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While these samples are representative of the content of NLEBeta,
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We encourage you to perform a real-time search of NLEBeta
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1

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

2

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

3

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

4

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

5

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...

6

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

7

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,...

8

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

9

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

10

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

11

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...

12

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

13

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.

14

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

15

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...

16

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

17

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

18

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

19

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

20

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.

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

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.

22

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

23

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.

24

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...

25

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

26

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

27

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

28

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

29

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.

30

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

31

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

32

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

33

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

34

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

35

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

36

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

37

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

38

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

39

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

40

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

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

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

42

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

43

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

44

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

45

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

46

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

47

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

48

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

49

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

50

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

51

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

52

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

53

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

54

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....

55

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

56

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

57

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

58

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

59

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

60

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

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

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

62

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

63

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

64

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

65

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

66

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

67

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

68

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

69

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

70

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

71

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

72

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

73

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

74

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

75

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

76

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

77

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

78

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:...

79

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

80

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

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

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

82

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

83

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

84

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

85

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

86

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

87

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.

88

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

89

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

90

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

91

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

92

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

93

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

94

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

95

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

96

Long-time protein folding dynamics from short-time molecular dynamics simulations  

E-Print Network [OSTI]

On the simulation of protein folding by short time scaleand W. A. Eaton, The protein folding “speed limit,” Curr.and T. Head-Gordon, Protein folding by distributed computing

Chodera, J D; Swope, W C; Pitera, J W; Dill, Ken A

2006-01-01T23:59:59.000Z

97

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

98

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

99

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

100

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

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101

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

102

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

103

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

104

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

105

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

106

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

107

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

108

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

109

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

110

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

111

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.

112

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

113

Dynamic Positioning Simulator Dynamic Positioning Simulator  

E-Print Network [OSTI]

Simulator 5 / 24 #12;Dynamic Positioning Simulator Dynamic Positioning Why Dynamic Positioning? Advantages Dynamic Positioning: No tugboats needed; Offshore set-up is quick; Power saving; Precision situations more on Ship: Wind Force Fw = 1 2 air V 2 rw CXw (rw )AT 1 2 air V 2 rw CYw (rw )AL Mw = 1 2 air V 2 rw CMw (rw

Vuik, Kees

114

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

115

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

116

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

117

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

118

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

119

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

120

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

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While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
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121

The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations  

E-Print Network [OSTI]

, ) 91 ps-1). The Folding@Home distributed computing project was used to generate an aggregate simulation

Snow, Christopher

122

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

123

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

124

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.

125

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

126

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

127

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

128

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...

129

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

130

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...

131

Molecular Simulation of Fracture Dynamics of Symmetric Tilt Grain Boundaries in Graphene  

E-Print Network [OSTI]

Atomistic simulations were utilized to obtain microscopic information of the elongation process in graphene sheets consisting of various embedded symmetric tilt grain boundaries (GBs). In contrast to pristine graphene, these GBs fractured in an extraordinary pattern under transverse uniaxial elongation in all but the largest misorientation angle case, which exhibited intermittent crack propagation and formed many stringy residual connections after quasi mechanical failure. The strings known as monoatomic carbon chains (MACCs), whose importance was recently highlighted, gradually extended to a maximum of a few nanometers as the elongation proceeded. These features, which critically affect the tensile stress and the shape of stress-strain curve, were observed in both armchair and zigzag-oriented symmetric tilt GBs. However, there exist remarkable differences in the population density and the achievable length of MACCs appearing after quasi mechanical failure which were higher in the zigzag-oriented GBs. In addi...

Jhon, Young In; Smith, Robert; Jhon, Myung S

2012-01-01T23:59:59.000Z

132

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

133

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

134

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

135

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

136

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

137

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

138

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,"

139

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

140

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

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

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

142

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

143

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.

144

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

145

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

146

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

147

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, 0.18simulated material. The sound velocity of transverse acoustic (TA) modes presents discontinuity at the same value of the thermodynamic derived Tg. It is proposed that the distinct behavior of high frequency TA modes is due to fast reorientational motions of NO3? anions that are able to relieve local shear stresses.

Mauro C. C. Ribeiro

2007-04-06T23:59:59.000Z

148

Dynamic simulation of Odoo  

Science Journals Connector (OSTI)

Abstract The thermal habits of Odoo were examined and energy consumption data were also predicted. Special tests were performed for the time of the competition, and whole year was also analysed. The climatic data were of Madrid as the competition took place there. The modelling environment was MATLAB's Simulink with a built-in module of Simscape. It is for especially examining thermal behaviours. MATLAB itself is capable of solving differential equations by time, for this reason dynamic simulations can be performed. First the building structure was created, and then the heatflows affecting the internal temperature were added. In this paper detailed process of creating the model is presented, and some results are discussed, including some possibilities of further improvements.

