philip D [ORNL] [ORNL; Berger, Mark [NVIDIA, Santa Clara, CA] [NVIDIA, Santa Clara, CA

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Cancer Genesis and Progression as Dynamics in Functional Landscape of Endogenous Molecular-Cellular Network  

E-Print Network [OSTI]

An endogenous molecular-cellular network for both normal and abnormal functions is assumed to exist. This endogenous network forms a nonlinear stochastic dynamical system, with many stable attractors in its functional landscape. Normal or abnormal robust states can be decided by this network in a manner similar to the neural network. In this context cancer is hypothesized as one of its robust intrinsic states. This hypothesis implies that a nonlinear stochastic mathematical cancer model is constructible based on available experimental data and its quantitative prediction is directly testable. Within such model the genesis and progression of cancer may be viewed as stochastic transitions between different attractors. Thus it further suggests that progressions are not arbitrary. Other important issues on cancer, such as genetic vs epigenetics, double-edge effect, dormancy, are discussed in the light of present hypothesis. A different set of strategies for cancer prevention, cure, and care, is therefore suggested.

P. Ao; D. Galas; L. Hood; X. -M. Zhu

2007-09-05T23:59:59.000Z

222

Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions  

E-Print Network [OSTI]

The effect of interfacial slip on steady-state and time-periodic flows of monatomic liquids is investigated using non-equilibrium molecular dynamics simulations. The fluid phase is confined between atomically smooth rigid walls, and the fluid flows are induced by moving one of the walls. In steady shear flows, the slip length increases almost linearly with shear rate. We found that the velocity profiles in oscillatory flows are well described by the Stokes flow solution with the slip length that depends on the local shear rate. Interestingly, the rate dependence of the slip length obtained in steady shear flows is recovered when the slip length in oscillatory flows is plotted as a function of the local shear rate magnitude. For both types of flows, the friction coefficient at the liquid-solid interface correlates well with the structure of the first fluid layer near the solid wall.

Nikolai V. Priezjev

2012-08-27T23:59:59.000Z

223

First-principles molecular-dynamics study of the (0001) ?-quartz surface  

Science Journals Connector (OSTI)

We present an ab initio investigation of the structural and electronic properties of the (0001) ?-quartz surface. Five different models of this surface are generated by cleavage of the bulk followed by atomic relaxation and constant-temperature molecular dynamics. The most favorable reconstruction presents an unexpected densification of the two uppermost layers of SiO2 tetrahedral units, with three-membered and six-membered rings that do not exist in bulk ?-quartz. The electronic density of states for this surface is very similar to the bulk one, except for a typical feature of SiO2 under pressure, namely the disappearance of the gap between Si-O bonding and O 2p nonbonding states.

G.-M. Rignanese; Alessandro De Vita; J.-C. Charlier; X. Gonze; Roberto Car

2000-05-15T23:59:59.000Z

224

Molecular dynamics investigations of boron doping in a-Si:H  

SciTech Connect (OSTI)

The rather low doping efficiency of B in a-Si:H is almost always explained by the argument that almost all of the B is incorporated into three-fold coordinated sites and that B is inert or non-doping in this configuration. Using ab initio molecular dynamics, the authors have studied the energetics and doping (electronic structure) consequences of B incorporation into a-Si:H both with and without H passivation. Their results suggest that the conventional view is in error and that the low doping efficiency is primarily due to H passivation. These results are consistent with the low doping efficiency of B as well as NMR studies on the large electric field gradients experienced by the B atoms and on NMR double resonance studies of B-H neighboring distances.

Fedders, P.A.; Drabold, D.A.

1997-07-01T23:59:59.000Z

225

Fabrication of nanopores in a graphene sheet with heavy ions: A molecular dynamics study  

SciTech Connect (OSTI)

Molecular dynamics simulations were performed to study the formation process of nanopores in a suspended graphene sheet irradiated by using energetic ions though a mask. By controlling the ion parameters including mass, energy, and incident angle, different kinds of topography were observed in the graphene sheet. Net-like defective structures with carbon atom chains can be formed at low ion fluences, which provide the possibility to functionalize the irradiated sample with subsequent chemical methods; finally a perfect nanopore with smooth edge appears when the ion fluence is high enough. We found that the dependence of ion damage efficiency on ion fluence, energy, and incident angle are different from that predicted by the semi-empirical model based on the binary-collision approximation, which results from the special structure of graphene. Our results demonstrate that it is feasible to fabricate controlled nanopores/nanostructures in graphene via heavy ion irradiation.

Li, Weisen; Liang, Li; Zhang, Shuo [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871 (China)] [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871 (China); Zhao, Shijun [Center for Applied Physics and Technology, Peking University, Beijing 100871, People's Republic China (China)] [Center for Applied Physics and Technology, Peking University, Beijing 100871, People's Republic China (China); Xue, Jianming [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871 (China) [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871 (China); Center for Applied Physics and Technology, Peking University, Beijing 100871, People's Republic China (China)

2013-12-21T23:59:59.000Z

226

The Melting Temperature of Bulk Silicon from ab initio Molecular Dynamics Simulations  

SciTech Connect (OSTI)

We estimated a melting temperature of Tm ~ 1540 ± 90 K at zero pressure for silicon from constant enthalpy and constant pressure (NPH) Born-Oppenheimer Molecular Dynamics (BOMD) simulations of a coexisting crystalline-liquid phase. The computed Tm is below the experimental melting point of 1685 K, but it is consistent with a previously predicted first-order liquid-liquid phase transition (LLPT) at a critical point Tc ~ 1232 K and Pc ~ - 12kB [Ganesh and Widom, Phys. Rev. Lett. 102, 075701 (2009)], which is in a highly supercooled state. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Chemical Sciences program. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

Yoo, Soohaeng; Xantheas, Sotiris S.; Zeng, Xiao Cheng

2009-10-19T23:59:59.000Z

227

Molecular simulations of the fluctuating conformational dynamics of intrinsically disordered proteins  

Science Journals Connector (OSTI)

Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP ?-synuclein that include geometric, attractive hydrophobic, and screened electrostatic interactions and are calibrated to the inter-residue separations measured in recent single-molecule fluorescence energy transfer (smFRET) experiments. We find that ?-synuclein is disordered, with conformational statistics that are intermediate between random walk and collapsed globule behavior. An advantage of calibrated molecular simulations over constraint methods is that physical forces act on all residues, not only on residue pairs that are monitored experimentally, and these simulations can be used to study oligomerization and aggregation of multiple ?-synuclein proteins that may precede amyloid formation.

W. Wendell Smith; Carl F. Schreck; Nabeem Hashem; Sherwin Soltani; Abhinav Nath; Elizabeth Rhoades; Corey S. O’Hern

2012-10-12T23:59:59.000Z

228

Superionicity in the hydrogen storage material Li2NH: Molecular dynamics simulations  

Science Journals Connector (OSTI)

We have employed ab initio molecular dynamics simulations in an attempt to study a temperature-induced order-disorder structural phase transformation that occurs in Li2NH at about 385 K. A structural phase transition was observed by us in the temperature range 300–400 K, in good agreement with experiment. This transition is associated with a melting of the cation sublattice (Li+), giving rise to a superionic phase, which in turn is accompanied by an order-disorder transition of the N-H bond orientation. The results obtained here can contribute to a better understanding of the hydrogen storage reactions involving Li2NH and furthermore broaden its possible technological applications toward batteries and fuel cells.

C. Moysés Araújo; Andreas Blomqvist; Ralph H. Scheicher; Ping Chen; Rajeev Ahuja

2009-05-08T23:59:59.000Z

229

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

230

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

231

Atomistic mechanisms of amorphization during nanoindentation of SiC: A molecular dynamics study  

Science Journals Connector (OSTI)

Atomistic mechanisms underlying the nanoindentation-induced amorphization in SiC crystal has been studied by molecular dynamics simulations on parallel computers. The calculated load-displacement curve consists of a series of load drops, corresponding to plastic deformation, in addition to a shoulder at a smaller displacement, which is fully reversible upon unloading. The peaks in the load-displacement curve are shown to reflect the crystalline structure and dislocation activities under the surface. The evolution of indentation damage and defect accumulation are also discussed in terms of bond angles, local pressure, local shear stress, and spatial rearrangements of atoms. These structural analyses reveal that the defect-stimulated growth and coalescence of dislocation loops are responsible for the crystalline-to-amorphous transition. The shortest-path-ring analysis is effectively employed to characterize nanoindentation-induced structural transformations and dislocation activities.

Izabela Szlufarska; Rajiv K. Kalia; Aiichiro Nakano; Priya Vashishta

2005-05-26T23:59:59.000Z

232

Glass transition line in C60: a mode-coupling/molecular-dynamics study  

E-Print Network [OSTI]

We report a study of the mode-coupling theory (MCT) glass transition line for the Girifalco model of C60 fullerene. The equilibrium static structure factor of the model, the only required input for the MCT calculations, is provided by molecular dynamics simulations. The glass transition line develops inside the metastable liquid-solid coexistence region and extends down in temperature, terminating on the liquid sideof the metastable portion of the liquid-vapor binodal. The vitrification locus does not show re-entrant behavior. A comparison with previous computer simulation estimates of the location of the glass line suggests that the theory accurately reproduces the shape of the arrest line in the density-temperature plane. The theoretical HNC and MHNC structure factors (and consequently the corresponding MCT glass line) compare well with the numerical counterpart. These evidences confirm the conclusion drawn in previous works about the existence of a glassy phase for the fullerene model at issue.

D. Costa; R. Ruberto; F. Sciortino; M. C. Abramo; C. Caccamo

2007-03-22T23:59:59.000Z

233

Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo  

E-Print Network [OSTI]

Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in excellent agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.

Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro

2014-01-01T23:59:59.000Z

234

Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo  

E-Print Network [OSTI]

Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in excellent agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.

Andrea Zen; Ye Luo; Guglielmo Mazzola; Leonardo Guidoni; Sandro Sorella

2014-12-09T23:59:59.000Z

235

Ab initio Molecular Dynamics and Elastic Properties of TiC and TiN Nanoparticles A. V. Postnikov and P. Entel  

E-Print Network [OSTI]

Ab initio Molecular Dynamics and Elastic Properties of TiC and TiN Nanoparticles A. V. Postnikov composition and compared to frozen phonon and molecular dynamics calculations for crystalline TiC and Ti range of frequencies, including the phonon band gap of pure crystalline TiC (near 15 THz). Similar

Entel, P.

236

Community Academic Profile Jon D. Fuller, MD  

E-Print Network [OSTI]

-1987 University of Utah School of Medicine MD Salt Lake City, Utah 1979-1983 University of Wyoming BS with honors-2001 Education & Community Professional Education Fellowship, Charles A. Dana. Foundation Fellowship Laramie, Wyoming Zoology/Physiology PROFESSIONAL TRAINING 1992-1993 Stanford University Charles A. Dana

Ford, James

237

Community Academic Profile Mina Charon, MD  

E-Print Network [OSTI]

.S., University of California, Davis, CA, 1992 Community & International Work RotaCare Free Clinic in Mountain View, CA Scientific Focus Publications Charon, M. Chapter on Yucca roots. In: Rotblatt MD, Ziment I Treadmill Testing · Medical staff scheduling VOLUNTEER: · RotaCare Free Clinic in Mountain View, California

Ford, James

238

Heart Valve Disease James S. Gammie, MD  

E-Print Network [OSTI]

Heart Valve Disease James S. Gammie, MD Professor and Chief Division of Cardiac Surgery University USA Source: CDC #12;#12;CARDIOTHORACIC SURGEON: A SURGEON THAT TREATS HEART AND LUNG DISEASE #12;Valvular Heart Disease: Common and Under-diagnosed 0 2 4 6 8 10 12 14 18 - 44 45 - 54 55 - 64 65 - 74 > 75

Weber, David J.

239

Strategic Plan Update Lydia Pleotis Howell MD  

E-Print Network [OSTI]

diagnostic testing that is tailored to the prevention and management of disease. 4. Develop a culture....where are we at and what have we accomplished?? #12; Maximized resources, efficiency and effectiveness CultureStrategic Plan Update 2014-2015 Lydia Pleotis Howell MD Professor and Chair Pathology

Leistikow, Bruce N.

240

Strategic Plan Update Lydia Pleotis Howell MD  

E-Print Network [OSTI]

diagnostic testing that is tailored to the prevention and management of disease. 4. Develop a culture....where are we at and what have we accomplished?? #12; Maximized resources, efficiency and effectiveness CultureStrategic Plan Update 2013-2014 Lydia Pleotis Howell MD Professor and Chair Pathology

Leistikow, Bruce N.

Note: This page contains sample records for the topic "molecular dynamics md" 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

Marylee M. Rothschild, MD Louisville, Kentucky  

E-Print Network [OSTI]

, which results in respiratory problems from indoor air pollution as well as burns. HELPS has installed Brookfield, Wisconsin Daniel L. Wegg, MD Winchester, Indiana Brett A. Wyrick, DO Hilo, Hawaii Solomon Adu the health effects of the stove program through a comparison of medical diagnoses before and after

242

An unusual dimeric structure and assembly for TLR4 regulator RP105?MD-1  

SciTech Connect (OSTI)

RP105-MD-1 modulates the TLR4-MD-2-mediated, innate immune response against bacterial lipopolysaccharide (LPS). The crystal structure of the bovine 1:1 RP105-MD-1 complex bound to a putative endogenous lipid at 2.9 {angstrom} resolution shares a similar overall architecture to its homolog TLR4-MD-2 but assembles into an unusual 2:2 homodimer that differs from any other known TLR-ligand assembly. The homodimer is assembled in a head-to-head orientation that juxtaposes the N-terminal leucine-rich repeats (LRRs) of the two RP105 chains, rather than the usual tail-to-tail configuration of C-terminal LRRs in ligand-activated TLR dimers, such as TLR1-TRL2, TLR2-TLR6, TLR3-TLR3 and TLR4-TLR4. Another unusual interaction is mediated by an RP105-specific asparagine-linked glycan, which wedges MD-1 into the co-receptor binding concavity on RP105. This unique mode of assembly represents a new paradigm for TLR complexes and suggests a molecular mechanism for regulating LPS responses.

Yoon, Sung-il; Hong, Minsun; Wilson, Ian A (Scripps)

2011-11-16T23:59:59.000Z

243

Molecular Dynamics Simulation of Heat Transfer Issues of Nanotubes. > Yasuhiro Igarashi, Yuki Taniguchi, Yasushi Shibuta and Shigeo Maruyama  

E-Print Network [OSTI]

Molecular Dynamics Simulation of Heat Transfer Issues of Nanotubes. ·> Yasuhiro Igarashi, Yuki 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Heat transfer between single-walled carbon nanotubes, which was 0.105 µm. In other words, when the length of SWNT is 0.105 µm, the radial heat transfer

Maruyama, Shigeo

244

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

245

Anisotropic Motion and Molecular Dynamics of Cholesterol, Lanosterol, and Ergosterol in Lecithin Bilayers Studied by Quasi-elastic Neutron Scattering  

E-Print Network [OSTI]

Bilayers Studied by Quasi-elastic Neutron Scattering Emil Endress, Helmut Heller,§ He´le`ne CasaltaVised Manuscript ReceiVed June 27, 2002 ABSTRACT: Quasi-elastic neutron scattering (QENS) was employed to study of motion within the bilayer on the molecular dynamics time scale. In a recent quasi-elastic neutron

Brown, Michael F.

246

The initial stages of bioglass dissolution: a Car–Parrinello molecular-dynamics study of the glass–water interface  

Science Journals Connector (OSTI)

...doi:10.1021/jp805206z ) Car, R. , and M. Parrinello1985Unified...amorphous silica surfaces:a Car-Parrinello simulation studyJ...multicomponent silicate glasses:Car-Parrinello molecular dynamics...layers on defect-free and defective anatase TiO2(101) surfacesJ...

2011-01-01T23:59:59.000Z

247

Friction anisotropy at Ni,,100...,,100... interfaces: Molecular dynamics studies Yue Qi and Yang-Tse Cheng  

E-Print Network [OSTI]

Friction anisotropy at Ni,,100...Ã?,,100... interfaces: Molecular dynamics studies Yue Qi and Yang of Technology, Pasadena, California, 91125 Received 8 March 2002; published 30 August 2002 The friction theories predict that most perfect clean incommensurate interfaces would produce no static friction

Goddard III, William A.

248

Solvation of Magnesium Dication: Molecular Dynamics Simulation and Vibrational Spectroscopic Study of Magnesium Chloride in Aqueous Solutions  

E-Print Network [OSTI]

Solvation of Magnesium Dication: Molecular Dynamics Simulation and Vibrational Spectroscopic Study of Magnesium Chloride in Aqueous Solutions Karen M. Callahan, Nadia N. Casillas-Ituarte, Martina Roeselova 26, 2010 Magnesium dication plays many significant roles in biochemistry. While it is available

249

Condensed phase spectroscopy from mixed-order semiclassical molecular dynamics: Absorption, emission, and resonant Raman spectra of I2  

E-Print Network [OSTI]

Condensed phase spectroscopy from mixed-order semiclassical molecular dynamics: Absorption, as a prototype of spectroscopy in condensed media in general. The method relies on constructing quantum correlations into system and bath are used to provide perspectives about condensed phase spectroscopy

Apkarian, V. Ara

250

Molecular Dynamics Simulations of End-to-End Contact Formation in Hydrocarbon Chains in Water and Aqueous Urea  

E-Print Network [OSTI]

Molecular Dynamics Simulations of End-to-End Contact Formation in Hydrocarbon Chains in Water is to probe contact formation between two ends of model hydrocarbon chains in water and 6 M aqueous urea "folding" event, namely, the formation of end-to-end contact in the linear hydrocarbon chain (HC) CH3(CH2

Thirumalai, Devarajan

251

Molecular dynamics simulation of shock induced ejection on fused silica surface  

SciTech Connect (OSTI)

Shock response and surface ejection behaviors of fused silica are studied by using non-equilibrium molecular dynamics combining with the Tersoff potential. First, bulk structure and Hugoniot curves of fused silica are calculated and compared with experimental results. Then, the dynamical process of surface ejection behavior is simulated under different loading velocities ranging from 3.5 to 5.0?km?s, corresponding to shock wave velocities from 7.1 to 8.8?km?s. The local atomistic shear strain parameter is used to describe the local plastic deformation under conditions of shock compression or releasing. Our result shows that the shear strain is localized in the bottom area of groove under the shock compression. Surface ejection is observed when the loading velocity exceeds 4.0?km?s. Meanwhile, the temperature of the micro-jet is ?5574.7?K, which is close to experiment measurement. Several kinds of structural defects including non-bridging oxygen are found in the bulk area of the sample after ejection.

Su, Rui [College of Physical Science and Technology, Sichuan University, Chengdu 610064 (China); Xiang, Meizhen; Jiang, Shengli [Institute of Applied Physics and Computational Mathematics, Beijing 100094 (China); Chen, Jun, E-mail: jun-chen@iapcm.ac.cn [Institute of Applied Physics and Computational Mathematics, Beijing 100094 (China); Center for Applied Physics and Technology, Peking University, Beijing 100087 (China); Wei, Han [Research Center of Laser Fusion, Mianyang 621900 (China)

2014-05-21T23:59:59.000Z

252

Molecular Dynamics Simulation of Cascade-Induced Ballistic Helium Resolutioning from Bubbles in Iron  

SciTech Connect (OSTI)

Molecular dynamics simulations have been used to assess the ability of atomic displacement cascades to eject helium from small bubbles in iron. This study of the ballistic resolutioning mechanism employed a recently-developed Fe-He interatomic potential in concert with an iron potential developed by Ackland and co-workers. The primary variables examined were: irradiation temperature (100 and 600K), cascade energy (5 and 20 keV), bubble radius (0.5 and 1.0 nm), and He-to-vacancy ratio in the bubble (0.25, 0.5 and 1.0). Systematic trends were observed for each of these variables. For example, ballistic resolutioning leads to a greater number of helium atoms being displaced from larger bubbles and from bubbles that have a higher He/vacancy ratio (bubble pressure). He resolutioning was reduced at 600K relative to 100K, and for 20 keV cascades relative to 5 keV cascades. Overall, the results indicate a modest level of He removal by ballistic resolutioning. The results can be used to provide guidance in selection of a resolution parameter that can be employed in cluster dynamics models to predict the bubble size distribution that evolves under irradiation.

Stoller, Roger E [ORNL] [ORNL

2013-01-01T23:59:59.000Z

253

Properties of gravitationally equilibrated Yukawa systems—A molecular dynamics study  

SciTech Connect (OSTI)

Using 2D Molecular Dynamics simulation, the equilibrium and dynamical properties of a gravitationally equilibrated Yukawa liquid are investigated. We observe that due to asymmetry introduced in one direction by gravity, several interesting features arise. For example, for a given value of coupling parameter ?, screening parameter ?, and according to a chosen value of gravitational force g (say in y-direction), the system is seen to exhibit super-, sub- or normal diffusion. Interestingly, x-averaged density profiles, unlike a barotropic fluid, acquires sharp, free surface with scale free linear y-dependence. As can be expected for a system with macroscopic gradients, self-diffusion calculated from Green-Kubo’s formalism does not agree with that obtained from Einstein-Smoluchowski diffusion. A 2D angular-radial pair correlation function g(r, ?) clearly indicates asymmetric features induced by gravity. We observe that due to compression in y-direction, though in liquid state for all values of gravity considered, the transverse mode is found to predominant as compared to the longitudinal mode, leading to a novel Anisotropic Solid-like Yukawa liquid.

Charan, Harish; Ganesh, Rajaraman, E-mail: ganesh@ipr.res.in; Joy, Ashwin [Institute for Plasma Research, Bhat-Village, Gujarat, Gandhinagar 382428 (India)] [Institute for Plasma Research, Bhat-Village, Gujarat, Gandhinagar 382428 (India)

2014-04-15T23:59:59.000Z

254

Molecular dynamics of shock-wave induced structural changes in silica glasses  

Science Journals Connector (OSTI)

We seek to model the shock wave induced structural changes in silicate glass at the atomic scale. We use both direct shock propagation with nonequilibrium molecular dynamics (NEMD) and bulk simulations in the Hugoniot ensemble to characterize the structure and topology of the shocked glass. Despite the lack of long-range interactions in our model, the close agreement between our structures and those obtained by experimental and simulation studies alike underlines the importance of the role played by first neighbor interactions on the structure of silicate glass. The results obtained from this study show that, in agreement with experimental work, the structure and topology of the shock-induced densified phase is unique in its structure as can be revealed by medium-range order measurements. The modifications include a reduction of the average tetrahedra size and an increase in the proportion of 3–4 and 8–10 membered Si-rings. Application of a Hugoniostat method based on constraint dynamics shows near-perfect agreement with the NEMD results. Besides validating the former method, this opens the prospect of studying shock-induced effects at a fraction of the cost required to run large scale shock simulations while using much more complicated potentials and setups.

F. Barmes; L. Soulard; M. Mareschal

2006-06-16T23:59:59.000Z

255

Chirped-pulse manipulated carrier dynamics in low-temperature molecular-beam-epitaxy grown GaAs  

SciTech Connect (OSTI)

Chirped pulse controlled carrier dynamics in low-temperature molecular-beam-epitaxy grown GaAs are investigated by degenerate pump-probe technique. Varying the chirped condition of excited pulse from negative to positive increases the carrier relaxation time so as to modify the dispersion and reshape current pulse in time domain. The spectral dependence of carrier dynamics is analytically derived and explained by Shockley-Read Hall model. This observation enables the new feasibility of controlling carrier dynamics in ultrafast optical devices via the chirped pulse excitations.

Lee, Chao-Kuei, E-mail: chuckcklee@yahoo.com [Department of Photonics, National Sun-Yat-Sen University, Kaohsiung 80400, Taiwan (China); Lin, Yuan-Yao [Department of Electrical Engineering, Institute of Photonics Technologies, National Tsing Hua University, Hsinchu 30010, Taiwan (China); Lin, Sung-Hui [Department of Photonics, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Lin, Gong-Ru [Department of Electrical Engineering, Graduate Institute of Photonics and Optoelectronics, National Taiwan University, No. 1, Roosevelt Road, Sec. 4, Taipei 10617, Taiwan (China); Pan, Ci-Ling [Department of Photonics, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Department of Physics, National Tsing Hwa University, Hsinchu 30010, Taiwan (China)

2014-04-28T23:59:59.000Z

256

Molecular-dynamics simulations of thin polyisoprene films confined between amorphous silica substrates  

SciTech Connect (OSTI)

Constant temperature–constant pressure (NpT) molecular-dynamics computer simulations have been carried out for the united-atom model of a non-crosslinked (1,4) cis-polyisoprene (PI) melt confined between two amorphous, fully coordinated silica surfaces. The Lennard-Jones 12-6 potential was implemented to describe the polymer–silica interactions. The thickness H of the produced PI–silica film has been varied in a wide range, 1 < H/R{sub g} < 8, where R{sub g} is the individual PI chain radius of gyration measured under the imposed confinement. After a thorough equilibration, the PI film stratified structure and polymer segmental dynamics have been studied. The chain structure in the middle of the films resembles that in a corresponding bulk, but the polymer-density profile shows a pronounced ordering of the polymer segments in the vicinity of silica surfaces; this ordering disappears toward the film middles. Tremendous slowing down of the polymer segmental dynamics has been observed in the film surface layers, with the segmental relaxation more than 150 times slower as compared to that in a PI bulk. This effect increases with decreasing the polymer-film thickness. The segmental relaxation in the PI film middles shows additional relaxation process which is absent in a PI bulk. Even though there are fast relaxation processes in the film middle, its overall relaxation is slower as compared to that in a bulk sample. The interpretation of the results in terms of polymer glassy bridges has been discussed.

Guseva, D. V., E-mail: d.v.guseva@tue.nl [Theory of Polymers and Soft Matter, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB, Eindhoven (Netherlands); Physics Department, Chair of Polymer and Crystal Physics, M. V. Lomonosov Moscow State University, 119991 Moscow (Russian Federation); Komarov, P. V. [Department of Theoretical Physics, Tver State University, Sadovyj per. 35, 170002 Tver, Russia and Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow (Russian Federation)] [Department of Theoretical Physics, Tver State University, Sadovyj per. 35, 170002 Tver, Russia and Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova st. 28, 119991 Moscow (Russian Federation); Lyulin, Alexey V. [Theory of Polymers and Soft Matter, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB, Eindhoven (Netherlands)] [Theory of Polymers and Soft Matter, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB, Eindhoven (Netherlands)

2014-03-21T23:59:59.000Z

257

TIME-DEPENDENT PROPERTIES OF LIQUID WATER: A COMPARISON OF CAR-PARRINELLO AND BORN-OPPENHIEMER MOLECULAR DYNAMICS SIMULATIONS  

SciTech Connect (OSTI)

A series of 30 ps first principles molecular dynamics simulations in the microcanonical ensemble were carried out to investigate transport and vibrational properties of liquid water. To allow for sufficient sampling, the thermodynamic constraints were set to an elevated temperature of around 423 K and a density of 0.71 g/cm{sup 3} corresponding to the saturated liquid density for the Becke-Lee-Yang-Parr (BLYP) representation of water. Four simulations using the Car-Parrinello molecular dynamics (CPMD) technique with varying values of the fictitious electronic mass ({mu}) and two simulations using the Born-Oppenheimer molecular dynamics (BOMD) technique are analyzed to yield structural and dynamical information. At the selected state point, the simulations are found to exhibit non-glassy dynamics and yield consistent results for the liquid structure and the self-diffusion coefficient, although the statistical uncertainties in the latter quantity are quite large. Consequently, it can be said that the CPMD and BOMD methods produce equivalent results for these properties on the time scales reported here. However, it was found that the choice of {mu} affects the frequency spectrum of the intramolecular modes, shifting them slightly to regions of lower frequency. Using a value of {mu} = 400 a.u. results in a significant drift in the electronic kinetic energy of the system over the course of 30 ps and a downward drift in the ionic temperature. Therefore, for long trajectories at elevated temperatures, lower values of this parameter are recommended for CPMD simulations of water.

Kuo, I W; Mundy, C; McGrath, M; Siepmann, J I

2005-12-29T23:59:59.000Z

258

DOE - Office of Legacy Management -- Johns Hopkins University - MD 02  

Office of Legacy Management (LM)

Johns Hopkins University - MD 02 Johns Hopkins University - MD 02 FUSRAP Considered Sites Site: JOHNS HOPKINS UNIVERSITY (MD.02 ) Eliminated from further consideration under FUSRAP Designated Name: Not Designated Alternate Name: None Location: Baltimore , Maryland MD.02-1 Evaluation Year: 1987 MD.02-2 Site Operations: Conducted spectroscopic studies under contract number AT(49-1)-309. MD.02-1 Site Disposition: Eliminated - Potential for contamination considered remote based on limited quantities of material used in a controlled environment MD.02-2 Radioactive Materials Handled: Yes Primary Radioactive Materials Handled: Tritium MD.02-1 Radiological Survey(s): None Indicated Site Status: Eliminated from further consideration under FUSRAP Also see Documents Related to JOHNS HOPKINS UNIVERSITY

259

E-Print Network 3.0 - alan menter md Sample Search Results  

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

MD (Chair) Psychiatry Psychiatry Marie Acierno, MD Ophthalmology... Ophthalmology David Smith, MD ... Source: Louisiana State University Health Sciences Center in New...

260

Non-Gaussian Fluctuation and Non-Markovian Effect in the Nuclear Fusion Process: Langevin Dynamics Emerging from Quantum Molecular Dynamics Simulations  

E-Print Network [OSTI]

Macroscopic parameters as well as precise information on the random force characterizing the Langevin type description of the nuclear fusion process are extracted from the microscopic dynamics of individual nucleons by exploiting the numerical simulation of the improved quantum molecular dynamics. It turns out that the dissipation dynamics of the relative motion between two fusing nuclei is caused by a non-Gaussian distribution of the random force. We find that the friction coefficient as well as the time correlation function of the random force takes particularly large values in a region a little bit inside of the Coulomb barrier. A clear non-Markovian effect is observed in the time correlation function of the random force. It is further shown that an emergent dynamics of the fusion process can be described by the generalized Langevin equation with memory effects by appropriately incorporating the microscopic information of individual nucleons through the random force and its time correlation function.

Wen, Kai; Li, Zhu-Xia; Wu, Xi-Zhen; Zhang, Ying-Xun; Zhou, Shan-Gui

2013-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Non-Gaussian Fluctuation and Non-Markovian Effect in the Nuclear Fusion Process: Langevin Dynamics Emerging from Quantum Molecular Dynamics Simulations  

E-Print Network [OSTI]

Macroscopic parameters as well as precise information on the random force characterizing the Langevin type description of the nuclear fusion process around the Coulomb barrier are extracted from the microscopic dynamics of individual nucleons by exploiting the numerical simulation of the improved quantum molecular dynamics. It turns out that the dissipation dynamics of the relative motion between two fusing nuclei is caused by a non-Gaussian distribution of the random force. We find that the friction coefficient as well as the time correlation function of the random force takes particularly large values in a region a little bit inside of the Coulomb barrier. A clear non-Markovian effect is observed in the time correlation function of the random force. It is further shown that an emergent dynamics of the fusion process can be described by the generalized Langevin equation with memory effects by appropriately incorporating the microscopic information of individual nucleons through the random force and its time correlation function.

Kai Wen; Fumihiko Sakata; Zhu-Xia Li; Xi-Zhen Wu; Ying-Xun Zhang; Shan-Gui Zhou

2013-05-02T23:59:59.000Z

262

Momentum imaging spectrometer for molecular fragmentation dynamics induced by pulsed electron beam  

SciTech Connect (OSTI)

A momentum imaging spectrometer has been built for studying the electron impact molecular fragmentation dynamics. The setup consists of a pulsed electron gun and a time of flight system as well as a two-dimensional time and position sensitive multi-hit detector. The charged fragments with kinetic energy up to 10 eV can be detected in 4? solid angles and their three-dimensional momentum vectors can be reconstructed. The apparatus is tested by electron impact ionization of Ar and dissociative ionization of CO{sub 2}. By analyzing the ion-ion coincidence spectra, the complete and incomplete Coulomb fragmentation channels for CO{sub 2}{sup 2+} and CO{sub 2}{sup 3+} are identified. The kinetic energy release (KER) and angular correlation for the two-body breakup channel CO{sub 2}{sup 2+*}? O{sup +}+ CO{sup +} are reported. The peak value of total KER is found to be 6.8 eV which is consistent with the previous photoion-photoion coincidence studies, and the correlation angle of O{sup +} and CO{sup +} is also explicitly determined to be 172.5°.

Wang, EnLiang; Shan, Xu; Shi, YuFeng; Tang, YaGuo; Chen, XiangJun [Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)] [Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

2013-12-15T23:59:59.000Z

263

Molecular Dynamic Simulation of Sodium in 7-Pin LMFBR Bundle Under Hypothetical Accident Conditions  

SciTech Connect (OSTI)

In the frame of safety analysis of liquid metal fast breeder reactors (LMFBRs) under hypothetical Unprotected Loss of Flow (ULOF) conditions two-phase flow of sodium is simulated in a 7-pin bundle, with hexagonal lattice. Molecular dynamics, with the application of the Direct Simulation Monte Carlo (DSMC) method, and a macroscopic model describing rewetting sequences due to the flow of a sodium liquid film along the pin surfaces, are applied to simulate the coolant in the bundle. The pin surfaces and the inner surface of the hexagonal canning are treated in the Monte Carlo simulation as diffusively reflecting surfaces. Collisions of sodium molecules are computed with the 'hard-sphere' model. With respect to previous work the following improvements of the computational code were made: i) The full bundle is simulated, thus allowing for asymmetries, like a skewed power distribution, to be accounted for; ii) A pin model calculates detailed temperature distributions in the pins, so that temperature boundary conditions are computed and not imposed; iii) Post processing visualisation of computed results was developed. An out of pile sodium boiling experiment run at the Nuclear Research Center of Karlsruhe, Germany, is simulated and conclusions are drawn about the applicability of the methodology in computer codes dedicated to breeder reactors safety analysis. (authors)

Bottoni, Maurizio [University of Ferrara, Physics Department, Via Paradiso 12, I-44100 Ferrara (Italy); Bottoni, Claudio; Scanu, John [University of Pisa, Lungarno Pacinotti, 43 - 56126 Pisa (Italy)

2006-07-01T23:59:59.000Z

264

Molecular dynamics simulation of elevated temperature interfacial behavior between silica glass and a model crystal  

SciTech Connect (OSTI)

Elevated temperature atomistic behavior was investigated using classical molecular dynamics simulations of solid state interfaces. Initially, observations on a Lennard-Jones (LJ) crystal surface interfaced with an ideal vacuum were made. Assignment of temperatures associated with specific amounts of crystal surface disorder was possible. A temperature was observed at and above which disorder propagated through all planes of mobile atoms, making it possible to establish an approximate transition temperature for surface nucleated melting of the LJ crystal. Similar high temperature simulations were then performed on silica glass/LJ crystal interfaces at two system stress levels. No significant dependence of interface behavior on the stress states which were studied was observed. The presence of the glass surface resulted in a depression of the temperature needed for the surface most planes of crystal atoms to roughen. This allowed LJ atoms to sample and occupy sites in the glass surface. Additional data presented shows this behavior was at least partly a function of the open structure inherent in glassy oxide surfaces. {copyright} {ital 1996 American Institute of Physics.}

Webb, E.B. III; Garofalini, S.H. [Department of Ceramics, Interfacial Molecular Science Laboratory, Rutgers University, Piscataway, New Jersey 08855 (United States)] [Department of Ceramics, Interfacial Molecular Science Laboratory, Rutgers University, Piscataway, New Jersey 08855 (United States)

1996-07-01T23:59:59.000Z

265

Structural and elastic properties of a confined 2D colloidal solid: a molecular dynamics study  

E-Print Network [OSTI]

We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This system can describe colloidal particles at the air-water interface. It is shown that the system characteristics depend sensitively on the boundary conditions at the two {\\it walls} providing the confinement. The walls exert perpendicular forces on their adjacent particles. The potential between walls and particles varies as the inverse power of ten. Structural quantities such as density profile, structure factor and orientational order parameter are computed. It is shown that orientational order persists near the walls even at temperatures where the system in the bulk is in fluid state. The dependence of elastic constants, stress tensor elements, shear and bulk modulii on density as well as the channel width is discussed. Moreover, the effect of channel incommensurability with the triangular lattice structure is discussed. It is shown that incommensurability notably affects the system properties. We compare our findings to those obtained by Monte Carlo simulations and also to the case with the periodic boundary condition along the channel width. .

M. Ebrahim Foulaadvand; Neda Ojaghlou

2014-09-27T23:59:59.000Z

266

Molecular Dynamics Modeling of Ion Adsorption to the Basal Surfaces of Kaolinite  

SciTech Connect (OSTI)

Molecular dynamics simulation is used to study the mechanisms involved in the adsorption of various ions to the basal surfaces of kaolinite. Analysis of simulation data indicates that cations and anions adsorb preferably on the siloxane and gibbsite surfaces of kaolinite, respectively. Strong inner-sphere adsorption of chlorine at aluminum vacancies on the gibbsite surface and the occurrence of chlorine-driven inner-sphere adsorption of cesium and sodium on the gibbsite surface for high ionic strengths are observed. Cesium ions form strong inner-sphere complexes at ditrigonal cavities on the siloxane surface. Outer-sphere cesium is highly mobile and only weak adsorption may occur. A small amount of sodium adsorbs on the siloxane surface as inner-sphere complexes at less clearly defined sites. Like cesium, sodium only forms very weak outer-sphere complexes on this surface. Inner-sphere complexes of cadmium and lead do not occur on either surface. Relatively strong outer-sphere cadmium and lead complexes are present on the siloxane surface at ditrigonal cavities.

Vasconcelos, Igor F.; Bunker, Bruce A.; Cygan, Randall T. (Sandia); (Notre)

2008-06-06T23:59:59.000Z

267

Molecular dynamics simulation study on surface structure and surface energy of anatase  

Science Journals Connector (OSTI)

Molecular dynamics simulations were performed to investigate the relaxed structures and surface energies of perfect and pit anatase TiO2 surfaces. It is shown that the slab containing more than two unit-cell layers away from the fixed layer expresses the surface characteristics of perfect anatase TiO2 (1?0?1) and (1?0?0) surfaces well, while the slab containing more than one unit-cell layer away from the fixed layer expresses the surface characteristics of the (0?0?1) surface well. Their surface energies follow the sequence (0?0?1) ] and [0?1?0] directions, and the changes in their surface energies are less than 0.05?J?m?2, while the surface energies increase sharply with the increase in pit depth within 1?nm. Therefore, for anatase (1?0?1) surface, in order to obtain a higher surface energy, one may increase the pit sizes, particularly along the [1?0?1] direction.

Dai-Ping Song; Ming-Jun Chen; Ying-Chun Liang; Chun-Ya Wu; Zhi-Jiang Xie; Qing-Shun Bai

2010-01-01T23:59:59.000Z

268

Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding  

E-Print Network [OSTI]

The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations that build out the transition state is particularly cumbersome, mainly because of the large computational cost of generating a statistically-sound set of folding trajectories. Here we show that a biasing algorithm, based on the physics of the ratchet-and-pawl, can be used to identify efficiently the transition state. The basic idea is that the algorithmic ratchet exerts a force on the protein when it is climbing the free-energy barrier, while it is inactive when it is descending. The transition state can be identified as the point of the trajectory where the ratchet changes regime. Besides discussing this strategy in general terms, we test it within a protein model whose transition state can be studied independently by plain molecular dynamics simulations. Finally, we show its power in explicit-solvent simulations, obtaining and characterizing a set of transition--state conformations for ACBP and CI2.

Guido Tiana; Carlo Camilloni

2012-07-05T23:59:59.000Z

269

Molecular dynamics simulations of the melting curve of NiAl alloy under pressure  

SciTech Connect (OSTI)

The melting curve of B2-NiAl alloy under pressure has been investigated using molecular dynamics technique and the embedded atom method (EAM) potential. The melting temperatures were determined with two approaches, the one-phase and the two-phase methods. The first one simulates a homogeneous melting, while the second one involves a heterogeneous melting of materials. Both approaches reduce the superheating effectively and their results are close to each other at the applied pressures. By fitting the well-known Simon equation to our melting data, we yielded the melting curves for NiAl: 1783(1 + P/9.801){sup 0.298} (one-phase approach), 1850(1 + P/12.806){sup 0.357} (two-phase approach). The good agreement of the resulting equation of states and the zero-pressure melting point (calc., 1850 ± 25 K, exp., 1911 K) with experiment proved the correctness of these results. These melting data complemented the absence of experimental high-pressure melting of NiAl. To check the transferability of this EAM potential, we have also predicted the melting curves of pure nickel and pure aluminum. Results show the calculated melting point of Nickel agrees well with experiment at zero pressure, while the melting point of aluminum is slightly higher than experiment.

Zhang, Wenjin; Peng, Yufeng [College of Physics and electronic Engineering, Henan Normal University, Xinxiang, 453007 (China)] [College of Physics and electronic Engineering, Henan Normal University, Xinxiang, 453007 (China); Liu, Zhongli, E-mail: zhongliliu@yeah.net [College of Physics and Electric Information, Luoyang Normal University, Luoyang, 471002 (China)] [College of Physics and Electric Information, Luoyang Normal University, Luoyang, 471002 (China)

2014-05-15T23:59:59.000Z

270

Oxidation of ligand-protected aluminum clusters: An ab initio molecular dynamics study  

SciTech Connect (OSTI)

We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O{sub 2} molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O{sub 2} diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material.

Alnemrat, Sufian; Hooper, Joseph P., E-mail: jphooper@nps.edu [Department of Physics, Naval Postgraduate School, Monterey, California 93943 (United States)

2014-03-14T23:59:59.000Z

271

Molecular dynamics simulations of damage production by thermal spikes in Ge  

SciTech Connect (OSTI)

Molecular dynamics simulation techniques are used to analyze damage production in Ge by the thermal spike process and to compare the results to those obtained for Si. As simulation results are sensitive to the choice of the inter-atomic potential, several potentials are compared in terms of material properties relevant for damage generation, and the most suitable potentials for this kind of analysis are identified. A simplified simulation scheme is used to characterize, in a controlled way, the damage generation through the local melting of regions in which energy is deposited. Our results show the outstanding role of thermal spikes in Ge, since the lower melting temperature and thermal conductivity of Ge make this process much more efficient in terms of damage generation than in Si. The study is extended to the modeling of full implant cascades, in which both collision events and thermal spikes coexist. Our simulations reveal the existence of bigger damaged or amorphous regions in Ge than in Si, which may be formed by the melting and successive quenching induced by thermal spikes. In the particular case of heavy ion implantation, defect structures in Ge are not only bigger, but they also present a larger net content in vacancies than in Si, which may act as precursors for the growth of voids and the subsequent formation of honeycomb-like structures.

Lopez, Pedro; Pelaz, Lourdes; Santos, Ivan; Marques, Luis A.; Aboy, Maria [Departamento de Electricidad y Electronica, Universidad de Valladolid, E.T.S.I. Telecomunicacion, Valladolid 47011 (Spain)

2012-02-01T23:59:59.000Z

272

On the performance of molecular dynamics applications on current high-end systems  

Science Journals Connector (OSTI)

...exploitation of current high performance computing (HPC) platforms in molecular...capability computing|high performance computing| 1. Introduction Molecular...places increasing demands on high performance computing (HPC) resources. A vast...

2005-01-01T23:59:59.000Z

273

DOE - Office of Legacy Management -- Maryland Disposal Site - MD 05  

Office of Legacy Management (LM)

Maryland Disposal Site - MD 05 Maryland Disposal Site - MD 05 FUSRAP Considered Sites Site: MARYLAND DISPOSAL SITE (MD.05 ) Eliminated from consideration under FUSRAP Designated Name: Not Designated Alternate Name: None Location: Baltimore - Vicinity , Maryland MD.05-1 Evaluation Year: 1989 MD.05-1 Site Operations: Proposed disposal site - never developed. MD.05-1 Site Disposition: Eliminated Radioactive Materials Handled: None Indicated Primary Radioactive Materials Handled: None Indicated Radiological Survey(s): None Indicated Site Status: Eliminated from consideration under FUSRAP Also see Documents Related to MARYLAND DISPOSAL SITE MD.05-1 - Report (DOE/OR/20722-131 Revision 0); Site Plan for the Maryland Disposal Site; April 1989 Historical documents may contain links which are no longer valid or to

274

Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature  

SciTech Connect (OSTI)

In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C{sub 60} collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C{sub 60} impact on the Si surface is in good agreement with our experimental findings.

Taioli, Simone [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Physics, University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Perugia (Italy); Department of Chemistry, University of Bologna, Bologna (Italy); Garberoglio, Giovanni [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Simonucci, Stefano [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Perugia (Italy); Department of Physics, University of Camerino, Camerino (Italy); Beccara, Silvio a [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Physics, University of Trento, Trento (Italy); Aversa, Lucrezia [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Trento (Italy); Nardi, Marco [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Trento (Italy); Institut fuer Physik, Humboldt-Universitaet zu Berlin, Berlin (Germany); Verucchi, Roberto [Institute of Materials for Electronics and Magnetism, FBK-CNR, Trento (Italy); Iannotta, Salvatore [Institute of Materials for Electronics and Magnetism, IMEM-CNR, Parma (Italy); Dapor, Maurizio [Interdisciplinary Laboratory for Computational Science, FBK-Center for Materials and Microsystems and University of Trento, Trento (Italy); Department of Materials Engineering and Industrial Technologies, University of Trento, Trento (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Padova (Italy); and others

2013-01-28T23:59:59.000Z

275

Local Depolarization in Hydrophobic and Hydrophilic Ionic Liquids/Water Mixtures: Car–Parrinello and Classical Molecular Dynamics Simulation  

Science Journals Connector (OSTI)

Local Depolarization in Hydrophobic and Hydrophilic Ionic Liquids/Water Mixtures: Car–Parrinello and Classical Molecular Dynamics Simulation ... Their analysis of the molecular electrostatic properties compared with the previous work on smaller number of ion pairs per unit cell shows that the immediate liquid environment predominantly affects the molecular electric dipole moments, whereas the bulk contributions appear to be minor. ... The ion-pair/water interaction energy (Einter), which is defined as the difference between the energy of the ion pair and water system (EIL-W) and the sum of the energies of the single ion pair (EIL) and water (EW), can be calculated by:(1)Each complex and corresponding water and anion were optimized for structure and energy at the B3LYP/6-311++G(d,p) level of theory by the above computational procedure. ...

Mohammad Hadi Ghatee; Amin Reza Zolghadr

2013-01-08T23:59:59.000Z

276

Molecular Beam and Surface Science Studies of Heterogeneous Reaction Kinetics Including Combustion Dynamics. Final Technical Report.  

SciTech Connect (OSTI)

This research program examined the heterogeneous reaction kinetics and reaction dynamics of surface chemical processes which are of direct relevance to efficient energy production, condensed phase reactions, and mateials growth including nanoscience objectives. We have had several notable scientific and technical successes. Illustrative highlights include: (1) a thorough study of how one can efficiently produce synthesis gas (SynGas) at relatively low Rh(111) catalyst temperatures via the reaction CH{sub4}+1/2 O{sub2} {r_arrow} CO+2H{sub2}. In these studies methane activation is accomplished utilizing high-kinetic energy reagents generated via supersonic molecular beams, (2) experiments which have incisively probed the partial oxidation chemistry of adsorbed 1- and 2- butene on Rh and ice, as well as partial oxidation of propene on Au; (3) investigation of structural changes which occur to the reconstructed (23x{radical}3)-Au(111) surface upon exposure to atomic oxygen, (4) a combined experimental and theoretical examination of the fundamental atomic-level rules which govern defect minimization during the formation of self-organizing stepped nanostructures, (5) the use of these relatively defect-free nanotemplates for growing silicon nanowires having atomically-dimensioned widths, (6) a combined scanning probe and atomic beam scattering study of how the presence of self-assembling organic overlayers interact with metallic supports substrates - this work hs led to revision of the currently held view of how such adsorbates reconfigure surface structure at the atomic level, (7) an inelastic He atom scattering study in which we examined the effect of chain length on the low-energy vibrations of alkanethiol striped phase self-assembled monolayers on Au(111), yielding information on the forces that govern interfacial self-assembly, (8) a study of the vibrational properties of disordered films of SF{sub6} adsorbed on Au(111), and (9) a study of the activated chemistry and photochemistry of NO on NiO/Ni. Innovative STM and molecular beam instrumentation has been fabricated to enable this program.

Sibener, S. J.

2006-06-23T23:59:59.000Z

277

Lithium Ion Transport Mechanism in Ternary Polymer Electrolyte-Ionic Liquid Mixtures - A Molecular Dynamics Simulation Study  

E-Print Network [OSTI]

The lithium transport mechanism in ternary polymer electrolytes, consisting of PEO/LiTFSI and various fractions of the ionic liquid N-methyl-N-propylpyrrolidinium bis(trifluoromethane)sulfonimide, are investigated by means of MD simulations. This is motivated by recent experimental findings [Passerini et al., Electrochim. Acta 2012, 86, 330-338], which demonstrated that these materials display an enhanced lithium mobility relative to their binary counterpart PEO/LiTFSI. In order to grasp the underlying microscopic scenario giving rise to these observations, we employ an analytical, Rouse-based cation transport model [Maitra at al., PRL 2007, 98, 227802], which has originally been devised for conventional polymer electrolytes. This model describes the cation transport via three different mechanisms, each characterized by an individual time scale. It turns out that also in the ternary electrolytes essentially all lithium ions are coordinated by PEO chains, thus ruling out a transport mechanism enhanced by the presence of ionic-liquid molecules. Rather, the plasticizing effect of the ionic liquid contributes to the increased lithium mobility by enhancing the dynamics of the PEO chains and consequently also the motion of the attached ions. Additional focus is laid on the prediction of lithium diffusion coefficients from the simulation data for various chain lengths and the comparison with experimental data, thus demonstrating the broad applicability of our approach.

Diddo Diddens; Andreas Heuer

2012-11-14T23:59:59.000Z

278

Final technical report [ACCELERATED MOLECULAR DYNAMICS SIMULATIONS OF REACTIVE HYDROCARBON SYSTEMS  

SciTech Connect (OSTI)

The research activities in this project consisted of four different sub-projects. Three different accelerated dynamics techniques (parallel replica dynamics, hyperdynamics, and temperature-accelerated dynamics) were applied to the modeling of pyrolysis of hydrocarbons. In addition, parallel replica dynamics was applied to modeling of polymerization.

Stuart, Steven J.