Gábor Haas-Schnabel; Csaba Szikra

2014-01-01T23:59:59.000Z

149

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:...

150

Crater formation by single ions in the electronic stopping regime: Comparison of molecular dynamics simulations with experiments on organic films  

E-Print Network [OSTI]

simulations with experiments on organic films E. M. Bringa* and R. E. Johnson Engineering Physics, University modification of materials by single-ion irradiation has been studied in insulators,1­6 semiconductors,7 energy deposition and yields, redepo- sition of the ejecta plus plastic deformation occurs, produc- ing

Johnson, Robert E.

151

Probing Conformational Disorder in Neurotensin by Two-Dimensional Solid-State NMR and Comparison to Molecular Dynamics Simulations  

E-Print Network [OSTI]

Probing Conformational Disorder in Neurotensin by Two-Dimensional Solid-State NMR and Comparison is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic simulations. For neurotensin, a peptide that binds with high affinity to a G-protein coupled receptor

de Groot, Bert

152

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

153

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.

154

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.

155

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

156

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

157

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

158

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

159

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

160

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

Note: This page contains sample records for the topic "molecular dynamics simulations" from the National Library of EnergyBeta (NLEBeta).
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161

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

162

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

163

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.

164

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

165

First-principles simulation of molecular dissociation-recombination equilibrium  

SciTech Connect (OSTI)

For the first time, the equilibrium composition of chemical dissociation-recombination reaction is simulated from first-principles, only. Furthermore, beyond the conventional ab initio Born-Oppenheimer quantum chemistry the effects from the thermal and quantum equilibrium dynamics of nuclei are consistently included, as well as, the nonadiabatic coupling between the electrons and the nuclei. This has been accomplished by the path integral Monte Carlo simulations for full NVT quantum statistics of the H{sub 3}{sup +} ion. The molecular total energy, partition function, free energy, entropy, and heat capacity are evaluated in a large temperature range: from below room temperature to temperatures relevant for planetary atmospheric physics. Temperature and density dependent reaction balance of the molecular ion and its fragments above 4000 K is presented, and also the density dependence of thermal ionization above 10 000 K is demonstrated.

Kylaenpaeae, Ilkka; Rantala, Tapio T. [Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere (Finland)

2011-09-14T23:59:59.000Z

166

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

167

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

168

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

169

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

170

Sandia National Laboratories: Computational Fluid Dynamics Simulations...  

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

Canal, Yakima Washington Sandia Publishes Five Reports on the Environmental Effects of Wave-Energy Converters Computational Fluid Dynamics Simulations Provide Insight for Rotor...

171

Dynamic Simulators | netl.doe.gov  

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

to Develop Dynamic Simulators for Supercritical Pulverized Coal and Natural Gas Combined Cycle Power Plants A screen shot of the new generic supercritical once-through...

172

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

173

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

174

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

175

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

176

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

177

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

178

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

179

DEMAND SIMULATION FOR DYNAMIC TRAFFIC ASSIGNMENT  

E-Print Network [OSTI]

of the response of travelers to real-time pre- trip information. The demand simulator is an extension of dynamicDEMAND SIMULATION FOR DYNAMIC TRAFFIC ASSIGNMENT Constantinos Antoniou, Moshe Ben-Akiva, Michel Bierlaire, and Rabi Mishalani Massachusetts Institute of Technology, Cambridge, MA 02139 Abstract

Bierlaire, Michel

180

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

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

Prediction of Transport Properties by Molecular Simulation: Methanol and Ethanol and their mixture  

E-Print Network [OSTI]

Transport properties of liquid methanol and ethanol are predicted by molecular dynamics simulation. The molecular models for the alcohols are rigid, non-polarizable and of united-atom type. They were developed in preceding work using experimental vapor-liquid equilibrium data only. Self- and Maxwell-Stefan diffusion coefficients as well as the shear viscosity of methanol, ethanol and their binary mixture are determined using equilibrium molecular dynamics and the Green-Kubo formalism. Non-equilibrium molecular dynamics is used for predicting the thermal conductivity of the two pure substances. The transport properties of the fluids are calculated over a wide temperature range at ambient pressure and compared with experimental and simulation data from the literature. Overall, a very good agreement with the experiment is found. For instance, the self-diffusion coefficient and the shear viscosity are predicted with average deviations of less 8% for the pure alcohols and 12% for the mixture. The predicted thermal...