2014-02-25T23:59:59.000Z

279

Computer Simulation of Diffusion of Pb-Bi Eutectic in Liquid Sodium by Molecular Dynamics Method  

SciTech Connect (OSTI)

Lead-bismuth eutectic is a potential candidate for coolant of secondary loops of sodium-cooled fast breeder reactors (FBR). The studies on the diffusion of liquid Pb-Bi in liquid Na are carried out corresponding to the case that liquid Pb-Bi leaks to liquid Na by accident. As the diffusion processes are the results of atomic motions, molecular dynamics method has been used to study the diffusion process. The self-diffusion coefficients of pure liquid Pb and Na, and liquid Pb-Bi are calculated and compared with ones by the empirical equations. The discrepancy between them could be eliminated by changing the densities of the liquids. The diffusion of lead-bismuth in sodium is simulated based on the changed densities under which the self-diffusion coefficients of individual liquid metals are close to those by the empirical equations. The simulation results show that the diffusion process of liquid Pb-Bi in liquid Na is a heat releasing process and the density of ternary liquid Na-Pb-Bi is higher than the average value of the densities of liquid Na and liquid Pb-Bi. It is also found that the diffusion coefficients of liquid Pb-Bi in liquid Na are much higher than their self-diffusion coefficients, indicating that liquid Pb-Bi are easy and quickly to diffuse in liquid Na. However, the diffusion coefficient of liquid Na is decreased due to the existence of liquid Pb-Bi, implying that liquid Na-Pb-Bi have a higher viscosity than that of pure liquid Na. (authors)

Yingxia Qi; Minoru Takahashi [Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550 (Japan)

2002-07-01T23:59:59.000Z

280

Time-resolved diffraction profiles and atomic dynamics in short-pulse laser-induced structural transformations: Molecular dynamics study  

E-Print Network [OSTI]

Time-resolved diffraction profiles and atomic dynamics in short-pulse laser-induced structural dynamics simulations of a 20 nm Au film irradiated with 200 fs laser pulses of different intensity in time-resolved x-ray and electron diffraction experiments. Three processes are found to be responsible

Zhigilei, Leonid V.

Note: This page contains sample records for the topic "molecular dynamics md" 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

Theoretical Design by First Principles Molecular Dynamics of a Bioinspired Electrode?Catalyst System for Electrocatalytic Hydrogen Production from Acidified Water  

Science Journals Connector (OSTI)

Our study is based on Car?Parrinello (CP)(26) FPMD simulations of the [FeFe]H cluster in a liquid-water environment with or without hydronium ions. ... To achieve these results, we have employed the first principles molecular dynamics method at an advanced level of system complexity and have illustrated thereby the utility and power of FPMD for molecular design. ...

Federico Zipoli; Roberto Car; Morrel H. Cohen; Annabella Selloni

2010-09-29T23:59:59.000Z

282

E-Print Network 3.0 - ab-initio molecular dynamics Sample Search...  

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

continuum models) investigate... -Lung Tsai, "Calculation of Thermophysical Properties of CO2 Gas Using an Ab Initio Potential Model... -Lung Tsai, "Molecular ... Source: Ragsdell,...

283

Phenomenology of Psychogenic Movement Disorders in Children Joseph Ferrara, MD and Joseph Jankovic, MD  

E-Print Network [OSTI]

Phenomenology of Psychogenic Movement Disorders in Children Joseph Ferrara, MD and Joseph Jankovic little has been published regarding the frequency and phenomenology of PMDs in children. We reviewed (61) 14 (26) 7 (13) Objective: To assess the frequency and phenomenology of psychogenic movement

Lichtarge, Olivier

284

Molecular Cell Genome-wide Consequences  

E-Print Network [OSTI]

,2 Margaret Dayhoff-Brannigan,3 Wen-Chih Cheng,2 Catherine E. Gilbert,1,2 Cierra N. Sing,2 Nicola L. Diny,2, Baltimore, MD 21205, USA 2W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns

Dunham, Maitreya

285

DOE - Office of Legacy Management -- Max Zuckerman and Sons Inc - MD 04  

Office of Legacy Management (LM)

Inc - MD 04 Inc - MD 04 FUSRAP Considered Sites Site: MAX ZUCKERMAN & SONS, INC. (MD.04 ) Eliminated from consideration under FUSRAP Designated Name: Not Designated Alternate Name: Maryland Alloys Corporation MD.04-1 Location: 5245 Fairlawn Avenue , Baltimore , Maryland MD.04-2 Evaluation Year: 1994 MD.04-1 MD.04-3 Site Operations: Scrap metals broker that arranged purchases of materials for third party buyers. MD.04-2 MD.04-4 Site Disposition: Eliminated - Potential for contamination remote MD.04-3 Radioactive Materials Handled: Yes Primary Radioactive Materials Handled: Uranium (Q-11) Oxide/Residue MD.04-2 MD.04-4 Radiological Survey(s): Yes MD.04-1 Site Status: Eliminated from consideration under FUSRAP MD.04-3 Also see Documents Related to MAX ZUCKERMAN & SONS, INC.

286

Dynamics  

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

Hydration Hydration Water on Rutile Studied by Backscattering Neutron Spectroscopy and Molecular Dynamics Simulation E. Mamontov,* ,† D. J. Wesolowski, ‡ L. Vlcek, § P. T. Cummings, §,| J. Rosenqvist, ‡ W. Wang, ⊥ and D. R. Cole ‡ Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6473, Chemical Sciences DiVision, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, Department of Chemical Engineering, Vanderbilt UniVersity, NashVille, Tennessee 37235-1604, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6496, and EnVironmental Sciences DiVision, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6036 ReceiVed: December 20, 2007; ReVised Manuscript ReceiVed: June 4, 2008 The high energy resolution, coupled with the wide dynamic range, of the new backscattering

287

Ion Association in AlCl3 Aqueous Solutions from Constrained First-Principles Molecular Dynamics  

SciTech Connect (OSTI)

Ab initio molecular dynamics was used to investigate the ion pairing behavior between Cl- and the Al3+ ion in an aqueous AlCl3 solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, by fixing the inter-nuclear separation (rAl-Cl) between the Al3+ ion and one of the Cl- ions. The calculated potential of mean force of the Al3+-Cl- ion pair shows a pronounced minimum at rAl-Cl = 2.3 Å corresponding to a contact ion pair (CIP). Two local minima assigned to solvent separated ion pairs (SSIP) are identified at rAl-Cl= 4.4 and 6.0 Å. The positions of the free energy minima coincide with the hydration shell intervals of the Al3+ cation suggesting that the Cl- ion is inclined to reside in regions of low concentration of waters, i.e. between the 1st and 2nd shells of Al3+ and between the 2nd shell and bulk. A detailed analysis of solvent structure around the Al3+ and Cl- ions as a function of rAl-Cl is presented. The results are compared to structure data from X-ray measurements and unconstrained AIMD simulations of single ions Al3+ and Cl- and AlCl3 solutions. The dipole moment of the water molecules inside the 1st and 2nd hydration shells of Al3+ and in the bulk region and those of the Clion were calculated as a function of rAl-Cl. Major changes in the electronic structure of the system result from the removal of Cl- from the 1st hydration shell of the Al3+ cation. Finally, two unconstrained AIMD simulations of aqueous AlCl3 solutions corresponding to CIP and SSIP configurations were performed (17 ps, 300 K). Only minor structural changes are observed in these systems, confirming their stability.

Cauet, Emilie L.; Bogatko, Stuart A.; Bylaska, Eric J.; Weare, John H.

2012-10-15T23:59:59.000Z

288

Ab initio molecular dynamics investigations on the SN2 reactions of OH? with NH2F and \\{NH2Cl\\}  

Science Journals Connector (OSTI)

The bimolecular nucleophilic substitution (SN2) reactions of hydroxide anion (OH?) with fluoroamine (NH2F) and chloramine (NH2Cl) have been investigated with ab initio molecular dynamics simulations. For the SN2 reaction of OH? with NH2F, there are two main dynamic reaction pathways after passing the [HO···NH2···F]? barrier. The first one is that the [HO···NH2···F]? transition state directly dissociates to the products of F? and NH2OH without involving any dynamic intermediate complex, and on the contrary, the other one involves the dynamic hydrogen bond F?···H?NH?OH and/or F?···H?O?NH2 intermediate complexes. As to the SN2 reaction of OH? with NH2Cl, there is only one dominant dynamic reaction pathway, which leads to the products of Cl? and NH2OH directly. According to our calculations, the statistical theories including the Rice–Ramsperger–Kassel–Marcus (RRKM) theory and transition state (TS) theory cannot be utilized to model the reaction kinetics for these two SN2 reactions.

Feng Yu; Lei Song; Xiaoguo Zhou

2011-01-01T23:59:59.000Z

289

Transport properties of dense fluid mixtures using nonequilibrium molecular dynamics. Final report, September 15, 1987--March 14, 1997  

SciTech Connect (OSTI)

Computer Simulation Studies were carried out using the method of equilibrium and nonequilibrium molecular dynamics (NEMD) to examine a wide range of transport processes in both fluids and fluid mixtures. This included testing a wide range of mixing rules for thermal conductivity and viscosity. In addition a method was developed to calculate the internal rotational contributions to thermal conductivity and the accuracy of current methods for predicting these contributions were examined. These comparisons were then used to suggest possible ways of improving these theories. The method of NEMD was also used to examine the critical enhancements of thermal conductivity. Finally, molecular simulations were carried out to study the various transport coefficients of fluids confined by membranes, as well as important transport processes such as osmosis, and reverse osmosis.

Murad, S.

1997-05-01T23:59:59.000Z

290

Molecular Dynamics Study of Alkanethiolate Self-Assembled Monolayer coated Gold Nanoparticle  

Science Journals Connector (OSTI)

Through molecular simulations we have observed that the surface of gold nanoparticles become highly corrugated by the adsorption of alkanethiolate self- assembled monolayers (SAMs). Furthermore, as the temperature is increased, the SAMs dissolve into ...

B. Henz; M. Zachairah

2007-06-01T23:59:59.000Z

291

Nanoscale Graphene Disk: A Natural Functionally Graded Material --The Thermal Conductivity of Nanoscale Graphene Disk by Molecular Dynamics Simulation  

E-Print Network [OSTI]

In this letter, we investigate numerically (by non-equilibrium molecular dynamics) and analytically the thermal conductivity of nanoscale graphene disks (NGDs), and discussed the possibility to realize FGM with only one material, NGDs. We found that the NGD has a graded thermal conductivity and can be used as FGM in a large temperature range. Moreover, we show the dependent of NGDs' thermal conductivity on radius and temperature. Our study may inspire experimentalists to develop NGD based FGMs and help heat removal of hot spots on chips by graphene.

Yang, Nuo; Ma, Dengke; Lu, Tingyu; Li, Baowen

2014-01-01T23:59:59.000Z

292

Solvation Structure and Mobility Mechanism of OH-:? A Car?Parrinello Molecular Dynamics Investigation of Alkaline Solutions  

Science Journals Connector (OSTI)

Solvation Structure and Mobility Mechanism of OH-:? A Car?Parrinello Molecular Dynamics Investigation of Alkaline Solutions ... Figure 17 Comparison of power spectra derived from deuterium velocity autocorrelation functions for pure water (dashed lines in both panels a and b), KOD (panel a) at 1.3 M (solid line) and 14 M (dotted line), and NaOD (panel b) at 1.5 M (solid line), 4.5 M (diamonds), and 15 M (dotted line). ... energy structure on the potential energy surface, because the water drifts to become attached to one of the first solvation shell waters. ...

Bin Chen; Ivaylo Ivanov; Jung Mee Park; Michele Parrinello; Michael L. Klein

2002-10-24T23:59:59.000Z

293

Comparison of the Properties of Xenon, Methane, and Carbon Dioxide Hydrates from Equilibrium and Nonequilibrium Molecular Dynamics Simulations  

Science Journals Connector (OSTI)

Comparison of the Properties of Xenon, Methane, and Carbon Dioxide Hydrates from Equilibrium and Nonequilibrium Molecular Dynamics Simulations† ... The VACFs of all three guests in the small cages oscillate between positive and negative values with the oscillation being damped out with increasing time. ... The oscillations are damped much more strongly for CO2 hydrate than for the Xe or methane hydrates, indicating that the coupling between the rattling motions of the encaged guest molecules and the vibrational motions of the host lattice is strongest for CO2 hydrate. ...

H. Jiang; K. D. Jordan

2009-11-11T23:59:59.000Z

294

Solvent Dependence on Bond Length Alternation and Charge Distribution in Phenol Blue: A Car?Parrinello Molecular Dynamics Investigation  

Science Journals Connector (OSTI)

Solvent Dependence on Bond Length Alternation and Charge Distribution in Phenol Blue: A Car?Parrinello Molecular Dynamics Investigation ... (4) The probing nature of these molecules is due to the effect of the polarity of the solvation shell in changing the electron excitation energy of the indicator dye. ... (23) The usual theoretical approach to tune the bond length alternation was to apply a static electric field(20, 25) or to optimize the structure by placing “sparkles” (negative or positive ions) close to the donor or acceptor groups of these conjugated systems. ...

N. Arul Murugan; Zilvinas Rinkevicius; Hans Ågren

2009-04-02T23:59:59.000Z

295

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

296

Can xenon in water inhibit ice growth? Molecular dynamics of phase transitions in water$-$Xe system  

E-Print Network [OSTI]

Motivated by recent experiments showing the promise of noble gases as cryoprotectants, we perform molecular dynamics modeling of phase transitions in water with xenon under cooling. We study the structure and dynamics of xenon water solution as a function of temperature. Homogeneous nucleation of clathrate hydrate phase is observed and characterized. As the temperature is further reduced we observe hints of dissociation of clathrate due to stronger hydrophobic hydration, pointing towards a possible instability of clathrate at cryogenic temperatures and conversion to an amorphous phase comprised of "xenon + hydration shell" Xe$\\cdot$(H$_{2}$O)$_{21.5}$ clusters. Simulations of ice$-$xenon solution interface in equilibrium and during ice growth reveal the effects of xenon on the ice$-$liquid interface, where adsorbed xenon causes roughening of ice surface but does not preferentially form clathrate. These results provide evidence against the ice-blocker mechanism of xenon cryoprotection.

Vasilii I. Artyukhov; Alexander Yu. Pulver; Alex Peregudov; Igor Artyuhov

2014-07-11T23:59:59.000Z

297

Structural investigation of liquid acetic acid by neutron scattering, DFT calculations and molecular dynamics simulations. Complementarity to x-ray scattering results  

Science Journals Connector (OSTI)

Abstract Neutron scattering experiments have been performed on fully deuterated liquid acetic acid (AA) at room temperature and atmospheric pressure. The scattering data are analyzed to yield the structure factor SM(Q), the molecular form factor F1(Q) and the pair correlation function g(r). To describe the intermolecular arrangement of the liquid, we have considered two dimers and two trimers, involving the isomer cis, already described in our x-ray scattering study. Neutron scattering data show that the local order of the liquid is well described by linear and ring cis trimers. Complementarity with recent x-ray results is then highlighted. Using four force fields, MD simulations show that x-ray and neutron scattering data are better reproduced by both OPLS-AA1 and OPLS-AA2 potentials.

Sonia Fathi; Salah Bouazizi; Sahbi Trabelsi; Miguel Angel Gonzalez; Mohamed Bahri; Salah Nasr; Marie-Claire Bellissent-Funel

2014-01-01T23:59:59.000Z

298

On the use of a Born-Oppenheimer type separation in the treatment of the dynamics of molecular collisions  

Science Journals Connector (OSTI)

The Born-Oppenheimer separation, commonly invoked in electronic/nuclear motions, is extended to separate the motions of light and heavy nuclei in the dynamics of molecular collisions. The method is applied to various heavy-light + heavy (hl + h) systems where the light atom is either H or D. The hydrogenic wavefunctions, which describe the motion of the light nucleus for clamped heavy nuclei, are found to have bonding, anti-bonding or non-bonding properties depending on the localisation of the light nucleus. The Born-Oppenheimer approximation is valid for quasi-diabatic states which maintain the localisation property, when the distance between the heavy nuclei changes. A small number of these states support quasi-bound states of the triatomic systems, which appear as resonances in the dynamics. The quasi-diabatic states can be used to explain the dynamics of light atom exchange in hl + h collisions and of dissociative photodetachment of the (hlh)? anion. The method is shown to give very accurate results and to allow for a clear understanding of the dynamics.

C. Kubach; N. Rougeau

1998-01-01T23:59:59.000Z

299

Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions, and Molecular Sizes  

E-Print Network [OSTI]

Dynamics of Single-Molecule Rotations on Surfaces that Depend on Symmetry, Interactions new nanoscale devices and materials. However, mechanisms of motion of these rotors at the single-molecule dynamics simulations and simple models to investigate what factors influence single-molecule rotations

300

Molecular vibration demonstrations  

Science Journals Connector (OSTI)

Molecular vibration demonstrations ... Two dynamic models that illustrate the normal-mode vibrations of the water and benzene molecules. ...

George Turrell; Robert Demol

1987-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Influence of ensemble boundary conditions (thermostat and barostat) on the deformation of amorphous polyethylene by molecular dynamics  

E-Print Network [OSTI]

Molecular dynamics simulations are increasingly being used to investigate the structural evolution of polymers during mechanical deformation, but relatively few studies focus on the influence of boundary conditions on this evolution, in particular the dissipation of both heat and pressure through the periodic boundaries during deformation. The research herein explores how the tensile deformation of amorphous polyethylene, modelled with a united atom method potential, is influenced by heat and pressure dissipation. The stress-strain curves for the pressure dissipation cases (uniaxial tension) are in qualitative agreement with experiments and show that heat dissipation has a large effect on the strain hardening modulus calculated by molecular dynamics simulations. The evolution of the energy associated with bonded and non-bonded terms was quantified as a function of strain as well as the evolution of stress in both the loading and non-loading directions to give insight into how the stress state is altered within the elastic, yield, strain softening, and strain hardening regions. The stress partitioning shows a competition between `tensile' Van der Waal's interactions and `compressive' bond stretching forces, with the characteristic yield stress peak clearly associated with the non-bonded stress. The lack of heat dissipation had the largest effect on the strain hardening regime, where an increase in the calculated temperature correlated with faster chain alignment in the loading direction and more rapid conformation changes. In part, these observations demonstrate the role that heat and pressure dissipation play on deformation characteristics of amorphous polymers, particularly for the strain hardening regime.

M. A. Tschopp; J. L. Bouvard; D. K. Ward; D. J. Bammann; M. F. Horstemeyer

2013-10-02T23:59:59.000Z

302

Short-and intermediate-range structural correlations in amorphous silicon carbide: A molecular dynamics study  

E-Print Network [OSTI]

Short- and intermediate-range structural correlations in amorphous silicon carbide: A molecular-range structural correlations in amorphous silicon carbide a-SiC are studied in terms of partial pair distributions.43.Dq, 61.43.Bn, 61.66.Dk, 81.05.Gc I. INTRODUCTION Silicon carbide SiC has been receiving increasing

Southern California, University of

303

Exceptional tools for studying the structure and dynamics of materials at the molecular level  

E-Print Network [OSTI]

to differentiate complex molecular structures. #12;09-G00911/arm Neutron Scattering Educational Resources ORNL is home to the Neutron Scattering portion of the National School on Neutron and X-ray Scattering (NXS/Optics · Powder Diffraction · Quasi-elastic Neutron Scattering · Magnetic Scattering · Small Angle Scat

304

Aqueous solutions: state of the art in ab initio molecular dynamics  

Science Journals Connector (OSTI)

...recent work by Car and co-workers...contributions to the free energy landscape of water...the g(r) (R. Car 2012, personal...charged by the applied electric field. He imagined...reactive potential energy surfaces using Car-Parrinello molecular...

2014-01-01T23:59:59.000Z

305

Molecular Dynamics Simulations: Methods and Value in the Folding Problem Devon Chandler-Brown  

E-Print Network [OSTI]

March 2013 Introduction The protein folding has been an outstanding problem in molecular biology for a long period of time. Stated simply, the question of protein folding is that of how the primary amino that govern protein folding are thought to be well established. Forces driven by ionic, Van der Waals

306

DOE - Office of Legacy Management -- Armco-Rustless Iron and Steel - MD 03  

Office of Legacy Management (LM)

Armco-Rustless Iron and Steel - MD Armco-Rustless Iron and Steel - MD 03 FUSRAP Considered Sites Site: Armco-Rustless Iron & Steel (MD.03 ) Eliminated from consideration under FUSRAP Designated Name: Not Designated Alternate Name: ARMCO Baltimore Works MD.03-1 Location: Baltimore , Maryland MD.03-2 Evaluation Year: 1987 MD.03-1 Site Operations: Test rolling of uranium billets. MD.03-2 MD.03-3 Site Disposition: Eliminated - Potential for contamination remote due to limited quantity of material and duration of test MD.03-1 Radioactive Materials Handled: Yes Primary Radioactive Materials Handled: Uranium MD.03-2 Radiological Survey(s): Health and safety monitoring conducted during operations MD.03-2 Site Status: Eliminated from consideration under FUSRAP MD.03-1 Also see

307

Serial Intraoperative MR Imaging of Brain Shift Arya Nabavi, M.D.1  

E-Print Network [OSTI]

Serial Intraoperative MR Imaging of Brain Shift Arya Nabavi, M.D.1 , Peter McL. Black, M.D. Ph.D.1 , David T. Gering, M.S.4 , Carl-Fredrik Westin, Ph.D3 , Vivek Mehta, M.D.1 , Richard S. Pergolizzi Jr., M, M.D., Ph.D.2 , William M. Wells III, Ph.D4 ., Ron Kikinis, M.D.3 , Ferenc A. Jolesz, M.D.3 1

308

Incoherent Quasielastic Neutron Scattering Study of Molecular dynamics of 4-n-cyano-4'-octylbiphenyl  

E-Print Network [OSTI]

We report incoherent quasielastic neutron scattering experiments on the thermotropic liquid crystal 4-n-cyano-4'-octylbiphenyl. The combination of time-of-flight and backscattering data allows analyzing the intermediate scattering function over about three decades of relaxation times. Translational diffusion and uniaxial molecular rotations are clearly identified as the major relaxation processes in respectively the nanosecond and picosecond time scales. The comparison with literature data obtained by other techniques is discussed.

Ronan Lefort; Denis Morineau; Régis Guégan; Claude Ecolivet; Mohammed Guendouz; Jean-Marc Zanotti; Bernhard Frick

2008-04-10T23:59:59.000Z

309

Computational Improvements to Quantum Wave Packet ab Initio Molecular Dynamics Using a Potential-Adapted,  

E-Print Network [OSTI]

for several dynamical methodologies in gas-phase1 and condensed-phase quantum mechanics.2 The Born-Adapted, Time-Dependent Deterministic Sampling Technique Jacek Jakowski, Isaiah Sumner, and Srinivasan S, we overcome this problem through the use of a time-dependent deterministic sampling measure

Iyengar, Srinivasan S.

310

Gas Phase Reaction with FT-ICR and Molecular Dynamics Simulation of Precursor Clusters for SWNTs  

E-Print Network [OSTI]

of the random cage delayed the annealing of the cage. Number of Carbon Atoms Intensity(arbitrary) NiC38 ­ CoC38 dynamics simulations of metal-containing carbon cluster formation were performed. Metal-carbon binary clusters were generated by the laser vaporization of Ni/Co or Ni/Y loaded carbon materials used

Maruyama, Shigeo

311

Molecular simulations of beta-amyloid protein near hydrated lipids (PECASE).  

SciTech Connect (OSTI)

We performed molecular dynamics simulations of beta-amyloid (A{beta}) protein and A{beta} fragment(31-42) in bulk water and near hydrated lipids to study the mechanism of neurotoxicity associated with the aggregation of the protein. We constructed full atomistic models using Cerius2 and ran simulations using LAMMPS. MD simulations with different conformations and positions of the protein fragment were performed. Thermodynamic properties were compared with previous literature and the results were analyzed. Longer simulations and data analyses based on the free energy profiles along the distance between the protein and the interface are ongoing.

Thompson, Aidan Patrick; Han, Kunwoo (Texas A& M University, College Station, TX); Ford, David M. (Texas A& M University, College Station, TX)

2005-12-01T23:59:59.000Z

312

Effects of boron-nitride substrates on Stone-Wales defect formation in graphene: An ab initio molecular dynamics study  

SciTech Connect (OSTI)

Ab initio molecular dynamics simulations are performed to investigate the effects of a boron nitride (BN) substrate on Stone-Wales (SW) defect formation and recovery in graphene. It is found that SW defects can be created by an off-plane recoil atom that interacts with the BN substrate. A mechanism with complete bond breakage for formation of SW defects in suspended graphene is also revealed for recoils at large displacement angles. In addition, further irradiation can result in recovery of the SW defects through a bond rotation mechanism in both graphene and graphene/BN, and the substrate has little effect on the recovery process. This study indicates that the BN substrate enhances the irradiation resistance of graphene.

Jin, K.; Xiao, H. Y. [Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States); Zhang, Y. [Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States); Weber, W. J., E-mail: wjweber@utk.edu [Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States); Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States)

2014-05-19T23:59:59.000Z

313

Biased interface between solid ion conductor LiBH{sub 4} and lithium metal: A first principles molecular dynamics study  

SciTech Connect (OSTI)

We use first-principles molecular dynamics to study the electrochemical solid-solid interface between lithium metal and lithium electrolyte LiBH{sub 4}. An external bias is applied by using an effective screening medium. We observe large polarization in the LiBH{sub 4}, because the lithium cations in LiBH{sub 4} are shifted more on one side of the double-well potential of Li{sup +}. This results in a large potential drop in the interface region and a large double-layer capacity corresponding to ca. 70 ?F/cm{sup 2}. H-coordination to the Li atoms plays an important role in the charge-transfer reaction and ion transfer.

Ikeshoji, Tamio [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan) [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan); Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568 (Japan); Ando, Yasunobu; Otani, Minoru; Tsuchida, Eiji [Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568 (Japan)] [Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568 (Japan); Takagi, Shigeyuki; Matsuo, Motoaki [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan)] [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan); Orimo, Shin-ichi [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan) [Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan); WPI-Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan)

2013-09-23T23:59:59.000Z

314

Cisplatin Binding to DNA Oligomers from Hybrid Car-Parrinello/Molecular Dynamics Simulations  

Science Journals Connector (OSTI)

The first-principles calculations are carried out with the Car-Parrinello approach,52 which has proven to reliably describe structure, dynamics, and electronic properties of platinum?nucleotide complexes in the solid state53 as well as in water solution. ... There are more than three waters in the first solvation shell of AM1. ... The predictive power of our computational setup was investigated by constructing a structural model of platinated DNA. ...

Katrin Spiegel; Ursula Rothlisberger; Paolo Carloni

2004-01-29T23:59:59.000Z

315

Dynamic molecular structure of plant biomass-derived black carbon (biochar)  

SciTech Connect (OSTI)

Char black carbon (BC), the solid residue of incomplete combustion, is continuously being added to soils and sediments due to natural vegetation fires, anthropogenic pollution, and new strategies for carbon sequestration ('biochar'). Here we present a molecular-level assessment of the physical organization and chemical complexity of biomass-derived chars and, specifically, that of aromatic carbon in char structures. BET-N{sub 2} surface area, X-ray diffraction (XRD), synchrotron-based Near-edge X-ray Absorption Fine Structure (NEXAFS), and Fourier transform infrared (FT-IR) spectroscopy are used to show how two plant materials (wood and grass) undergo analogous, but quantitatively different physical-chemical transitions as charring temperature increases from 100 to 700 C. These changes suggest the existence of four distinct categories of char consisting of a unique mixture of chemical phases and physical states: (i) in transition chars the crystalline character of the precursor materials is preserved, (ii) in amorphous chars the heat-altered molecules and incipient aromatic polycondensates are randomly mixed, (iii) composite chars consist of poorly ordered graphene stacks embedded in amorphous phases, and (iv) turbostratic chars are dominated by disordered graphitic crystallites. The molecular variations among the different char categories translate into differences in their ability to persist in the environment and function as environmental sorbents.

Keiluweit, M.; Nico, P.S.; Johnson, M.G.; Kleber, M.

2009-11-15T23:59:59.000Z

316

The 1st International Symposium on Micro & Nano Technology, 14-17 March, 2004, Honolulu, Hawaii, USA MOLECULAR DYNAMICS SIMULATIONS OF HEAT TRANSFER ISSUES  

E-Print Network [OSTI]

, USA MOLECULAR DYNAMICS SIMULATIONS OF HEAT TRANSFER ISSUES IN CARBON NANOTUBES S. Maruyama, Y-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, JAPAN ABSTRACT Several heat transfer problems related to single, and thermal boundary resistance in a junction of nanotubes are reviewed. Then, the heat transfer from an SWNT

Maruyama, Shigeo

317

Molecular dynamics simulations of hydrogen bombardment of tungsten carbide surfaces P. Trskelin,1 N. Juslin,1 P. Erhart,2 and K. Nordlund1  

E-Print Network [OSTI]

Molecular dynamics simulations of hydrogen bombardment of tungsten carbide surfaces P. Träskelin,1 and tungsten carbide WC is of interest both due to the use of hydrogen-containing plasmas in thin. INTRODUCTION Tungsten carbide WC exhibits extraordinary hardness and temperature resistance. It has long been

Nordlund, Kai

318

On the Mechanisms of OH Radical Induced DNA-Base Damage:? A Comparative Quantum Chemical and Car?Parrinello Molecular Dynamics Study  

Science Journals Connector (OSTI)

We present a detailed Car?Parrinello molecular dynamics study of DNA bases in explicit water interacting with an OH radical. ... Thus, we choose to compute the power spectrum of guanine in the gas phase and in the presence of 21 and 56 waters. ...

Yudong Wu; Christopher J. Mundy; Michael E. Colvin; Roberto Car

2004-02-25T23:59:59.000Z

319

Vibrational Sum Frequency Spectroscopy and Molecular Dynamics Simulation of the Carbon Tetrachloride-Water and 1,2-Dichloroethane-Water Interfaces  

E-Print Network [OSTI]

and bonding at the carbon tetrachloride-water (CCl4-H2O) and the 1,2-dichloroethane-water (DCE-H2O) liquidVibrational Sum Frequency Spectroscopy and Molecular Dynamics Simulation of the Carbon Tetrachloride-Water and 1,2-Dichloroethane-Water Interfaces Dave S. Walker, Fred G. Moore, and Geraldine L

Richmond, Geraldine L.

320

Hybrid DFT Functional-Based Static and Molecular Dynamics Studies of Excess Electron in Liquid Ethylene Carbonate  

SciTech Connect (OSTI)

We applied static and dynamic hybrid functional density functional theory (DFT) calculations to study the interactions of one and two excess electrons with ethylene carbonate (EC) liquid and clusters. Optimal structures of (EC){sub n} and (EC){sup ?}{sub n} clusters devoid of Li{sub +} ions, n?=?1–6, were obtained. The excess electron was found to be localized on a single EC in all cases, and the EC dimeric radical anion exhibits a reduced barrier associated with the breaking of the ethylene carbon–oxygen covalent bond compared to EC{sub ?}. In ab initio molecular dynamics (AIMD) simulations of EC{sub ?} solvated in liquid EC, large fluctuations in the carbonyl carbon–oxygen bond lengths were observed. AIMD simulations of a two-electron attack on EC in EC liquid and on Li metal surfaces yielded products similar to those predicted using nonhybrid DFT functionals, except that CO release did not occur for all attempted initial configurations in the liquid state.

Yu, J M; Balbuena, P B; Budzien, J L; Leung, Kevin

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Terrigal Burn MD Lean Physician Champion  

E-Print Network [OSTI]

Scientific reductionism is not definitive: dynamic, adaptive and interrelated systems, models of individuals of the processes of work, and the processes that support those processes, to support the people who create value for the patient (caregivers) 11 #12;lean six sigma Continuous improvement Process improvement The xx Way

Soloveichik, David

322

Molecular Dynamics Investigation of Adhesion between TATB Surfaces and Amorphous Fluoropolymers  

SciTech Connect (OSTI)

Atomistic simulations are used to study the adhesion properties of amorphous perfluoro- and fluoro-polymers onto two different crystal surfaces of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Properties of the bulk amorphous polymer melts are also investigated. The fluoropolymers studied in this article include Kel-F 800, Teflon{reg_sign} AF, Hyflon AD{reg_sign}, and Cytop{reg_sign}. Simulations of the bulk polymer melts were performed over a wide range of temperatures including the volumetric glass transition temperature, so as to validate the interaction parameters used. The computed glass transition temperatures and densities compare well with experiment. The solubility parameters for the various polymers also compare well with calculations based on group additive methods. The local molecular structure at the TATB interface, as well as the degree of adhesion varies from one polymer to another. All polymers except Hyflon show a propensity to readily wet the two TATB surfaces studied.

Gee, R H; Maiti, A; Bastea, S; Fried, L

2007-01-25T23:59:59.000Z

323

Circularly Polarized X Rays: Another Probe of Ultrafast Molecular Decay Dynamics  

SciTech Connect (OSTI)

Dissociative nuclear motion in core-excited molecular states leads to a splitting of the fragment Auger lines: the Auger-Doppler effect. We present here for the first time experimental evidence for an Auger-Doppler effect following F1s{yields}a{sub 1g}* inner-shell excitation by circularly polarized x rays in SF{sub 6}. In spite of a uniform distribution of the dissociating S-F bonds near the polarization plane of the light, the intersection between the subpopulation of molecules selected by the core excitation with the cone of dissociation induces a strong anisotropy in the distribution of the S-F bonds that contributes to the scattering profile measured in the polarization plane.

Travnikova, Oksana; Lindblad, Andreas; Nicolas, Christophe; Soederstroem, Johan; Kimberg, Victor; Miron, Catalin [Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, B.P. 48, F-91192 Gif-sur-Yvette Cedex (France); Liu Jicai; Gel'mukhanov, Faris [Department of Theoretical Chemistry, Roslagstullsbacken 15, Royal Institute of Technology, S-106 91 Stockholm (Sweden)

2010-12-03T23:59:59.000Z

324

Nonlinear Relaxation Dynamics in Elastic Networks and Design Principles of Molecular Machines  

E-Print Network [OSTI]

Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these motions are robust against external perturbations. We show that this behavior is not characteristic for random elastic networks. However, special network architectures with such properties can be designed by evolutionary optimization methods. Using them, an example of an artificial elastic network, operating as a cyclic machine powered by ligand binding, is constructed.

Yuichi Togashi; Alexander S. Mikhailov

2007-05-17T23:59:59.000Z

325

Structural Evolution of Polylactide Molecular Bottlebrushes: Kinetics Study by Size Exclusion Chromatography, Small Angle Neutron Scattering and Simulations  

SciTech Connect (OSTI)

Structural evolution from poly(lactide) (PLA) macromonomer to resultant PLA molecular bottlebrush during ring opening metathesis polymerization (ROMP) was investigated for the first time by combining size exclusion chromatography (SEC), small-angle neutron scattering (SANS) and coarse-grained molecular dynamics (CG-MD) simulations. Multiple aliquots were collected at various reaction times during ROMP, and subsequently analyzed by SEC and SANS. The two complementary techniques enable the understanding of systematic changes in conversion, molecular weight and dispersity as well as structural details of PLA molecular bottlebrushes. CG-MD simulation not only predicts the experimental observations, but it also provides further insight into the analysis and interpretation of data obtained in SEC and SANS experiments. We find that PLA molecular bottlebrushes undergo three conformational transitions with increasing conversion (i.e., increasing the backbone length): (1) from an elongated to a globular shape due to longer side chain at lower conversion, (2) from a globular to an elongated shape at intermediate conversion caused by excluded volume of PLA side chain, and (3) the saturation of contour length at higher conversion due to chain transfer reactions.

Pickel, Deanna L [ORNL; Kilbey, II, S Michael [ORNL; Uhrig, David [ORNL; Hong, Kunlun [ORNL; Carrillo, Jan-Michael Y [ORNL; Sumpter, Bobby G [ORNL; Ahn, Suk-Kyun [ORNL; Han, Youngkyu [ORNL; Kim, Dr. Tae-Hwan [Korea Atomic Energy Research Institute; Smith, Gregory Scott [ORNL; Do, Changwoo [ORNL

2014-01-01T23:59:59.000Z

326

Non-adiabatic molecular dynamics with complex quantum trajectories. II. The adiabatic representation  

SciTech Connect (OSTI)

We present a complex quantum trajectory method for treating non-adiabatic dynamics. Each trajectory evolves classically on a single electronic surface but with complex position and momentum. The equations of motion are derived directly from the time-dependent Schroedinger equation, and the population exchange arises naturally from amplitude-transfer terms. In this paper the equations of motion are derived in the adiabatic representation to complement our work in the diabatic representation [N. Zamstein and D. J. Tannor, J. Chem. Phys. 137, 22A517 (2012)]. We apply our method to two benchmark models introduced by John Tully [J. Chem. Phys. 93, 1061 (1990)], and get very good agreement with converged quantum-mechanical calculations. Specifically, we show that decoherence (spatial separation of wavepackets on different surfaces) is already contained in the equations of motion and does not require ad hoc augmentation.

Zamstein, Noa; Tannor, David J. [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel)

2012-12-14T23:59:59.000Z

327

Adapting SAFT-? perturbation theory to site-based molecular dynamics simulation. I. Homogeneous fluids  

SciTech Connect (OSTI)

In this work, we aim to develop a version of the Statistical Associating Fluid Theory (SAFT)-? equation of state (EOS) that is compatible with united-atom force fields, rather than experimental data. We rely on the accuracy of the force fields to provide the relation to experimental data. Although, our objective is a transferable theory of interfacial properties for soft and fused heteronuclear chains, we first clarify the details of the SAFT-? approach in terms of site-based simulations for homogeneous fluids. We show that a direct comparison of Helmholtz free energy to molecular simulation, in the framework of a third order Weeks-Chandler-Andersen perturbation theory, leads to an EOS that takes force field parameters as input and reproduces simulation results for Vapor-Liquid Equilibria (VLE) calculations. For example, saturated liquid density and vapor pressure of n-alkanes ranging from methane to dodecane deviate from those of the Transferable Potential for Phase Equilibria (TraPPE) force field by about 0.8% and 4%, respectively. Similar agreement between simulation and theory is obtained for critical properties and second virial coefficient. The EOS also reproduces simulation data of mixtures with about 5% deviation in bubble point pressure. Extension to inhomogeneous systems and united-atom site types beyond those used in description of n-alkanes will be addressed in succeeding papers.

Ghobadi, Ahmadreza F.; Elliott, J. Richard, E-mail: elliot1@uakron.edu [Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325 (United States)

2013-12-21T23:59:59.000Z

328

TO J. A. QuigUy, M.D. NATIONALLPADCW~  

Office of Legacy Management (LM)

J. A. QuigUy, M.D. J. A. QuigUy, M.D. NATIONALLPADCW~ OF oliI0 Cincbnati 39, Ohio September 23, 1960 TRIP RBPCRT TO PIONRBR DIVISION, BENDIX AVI4TIONC~ ION, DAVBNPQRT, SOWA,oNSEPTEMBR6-9,196O F. J. Klein CENTRAL FILE The purpose of this trip was tot (1) determine if a Bendix ronic energy cleaning system can clean uranium-contaminated drums to the extent of rcduciug the @ha ccmtazuinatiou level belav that required for sale as %oa-contaminatecl** by AEC Manual Chapter 5182-0s UOOO a dMlOO& average and at peak not more than 25,OOO a d~lOOcm2, and (2) observe . the health and safety aspects of the wotk and insure the adequate decontauimtiou of the machinery, tools, equi~t, aud teat area. This waa a wet operation Md the tauk waa not ventilated; hawever, should

329

Neutron scattering in molecular liquids: Influence of orientational degrees of freedom and the prepeak in a fragile glass former  

E-Print Network [OSTI]

The intermediate scattering function S(q,t) for neutron scattering is expanded with respect to a complete set of correlation functions which describe the dynamical correlations in a molecular liquid. For the static ns-structure factor S(q) of a system of diatomic molecules the results of the expansion are compared with the exact results from a MD-imulation and it is shown that the Sears-expansion, which is commonly used to interpret such data, fails in the supercooled regime. The representation for S(q) is used to draw conclusions about the q-dependence and especially the origin of the prepeak.

Christoph Theis; Rolf Schilling

1998-08-07T23:59:59.000Z

330

Monitoring attosecond dynamics of coherent electron-nuclear wave packets by molecular high-order-harmonic generation  

SciTech Connect (OSTI)

A pump-probe scheme for preparing and monitoring electron-nuclear motion in a dissociative coherent electron-nuclear wave packet is explored from numerical solutions of a non-Born-Oppenheimer time-dependent Schroedinger equation. A mid-ir intense few-cycle probe pulse is used to generate molecular high-order-harmonic generation (MHOHG) from a coherent superposition of two or more dissociative coherent electronic-nuclear wave packets, prepared by a femtosecond uv pump pulse. Varying the time delay between the intense ir probe pulse and the uv pump pulse by a few hundreds of attoseconds, the MHOHG signal intensity is shown to vary by orders of magnitude, thus showing the high sensitivity to electron-nuclear dynamics in coherent electron-nuclear wave packets. We relate this high sensitivity of MHOHG spectra to opposing electron velocities (fluxes) in the electron wave packets of the recombining (recolliding) ionized electron and of the bound electron in the initial coherent superposition of two electronic states.

Bredtmann, Timm [Laboratoire de Chimie Theorique, Faculte des Sciences, Universite de Sherbrooke, Sherbrooke, Quebec, J1K 2R1 (Canada); Institut fuer Chemie und Biochemie, Freie Universitaet Berlin, Takustrasse 3, D-14195 Berlin (Germany); Chelkowski, Szczepan; Bandrauk, Andre D. [Laboratoire de Chimie Theorique, Faculte des Sciences, Universite de Sherbrooke, Sherbrooke, Quebec, J1K 2R1 (Canada)

2011-08-15T23:59:59.000Z

331

Thermodynamic properties and shear viscosity over entropy density ratio of nuclear fireball in a quantum-molecular dynamics model  

E-Print Network [OSTI]

Thermodynamic and transport properties of nuclear fireball created in the central region of heavy-ion collisions below 400 MeV/nucleon are investigated within the isospin-dependent quantum molecular dynamic (IQMD) model. These properties including the density, temperature, chemical potential, entropy density ($s$) and shear viscosity ($\\eta$), are calculated by a generalized hot Thomas Fermi formulism and a parameterized function, which was developed by Danielewicz. As the collision goes on, a transient minimal $\\eta/s=5/4\\pi-10/4\\pi$ occurs in the largest compression stage. Besides, the relationship of $\\eta/s$ to temperature ($T$) in the freeze-out stage displays a local minimum which is about 9-20 times $1/4\\pi$ around $T$ = 8-12 MeV, which can be argued as indicative of a liquid gas phase transition. In addition, the influences of nucleon-nucleon (NN) cross section ($\\sigma_{NN}$) and symmetry energy coefficient ($C_{s}$) are also discussed, and it is found that the results are sensitive to $\\sigma_{NN}$ but not to $C_{s}$.

C. L. Zhou; Y. G. Ma; D. Q. Fang; G. Q. Zhang

2012-12-20T23:59:59.000Z

332

DOE - Office of Legacy Management -- Bendix Corp Frieze Division - MD 0-01  

Office of Legacy Management (LM)

Bendix Corp Frieze Division - MD Bendix Corp Frieze Division - MD 0-01 FUSRAP Considered Sites Site: BENDIX CORP., FRIEZE DIVISION (MD.0-01 ) Eliminated from further consideration under FUSRAP Designated Name: Not Designated Alternate Name: None Location: Baltimore , Maryland MD.0-01-1 Evaluation Year: 1987 MD.0-01-3 Site Operations: Produced "classified units" believed to be electronics components - no radioactive materials involved. MD.0-01-1 MD.0-01-3 Site Disposition: Eliminated - No radioactive materials handled at this site MD.0-01-3 Radioactive Materials Handled: No Primary Radioactive Materials Handled: None MD.0-01-3 Radiological Survey(s): No Site Status: Eliminated from further consideration under FUSRAP Also see Documents Related to BENDIX CORP., FRIEZE DIVISION

333

DOE - Office of Legacy Management -- Naval Ordnance Laboratory - MD 0-03  

Office of Legacy Management (LM)

Ordnance Laboratory - MD 0-03 Ordnance Laboratory - MD 0-03 FUSRAP Considered Sites Site: NAVAL ORDNANCE LABORATORY (MD.0-03 ) Eliminated from further consideration under FUSRAP - Referred to DOD Designated Name: Not Designated Alternate Name: Naval Ordnance Laboratory - White Oak Location: White Oak Area , Silver Spring , Maryland MD.0-03-1 MD.0-03-2 Evaluation Year: 1987 MD.0-03-2 Site Operations: Research and development - may have involved radioactive materials because the site was identified on a 1955 Accountability Station List. MD.0-03-1 Site Disposition: Eliminated - NRC licensed MD.0-03-2 Radioactive Materials Handled: None Specifically Identified Primary Radioactive Materials Handled: None specifically indicated Radiological Survey(s): None Indicated Site Status: Eliminated from further consideration under FUSRAP - Referred to DOD MD.0-03-2

334

A Car–Parrinello and path integral molecular dynamics study of the intramolecular lithium bond in the lithium 2-pyridyl- N -oxide acetate  

Science Journals Connector (OSTI)

Lithium bonding in lithium 2-pyridyl- N -oxide acetate has been investigated using classic Car–Parrinello molecular dynamics (CPMD) and the path integral approach [path integrals molecular dynamics (PIMD)]. The simulations have been performed in 300 K. Structures energies and lithium trajectories have been determined. The CPMD results show that the lithium atom is generally equidistant between heavy atoms in the ( O ? Li ? O ) bridge. Applying quantum effects through the PIMD leads to similar conclusion. The theoretical lithium 2-pyridyl- N -oxide acetate infrared spectrum has also been determined using the CPMD calculations. This shows very good agreement with available experimental results and reproduces well the broad low-frequency band observed experimentally. In order to gain deeper understanding of the nature of the lithium bonding topological analysis of the electron localization function has been applied.

Piotr Durlak; Zdzis?aw Latajka; S?awomir Berski

2009-01-01T23:59:59.000Z

335

Theinfluence of a hierarchical porous carbon network on the coherent dynamics of a nanoconfined room temperature ionic liquid: A neutron spin echo and atomistic simulation investigation  

SciTech Connect (OSTI)

The molecular-scale dynamic properties of the room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, or [C4mim+ ][Tf2N ], confined in hierarchical microporous mesoporous carbon, were investigated using neutron spin echo (NSE) and molecular dynamics (MD) simulations. Both NSE and MD reveal pronounced slowing of the overall collective dynamics, including the presence of an immobilized fraction of RTIL at the pore wall, on the time scales of these approaches. A fraction of the dynamics, corresponding to RTIL inside 0.75 nm micropores located along the mesopore surfaces, are faster than those of RTIL in direct contact with the walls of 5.8 nm and 7.8 nm cylindrical mesopores. This behavior is ascribed to the near-surface confined-ion density fluctuations resulting from the ion ion and ion wall interactions between the micropores and mesopores as well as their confinement geometries. Strong micropore RTIL interactions result in less-coordinated RTIL within the micropores than in the bulk fluid. Increasing temperature from 296 K to 353 K reduces the immobilized RTIL fraction and results in nearly an order of magnitude increase in the RTIL dynamics. The observed interfacial phenomena underscore the importance of tailoring the surface properties of porous carbons to achieve desirable electrolyte dynamic behavior, since this impacts the performance in applications such as electrical energy storage devices.

Banuelos, Jose Leo [ORNL; Feng, Guang [ORNL; Fulvio, Pasquale F [ORNL; Li, Song [Vanderbilt University, Nashville; Rother, Gernot [ORNL; Arend, Nikolas [ORNL; Faraone, Antonio [National Institute of Standards and Technology (NIST); Dai, Sheng [ORNL; Cummings, Peter T [ORNL; Wesolowski, David J [ORNL

2014-01-01T23:59:59.000Z

336

MD6151-8-10 Murdoch Counselling Service  

E-Print Network [OSTI]

MD6151-8-10 Murdoch Counselling Service Stress management What is stress? Stress is the way your to gather physical and emotional energy which helps you deal with changes and challenges in your daily life which drains you of emotional and physical energy. How is university stressful? University life can

337

GRANT AWARDS Justin Annes, MD, PhD  

E-Print Network [OSTI]

Therapy POSTDOCS AWARDS Joseph Cheng, PhD, MEng, BS Postdoctoral fellow, Radiology Pediatric Radiology, Pediatrics Gastroenterology Project: Translational Studies using Immune and Microbiota markers in Vancomycin-treated Children with GI disease Adam Frymoyer, MD Instructor, Pediatrics General Pediatrics & Neonatal

Bejerano, Gill

338

Joseph P. Vacanti, MD Chief of Pediatric Surgery  

E-Print Network [OSTI]

, neurosurgery, radiology, pediatric intensive care, genetic counseling, social work and palliative careJoseph P. Vacanti, MD Chief of Pediatric Surgery and Surgeon-in-Chief MassGeneral Hospital Pediatrics Debra Burke, RN, MSN, MBA Associate Chief Nurse Chiefs' Notes To provide optimal support

Mootha, Vamsi K.

339

Ionic dynamics in the glass-forming liquid Ca0.4K0.6(NO3)1.4: A molecular dynamics study with a polarizable model  

Science Journals Connector (OSTI)

The microscopic dynamics of the fragile glass-forming liquid Ca0.4K0.6(NO3)1.4 is investigated by molecular dynamics simulation with a polarizable model. Polarization effects are included within a fluctuating partial charges approach for the nitrate ion. Single-particle time-correlation functions are compared with the ones obtained by the nonpolarizable model counterpart. It is argued that the increased ionic mobility due to polarization effects corrects the stiff dynamics of the nonpolarizable model. Among the collective functions that have been calculated with the polarizable model, special attention is paid to the density fluctuations in wave vectors around the first sharp diffraction peak of the static structure factor. In line with recent neutron-scattering experiments, an intermediate-range-order dynamics has been observed in the simulated system.

Mauro C. C. Ribeiro

2001-02-12T23:59:59.000Z

340

Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations  

Science Journals Connector (OSTI)

Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein X-ray crystallography, were constructed and biochemically characterized. The mutants showed distinct catalytic efficiencies with the halogenated substrate 1,2,3-trichloropropane. Release pathways for the two dehalogenation products, 2,3-dichloropropane-1-ol and the chloride ion, and exchange pathways for water molecules, were studied using classical and random acceleration molecular dynamics simulations. Five different pathways, denoted p1, p2a, p2b, p2c, and p3, were identified. The individual pathways showed differing selectivity for the products: the chloride ion releases solely through p1, whereas the alcohol releases through all five pathways. Water molecules play a crucial role for release of both products by breakage of their hydrogen-bonding interactions with the active-site residues and shielding the charged chloride ion during its passage through a hydrophobic tunnel. Exchange of the chloride ions, the alcohol product, and the waters between the buried active site and the bulk solvent can be realized by three different mechanisms: (i) passage through a permanent tunnel, (ii) passage through a transient tunnel, and (iii) migration through a protein matrix. We demonstrate that the accessibility of the pathways and the mechanisms of ligand exchange were modified by mutations. Insertion of bulky aromatic residues in the tunnel corresponding to pathway p1 leads to reduced accessibility to the ligands and a change in mechanism of opening from permanent to transient. We propose that engineering the accessibility of tunnels and the mechanisms of ligand exchange is a powerful strategy for modification of the functional properties of enzymes with buried active sites.