Guevara-Carrion, Gabriela; Vrabec, Jadran; Hasse, Hans

2009-01-01T23:59:59.000Z

182

VALIDATION OF MASSIVELY PARALLEL SIMULATIONS OF DYNAMIC FRACTURE AND  

E-Print Network [OSTI]

VALIDATION OF MASSIVELY PARALLEL SIMULATIONS OF DYNAMIC FRACTURE AND FRAGMENTATION OF BRITTLE element simulations of dynamic fracture and fragmentation of brittle solids are presented. Fracture the results of massively parallel numerical simulations of dynamic fracture and fragmentation in brittle

Barr, Al

183

Model Validation with Hybrid Dynamic Simulation  

SciTech Connect (OSTI)

Abstract—Model validation has been one of the central topics in power engineering studies for years. As model validation aims at obtaining reasonable models to represent actual behavior of power system components, it has been essential to validate models against actual measurements or known benchmark behavior. System-wide model simulation results can be compared with actual recordings. However, it is difficult to construct a simulation case for a large power system such as the WECC system and to narrow down to problematic models in a large system. Hybrid dynamic simulation with its capability of injecting external signals into dynamic simulation enables rigorous comparison of measurements and simulation in a small subsystem of interest. This paper presents such a model validation methodology with hybrid dynamic simulation. Two application examples on generator and load model validation are presented to show the validity of this model validation methodology. This methodology is further extended for automatic model validation and dichotomous subsystem model validation.

Huang, Zhenyu; Kosterev, Dmitry; Guttromson, Ross T.; Nguyen, Tony B.

2006-06-18T23:59:59.000Z

184

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

185

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

186

Annual Report 1999 Environmental Dynamics and Simulation  

SciTech Connect (OSTI)

This annual report describes selected 1999 research accomplishments for the Environmental Dynamics and Simulation (ED and S) directorate, one of six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). These accomplishments are representative of the different lines of research underway in the ED and S directorate. EMSL is one of US Department of Energy's (DOE) national scientific user facilities and is the centerpiece of DOE's commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems. Capabilities in the EMSL include over 100 major instrument systems for use by the resident research staff, their collaborators, and users of the EMSL. These capabilities are used to address the fundamental science that will be the basis for finding solutions to national environmental issues such as cleaning up contamianted areas at DOE sites across the country and developing green technologies that will reduce or eliminate future pollution production. The capabilities are also used to further the understanding of global climate change and environmental issues relevant to energy production and use and health effects resulting from exposure to contaminated environments.

NS Foster-Mills

2000-06-28T23:59:59.000Z

187

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

188

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

189

Dynamics Simulation in a Wave Environment  

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

Coupled Dynamic Simulation in a Wave Coupled Dynamic Simulation in a Wave Environment (Navatek, AEGIR, and WECs) Marine and Hydrokinetics Instrumentation Workshop 9 July 2012 David Kring, Navatek Ltd. Presentation Overview * Introduction to Navatek * AEGIR brief: resistance, seakeeping, global and local loads a 3D, NURBS-based, high-order, Rankine boundary element method ... from same lab as at MIT as WAMIT and SWAN, with pFFT acceleration coupling with controls, structures, aerodynamics, power take-offs * Some WEC applications at Navatek 2 Honolulu, Hawaii, USA Company Background A "Research Shipyard" based in Honolulu, HI Combining simulation-based design with prototype construction

190

Physical simulation study of dynamic voltage instability  

SciTech Connect (OSTI)

This paper presents a physical simulation of the dynamic behavior of voltage instability in an interconnected multimachine environment. The dynamic evolving process leading to eventual voltage collapse, the scenario of the progressive reactive support reduction resulting from the MXL protection relays, the OLTC operation, and the effect of switched-in capacitor banks are examined using physical facilities in the laboratory. The physical simulation results are also compared with digital simulation results. This physical investigation provides a reliable foundation for the effective development of assessment approaches and countermeasures.

Tso, S.K.; Zhu, T.X. [Univ. of Hong Kong (Hong Kong); Zeng, Q.Y. [Electric Power Research Inst., Beijing (China); Lo, K.L. [Univ. of Strathclyde, Glasgow (United Kingdom). Dept. of Electrical and Electrical Engineering

1995-12-31T23:59:59.000Z

191

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

192

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:...