Martin Klvana; Martina Pavlova; Tana Koudelakova; Radka Chaloupkova; Pavel Dvorak; Zbynek Prokop; Alena Stsiapanava; Michal Kuty; Ivana Kuta-Smatanova; Jan Dohnalek; Petr Kulhanek; Rebecca C. Wade; Jiri Damborsky

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Structures of disordered alkali chlorides in normal and compressed states: An isothermal-isobaric molecular-dynamics study  

Science Journals Connector (OSTI)

Isothermal-isobaric molecular-dynamics simulations have been performed to investigate the glassy and liquid structures of two alkali chloride systems [mixture (LiCl)0.50(KCl)0.40(CsCl)0.10 and pure LiCl]. With the use of an ionic interaction model, the basic thermodynamic properties of the crystalline, liquid, and glassy states are successfully reproduced in the simulations. At normal pressure (101.3 MPa), it is found that the predominant short-range order in both systems is the LiCl4 tetrahedral units, each pair of which is mutually connected by sharing not only the vertices but also the edges of the tetrahedra. In the glassy and liquid states of LiCl-KCl-CsCl, the network structure is formed by polytetrahedral medium-range order (LiLi4) consisting of five connected LiCl4 tetrahedra. Some portions of this network are truncated by the K+ and Cs+ ions adjacent to the vertex Cl- ions. On the other hand, liquid and glassy LiCl has a disordered structure approximately analogous to zinc-blende structure, also including the wurtzitelike ionic arrangement. For LiCl in the amorphous and crystalline states, we performed isothermal-compression simulations up to 30 GPa. As in the experimental findings, no structural transformation occurs for the rocksalt LiCl crystal. The compression causes the crystallization of amorphous LiCl into rocksalt structure at more than 3–10 GPa with continuous structural change. This structural transformation is analogous to the pressure-induced polymorphic transition (zinc blende?rocksalt) that occurs in the crystals of more covalent compounds such as CdS.

Kenichi Kinugawa

1993-10-01T23:59:59.000Z

342

Structural Assignments and Dynamics of the A Substates of MbCO: Spectrally Resolved Vibrational Echo Experiments and Molecular Dynamics Simulations  

E-Print Network [OSTI]

Structural Assignments and Dynamics of the A Substates of MbCO: Spectrally Resolved Vibrational of the A1 and A3 spectroscopic substates in the IR spectrum of the carbon monoxide (CO) stretch of carbonmonoxymyoglobin (MbCO). The measured dephasing dynamics of these substates is compared to the dephasing dynamics

Fayer, Michael D.

343

Conformational and Structural Relaxations of Poly(ethylene oxide) and Poly(propylene oxide) Melts: Molecular Dynamics Study of Spatial Heterogeneity, Cooperativity, and Correlated Forward-Backward Motion  

E-Print Network [OSTI]

Performing molecular dynamics simulations for all-atom models, we characterize the conformational and structural relaxations of poly(ethylene oxide) and poly(propylene oxide) melts. The temperature dependence of these relaxation processes deviates from an Arrhenius law for both polymers. We demonstrate that mode-coupling theory captures some aspects of the glassy slowdown, but it does not enable a complete explanation of the dynamical behavior. When the temperature is decreased, spatially heterogeneous and cooperative translational dynamics are found to become more important for the structural relaxation. Moreover, the transitions between the conformational states cease to obey Poisson statistics. In particular, we show that, at sufficiently low temperatures, correlated forward-backward motion is an important aspect of the conformational relaxation, leading to strongly nonexponential distributions for the waiting times of the dihedrals in the various conformational states

Michael Vogel

2007-10-30T23:59:59.000Z

344

Fermi molecular dynamics  

SciTech Connect (OSTI)

classical many body models supplemented by repulsive momentum-dependent potentials to simulate the Pauli and Heisenberg principles have been use with some success for nuclear and atomic bound state and collision problems. They are capable of describing mean ground state properties, hydrodynamics, shocks (if warranted by the physics), viscosity, correlations, clustering, fragmentation, etc. We have become interested in the Feldmeier Gaussian packet formulation since it is based on a variational principle using trial wave functions. We discuss some limitations of the model and discuss further directions of investigation.

Wilets, L.; Beck, W.

1991-01-01T23:59:59.000Z

345

Asbestos-related diseases in automobile mechanics Jacques Ameille, MD1  

E-Print Network [OSTI]

1 Asbestos-related diseases in automobile mechanics Jacques Ameille, MD1 , Nicole Rosenberg, MD2-related diseases in automobile mechanics Corresponding author Jacques Ameille, MD, Unité de pathologie plaques, automobile mechanics, HRCT inserm-00671970,version1-20Feb2012 Author manuscript, published

Paris-Sud XI, Université de

346

Crystal Structure and Structural Mechanism of a Novel Anti-Human Immunodeficiency Virus and d-Amino Acid-Containing Chemokine  

Science Journals Connector (OSTI)

...Molecular-modeling studies of ligand-CXCR4...molecular-dynamics (MD) simulation was performed...used homology modeling and MD simulation to predict the...suggested by the modeling studies, is...during the MD simulations, as described...

Dongxiang Liu; Navid Madani; Ying Li; Rong Cao; Won-Tak Choi; Sameer P. Kawatkar; Mi Youn Lim; Santosh Kumar; Chang-Zhi Dong; Jun Wang; Julie D. Russell; Caroline R. Lefebure; Jing An; Scott Wilson; Yi-Gui Gao; Luke A. Pallansch; Joseph G. Sodroski; Ziwei Huang

2007-08-08T23:59:59.000Z

347

Insights into the Mechanical Properties of the Kinesin Neck Linker Domain from Sequence Analysis and Molecular Dynamics Simulations  

E-Print Network [OSTI]

domain links the core motor to the coiled-coil dimerization domain. One puzzle is that the neck linker as an entropic spring, high inter- head forces are predicted when both heads are bound to the microtubule. We--Molecular biomechanics, Entropic spring, Bioin- formatics, Worm-like chain, Molecular motor, Microtubule. INTRODUCTION

Hancock, William O.

348

Electronic structure, molecular orientation, charge transfer dynamics and solar cells performance in donor/acceptor copolymers and fullerene: Experimental and theoretical approaches  

SciTech Connect (OSTI)

By combining experimental and theoretical approaches, the electronic structure, molecular orientation, charge transfer dynamics and solar cell performance in donor/acceptor copolymer poly[2,7-(9,9-bis(2-ethylhexyl)-dibenzosilole)-alt-4,7-bis(thiophen-2-yl) benzo-2,1,3-thiadiazole] (PSiF-DBT) films and blended with 6,6.-phenyl-C 61-butyric acid methyl ester (PSiF-DBT:PCBM) were investigated. Good agreement between experimental and theoretical PSiF-DBT UV-Vis absorption spectrum is observed and the main molecular orbitals contributing to the spectrum were determined using DFT single point calculations. Non-coplanar configuration was determined by geometric optimization calculation in isolated PSiF-DBT pentamer and corroborated by angular variation of the sulphur 1s near-edge X-ray absorption fine structure (NEXAFS) spectra. Edge-on and plane-on molecular orientations were obtained for thiophene and benzothiadiazole units, respectively. A power conversion efficiency up to 1.58%, open circuit voltage of 0.51 V, short circuit current of 8.71 mA/cm{sup 2} and a fill factor of 35% was obtained using blended PSiF-DBT:PCBM as active layer in a bulk heterojunction solar cell. Ultrafast electron dynamics in the low-femtosecond regime was evaluated by resonant Auger spectroscopy using the core-hole clock methodology around sulphur 1s absorption edge. Electron delocalization times for PSiF-DBT and PSiF-DBT:PCBM polymeric films were derived for selected excitation energies corresponding to the main transitions in the sulphur 1s NEXAFS spectra. The mixture of PSiF-DBT with PCBM improves the charge transfer process involving the ?* molecular orbital of the thiophene units.

Garcia-Basabe, Y.; Borges, B. G. A. L.; Rocco, M. L. M., E-mail: lsroman@fisica.ufpr.br, E-mail: luiza@iq.ufrj.br [Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909 (Brazil); Marchiori, C. F. N.; Yamamoto, N. A. D.; Koehler, M.; Roman, L. S., E-mail: lsroman@fisica.ufpr.br, E-mail: luiza@iq.ufrj.br [Departament of Physics, Federal University of Paraná, Curitiba 81531-990 (Brazil); Macedo, A. G. [Departament of Physics, Technological Federal University of Paraná, Curitiba 80230-901 (Brazil)

2014-04-07T23:59:59.000Z

349

Exploring kinetics and thermodynamics in fast-ion conductors and hydrogen-storage materials using ab-initio molecular dynamics  

E-Print Network [OSTI]

We investigate the interplay between various kinetic processes and thermodynamic factors in three materials--silver iodide (AgI), cesium hydrogen sulfate (CsHSO4), and sodium alanate (NaAlH4)-using ab-initio molecular ...

Wood, Brandon C. (Brandon Christopher)

2007-01-01T23:59:59.000Z

350

A classical approach in simple nuclear fusion reaction {sub 1}H{sup 2}+{sub 1}H{sup 3} using two-dimension granular molecular dynamics model  

SciTech Connect (OSTI)

Molecular dynamics in 2-D accompanied by granular model provides an opportunity to investigate binding between nuclei particles and its properties that arises during collision in a fusion reaction. A fully classical approach is used to observe the influence of initial angle of nucleus orientation to the product yielded by the reaction. As an example, a simplest fusion reaction between {sub 1}H{sup 2} and {sub 1}H{sup 3} is observed. Several products of the fusion reaction have been obtained, even the unreported ones, including temporary {sub 2}He{sup 4} nucleus.

Viridi, S.; Kurniadi, R.; Waris, A.; Perkasa, Y. S. [Nuclear Physics and Biophysics Research Division, Institut Teknologi Bandung, Bandung 40132 (Indonesia); Doctoral Program in Physics, Institut Teknologi Bandung, Bandung 40132 Physics Department, Universitas Islam Negeri Sunan Gunung Djati, Bandung 40614 (Indonesia)

2012-06-06T23:59:59.000Z

351

Polyethylene under tensile load: strain energy storage and breaking of linear and knotted alkanes probed by first-principles molecular dynamics calculations  

E-Print Network [OSTI]

The mechanical resistance of a polyethylene strand subject to tension and the way its properties are affected by the presence of a knot is studied using first-principles molecular dynamics calculations. The distribution of strain energy for the knotted chains has a well-defined shape that is very different from the one found in the linear case. The presence of a knot significantly weakens the chain in which it is tied. Chain rupture invariably occurs just outside the entrance to the knot, as is the case for a macroscopic rope.

A. Marco Saitta; Michael L. Klein

1999-09-01T23:59:59.000Z

352

Molecular dynamics beyonds the limits: massive scaling on 72 racks of a BlueGene/P and supercooled glass transition of a 1 billion particles system  

E-Print Network [OSTI]

We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the atomic dynamics in structural glasses and amorphous materials. The code was able to scale up to 72 racks of an IBM BlueGene/P, with a measured 89% efficiency for a system with 100 billion particles. The code speed, with less than 0.14 seconds per iteration in the case of 1 billion particles, paves the way to the study of billion-body structural glasses with a resolution increase of two orders of magnitude with respect to the largest simulation ever reported. We demonstrate the effectiveness of our code by studying the liquid-glass transition of an exceptionally large system made by a binary mixture of 1 billion particles.

Allsopp, N; Fratalocchi, A

2011-01-01T23:59:59.000Z

353

Nanosecond quantum molecular dynamics simulations of the lithium superionic conductor Li4?xGe1?xPxS4  

Science Journals Connector (OSTI)

The microscopic origin of high conductivity at room temperatures in lithium superionic conductors has remained a fundamental unsolved problem, although the recent discovery of Li10GeP2S12 was a great step toward the application of solid electrolytes. We achieve long-time (2-ns) tight-binding molecular dynamics simulations of Li4?xGe1?xPxS4 and observe the diffusion process where lithium atoms collectively hop into neighboring lithium sites by kicking the lithium atoms occupying these sites out. Furthermore, it is found that excess lithium atoms or doped lithium vacancies trigger a new diffusion process and drastically reduce the activation energy. We discuss the dynamic properties of lithium atoms in these materials, such as the diffusion constant, the activation energy, and the diffusion path.

Shinya Nishino; Takeo Fujiwara; Hisatsugu Yamasaki

2014-07-18T23:59:59.000Z

354

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

355

Potential-tuning molecular dynamics studies of fusion, and the question of ideal glassformers: (I) The Gay-Berne model  

E-Print Network [OSTI]

The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and/or crystal growth) becoming small [1] - thus a matter of kinetics. However there is evidence, dating back to the empirics of coal briquetting for maximum trucking efficiency [2] that some object shapes find little advantage in self- assembly to ordered structures - meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [3,4] or spherocylinders [5] into the world of molecules with attractive forces, we have carried out potential tuning MD studies on the behavior of the Gay-Berne (G-B) model [6] at aspect ratios in the range of the hard ellipsoid studies. Here we report that, in the aspect ratio range of maximum ellipsoid packing efficiency, some G-B crystalline states disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Cooling of the liquids in this range...

Kapko, Vitaliy; Angell, C Austen

2010-01-01T23:59:59.000Z

356

Dynamic  

Office of Legacy Management (LM)

Dynamic Dynamic , and Static , Res.ponse of the Government Oil Shale Mine at ' , . , Rifle, Colorado, to the Rulison Event. , . ; . . DISCLAIMER Portions of this document may be illegible in electronic image products. Images are produced from the best available original document. p ( y c - - a 2-1 0 -4- REPORT AT (29-2) 914 USBM 1 0 0 1 UNITED STATES DEPARTMENT O F THE I NTERIOR BUREAU OF MINES e s.09 P. L. R U S S E L L RESEARCH D l RECTOR Februory 2, lB7O DYNAMIC AND STATIC RESPONSE 'OF THE GOVERNMENT OIL SHALE MINE A T RIFLE, COLORADO, T O THE, RULISON EVENT ORDER FROM CFSTl A S ~ B ~ &J C / This page intentionally left blank CONTENTS Page . . . . . . . . . . . . . . . . . . . . . . . . . H i s t o r i c . a l Des c r i p t i o n 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Summary 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Introduction 3

357

UW Team Creates High-Performance Workflow To Explore Molecular Dynamics of Proteins UW Team Creates High-Performance Workflow  

E-Print Network [OSTI]

. That's a static repository, which, in some cases, will help you say something about function. It for what we do. But you really need to get that dynamic component to say something. Let

Daggett, Valerie

358

14th international symposium on molecular beams  

SciTech Connect (OSTI)

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

Not Available

1992-01-01T23:59:59.000Z

359

14th international symposium on molecular beams  

SciTech Connect (OSTI)

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

Not Available

1992-09-01T23:59:59.000Z

360

E-Print Network 3.0 - antioxidants bethesda md Sample Search...  

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

Content and Inflammatory Cytokines Tumor Necrosis Summary: Cells. Lipid O staining and Image-Pro analysis (Media Cybernetics, Inc., Bethesda, MD) revealed that h... in human...

Note: This page contains sample records for the topic "molecular dynamics md" 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

Molecular Dynamics Simulation of the Effect of Hydrophobic Cosolutes on the Neutral Hydrolysis of an Activated Ester  

Science Journals Connector (OSTI)

Physical Organic Chemistry Unit, Stratingh Institute, University of Groningen, and Groningen Biochemistry and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands ... (17)?Postma, J. P. M. Ph.D. Thesis, University of Groningen, The Netherlands, 1985. ... (32)?van Gunsteren, W. F.; Berendsen, H. J. C. GROMOS, Groningen Molecular Simulation Package; Biomos B.V.:? Nijenborgh 16, 9747 AG Groningen, The Netherlands, 1987. ...

Theo Rispens; Marc F. Lensink; Herman J. C. Berendsen; Jan B. F. N. Engberts

2004-04-06T23:59:59.000Z

362

Interfacial Complex Formation in Uranyl Extraction by Tributyl-Phosphate in Dodecane Diluent: A Molecular Dynamics Study  

SciTech Connect (OSTI)

Atomistic simulations have been carried out in a multicomponent two-phase system (aqueous and organic phases in direct contact) to investigate the interfacial molecular mechanisms leading to uranyl extractionfrom the aqueous to organic phase. The aqueous phase consists of the dissolved ions UO2^2+ and nitrate NO3-,with or without H3O+, in water to describe acidic or neutral condition; the organic phase consists of tributyl phosphate, the extractant, in dodecane as the diluent. We find that the interface facilitates the formation of various uranyl complexes, with a general formula UO2^2+(NO3-)n mTBP kH2O, with n + m + k ) 5, suggesting a 5-fold coordination. The coordination for all three molecular entities has the common feature that they all bind to the uranyl at the uranium atom with an oxygen atom in the equatorial plane perpendicular to the molecular axis of the uranyl, forming a 5-fold symmetry plane. Nitric acid has a strong effect in enhancing the formation of extractable species, which is consistent with experimental findings.

de Almeida, Valmor F [ORNL; Cui, Shengting [ORNL; Ye, Xianggui [ORNL; Khomami, Bamin [ORNL

2009-01-01T23:59:59.000Z

363

Oral Histories: Oncologist Helen Vodopick, M.D.  

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

2 2 HUMAN RADIATION STUDIES: REMEMBERING THE EARLY YEARS Oral History of Oncologist Helen Vodopick, M.D. Conducted December 28, 1994 United States Department of Energy Office of Human Radiation Experiments August 1995 CONTENTS Foreword Short Biography Academic Fellowship at Oak Ridge Institute for Nuclear Studies (ORINS), 1960 Appointment to the Staff at ORINS Medical Division The Medium-Exposure-Rate Total Body Irradiator (METBI) ORINS Radioisotope Tracer Studies Participation by Regional Universities at Oak Ridge Associated Universities (ORAU) Treatment of Cancer Patients with the METBI Introduction of Immunotherapy Radiation Treatment for Leukemia Patients Bone Marrow Treatment of Leukemia Low-Exposure-Rate Total Body Irradiator (LETBI) Treatment of Radiation Accident Victims at ORAU

364

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

365

An M.D. or Ph.D.? Good. Now, what are your choices?  

E-Print Network [OSTI]

1 An M.D. or Ph.D.? Good. Now, what are your choices? Martha A. Reitman, MD Stanford University-American Studies President & CEO Reitman Corporation HARVARD-BWH Trial #12;3 Products on Market · Aleve · Femstat · Palenosetron · Taxus stent · Nicardipine · Ticlopidine (predecessor to Plavix) #12;4 Products in Development

Puglisi, Joseph

366

Harry Greenspun, M.D. Senior Advisor, Health Care Transformation & Technology  

E-Print Network [OSTI]

Harry Greenspun, M.D. Senior Advisor, Health Care Transformation & Technology Deloitte Center for Health Solutions Deloitte LLP Bio highlights Harry Greenspun, M.D., is the Senior Advisor for Health Care a diverse range of clinical and executive roles, and is now responsible for helping Deloitte's health care

Stanford, Kyle

367

Application of U(2)?O(2) and U(2)?U(1) dynamical symmetries to diatomic molecular vibrations  

Science Journals Connector (OSTI)

Algebraic Hamiltonians based on the Casimir invariants of U(1) and O(2) dynamical symmetries of U(2) are used to describe the vibrational energy level spectrum of a diatomic molecule. The set of vibrational eigenstates arising from the U(1) chain remains closed under the operation of the appropriate ladder operators, whereas no such closure occurs in the case of the O(2) chain. This result is shown to be a consequence of the differing roles of the dimension of the irreducible representation of U(2), the so-called vibron number, in the two dynamical symmetry chains. A simple procedure is proposed to effect closure in the O(2) chain, as required for the eigenstates of a Morse oscillator Hamiltonian, to which the algebraic Hamiltonian based on the quadratic Casimir invariant of O(2) reduces within a coordinate representation. For each symmetry chain, application of the Holstein-Primakoff transformation leads to a set of ladder operators that act on one-dimensional harmonic oscillator eigenstates. Explicit comparison of the two dynamical symmetry chains is made with respect to the vibrational energy spectrum of the hydrogen molecule in its ground electronic state.

Ian L. Cooper and Raj K. Gupta

1997-06-01T23:59:59.000Z

368

EA-1942: Cove Point Liquefaction Project, Lusby, MD | Department of Energy  

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

2: Cove Point Liquefaction Project, Lusby, MD 2: Cove Point Liquefaction Project, Lusby, MD EA-1942: Cove Point Liquefaction Project, Lusby, MD SUMMARY The Federal Energy Regulatory Commission (FERC) is preparing, with DOE as a cooperating agency, an EA, to analyze the potential environmental impacts of a proposal to add natural gas liquefaction and exportation capabilities to an existing Cove Point LNG Terminal located on the Chesapeake Bay in Lusby, Maryland. PUBLIC COMMENT OPPORTUNITIES None available at this time. DOCUMENTS AVAILABLE FOR DOWNLOAD September 28, 2012 EA-1942: Notice of Intent to Prepare an Environmental Assessment Cove Point Liquefaction Project, Lusby, MD September 24, 2012 EA-1942: Notice of Intent of to Prepare an Environmental Assessment Cove Point Liquefaction Project, Lusby, MD

369

The Reactivity and Structural Dynamics of Supported Metal Nanoclusters Using Electron Microscopy, in situ X-Ray Spectroscopy, Electronic Structure Theories, and Molecular Dynamics Simulations.  

SciTech Connect (OSTI)

The distinguishing feature of our collaborative program of study is the focus it brings to emergent phenomena originating from the unique structural/electronic environments found in nanoscale materials. We exploit and develop frontier methods of atomic-scale materials characterization based on electron microscopy (Yang) and synchrotron X-ray absorption spectroscopy (Frenkel) that are in turn coupled innately with advanced first principles theory and methods of computational modeling (Johnson). In the past year we have made significant experimental advances that have led to important new understandings of the structural dynamics of what are unquestionably the most important classes of heterogeneous catalysts—the materials used to both produce and mitigate the consequences of the use of liquid hydrocarbon fuels.

Judith C. Yang; Ralph G. Nuzzo, Duane Johnson, Anatoly Frenkel

2008-07-01T23:59:59.000Z

370

Center for Understanding and Control of Acid Gas-induced Evolution...  

Office of Science (SC) Website

and scattering, electron microscopy, scanning probe microscopy, surface science, neutron diffraction and scattering, molecular dynamics (MD), density functional theory...

371

Intermediate-range order and collective dynamics in an aqueous solution of trivalent cations  

Science Journals Connector (OSTI)

Molecular dynamics (MD) simulations of a concentrated aqueous solution of high-valence cations M3+ demonstrate the occurrence of intermediate-range order (IRO) by a pronounced prepeak at k?1.0Å?1 in the static structure factor. The IRO effect on the high-frequency collective dynamics of acoustic modes is investigated in a model system which mimics a 2.8M EuCl3 aqueous solution. A single branch in the dispersion relation of longitudinal acoustic (LA) modes in solution is obtained up to k?0.5Å?1, and then it splits into two branches for higher wave vectors. The low-frequency branch of LA modes in solution is not the well-known transverselike branch seen in MD simulation of pure water. It is assigned instead to a subsystem of M3+ cations plus water molecules belonging to the cations’ first hydration shell. The excitation energy of the low-frequency branch reaches a maximum in a k range half of the prepeak value, so that IRO plays the role of a pseudo–Brillouin zone for the cation subsystem. The high-frequency branch of the LA modes in solution follows the corresponding one in pure water, and in fact a subsystem of “bulk” water molecules is identified in solution showing high-frequency short-range structural relaxation similar to that of pure water.

Mauro C. C. Ribeiro

2006-01-10T23:59:59.000Z

372

Graduate Student Handbook Cell, Molecular, Developmental Biology and  

E-Print Network [OSTI]

Graduate Student Handbook Cell, Molecular, Developmental Biology and Biophysics Graduate Program The Johns Hopkins University Baltimore, MD This handbook is subject to change and corrections. September 1, and developmental biology and genetics. The core curriculum covers the fundamentals in each area at a rigorous

von der Heydt, Rüdiger

373

BERAC Meeting, October 6-7, 2011, Rockville, MD| U.S. DOE Office of Science  

Office of Science (SC) Website

Meeting, October 6-7, 2011, Rockville, MD Meeting, October 6-7, 2011, Rockville, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting, October 6-7, 2011, Rockville, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting October 6-7, 2011 Rockville, MD Agenda .docx file (13KB) Presentations Sharlene Weatherwax, State of BER Report .pptx file (2.0MB) Gary Geernaert, Climate and Environmental Sciences Division Update .pptx file (24.0MB) Todd Anderson, Biological Systems Science Division Update .pptx file (8.0MB) Susan Hubbard, Science Talk - Geophysical Signatures of Subsurface Microbially-Mediated Processes: Toward Quantification of In-Situ Ecosystem

374

BERAC Meeting October 16, 2006 North Bethesda, MD | U.S. DOE Office of  

Office of Science (SC) Website

October 16, 2006 North Bethesda, MD October 16, 2006 North Bethesda, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting October 16, 2006 North Bethesda, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting October 16, 2006 North Bethesda, MD Agenda .pdf file (8KB) Presentations Jerry Elwood .ppt file (4.1MB), State of BER James Ehleringer .ppt file (6.7MB), Report on BERAC Review of FACE Experiments David Kingsbury .ppt file (10.4MB), CAMERA-Metagenomics meets the Cyberinfrastructure Chris Somerville .ppt file (59KB), Life Sciences PART Measure Progress Report Joyce Penner .ppt file (116KB), Climate Change Science PART Measure

375

BERAC Meeting February 18 - 19, 2009 North Bethesda, MD | U.S. DOE Office  

Office of Science (SC) Website

18 - 19, 2009 North Bethesda, MD 18 - 19, 2009 North Bethesda, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting February 18 - 19, 2009 North Bethesda, MD Print Text Size: A A A RSS Feeds FeedbackShare Page Biological and Environmental Research Advisory Committee Meeting February 18-19, 2009 North Bethesda, MD Meeting Agenda .pdf file (9KB) Presentations Anna Palmisano .ppt file (11.7MB), State of BER Sharlene Weatherwax .ppt file (8.7MB), Biological Systems Science Division Update Wanda Ferrell .ppt file (16.9MB), Climate and Environmental Sciences Division Update Jeff Amthor, Report on the Climate Change Research Strategic Plan

376

BERAC Meeting February 23-24, 2010 Gaithersburg, MD | U.S. DOE Office of  

Office of Science (SC) Website

February 23-24, 2010 Gaithersburg, MD February 23-24, 2010 Gaithersburg, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting February 23-24, 2010 Gaithersburg, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting February 23-24,2010 Gaithersburg MD Agenda .pdf file (8KB) Presentations Patricia Dehmer .ppt file (7.4MB), News from the Office of Science Anna Palmisano .ppt file (18.0MB), State of BER Jeff Marqusee .ppt file (5.0MB), SERDP & ESTCP Phil Robertson .pdf file (3.1MB), Bioenergy & Sustainability (pdf format) Wanda Ferrell .ppt file (5.1MB), Climate and Environmental Sciences Division Update

377

BERAC Meeting September 1-2, 2009 Gaithersburg, MD | U.S. DOE Office of  

Office of Science (SC) Website

-2, 2009 Gaithersburg, MD -2, 2009 Gaithersburg, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting September 1-2, 2009 Gaithersburg, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting September 1-2, 2009 Gaithersburg, MD Agenda .pdf file (8KB) Presentations Patricia Dehmer .ppt file (25.0MB), News from the Office of Science Anna Palmisano .pptx file (6.6MB), State of BER Barbara Alving, NIH .ppt file (6.6MB), Connecting the Nation's Researchers, Patients and Communities: Next Steps Horst Simon .pdf file (2.6MB), Future Trends in Computing Sharlene Weatherwax .pdf file (928KB), Biological Systems Science

378

BERAC Meeting May 19-20, 2008 Hilton Hotel Gaithersburg, MD | U.S. DOE  

Office of Science (SC) Website

9-20, 2008 Hilton Hotel Gaithersburg, MD 9-20, 2008 Hilton Hotel Gaithersburg, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting May 19-20, 2008 Hilton Hotel Gaithersburg, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting May 19-20, 2008 Hilton Hotel Gaithersburg, MD Agenda .pdf file (17KB) Presentations Mike Hochella .ppt file (388KB), Environmental Remediation Sciences Division Committee of Visitors Report Jim Adelstein .ppt file (1.1MB), Report on the Low Dose Radiation Research Program Himadri Pakrasi .ppt file (22.3MB), Science Talk, Membrane Biology Grand Challenge Jeff Amthor .ppt file (11.7MB), Update on BER Program for Ecosystems

379

BERAC Meeting, June 6-7, 2012 Gaithersburg, MD| U.S. DOE Office of Science  

Office of Science (SC) Website

June 6-7, 2012 Gaithersburg, MD June 6-7, 2012 Gaithersburg, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting, June 6-7, 2012 Gaithersburg, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting June 6-7, 2012 Gaithersburg, MD Agenda .pdf file (424KB) Presentations Sharlene Weatherwax, BER Associate Director State of BER Report .pdf file (482KB) Todd Anderson, Director, Biological Systems Science Division Biological Systems Science Division Update .pdf file (1.9MB) Gary Geernaert, Director, Climate and Environmental Sciences Division Climate and Environmental Sciences Division Update .pdf file (1.6MB) Jonathan Petters,

380

BERAC Meeting, February 21-22, 2013, Rockville, MD | U.S. DOE Office of  

Office of Science (SC) Website

February 21-22, 2013 BERAC Rockville, MD February 21-22, 2013 BERAC Rockville, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings February 21-22, 2013 BERAC Rockville, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting, February 21-22, 2013, Rockville, MD Agenda .pdf file (10KB) Presentations: Sharlene Weatherwax .pdf file (1.9MB) - Office of Biological and Environmental Research Update Todd Anderson .pdf file (1.7MB) - Biological Systems Science Division Update Gary Geernaert .pdf file (2.3MB) - Climate and Environmental Sciences Division Update Judy Wall .pdf file (3.5MB) - The Genetic Basis for Bacterial Mercury Methylation

Note: This page contains sample records for the topic "molecular dynamics md" 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

BERAC Meeting May 14-15, 2007 North Bethesda, MD | U.S. DOE Office of  

Office of Science (SC) Website

4-15, 2007 North Bethesda, MD 4-15, 2007 North Bethesda, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting May 14-15, 2007 North Bethesda, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting May 14-15, 2007 North Bethesda, MD Agenda .pdf file (10KB) Presentations Joyce Penner .ppt file (74KB), Report on ARM Facilities Charge William Pizer .pdf file (292KB), Report on Integrated Assessment Charge John Ferrell .ppt file (2.7MB), Report on DOE Energy Efficiency and Renewable Energy Biomass Program Paul Vaska .ppt file (23.6MB), Science Talk, Advances in Instrumentation for Small-Animal PET Imaging Mike Viola .ppt file (2.3MB), State of BER

382

BERAC Meeting September 16-17, 2010 Gaithersburg, MD | U.S. DOE Office of  

Office of Science (SC) Website

6-17, 2010 Gaithersburg, MD 6-17, 2010 Gaithersburg, MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting September 16-17, 2010 Gaithersburg, MD Print Text Size: A A A RSS Feeds FeedbackShare Page BERAC Meeting September 16-17, 2010 Gaithersburg, MD Agenda .pdf file (8KB) Presentations Anna Palmisano .pptx file (6.5MB), State of BER Judy Wall .pptx file (904KB), CESD COV Report Gary Sayler .ppt file (65.0MB), Science Lecture, "From Microbes to Man: Environmental Biosensing with Bacterial Bioluminescence" Gary Geernaert .pptx file (4.5MB), Climate and Environmental Sciences Division Update Sharlene Weatherwax .pptx file (5.6MB), Biological Systems Science

383

Price of Cove Point, MD Natural Gas LNG Imports from Egypt (Nominal...  

U.S. Energy Information Administration (EIA) Indexed Site

Egypt (Nominal Dollars per Thousand Cubic Feet) Price of Cove Point, MD Natural Gas LNG Imports from Egypt (Nominal Dollars per Thousand Cubic Feet) Decade Year-0 Year-1 Year-2...

384

Price of Cove Point, MD Natural Gas LNG Imports from Algeria...  

U.S. Energy Information Administration (EIA) Indexed Site

Algeria (Dollars per Thousand Cubic Feet) Price of Cove Point, MD Natural Gas LNG Imports from Algeria (Dollars per Thousand Cubic Feet) Decade Year-0 Year-1 Year-2 Year-3 Year-4...

385

E-Print Network 3.0 - amory codman md Sample Search Results  

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

proud. During... , Emergency Surgery, and Surgical Critical Care (TESSCC), led by George P. Velmahos, MD, PhD, MSEd. George... is a skilled and committed teacher who has recruited...

386

Intelligent Mobile Health Monitoring System (IMHMS) Rifat Shahriyar, Md. Faizul Bari, Gourab Kundu, Sheikh Iqbal Ahamed,  

E-Print Network [OSTI]

, Sheikh Iqbal Ahamed, Md. Mostofa Akbar Department of Computer Science and Engineering, Bangladesh.com, sheikh.ahamed@mu.edu, mostofa@cse.buet.ac.bd Abstract. Health monitoring is repeatedly mentioned as one

Boutaba, Raouf

387

NATIONAL HARBOR, Md.,May 21, 2013-Los Alamos National Laboratory...  

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

director echoes cyber concerns May 21, 2013 Securing the grid will be key for energy security going forward NATIONAL HARBOR, Md.,May 21, 2013-Los Alamos National Laboratory...

388

High frequency sound velocity in the glass former 2Ca(NO3)2?3KNO3: Molecular dynamics simulations  

Science Journals Connector (OSTI)

Molecular dynamics simulations of the fragile glass-forming liquid 2Ca(NO3)2?3KNO3 (CKN) were performed from its molten state at 800K down to its glassy state at 250K. Time correlation functions of mass current fluctuations were calculated in order to investigate sound waves of high wave vectors, 0.18

Mauro C. C. Ribeiro

2007-04-06T23:59:59.000Z

389

Strong Electronic Polarization of the C60 Fullerene by the Imidazolium-Based Ionic Liquids: Accurate Insights from Born-Oppenheimer Molecular Dynamics Simulations  

E-Print Network [OSTI]

Fullerenes are known to be polarizable due to the strained carbon-carbon bonds and high surface curvature. Electronic polarization of fullerenes is of steady practical importance, since it leads to non-additive interactions and, therefore, to unexpected phenomena. For the first time, hybrid density functional theory (HDFT) powered Born-Oppenheimer molecular dynamics (BOMD) simulations have been conducted to observe electronic polarization and charge transfer phenomena in the C60 fullerene at finite temperature (350 K). The non-additive phenomena are fostered by the three selected imidazolium-based room-temperature ionic liquids (RTILs). We conclude that although charge transfer appears nearly negligible in these systems, an electronic polarization is indeed significant leading to a systematically positive effective electrostatic charge on the C60 fullerene: +0.14e in [EMIM][Cl], +0.21e in [EMIM][NO3], +0.17e in [EMIM][PF6]. These results are, to certain extent, unexpected providing an inspiration to consider ...

Chaban, Vitaly V

2015-01-01T23:59:59.000Z

390

Influence of longitudinal isotope substitution on the thermal conductivity of carbon nanotubes: Results of nonequilibrium molecular dynamics and local density functional calculations  

SciTech Connect (OSTI)

We report reverse nonequilibrium molecular dynamics calculations of the thermal conductivity of isotope substituted (10,10) carbon nanotubes (CNTs) at 300 K. {sup 12}C and {sup 14}C isotopes both at 50% content were arranged either randomly, in bands running parallel to the main axis of the CNTs or in bands perpendicular to this axis. It is found that the systems with randomly distributed isotopes yield significantly reduced thermal conductivity. In contrast, the systems where the isotopes are organized in patterns parallel to the CNTs axis feature no reduction in thermal conductivity when compared with the pure {sup 14}C system. Moreover, a reduction of approximately 30% is observed in the system with the bands of isotopes running perpendicular to the CNT axis. The computation of phonon dispersion curves in the local density approximation and classical densities of vibrational states reveal that the phonon structure of carbon nanotubes is conserved in the isotope substituted systems with the ordered patterns, yielding high thermal conductivities in spite of the mass heterogeneity. In order to complement our conclusions on the {sup 12}C-{sup 14}C mixtures, we computed the thermal conductivity of systems where the {sup 14}C isotope was turned into pseudo-atoms of 20 and 40 atomic mass units.

Leroy, Frédéric, E-mail: f.leroy@theo.chemie.tu-darmstadt.de; Böhm, Michael C., E-mail: boehm@theo.chemie.tu-darmstadt.de [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt (Germany); Schulte, Joachim [Bruker Biospin GmbH, Silberstreifen, D-76287 Rheinstetten (Germany)] [Bruker Biospin GmbH, Silberstreifen, D-76287 Rheinstetten (Germany); Balasubramanian, Ganesh [Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011 (United States)] [Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011 (United States)

2014-04-14T23:59:59.000Z

391

Molecular dynamics simulations of the electrical double layer on smectite surfaces contacting concentrated mixed electrolyte (NaCl-CaCl2)  

SciTech Connect (OSTI)

We report new molecular dynamics results elucidating the structure of the electrical double layer (EDL) on smectite surfaces contacting mixed NaCl-CaCl{sup 2} electrolyte solutions in the range of concentrations relevant to pore waters in geologic repositories for CO{sub 2} or high-level radioactive waste (0.34-1.83 mol{sub c} dm{sup -3}). Our results confirm the existence of three distinct ion adsorption planes (0-, {beta}-, and d-planes), often assumed in EDL models, but with two important qualifications: (1) the location of the {beta}- and d-planes are independent of ionic strength or ion type and (2) 'indifferent electrolyte' ions can occupy all three planes. Charge inversion occurred in the diffuse ion swarm because of the affinity of the clay surface for CaCl{sup +} ion pairs. Therefore, at concentrations 0.34 mol{sub c} dm{sup -3}, properties arising from long-range electrostatics at interfaces (electrophoresis, electro-osmosis, co-ion exclusion, colloidal aggregation) will not be correctly predicted by most EDL models. Co-ion exclusion, typically neglected by surface speciation models, balanced a large part of the clay mineral structural charge in the more concentrated solutions. Water molecules and ions diffused relatively rapidly even in the first statistical water monolayer, contradicting reports of rigid 'ice-like' structures for water on clay mineral surfaces.

Bourg, I.C.; Sposito, G.

2011-04-01T23:59:59.000Z

392

CORS -A Cost Optimized Resource Reservation Scheme for Grid Rifat Shahriyar, Md. Mostofa Akbar, M. Sohel Rahman, Md. Faizul Bari and Shampa Shahriyar  

E-Print Network [OSTI]

management in different areas of computer science. Some approach uses data structures [2] [3] [4 problem. Some approaches apply algo- rithms for resource management to grid but fails to provide any. Sohel Rahman, Md. Faizul Bari and Shampa Shahriyar Department of Computer Science and Engineering (CSE

Boutaba, Raouf

393

Molecular dynamics simulation comparison of atomic scale intermixing at the amorphous Al2O3/semiconductor interface for a-Al2O3/Ge, a-Al2O3/InGaAs,  

E-Print Network [OSTI]

Molecular dynamics simulation comparison of atomic scale intermixing at the amorphous Al2O3/semiconductor interface for a-Al2O3/Ge, a-Al2O3/InGaAs, and a-Al2O3/InAlAs/InGaAs Evgueni A. Chagarov *, Andrew oxides Ge InGaAs InAlAs Oxide­semiconductor stack High-K oxide a b s t r a c t The structural properties

Kummel, Andrew C.

394

Collective dynamics at high wave vector in the glass-forming liquid Ca 0.4 K 0.6 ( NO 3 ) 1.4  

Science Journals Connector (OSTI)

The nature of the phonons at high wave vectors (0.2molecular dynamics (MD) simulations. The MD simulations have been performed with a previously proposed polarizable model for the nitrate anion [M. C. C. Ribeiro Phys. Rev. B 61 3297 (2000)]. Time correlation functions of mass and charge current fluctuations have been calculated in order to obtain the spectra of the acoustic and the optic modes respectively both the longitudinal and the transverse ones (LA TA LO and TO). Phonon dispersion curves ?(k) and the damping ?(k) of the LA modes are shown to oscillate out of phase with the static structure factor S(k) in a wide range of wave vectors. Corresponding dynamic structure factors S(k ?) are calculated as k-dependent ?-constant cuts of the LA spectra. It is shown that S(k ?) oscillates in phase with S(k) for low energy modes. A similar analysis is applied to the LO spectra the corresponding dynamic structure factor following the charge static structure factor S q (k).

Mauro C. C. Ribeiro

2001-01-01T23:59:59.000Z

395

Benzene Dimer: Dynamic Structure and Thermodynamics Derived from...  

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

Benzene Dimer: Dynamic Structure and Thermodynamics Derived from On-the-Fly ab initio DFT-D Molecular Dynamic Simulations. Benzene Dimer: Dynamic Structure and Thermodynamics...

396

Single molecule measurements and molecular motors  

Science Journals Connector (OSTI)

...Hideyuki Okano and Atsushi Iriki Single molecule measurements and molecular motors...Suita, Osaka 565-0871, Japan Single molecule imaging and manipulation are...machines like molecular motors. The single molecule measurements allow a dynamic...

2008-01-01T23:59:59.000Z

397

Analysis of Borderline Substitution/Electron Transfer Pathways from Direct ab initio MD Simulations  

SciTech Connect (OSTI)

Ab initio molecular dynamics simulations were carried out for the borderline reaction pathways in the reaction of CH2O?- with CH3Cl. The simulations reveal distinctive features of three types of mechanisms passing through the SN2-like transition state (TS): (i) a direct formation of SN2 products, (ii) a direct formation of ET products, and (iii) a 2-step formation of ET products via the SN2 valley. The direct formation of the ET product through the SN2-like TS appears to be more favorable at higher temperatures. The 2-step process depends on the amount of energy that goes into the C-C stretching mode.

Yamataka, H (Osaka University, Japan); Aida, M A. (Department of Chemistry, Graduate School of Science, Hiroshima University); Dupuis, Michel (BATTELLE (PACIFIC NW LAB))

2001-12-01T23:59:59.000Z

398

Molecular Foundry  

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

Theory of Nanostructured Materials Theory of Nanostructured Materials The Theory of Nanostructured Materials Facility at the Molecular Foundry is focused on expanding our understanding of materials at the nanoscale. Our research connects the structural and dynamical properties of materials to their functions, such as electrical conductivity and storage, light-harvesting for electricity and fuel, or gas separation and sequestration. We develop and employ a broad range of tools, including advanced electronic-structure theory, excited-state methods, model Hamiltonians, and statistical mechanical models. This combination of approaches reveals how materials behave at the nanoscale, in pursuit of materials and devices that meet global energy and sustainability needs. Electronic structure of complex materials and interfaces for energy

399

Vibrational Spectra of Small Protonated Peptides from Finite Temperature MD Simulations and IRMPD Spectroscopy  

Science Journals Connector (OSTI)

Finite temperature Born?Oppenheimer DFT-based molecular dynamics simulations are presented for the vibrational spectroscopy of the prototype gas-phase Ala2H+ and Ala3H+ protonated peptides. ... This is due to the natural broadening arising from the finite temperature of the calculations, the conformational dynamics of the molecules in the simulations, and all anharmonicities which are naturally taken into account in the present calculations. ... We are grateful to the Royal Society for a USA/Canada Research Fellowship (T.D.V.) and a University Research Fellowship (L.C.S.), to The Leverhulme Trust (T.B., L.C.S., Grant F/08788G), and to Linacre College (T.D.V.) and Corpus Christi College, Oxford (T.B., L.C.S.) for support. ...

A. Cimas; T. D. Vaden; T. S. J. A. de Boer; L. C. Snoek; M.-P. Gaigeot

2009-03-20T23:59:59.000Z

400

Studies of structure and dynamics of biological macro-molecular assemblies by low angle neutron diffraction and inelastic X-ray scattering  

E-Print Network [OSTI]

This thesis is organized into two parts which focus on the studies of the dynamic structure factor and static inter-particle structure factor respectively. In the first part, we have measured and analyzed the dynamic ...

Liu, Yun, 1973-

2005-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" 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

Comment on "Structure and dynamics of liquid water on rutile TiO2(110)  

SciTech Connect (OSTI)

Liu and co-workers [Phys. Rev. B 82, 161415 (2010)] discussed the long-standing debate regarding whether H2O molecules on the defect-free (110) surface of rutile ( -TiO2) sorb associatively, or there is dissociation of some or all first-layer water to produce hydroxyl surface sites. They conducted static density functional theory (DFT) and DFT molecular dynamics (DFT-MD) investigations using a range of cell configurations and functionals. We have reproduced their static DFT calculations of the influence of crystal slab thickness on water sorption energies. However, we disagree with several assertions made by these authors: (a) that second-layer water structuring and hydrogen bonding to surface oxygens and adsorbed water molecules are weak ; (b) that translational diffusion of water molecules in direct contact with the surface approaches that of bulk liquid water; and (c) that there is no dissociation of adsorbed water at this surface in contact with liquid water. These assertions directly contradict our publishedwork, which compared synchrotron x-ray crystal truncation rod, second harmonic generation, quasielastic neutron scattering, surface charge titration, and classical MD simulations of rutile (110) single-crystal surfaces and (110)-dominated powders in contact with bulk water, and (110)-dominated rutile nanoparticles with several monolayers of adsorbed water.

Wesolowski, David J [ORNL; Sofo, Jorge O. [Pennsylvania State University; Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Zhang, Zhan [Argonne National Laboratory (ANL); Mamontov, Eugene [ORNL; Predota, M. [University of South Bohemia, Czech Republic; Kumar, Nitin [ORNL; Kubicki, James D. [Pennsylvania State University; Kent, Paul R [ORNL; Vlcek, Lukas [ORNL; Machesky, Michael L. [Illinois State Water Survey, Champaign, IL; Fenter, Paul [Argonne National Laboratory (ANL); Cummings, Peter T [ORNL; Anovitz, Lawrence {Larry} M [ORNL; Skelton, A A [Vanderbilt University; Rosenqvist, Jorgen K [ORNL

2012-01-01T23:59:59.000Z

402

BERAC Meeting September 5 2008 Gaithersburg MD | U.S. DOE Office of Science  

Office of Science (SC) Website

September 5 2008 Gaithersburg MD September 5 2008 Gaithersburg MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting September 5 2008 Gaithersburg MD Print Text Size: A A A RSS Feeds FeedbackShare Page BER September 5, 2008 Arlington, VA Agenda Presentations Peg Riley .ppt file (357KB), Life and Medical Sciences Division Committee of Visitors Report Patricia Dehmer .ppt file (2.6MB), Report from the Office of Science Todd Anderson .ppt file (1.2MB), Scientific Focus Area (SFA) Rollout & Discussion Robert Dickinson .ppt file (6.1MB), Report on Climate Research Grand Challenges Mike Kuperberg .ppt file (975KB), Climate & Environmental Sciences

403

Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media  

SciTech Connect (OSTI)

In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer 'compartments.' We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D{sub interlayer} of water tracers and representative cations (Na{sup +}, Cs{sup +}, Sr{sup 2+}) in Na-smectite interlayers. We find that a remarkably simple expression relates D{sub interlayer} to the pore-scale parameter {delta}{sub nanopore} {<=} 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: {delta}{sub nanopore} = D{sub interlayer}/D{sub 0}, where D{sub 0} is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracer H{sub 2}O, Na{sup +}, Sr{sup 2+} and Cs{sup +}+ in compacted Na-smectite-rich materials.

Bourg, I.C.; Sposito, G.

2009-12-01T23:59:59.000Z

404

Cost Analysis of NEMO Protocol Entities Md. Shohrab Hossain, Mohammed Atiquzzaman, William Ivancic  

E-Print Network [OSTI]

Cost Analysis of NEMO Protocol Entities Md. Shohrab Hossain, Mohammed Atiquzzaman, William Ivancic to ensure connectivity of the mobile nodes with the Internet. However, there has been no comprehensive cost analysis of mobility protocol entities that considers all possible costs. In this paper, we have developed

Atiquzzaman, Mohammed

405

DEWS: A Decentralized Engine for Web Search Reaz Ahmed, Rakibul Haque, Md. Faizul Bari, Raouf Boutaba  

E-Print Network [OSTI]

. Centrally controlled, company owned search engines, like Google, Yahoo and Bing, may not be sufficientDEWS: A Decentralized Engine for Web Search Reaz Ahmed, Rakibul Haque, Md. Faizul Bari, Raouf search engines, which is not healthy for our freedom in the Internet. A better solution is to enable

Waterloo, University of

406

says Michel Torbey, MD, medical director of OSU Medical Center's Neurovascular Stroke Center.  

E-Print Network [OSTI]

stroke says Michel Torbey, MD, medical director of OSU Medical Center's Neurovascular Stroke Center. "That means calling 911 as soon as you recognize signs in yourself or in someone nearby." When a stroke is brain,'" Dr. Torbey explains. `aMeriCa's best' stroke Care When a stroke patient arrives at The Ohio

407

Vendor Location PHS Assurance# A&G Pharmaceutical, Inc. MD A4404-01  

E-Print Network [OSTI]

BioScience Labs MD A3467-01 Alpha Genesis, Inc. SC A3645-01 Antibody Research Corporation MO A4489. On the BPA Program website open the current 'BPA Commodity List' and use the 'animal services', 'biological materials' or 'blood/blood products' tabs to search for these vendors. If a vendor is listed, the purchaser

Bandettini, Peter A.

408

RESEARCH Open Access HIV-1 Tat protein binds to TLR4-MD2 and signals  

E-Print Network [OSTI]

RESEARCH Open Access HIV-1 Tat protein binds to TLR4-MD2 and signals to induce TNF- and IL-10 Nawal in a TLR4 dependent manner. Conclusions: Collectively, our data showed for the first time that, HIV-1 Tat progression. Keywords: HIV-1, TLR4, Tat, IL-10, TNF- Background HIV-1 infects numerous cells of the immune

Boyer, Edmond

409

Hot Water DJ: Saving Energy by Pre-mixing Hot Water Md Anindya Prodhan  

E-Print Network [OSTI]

Hot Water DJ: Saving Energy by Pre-mixing Hot Water Md Anindya Prodhan Department of Computer University of Virginia whitehouse@virginia.edu Abstract After space heating and cooling, water heating consumption. Current water heating systems waste up to 20% of their energy due to poor insulation in pipes

Whitehouse, Kamin

410

Lupus research updateLupus research update Jennifer H. Anolik, MD, PhD  

E-Print Network [OSTI]

Lupus research updateLupus research update Jennifer H. Anolik, MD, PhD Division of Allergy · Yet, SLE is clearly multifactorial: ­ Genetic factors ­ Immunologic factors ­ Hormonal factors ­ Environmental factors EBV?EBV? Genetic predispoGenetic predispositionsition InfectionInfection Abnormal (control

Goldman, Steven A.

411

8501 La Salle Road Baltimore, MD 21284 USA SYRACUSE UNIVERSITY PARTICIPANTS  

E-Print Network [OSTI]

8501 La Salle Road Baltimore, MD 21284 USA SYRACUSE UNIVERSITY PARTICIPANTS ENGAGED IN INTERNATIONAL STUDIES SPONSOR TODAY'S DATE Syracuse University Month Day Year Date of Arrival in U.S.A. From Month Day Year * Valid for 1 year from enrollment date ENROLLMENT INFORMATION Last Name First Name USA

Kovalev, Leonid

412

HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations  

E-Print Network [OSTI]

HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD translocation, were provided by wide-angle X-ray scattering (WAXS) and neutron scattering. CD spectroscopy for Neutron Research, 100 Bureau Drive, Stop 6102, Gaithersburg, MD 20899, United States d CHESS, Cornell

Nagle, John F.

413

Intramolecular and nonlinear dynamics  

SciTech Connect (OSTI)

Research in this program focuses on three interconnected areas. The first involves the study of intramolecular dynamics, particularly of highly excited systems. The second area involves the use of nonlinear dynamics as a tool for the study of molecular dynamics and complex kinetics. The third area is the study of the classical/quantum correspondence for highly excited systems, particularly systems exhibiting classical chaos.

Davis, M.J. [Argonne National Laboratory, IL (United States)

1993-12-01T23:59:59.000Z

414

Interfacial Ionic Liquids: Connecting Static and Dynamic Structures  

E-Print Network [OSTI]

It is well-known that room temperature ionic liquids (RTILs) often adopt a charge-separated layered structure, i.e., with alternating cation- and anion-rich layers, at electrified interfaces. However, the dynamic response of the layered structure to temporal variations in applied potential is not well understood. We used in situ, real-time X-ray reflectivity (XR) to study the potential-dependent electric double layer (EDL) structure of an imidazolium-based RTIL on charged epitaxial graphene during potential cycling as a function of temperature. The results suggest that the graphene-RTIL interfacial structure is bistable in which the EDL structure at any intermediate potential can be described by the combination of two extreme-potential structures whose proportions vary depending on the polarity and magnitude of the applied potential. This picture is supported by the EDL structures obtained by fully atomistic molecular dynamics (MD) simulations at various static potentials. The potential-driven transition between the two structures is characterized by an increasing width but with an approximately fixed hysteresis magnitude as a function of temperature. The results are consistent with the coexistence of distinct anion and cation adsorbed structures separated by an energy barrier (~0.15 eV).

Ahmet Uysal; Hua Zhou; Guang Feng; Sang Soo Lee; Song Li; Peter T. Cummings; Pasquale F. Fulvio; Sheng Dai; John K. McDonough; Yury Gogotsi; Paul Fenter

2014-12-06T23:59:59.000Z

415

The influence of Zn vacancy on thermal conductivity of {beta}-Zn{sub 4}Sb{sub 3}: A molecular dynamics study  

SciTech Connect (OSTI)

The influence of Zn vacancy on lattice thermal conductivity of {beta}-Zn{sub 4}Sb{sub 3} is studied by non-equilibrium molecular dynamics approach. The lattice thermal conductivity of single-crystal bulk {beta}-Zn{sub 4}Sb{sub 3} decreases rapidly when there is Zn vacancy, and then when the vacancy grows, the lattice thermal conductivity decreases further but rather slowly, which suggests a scaling law of k{sub v}{approx}n{sub v}{sup -{alpha}} of Zn atom vacancy (n{sub v}) to lattice thermal conductivity (k{sub vac}). This phenomenon is attributed to the fact that the existence of vacancy scattering can significantly decrease the mean free path. When the Zn atom vacant proportion reaches 10%, that is the vacancy model of {beta}-Zn{sub 4}Sb{sub 3}, the lattice thermal conductivity is 1.32 W/mk along the x-axis and 1.62 W/mk along the z-axis, respectively, which drops by {approx}90% that of its full occupancy model. Therefore, our calculations show that the 10% Zn atom vacancy in {beta}-Zn{sub 4}Sb{sub 3} is the main reason for its exceptionally low thermal conductivity, and the interstitial Zn atoms have little effect on the thermal conductivity of single-crystal {beta}-Zn{sub 4}Sb{sub 3}. - Graphical abstract: The bulk thermal conductivity (k{sub pure}) is 11.88 W/mk along the x-axis and 20.00 W/mk the z-axis. When it is 10% vacancy, namely the vacancy model of {beta}-Zn{sub 4}Sb{sub 3}, the thermal conductivity of {beta}-Zn{sub 4}Sb{sub 3} is 1.32 W/mk along the x-axis and 1.62 W/mk along the z-axis, respectively, which reduces by {approx}90% that of its full occupancy model. Our calculations show that the 10% Zn atom vacancy in the crystal structure of {beta}-Zn{sub 4}Sb{sub 3} is the main reason for its exceptionally low thermal conductivity, and the interstitial Zn atoms have little effect on the thermal conductivity of single-crystal {beta}-Zn{sub 4}Sb{sub 3}. Highlights: Black-Right-Pointing-Pointer The lattice stability of {beta}-Zn{sub 4}Sb{sub 3} decreases remarkably with the growing vacancy. Black-Right-Pointing-Pointer 10% Zn vacancy leads to its low thermal conductivity and structural instability. Black-Right-Pointing-Pointer Interstitial Zn atoms in {beta}-Zn{sub 4}Sb{sub 3} mainly stabilize the crystal structure.

Zhai, Pengcheng [Department of Engineering Structure and Mechanics, Wuhan University of Technology, Wuhan 430070 (China) [Department of Engineering Structure and Mechanics, Wuhan University of Technology, Wuhan 430070 (China); State Key Laboratory of Advanced Technology of Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070 (China); Li, Guodong; Wen, Pengfei [Department of Engineering Structure and Mechanics, Wuhan University of Technology, Wuhan 430070 (China)] [Department of Engineering Structure and Mechanics, Wuhan University of Technology, Wuhan 430070 (China); Li, Yao, E-mail: liyao06@126.com [Department of Engineering Structure and Mechanics, Wuhan University of Technology, Wuhan 430070 (China)] [Department of Engineering Structure and Mechanics, Wuhan University of Technology, Wuhan 430070 (China); Zhang, Qingjie; Liu, Lisheng [State Key Laboratory of Advanced Technology of Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070 (China)] [State Key Laboratory of Advanced Technology of Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070 (China)

2012-09-15T23:59:59.000Z

416

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

417

Computer simulation study of collective dynamics in the glass former Ca(NO3)2·4H2O  

Science Journals Connector (OSTI)

Time correlation functions of current fluctuations were calculated by molecular dynamics (MD) simulations in order to investigate sound waves of high wavevectors in the glass-forming liquid Ca(NO3)2·4H2O. Dispersion curves ?(k) were obtained for longitudinal (LA) and transverse acoustic (TA) modes and also for longitudinal optic (LO) modes. Spectra of LA modes calculated by MD simulations were modeled by a viscoelastic model within the memory function framework. The viscoelastic model is used to rationalize the change of slope taking place at k ? 0.3 Å?1 in the ?(k) curve of acoustic modes. For still larger wavevectors mixing of acoustic and optic modes is observed. Partial time correlation functions of longitudinal mass currents were calculated separately for the ions and the water molecules. The wavevector dependence of excitation energies of the corresponding partial LA modes indicates the coexistence of a relatively stiff subsystem made of cations and anions and a softer subsystem made of water molecules.

Mauro C. C. Ribeiro

2012-01-01T23:59:59.000Z

418

Molecular Foundry  

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

The Molecular Foundry The Molecular Foundry Lawrence Berkeley National Laboratory One Cyclotron Road Building 67 Berkeley, CA 94720 Screen reader users: click here for plain HTML Go to Google Maps Home Molecular Foundry, Berkeley, CA Loading... Map Sat Ter Did you mean a different: Did you mean a different: Did you mean a different: Add Destination - Show options Hide options Get Directions Note: Public transit coverage may not be available in this area. Molecular Foundry, Berkeley, CA A Molecular Foundry 67 Cyclotron Rd, Berkeley, CA ‎ foundry.lbl.gov 3 reviews · "Berkeley Lab. About the Foundry. What is the Molecular Foundry? Research Themes; Foundry Careers; Media Gallery; Other User Facilities external link; Contact Us" - lbl.gov Directions Search nearby more See all 14 results for Molecular Foundry, Berkeley, CA

419

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations  

Science Journals Connector (OSTI)

Adenosine Triphosphate Hydrolysis Mechanism in Kinesin Studied by Combined Quantum-Mechanical/Molecular-Mechanical Metadynamics Simulations ... Future extensive molecular mechanical MD simulations exploring the stability of the various states would be very beneficial, although they are outside the scope of the present work. ... Here, we discuss the functions and mechanisms of action of three such crosslinkers: the motors kinesin-5 and kinesin-14, and the non-motor MAPs of the Ase1p family. ...

Matthew J. McGrath; I.-F. Will Kuo; Shigehiko Hayashi; Shoji Takada

2013-05-23T23:59:59.000Z

420

FINDING OF MD SIGNIFICANT IMPACT FORMERLY UTILIZED HED/AEC SITES REMEDIAL ACTION PROGRAM:  

Office of Legacy Management (LM)

FINDING OF MD SIGNIFICANT IMPACT FINDING OF MD SIGNIFICANT IMPACT FORMERLY UTILIZED HED/AEC SITES REMEDIAL ACTION PROGRAM: BAY0 CANYONS, NEW MEXICO Under the Formerly Utilized Sites Remedial Action Program (FUSRAP), the U.S. Department of Energy (DOE) has proposed to carry out rcmedfrl action at a site located in Bayo Canyon, Los Alamos County, New Mexico. Although the site as partially decontaminated and decommissioned in the 196Os, there remain above-background amounts of radionuclides. DOE has determined that strontium-90 in excess of DDE's proposed remedial- action criterir exists in subsurface materials underlying an area of about 0.6 ha (1.5 acres) at the Bayo Canyon site. The proposed action is to demarcate this are8 and restrict its use to activities that will not disturb this sub-

Note: This page contains sample records for the topic "molecular dynamics md" 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

Ceramic Composites, Inc. 1110 Benfield Blvd, Ste Q, Millersville, MD 21108  

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

Composites, Inc. Composites, Inc. 1110 Benfield Blvd, Ste Q, Millersville, MD 21108 A subsidiary of Technology Assessment and Transfer, Inc. 410-987-3435 fax 410-987-7172 www.techassess.com AGENCY: DOE / NETL CONTRACT: DE-FG02-03ER83627 TITLE: Enhanced Performance Carbon Foam Heat Exchanger for Power Plant Cooling REPORT: Final Technical Report PERIOD: 21 July 2003 - 13 July 2007 TPOC: Barbara Carney carney@netl.doe.gov PHONE: 304-285-4671 PI: Steven Seghi steve@techassess.com PHONE: 410-987-3435 COMPANY: Ceramic Composites, Inc. 133 Defense Hwy, Ste 212 Annapolis, MD 21401 SBIR/STTR Rights Notice These SBIR/STTR data are furnished with SBIR/STTR rights under Grant No. DE-FG02- 03ER83627. For a period of 4 years after the acceptance of all items to be delivered under this

422

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations  

Science Journals Connector (OSTI)

Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations ... To form the hydrated intermediate, a water molecule (WAT) must attack the carbonyl carbon of SUB15,17,18,21,31 (chemical step 1). ... This result, surprising at first, can be rationalized by realizing that a fundamental ingredient of HIV-1 PR catalytic power is the low polarity of the cleavage site environment15 that destabilizes the negatively charged Asp dyad. ...

Stefano Piana; Denis Bucher; Paolo Carloni; Ursula Rothlisberger

2004-06-25T23:59:59.000Z

423

Letter from the President Hossein Jadvar, MD, PhD, MPH, MBA, FACNM  

E-Print Network [OSTI]

Letter from the President Hossein Jadvar, MD, PhD, MPH, MBA, FACNM This is my first presi- dent regarded jour- nal, Clinical Nuclear Medicine (with an impact factor of 3.674, ranking 16th of 116, PhD, MPH, MBA, FACNM SCANNERT H E O F F I C I A L N E W S L E T T E R O F A C N M The NMRO Board had

Jadvar, Hossein

424

Molecular eigenstate spectroscopy: Application to the intramolecular dynamics of some polyatomic molecules in the 3000 to 7000 cm{sup {minus}1} region  

SciTech Connect (OSTI)

Intramolecular vibrational redistribution (IVR) appears to be a universal property of polyatomic molecules in energy regions where the vibrational density of states is greater than about 5 to 30 states per cm{sup {minus}1}. Interest in IVR stems from its central importance to the spectroscopy, photochemistry, and reaction kinetics of these molecules. A bright state, {var_phi}{sub s}, which may be a C-H stretching vibration, carries the oscillator strength from the ground state. This bright state may mix with bath rotational-vibrational levels to form a clump of molecular eigenstates, each of which carries a portion of the oscillator strength from the ground state. In this work the authors explicitly resolve transitions to each of these molecular eigenstates. Detailed information about the nature of IVR is contained in the frequencies and intensities of the observed discrete transitions. The primary goal of this research is to probe the coupling mechanisms by which IVR takes place. The most fundamental distinction to be made is between anharmonic coupling which is independent of molecular rotation and rotationally-mediated coupling. The authors are also interested in the rate at which IVR takes place. Measurements are strictly in the frequency domain but information is obtained about the decay of the zero order state, {var_phi}{sub s}, which could be prepared in a hypothetical experiment as a coherent excitation of the clump of molecular eigenstates. As the coherent superposition dephases, the energy would flow from the initially prepared mode into nearby overtones and combinations of lower frequency vibrational modes. The decay of the initially prepared mode is related to a pure sequence infrared absorption spectrum by a Fourier transform.

Perry, D.S. [Univ. of Akron, OH (United States)

1993-12-01T23:59:59.000Z

425

Figure 1. FA, MD, MK maps of a representative rat at baseline and 2 hour and 7 days after TBI.  

E-Print Network [OSTI]

, and R. Gullapalli1,2 1 Radiology, University of Maryland School of Medicine, Baltimore, MD, United) were subjected to left parietal CCI injury6 . A high-speed dental drill was used to perform a left

Simon, Jonathan Z.

426

A Linear Algorithm for Compact Box-Drawings of Trees Masud Hasan , Md. Saidur Rahman y , and Takao Nishizeki z  

E-Print Network [OSTI]

A Linear Algorithm for Compact Box-Drawings of Trees Masud Hasan #3; , Md. Saidur Rahman y, Bangladesh. Email: m2hasan@hopper.math.uwaterloo.ca y Graduate School of Information Sciences, Tohoku Univer

Wismath, Stephen

427

Computer, MD  

E-Print Network [OSTI]

Clinical decision support is an emerging type of healthcare information technology that aims to actively guide doctors' decision-making processes. In its various forms, it can help physicians design treatment regimens, ...

Feblowitz, Joshua

2010-01-01T23:59:59.000Z

428

Heart Rate Dynamics Before Spontaneous Onset of Ventricular  

E-Print Network [OSTI]

Heart Rate Dynamics Before Spontaneous Onset of Ventricular Fibrillation in Patients With Healed V. Huikuri, MD The traditional methods of analyzing heart rate (HR) variability have failed myocardial infarction has been shown to be in- creased in patients with reduced heart rate (HR) vari- ability

429

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...

430

Direct ab initio molecular dynamics study on a microsolvated S{sub N}2 reaction of OH{sup -}(H{sub 2}O) with CH{sub 3}Cl  

SciTech Connect (OSTI)

Reaction dynamics for a microsolvated S{sub N}2 reaction OH{sup -}(H{sub 2}O)+CH{sub 3}Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH{sub 3}OH+Cl{sup -}+H{sub 2}O: denoted by channel I), (2) a solvation channel (the products are Cl{sup -}(H{sub 2}O)+CH{sub 3}OH: channel II), and (3) a complex formation channel (the products are CH{sub 3}OH{center_dot}{center_dot}{center_dot}H{sub 2}O+Cl{sup -}: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.

Tachikawa, Hiroto [Division of Materials Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628 (Japan)

2006-10-07T23:59:59.000Z

431

Material dynamics under extreme conditions of pressure and strain rate  

SciTech Connect (OSTI)

Solid state experiments at extreme pressures (10-100 GPa) and strain rates ({approx}10{sup 6}-10{sup 8}s{sup -1}) are being developed on high-energy laser facilities, and offer the possibility for exploring new regimes of materials science. These extreme solid-state conditions can be accessed with either shock loading or with a quasi-isentropic ramped pressure drive. Velocity interferometer measurements establish the high pressure conditions. Constitutive models for solid-state strength under these conditions are tested by comparing 2D continuum simulations with experiments measuring perturbation growth due to the Rayleigh-Taylor instability in solid-state samples. Lattice compression, phase, and temperature are deduced from extended x-ray absorption fine structure (EXAFS) measurements, from which the shock-induced {alpha}-{omega} phase transition in Ti and the {alpha}-{var_epsilon} phase transition in Fe are inferred to occur on sub-nanosec time scales. Time resolved lattice response and phase can also be measured with dynamic x-ray diffraction measurements, where the elastic-plastic (1D-3D) lattice relaxation in shocked Cu is shown to occur promptly (< 1 ns). Subsequent large-scale molecular dynamics (MD) simulations elucidate the microscopic dynamics that underlie the 3D lattice relaxation. Deformation mechanisms are identified by examining the residual microstructure in recovered samples. The slip-twinning threshold in single-crystal Cu shocked along the [001] direction is shown to occur at shock strengths of {approx}20 GPa, whereas the corresponding transition for Cu shocked along the [134] direction occurs at higher shock strengths. This slip-twinning threshold also depends on the stacking fault energy (SFE), being lower for low SFE materials. Designs have been developed for achieving much higher pressures, P > 1000 GPa, in the solid state on the National Ignition Facility (NIF) laser.

Remington, B A; Allen, P; Bringa, E; Hawreliak, J; Ho, D; Lorenz, K T; Lorenzana, H; Meyers, M A; Pollaine, S W; Rosolankova, K; Sadik, B; Schneider, M S; Swift, D; Wark, J; Yaakobi, B

2005-09-06T23:59:59.000Z

432

Molecular biochemistry  

Science Journals Connector (OSTI)

... THIS text forms a very readable handbook which outlines the ... which outlines the fundamentals of electrostatic and dielectric theory on the one hand and of chemical bonding and molecular ...

B. Jennings

1978-09-07T23:59:59.000Z

433

MD-Predicted Phase diagrams for Pattern Formation due to Ion Irradiation  

E-Print Network [OSTI]

Energetic particle irradiation of solids can cause surface ultra-smoothening, self-organized nanoscale pattern formation, or degradation of the structural integrity of nuclear reactor components. Periodic patterns including high-aspect ratio quantum dots, with occasional long-range order and characteristic spacing as small as 7 nm, have stimulated interest in this method as a means of sub-lithographic nanofabrication. Despite intensive research there is little fundamental understanding of the mechanisms governing the selection of smooth or patterned surfaces, and precisely which physical effects cause observed transitions between different regimes has remained a matter of speculation. Here we report the first prediction of the mechanism governing the transition from corrugated surfaces to flatness, using only parameter-free molecular dynamics simulations of single-ion impact induced crater formation as input into a multi-scale analysis, and showing good agreement with experiment. Our results overturn the paradigm attributing these phenomena to the removal of target atoms via sputter erosion. Instead, the mechanism dominating both stability and instability is shown to be the impact-induced redistribution of target atoms that are not sputtered away, with erosive effects being essentially irrelevant. The predictions are relevant in the context of tungsten plasma-facing fusion reactor walls which, despite a sputter erosion rate that is essentially zero, develop, under some conditions, a mysterious nanoscale topography leading to surface degradation. Our results suggest that degradation processes originating in impact-induced target atom redistribution effects may be important, and hence that an extremely low sputter erosion rate is an insufficient design criterion for morphologically stable solid surfaces under energetic particle irradiation.

Scott A. Norris; Juha Samela; Laura Bukonte; Marie Backman; Djurabekova Flyura; Kai Nordlund; Charbel S. Madi; Michael P. Brenner; Michael J. Aziz

2010-12-23T23:59:59.000Z

434

Hydrogen storage and delivery mechanism of metal nanoclusters on a nanosheet.  

E-Print Network [OSTI]

??In this study, we used the Density functional theory (DFT) and Molecular dynamics (MD) to obtain the suitable hydrogen storage structure of Rh nanoclusters on… (more)

Huang, Li-Fan

2012-01-01T23:59:59.000Z

435

Effects of Oxygen-Containing Functional Groups on Supercapacitor...  

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

Oxygen-Containing Functional Groups on Supercapacitor Performance. Effects of Oxygen-Containing Functional Groups on Supercapacitor Performance. Abstract: Molecular dynamics (MD)...

436

Molecular Foundry  

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

Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE About the Foundry What is the Molecular Foundry? Research Themes Foundry Careers Media Gallery Other User Facilities external link Contact Us Go News & Highlights Users People Facilities Imaging and Manipulation Nanofabrication Theory Inorganic Biological Organic NCEM external link Seminars & Events Publications The Molecular Foundry is a Department of Energy-funded nanoscience research facility that provides users from around the world with access to cutting-edge expertise and instrumentation in a collaborative, multidisciplinary environment. Call for Proposals: The next deadline for standard proposals is Through March 31, 2014 Find out more information about becoming a Molecular Foundry facilities User. 2013 Annual User Meeting Postponed - Date TBD

437

The structures and dynamics of atomic and molecular adsorbates on metal surfaces by scanning tunneling microscopy and low energy electron diffraction  

SciTech Connect (OSTI)

Studies of surface structure and dynamics of atoms and molecules on metal surfaces are presented. My research has focused on understanding the nature of adsorbate-adsorbate and adsorbate-substrate interactions through surface studies of coverage dependency and coadsorption using both scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). The effect of adsorbate coverage on the surface structures of sulfur on Pt(111) and Rh(111) was examined. On Pt(111), sulfur forms p(2x2) at 0.25 ML of sulfur, which transforms into a more compressed ({radical}3x{radical}3)R30{degrees} at 0.33 ML. On both structures, it was found that sulfur adsorbs only in fcc sites. When the coverage of sulfur exceeds 0.33 ML, it formed more complex c({radical}3x7)rect structure with 3 sulfur atoms per unit cell. In this structure, two different adsorption sites for sulfur atoms were observed - two on fcc sites and one on hcp site within the unit cell.

Yoon, Hyungsuk Alexander

1996-12-01T23:59:59.000Z

438

DOE Challenge Home Case Study, Nexus EnergyHomes, Frederick, MD, Production  

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

Nexus Nexus EnergyHomes Frederick, MD BUILDING TECHNOLOGIES OFFICE DOE Challenge Home builders are in the top 1% of builders in the country meeting the extraordinary levels of excellence and quality specifi ed by the U.S. Department of Energy. Every DOE Challenge Home starts with ENERGY STAR for Homes Version 3 for an energy-effi cient home built on a solid foundation of building science research. Then, even more advanced technologies are designed in for a home that goes above and beyond current code to give you the superior quality construction, HVAC, appliances, indoor air quality, safety, durability, comfort, and solar-ready components along with ultra-low or no utility bills. This provides homeowners with a quality home that will last for generations to come.

439

DEPARTMENT OF HEALTH AN~~.N~dtAN, MD. Y.P.H.  

Office of Legacy Management (LM)

,' ,...- ,' ,...- -., -.- . . we#lnty..: - DEPARTMENT OF HEALTH AN~~.N~dtAN, MD. Y.P.H. April 30, 1979 . _-- _' . U.S.E.P.A. Radiation Branch 26 Federal Plaz;a, Boom 9079 New York, N. Y. 10007 Attention: Miss Feldman:, Gentlemen: In accordance with your request to Calvin E. Weber, P.E., Assistant Commissioner of Health for Environmental Quality, I am forwarding a copy of a report prepared by him concerning a radiation survey conducted in the vicinity of the former Canadian Radium and Uranium Corpora+on plant on Railroad Avenue in the Village of Mount Kisco, Westchester County, New Yor Please transmit any comments you may have regarding this matter directly to Mr. Weber. Very truly Yours, Conmissioner of Health xc:rr cc: Sherwood Davies, P.E. lbm Cashman

440

Recipient: County of Howard, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA COMPLIANCE FORM  

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

2 2 Recipient: County of Howard, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA COMPLIANCE FORM Activities Determination/ Categorical Exclusion Reviewer's Specific Instructions and Rationale (Restrictions and Allowable Activity) Electric Pick-up truck for on- site use at Alpha Ridge Landfill B5.1 None Landfill Forced Draft Heater A9 This CX applies to preliminary engineering and design tasks only. Additional information is required to make a NEPA determination for construction and operation tasks. Diesel Hybrid Truck B5.1 None Home Energy Audits A9 None Park Ballfield Lights Energy Efficiency B5.1 Waste Stream Clause Energy Efficiency Analysis via Monitoring of Sub-Meters Installation B5.1 None Energy Management Consultant A9 None High Efficiency Lighting - Rec & Parks B5.1

Note: This page contains sample records for the topic "molecular dynamics md" 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

Recipient. County of Baltimore, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA  

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

0 0 Recipient. County of Baltimore, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA COMPLIANCE FORM Activities Determination/ Categorical Exclusion Reviewer's Specific Instructions and Rationale (Restrictions and Allowable Activity) Renovation for the Green Resource Center B5.1 All administrative activities, audits, outreach, and technical advice should be CX'd. All EE activities are subject to the Waste Stream Clause, Historic Preservation clause, and Engineering clause. Energy Audits for Business & Government Structures A9, All, B5.1 None Revolving Loan Fund A9, All, B5.1 All administrative activities, audits, outreach, and technical advice should be CX'd. All EE activities are subject to the Waste Stream Clause, Historic Preservation clause, and Engineering clause.

442

Oral Histories: Dr. John W. Gofman, M.D., Ph.D.  

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

7 7 HUMAN RADIATION STUDIES: REMEMBERING THE EARLY YEARS Oral History of Dr. John W. Gofman, M.D., Ph.D. Conducted December 20, 1994 United States Department of Energy Office of Human Radiation Experiments June 1995 CONTENTS Foreword Short Biography Oberlin College, Enrollment in Western Reserve Medical School To University of California, Berkeley to Study Physical Chemistry Assisting Seaborg's Research, Discovery of Uranium-233 The Manhattan Project From Research to Laboratory Production of Plutonium Joe Hamilton's Cavalier Approach to Radiation Medical Treatments With Radioactive Phosphorus (32P) Conflict Between University of California San Francisco and Berkeley Reflections on Ernest Lawrence Heart Disease Studies AEC Support for Heart Disease Studies Heparin and Lipoprotein Research With Human Subjects

443

Oral Histories: Oral History of Radiologist Henry I. Kohn, M.D., Ph.D.  

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

1 1 HUMAN RADIATION STUDIES: REMEMBERING THE EARLY YEARS Oral History of Radiologist Henry I. Kohn, M.D., Ph.D. Conducted September 13, 1994 United States Department of Energy Office of Human Radiation Experiments June 1995 CONTENTS Foreword Short Biography Studying the Effects of X Rays on Animal Blood Chemistry at Oak Ridge Work at UCSF's Radiological Laboratory Advantages of Yeast Cells for Studying Radiation Effects Reflections on Bert Low-Beer and Joseph Hamilton Radiation Genetics Experiments on Mice Reflections on Reynold Brown and Henry Kaplan Establishment of Harvard's Joint Center for Radiation Therapy (Mid '60s) Radiological Assessment for the National Academy of Science Survey of Nuclear and Alternative Energy (1975–79) Biologist and Physicist Perspectives on Radiological Effects

444

Felix F? Camacho Governor Michael W. Cruz, M.D. Lieutenant Governor  

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

O. Box 2950 Haghiia, Guam 96932 O. Box 2950 Haghiia, Guam 96932 TEL: (671) 472-8931 FAX: (671) 477-4826 EMAIL: governo@mail.gov.gu Felix F? Camacho Governor Michael W. Cruz, M.D. Lieutenant Governor 0 6 MAW 2009 The Honorable Steven Chu Secretary U.S. Department of Energy 1000 Independence Avenue, S. W. Washington, D.C. 20585 Re: State Energy Program Assurances Dear Secretary Chu: As a condition of receiving Guam's share of the $3.1 billion funding for the State Energy Program (SEP) under the American Recovery and Renewal Act of 2009 (H.R. l)(ARRA), I am providing the following assurances. I have written to the Consolidated Commission on Utilities, Guam's public utility commission, and requested that they consider additional actions to promote energy efficiency, consistent with the Federal

445

ANL/ALCF/ESP-13/14 NAMD - The Engine for Large-Scale Classical MD  

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

4 4 NAMD - The Engine for Large-Scale Classical MD Simulations of Biomolecular Systems Based on a Polarizable Force Field ALCF-2 Early Science Program Technical Report Argonne Leadership Computing Facility About Argonne National Laboratory Argonne is a U.S. Department of Energy laboratory managed by UChicago Argonne, LLC under contract DE-AC02-06CH11357. The Laboratory's main facility is outside Chicago, at 9700 South Cass Avenue, Argonne, Illinois 60439. For information about Argonne and its pioneering science and technology programs, see www.anl.gov. Availability of This Report This report is available, at no cost, at http://www.osti.gov/bridge. It is also available on paper to the U.S. Department of Energy and its contractors, for a processing fee, from:

446

A study of QM/Langevin-MD simulation for oxygen-evolving center of photosystem II  

SciTech Connect (OSTI)

We have performed three QM/Langevin-MD simulations for oxygen-evolving complex (OEC) and surrounding residues, which are different configurations of the oxidation numbers on Mn atoms in the Mn{sub 4}O{sub 5}Ca cluster. By analyzing these trajectories, we have observed sensitivity of the change to the configuration of Mn oxidation state on O atoms of carboxyl on three amino acids, Glu354, Ala344, and Glu333. The distances from Mn to O atoms in residues contacting with the Mn{sub 4}O{sub 5}Ca cluster were analyzed for the three trajectories. We found the good correlation of the distances among the simulations. However, the distances with Glu354, Ala344, and Glu333 have not shown the correlation. These residues can be sensitive index of the changes of Mn oxidation numbers.

Uchida, Waka; Kimura, Yoshiro; Wakabayashi, Masamitsu [Department of Biomolecular Engineering, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8503 (Japan); Hatakeyama, Makoto; Ogata, Koji; Nakamura, Shinichiro [RIKEN Research Cluster for Innovation, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Yokojima, Satoshi [Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan and RIKEN Research Cluster for Innovation, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

2013-12-10T23:59:59.000Z

447

Nano-crystallization and magnetic mechanisms of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy by ab initio molecular dynamics simulation  

SciTech Connect (OSTI)

Iron-based amorphous and nano-crystalline alloys have attracted a growing interest due to their potential in the application of magnetic coil production. However, fundamental understanding of the nano-crystallization mechanisms and magnetic features in the amorphous structure are still lack of knowledge. In the present work, we performed ab initio molecular dynamics simulation to clarify the ionic and electronic structure in atomic scale, and to derive the origin of the good magnetic property of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy. The simulation gave a direct evidence of the Cu-P bonding preference in the amorphous alloy, which may promote nucleation in nano-crystallization process. On the other hand, the electron transfer and the band/orbital features in the amorphous alloy suggests that alloying elements with large electronegativity and the potential to expand Fe disordered matrix are preferred for enhancing the magnetization.

Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro [Institute for Material Research, Tohoku University, Sendai 980-8577 (Japan); Liang, Yunye [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kawazoe, Yoshiyuki [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kutateladze Institute of Thermophysics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk (Russian Federation)

2014-05-07T23:59:59.000Z

448

Accurate equations of state for CF4, CF4–Ar, and CF4–CH4 fluids using two-body and three-body intermolecular potentials from molecular dynamics simulation  

Science Journals Connector (OSTI)

Abstract Molecular dynamics simulations have been performed to obtain pressures and equations of state of CF4, CF4–Ar, and CF4–CH4 fluids using different inversion and ab initio pair-potentials. To take many-body forces into account, the three-body potentials of Hauschild and Prausnitz, Mol. Simul. 11 (1993) 177–185, Wang and Sadus, J. Chem. Phys. 125 (2006) 144509–144513, and Guzman et al., Mol. Phys. 109 (2011) 955–967 have been used with the pair-potentials. The significance of this work is that the many-body potential of Hauschild and Prausnitz is extended as a function of density, temperature, and molar fraction and is used with the HFD-like pair-potentials of CF4, CF4–Ar, and CF4–CH4 systems to improve the prediction of the pressure values without requiring an expensive three-body calculation. We have also simulated the self-diffusion coefficient of CF4 in good agreement with experimental data.

Mohsen Abbaspour; Maryam Sheykh

2014-01-01T23:59:59.000Z

449

Molecular nanostructure and nanotechnology  

Science Journals Connector (OSTI)

...Molecular nanostructure and nanotechnology compiled and edited by Chunli...Molecular nanostructure and nanotechnology Chunli Bai 1 Chen Wang 2...Molecular nanostructure and nanotechnology . This Theme Issue exemplifies...

2013-01-01T23:59:59.000Z

450

Surface Tensions in NaCl-Water-Air Systems from MD Simulations Ranjit Bahadur, Lynn M. Russell,*, and Saman Alavi  

E-Print Network [OSTI]

Surface Tensions in NaCl-Water-Air Systems from MD Simulations Ranjit Bahadur, Lynn M. Russell, Ottawa, Ontario K1A 0R6, Canada ReceiVed: July 9, 2007; In Final Form: July 30, 2007 Surface tensions to the surface tension, while the energy-integral and test area methods provide direct estimates. At 1 atm

Russell, Lynn

451

DSM-5What's new, what's controversial, and how does it fit with ICD? Presented by JanTerpstra, MD  

E-Print Network [OSTI]

The DSM-5What's new, what's controversial, and how does it fit with ICD? Presented by Jan of the development of the DSM-5. · Understand why some of the changes to diagnostic categories and specific mental. · Understand the current state of DSM and ICD integration. JanTerpstra, MD, is an assistant professor

Tipple, Brett

452

Alamethicin in lipid bilayers: Combined use of X-ray scattering and MD simulations Jianjun Pan a  

E-Print Network [OSTI]

Alamethicin in lipid bilayers: Combined use of X-ray scattering and MD simulations Jianjun Pan of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA d Canadian Neutron Beam Centre:1PC with varying amounts of alamethicin (Alm). We combine the use of X-ray diffuse scattering

Nagle, John F.

453

Transient Analysis of a Preemptive Resume M/D/1/2/2 through Petri Nets \\Lambda  

E-Print Network [OSTI]

Transient Analysis of a Preemptive Resume M/D/1/2/2 through Petri Nets \\Lambda Andrea Bobbio a semantical generalization of the DSPNs by including preemptive mechanisms of resume type. This generalization different preemptive resume policies. Key words: Markov regenerative processes, Stochastic Petri Nets

Telek, Miklós

454

Symmetry and dynamics of molecular rotors in amphidynamic molecular crystals  

Science Journals Connector (OSTI)

...similar in magnitude to the gas phase rotational barrier for the methyl groups...Medicine, University of Missouri-Columbia, 1514 Research...dispersion in mineral oil) in 500 mL of 1,2-dimethoxyethane...Eibling and J. Li, Unique gas and hydrocarbon adsorption...

Steven D. Karlen; Horacio Reyes; R. E. Taylor; Saeed I. Khan; M. Frederick Hawthorne; Miguel A. Garcia-Garibay

2010-01-01T23:59:59.000Z

455

Molecular Foundry  

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

See the Foundry's full equipment list See the Foundry's full equipment list Organic and Macromolecular Synthesis Capabilities & Tools Major Instruments and Capabilities AB SCIEX TF4800 MALDI TOF-TOF Mass Spectrometer This instrument is the tandem time-of-flight mass spectrometer systems, providing the excellent level of molecular mass coverage in the range of molecular masses 500 and 150,000 Da, high throughput, and confidence in both qualitative and quantitative analyses. The analyzer combines all of the advantages of MALDI in a flexible, easy-to-use, ultra-high-performance mass spectrometer with all the advanced capabilities of software. On-axis laser provides high sensitivity to identify and quantitate low-abundance compounds in complex samples. High-resolution precursor ion selection lets

456

Molecular Science Computing | EMSL  

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

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

457

Determination of the Dynamic Characteristics in the CO Transient Process in a PEM Fuel Cell Woo-kum Lee and J. W. Van Zee  

E-Print Network [OSTI]

Determination of the Dynamic Characteristics in the CO Transient Process in a PEM Fuel Cell Woo Road, Elkton, MD 21922-1488 Key words: PEM Fuel Cell, CO transient, Time constant Prepared publications #12;1 Determination of the Dynamic Characteristics in the CO Transient Process in a PEM Fuel Cell

Van Zee, John W.

458

Oral Histories: Physician James S. Robertson, M.D., Ph.D.  

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

8 8 HUMAN RADIATION STUDIES: REMEMBERING THE EARLY YEARS Oral History of Physician James S. Robertson, M.D., Ph.D. Conducted January 20, 1995 United States Department of Energy Office of Human Radiation Experiments September 1995 CONTENTS Foreword Short Biography Education Research on Human Subjects at Berkeley Invited to Join the New Lab at Brookhaven (1950) Boron Neutron Capture Therapy Other AEC Biomedical Programs Brookhaven Human Use Committee Castle Bravo Atomic Weapon Test (March 1, 1954) Studies on Marshallese at Brookhaven Modern BNCT Treatment Leaves Brookhaven for the Mayo Clinic (1975) Joins the Department of Energy (1983) Work at the Naval Radiological Defense Laboratory (1953–55) Controversial Treatments and the "Crackpot File" FOREWORD I n December 1993, U.S. Secretary of Energy Hazel R. O'Leary announced her Openness Initiative. As part of this initiative, the Department of Energy undertook an effort to identify and catalog historical documents on radiation experiments that had used human subjects. The Office of Human Radiation Experiments coordinated the Department's search for records about these experiments. An enormous volume of historical records has been located. Many of these records were disorganized; often poorly cataloged, if at all; and scattered across the country in holding areas, archives, and records centers.

459

Electron Trapping by Molecular Vibration  

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

Electron Trapping by Molecular Vibration Print Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping, giving rise to a broad feature in the photoelectron spectrum known as a shape resonance. This process represents a novel type of symmetry-breaking phenomenon that has not been observed previously but appears to be widespread. Such coupling between electronic motion and nuclear motion becomes increasingly important as scientists learn more about the geometry and dynamics of novel chemical structures such as those found in nanodevices and transient chemical species, and the results have implications for studies that use photoelectron spectroscopy as a diagnostic tool.

460

Atomic, Molecular & Optical Sciences  

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

Atomic, Molecular and Optical Sciences Atomic, Molecular and Optical Sciences The goal of the program is to understand the structure and dynamics of atoms and molecules using photons and ions as probes. The current program is focussed on studying inner-shell photo-ionization and photo-excitation of atoms and molecules, molecular orientation effects in slow collisions, slowing and cooling molecules, and X-ray photo-excitation of laser-dressed atoms. The experimental and theoretical efforts are designed to break new ground and to provide basic knowledge that is central to the programmatic goals of the Department of Energy (DOE). Unique LBNL facilities such as the Advanced Light Source (ALS), the ECR ion sources at the 88-inch cyclotron, and the National Energy Research Scientific Computing Center (NERSC) are

Note: This page contains sample records for the topic "molecular dynamics md" 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

Electron Trapping by Molecular Vibration  

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

Electron Trapping by Molecular Vibration Print Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping, giving rise to a broad feature in the photoelectron spectrum known as a shape resonance. This process represents a novel type of symmetry-breaking phenomenon that has not been observed previously but appears to be widespread. Such coupling between electronic motion and nuclear motion becomes increasingly important as scientists learn more about the geometry and dynamics of novel chemical structures such as those found in nanodevices and transient chemical species, and the results have implications for studies that use photoelectron spectroscopy as a diagnostic tool.

462

Molecular Dynamics Simulation of Liquid Sulfur Dioxide  

Science Journals Connector (OSTI)

Mauro C. C. Ribeiro * ... Ribeiro, Mauro C. C. ... Marcelo J. Monteiro, Ro?mulo A. Ando, Leonardo J. A. Siqueira, Fernanda F. Camilo, Paulo S. Santos, Mauro C. C. Ribeiro, and Roberto M. Torresi ...

Mauro C. C. Ribeiro

2006-04-11T23:59:59.000Z

463

Molecular dynamics in intense laser fields  

Science Journals Connector (OSTI)

...simpleman's model for above threshold ionization (ATI), where excess photons are absorbed on top of the minimum amount required...process for heavy molecules. Fragment atoms such as hydrogen and lithium, and their isotopes, are more difficult to study in this...

1999-01-01T23:59:59.000Z

464

Dynameomics Database of Molecular Dynamics Simulations Project...  

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

in determining protein behavior and function. Accomplishments: Over 11,000 protein folding simulations are now available in the world's largest public database of protein...

465

Molecular Science and Technology (MST) Program The Taiwan International Graduate Program (TIGP), Academia Sinica  

E-Print Network [OSTI]

Molecular Science and Technology (MST) Program The Taiwan International Graduate Program (TIGP Science and Technology (MST) graduate program: (1) Chemical dynamics and molecular spectroscopy, and transient species, and covers mechanisms involved in photodissociation, reactive scattering, energy transfer

466

Applied Statistical Physics Molecular Engineering Conference Puerto Vallarta, Mexico, 24-29 August 2003  

E-Print Network [OSTI]

of the sessions: Complex Fluids: Equilibrium and Dynamics, Nano-biotechnology, Nanoscience, Quantum EngineeringFOREWORD Applied Statistical Physics Molecular Engineering Conference Puerto Vallarta, Mexico, 24, RS, Brazil The Second International Conference on `Applied Statistical Physics: Molecular Engineering

Barbosa, Marcia C. B.

467

Molecular Foundry  

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

See the Foundry's full equipment list See the Foundry's full equipment list Nanofabrication Capabilities & Tools Major Capabilities: Instruments and Labs Zeiss Crossbeam 1540 EsB The Molecular Foundry Zeiss Cross-beam is one of the most versatile lithographic and inspection tools allowing fabrication of complex prototypes for nanoelectronics, nano-optical antenna, modifying scanning probe tips, rapid electrical contacting and many other applications. The 1500XB Cross Beam combines the Gemini field emission column (FESEM) with the Orsay Physics focused ion beam (FIB). In addition, the instrument offers a multi-channel gas injection system to allow ion and electron beam induced deposition (IBID and EBID) and chemically assisted ion beam etching (CAIBE). The tool can be used for lithographic patterning of materials or

468

Traffic of Molecular Motors  

E-Print Network [OSTI]

Molecular motors perform active movements along cytoskeletal filaments and drive the traffic of organelles and other cargo particles in cells. In contrast to the macroscopic traffic of cars, however, the traffic of molecular motors is characterized by a finite walking distance (or run length) after which a motor unbinds from the filament along which it moves. Unbound motors perform Brownian motion in the surrounding aqueous solution until they rebind to a filament. We use variants of driven lattice gas models to describe the interplay of their active movements, the unbound diffusion, and the binding/unbinding dynamics. If the motor concentration is large, motor-motor interactions become important and lead to a variety of cooperative traffic phenomena such as traffic jams on the filaments, boundary-induced phase transitions, and spontaneous symmetry breaking in systems with two species of motors. If the filament is surrounded by a large reservoir of motors, the jam length, i.e., the extension of the traffic jams is of the order of the walking distance. Much longer jams can be found in confined geometries such as tube-like compartments.

Stefan Klumpp; Melanie J. I. Müller; Reinhard Lipowsky

2005-12-06T23:59:59.000Z

469

E-Print Network 3.0 - ag-thiocrownethers molecular stability...  

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

92710 102910 Summary: to protein stability, the thermodynamics and kinetics of protein folding, and molecular dynamics simulations... Department of Biochemistry Module II: 9...

470

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

471

Molecular Science Computing | EMSL  

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

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

472

ANL/ALCF/ESP-13/14 NAMD -The Engine for Large-Scale Classical MD  

E-Print Network [OSTI]

of the potential energy function and the efficiency of the dynamic algorithm enabling the adequate configurational the leadership supercomputer Blue Gene/Q Mira. To address the issue of potential energy accuracy, classical Drude Systems Based on a Polarizable Force Field ALCF-2 Early Science Program Technical Report Argonne

Kemner, Ken

473

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

474

ChargeTransfer EAM Studies of Kinesin Molecular Motor  

E-Print Network [OSTI]

ChargeTransfer EAM Studies of Kinesin Molecular Motor Protein Mechanochemistry Vijay species. As a first step toward simulating the catalytic core of the molecular motor protein kinesin and dynamical studies of liquid water [5]. This research has the longterm goal of enabling a detailed

Maccabe, Barney

475

Electron Trapping by Molecular Vibration  

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

Electron Trapping by Molecular Electron Trapping by Molecular Vibration Electron Trapping by Molecular Vibration Print Wednesday, 27 April 2005 00:00 In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping, giving rise to a broad feature in the photoelectron spectrum known as a shape resonance. This process represents a novel type of symmetry-breaking phenomenon that has not been observed previously but appears to be widespread. Such coupling between electronic motion and nuclear motion becomes increasingly important as scientists learn more about the geometry and dynamics of novel chemical structures such as those found in nanodevices and transient chemical species, and the results have implications for studies that use photoelectron spectroscopy as a diagnostic tool.

476

Observation of a Rotational Band in the Odd-Z Transfermium Nucleus {sub 101}{sup 251}Md  

SciTech Connect (OSTI)

A rotational band has been unambiguously observed in an odd-proton transfermium nucleus for the first time. An in-beam {gamma}-ray spectroscopic study of {sub 101}{sup 251}Md has been performed using the {gamma}-ray array JUROGAM combined with the gas-filled separator RITU and the focal plane device GREAT. The experimental results, compared to Hartree-Fock-Bogolyubov calculations, lead to the interpretation that the rotational band is built on the [521]1/2{sup -} Nilsson state.

Chatillon, A.; Theisen, Ch.; Bouchez, E.; Clement, E.; Goergen, A.; Huerstel, A.; Korten, W.; Le Coz, Y.; Wilson, J. N. [CEA-SACLAY, DSM/DAPNIA/SPhN, F-91191 Gif-sur-Yvette Cedex (France); Butler, P. A.; Herzberg, R.-D.; Jones, G. D. [Oliver Lodge Laboratory, University of Liverpool, L697ZE (United Kingdom); Dorvaux, O.; Gall, B. J. P.; Khalfallah, F.; Rousseau, M. [Institut Pluridisciplinaire Hubert Curien, F-67037 Strasbourg (France); Eeckhaudt, S.; Grahn, T.; Greenlees, P. T.; Jones, P. [Department of Physics, University of Jyvaeskylae, Fin-40500 (Finland)] (and others)

2007-03-30T23:59:59.000Z

477

Dudley Herschbach: Chemical Reactions and Molecular Beams  

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

Dudley Herschbach: Dudley Herschbach: Chemical Reactions and Molecular Beams Resources with Additional Information Dudley Herschbach Courtesy of Texas A&M University As a co-recipient of the 1986 Nobel Prize in Chemistry, 'Dudley Herschbach was cited for "providing a much more detailed understanding of how chemical reactions take place". Using molecular beams, he studied elementary reactions such as K + CH3I and K + Br2, where it became possible to correlate reaction dynamics with the electronic structures of reactants and products. Exchanges proceeded through a persistent complex that lasted for many rotational periods, with product angular distributions reflecting the degree of reagent entanglement. Later this work was extended to H + Cl2, Cl + HI, halogen substitution reactions with vinyl and allyl halides, as well as such systems as Xe + Ar2 → XeAr + Ar. Herschbach has been a pioneer in the measurement and theoretical interpretation of vector properties of reaction dynamics, a field known as "molecular stereodynamics".

478

Molecular-To-Continuum Fracture Analysis of Thermosetting Polymer/Solid Interfaces  

SciTech Connect (OSTI)

This report focuses on the relationship between the fundamental interactions acting across an interface and macroscopic engineering observable such as fracture toughness or fracture stress. The work encompasses experiment, theory, and simulation. The model experimental system is epoxy on polished silicon. The interfacial interactions between the substrate and the adhesive are varied continuously using self-assembling monolayer. Fracture is studied in two specimen geometries: a napkin-ring torsion geometry and a double cantilevered beam specimen. Analysis and modeling involves molecular dynamics simulations and continuum mechanics calculations. Further insight is gained from analysis of measurements in the literature of direct force measurements for various fundamental interactions. In the napkin-ring test, the data indicate a nonlinear relationship between interface strength and fracture stress. In particular, there is an abrupt transition in fracture stress which corresponds to an adhesive-to-cohesive transition. Such nonlinearity is not present in the MD simulations on the tens-of-nanometer scale, which suggests that the nonlinearity comes from bulk material deformation occurring on much larger length scales. We postulate that the transition occurs when the interface strength becomes comparable to the yield stress of the material. This postulate is supported by variation observed in the fracture stress curve with test temperature. Detailed modeling of the stress within the sample has not yet been attempted. In the DCB test, the relationship between interface strength and fracture toughness is also nonlinear, but the fracture mechanisms are quite different. The fracture does not transition from adhesive to cohesive, but remains adhesive over the entire range of interface strength. This specimen is modeled quantitatively by combining (i) continuum calculations relating fracture toughness to the stress at 90 {angstrom} from the crack tip, and (ii) a relationship from molecular simulations between fracture stress on a {approx} 90 {angstrom} scale and the fraction of surface sites which chemically bond. The resulting relationship between G{sub c} and fraction of bonding sites is then compared to the experimental data. This first order model captures the nonlinearity in the experimentally-determined relationship. A much more extensive comparison is needed (calculations extending to higher G{sub c} values, experimental data extending to lower G{sub c} values) to guide further model development.

KENT,MICHAEL S.; REEDY JR.,EARL DAVID; STEVENS,MARK J.

2000-01-01T23:59:59.000Z

479

Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations  

Science Journals Connector (OSTI)

Adenine and cytosine methylation are two important epigenetic modifications of DNA sequences at the levels of the genome and transcriptome. To characterize the differential roles of methylating adenine or cytosine with respect to their hydration properties we performed conventional MD simulations and free energy perturbation calculations for two particular DNA sequences namely the brain-derived neurotrophic factor (BDNF) promoter and the R.DpnI-bound DNA that are known to undergo methylation of C5-methyl cytosine and N6-methyl adenine respectively. We found that a single methylated cytosine has a clearly favorable hydration free energy over cytosine since the attached methyl group has a slightly polar character. In contrast capping the strongly polar N6 of adenine with a methyl group gives a slightly unfavorable contribution to its free energy of solvation. Performing the same demethylation in the context of a DNA double-strand gave quite similar results for the more solvent-accessible cytosine but much more unfavorable results for the rather buried adenine. Interestingly the same demethylation reactions are far more unfavorable when performed in the context of the opposite (BDNF or R.DpnI target) sequence. This suggests a natural preference for methylation in a specific sequence context. In addition free energy calculations for demethylating adenine or cytosine in the context of B-DNA vs. Z-DNA suggest that the conformational B-Z transition of DNA transition is rather a property of cytosine methylated sequences but is not preferable for the adenine-methylated sequences investigated here.

2014-01-01T23:59:59.000Z

480

Stochastic molecular dynamics: A combined Monte Carlo and molecular dynamics technique for isothermal simulations  

E-Print Network [OSTI]

distribution, and while this precludes the study of dy- namics, it does allow the trajectory to be optimized with it.1,2 The question naturally arises as to the physi- cal meaning of these extensions and whetherFi t . This has been written in the simplest form. In practice one often solves the natural motion to higher order

Attard, Phil

Note: This page contains sample records for the topic "molecular dynamics md" 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

Transport and Self-Assembly in Molecular Nanosystems  

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

Transport and Transport and Self-Assembly in Molecular Nanosystems Transport and Self-Assembly in Molecular Nanosystems Key Challenges: Use classical molecular dynamics and coarse grain molecular dynamics to enable "bottom-up" material design of a wide variety of nanostructures possessing a wealth of unique properties. The goal is to guide and inform synthetic investigations and understand molecular and electronic transport, self-assembly, catalysis, and other phenomena. Ab-initio electronic structure and quantum transport methods are also used. The modeling often involves large systems (500,000 atoms) and cooperative use of several codes such as Gaussian and NAMD. Free-energy calculations typically require good ensemble averaging and therefore, must be performed

482

EMSL - Molecular Science Computing  

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

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