193

Molecular simulation of mineral surfaces and the role of impurities on surface stability  

SciTech Connect (OSTI)

Molecular simulation techniques represent a powerful complement to experiment for studying the surfaces and interfaces of minerals, not least because we can easily visualize the surface processes. The aim of this presentation is to describe recent work using molecular simulation methods to model the structure, stability and reactivity of mineral surfaces and how the simulation of these properties can be used to predict morphologies. Initially, we will describe how molecular simulation techniques can be used to give a reliable description of the surfaces. One of the significant contributions that atom-based simulation methods can make is in the investigation of competitive adsorption of impurities at surfaces and several examples are shown. Finally, two approaches for increasing the scope and reliability of the simulations are discussed, namely, electronic structure calculations, which enable us to explore the mineral surface stoichiometry and potential-based molecular dynamics simulations, which introduce dynamical contribution to the surface processes and hence allows for detailed characterization of the mineral-water interface.

Parker, Stephen C.; Allen, Jeremy P.; Arrouvel, Corrine; Spagnoli, Dino; Kerisit, Sebastien N.; Dean, Sayle C.

2008-08-08T23:59:59.000Z

194

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

195

Dynamic procedure for filtered gyrokinetic simulations  

SciTech Connect (OSTI)

Large eddy simulations (LES) of gyrokinetic plasma turbulence are investigated as interesting candidates to decrease the computational cost. A dynamic procedure is implemented in the gene code, allowing for dynamic optimization of the free parameters of the LES models (setting the amplitudes of dissipative terms). Employing such LES methods, one recovers the free energy and heat flux spectra obtained from highly resolved direct numerical simulations. Systematic comparisons are performed for different values of the temperature gradient and magnetic shear, parameters which are of prime importance in ion temperature gradient driven turbulence. Moreover, the degree of anisotropy of the problem, which can vary with parameters, can be adapted dynamically by the method that shows gyrokinetic large eddy simulation to be a serious candidate to reduce numerical cost of gyrokinetic solvers.

Morel, P.; Banon Navarro, A.; Albrecht-Marc, M.; Carati, D. [Statistical and Plasma Physics Laboratory, Universite Libre de Bruxelles, Bruxelles 1050 (Belgium); Merz, F.; Goerler, T.; Jenko, F. [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, D-85748 Garching (Germany)

2012-01-15T23:59:59.000Z

196

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

197

A visual simulation playground for engineering dynamics  

E-Print Network [OSTI]

A VISUAL SIMULATION PLAYGROUND FOR ENGINEERING DYNAMICS A Thesis by DONALD BRIAN FONG Submitted to the O ce of Graduate Studies of Texas A&M University in partial ful llment of the requirements for the degree of MASTER OF SCIENCE August 2008 Major... Subject: Visualization Sciences A VISUAL SIMULATION PLAYGROUND FOR ENGINEERING DYNAMICS A Thesis by DONALD BRIAN FONG Submitted to the O ce of Graduate Studies of Texas A&M University in partial ful llment of the requirements for the degree of MASTER...

Fong, Donald Brian

2008-10-10T23:59:59.000Z

198

Model Validation with Hybrid Dynamic Simulation  

SciTech Connect (OSTI)

Abstract—Model validation has been one of the central topics in power engineering studies for years. As model validation aims at obtaining reasonable models to represent actual behavior of power system components, it has been essential to validate models against actual measurements or known benchmark behavior. System-wide model simulation results can be compared with actual recordings. However, it is difficult to construct a simulation case for a large power system such as the WECC system and to narrow down to problematic models in a large system. Hybrid dynamic simulation with its capability of injecting external signals into dynamic simulation enables rigorous comparison of measurements and simulation in a small subsystem of interest. This paper presents such a model validation methodology with hybrid dynamic simulation. Two application examples on generator and load model validation are presented to show the validity of this model validation methodology. This methodology is further extended for automatic model validation and dichotomous subsystem model validation. A few methods to define model quality indices have been proposed to quantify model error for model validation criteria development.

Huang, Zhenyu; Kosterev, Dmitry; Guttromson, Ross T.; Nguyen, Tony B.

2006-06-22T23:59:59.000Z

199

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

200

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

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

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

202

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

203

Dynamic simulation of a reverse Brayton refrigerator  

SciTech Connect (OSTI)

A test refrigerator based on the modified Reverse Brayton cycle has been developed in the Chinese Academy of Sciences recently. To study the behaviors of this test refrigerator, a dynamic simulation has been carried out. The numerical model comprises the typical components of the test refrigerator: compressor, valves, heat exchangers, expander and heater. This simulator is based on the oriented-object approach and each component is represented by a set of differential and algebraic equations. The control system of the test refrigerator is also simulated, which can be used to optimize the control strategies. This paper describes all the models and shows the simulation results. Comparisons between simulation results and experimental data are also presented. Experimental validation on the test refrigerator gives satisfactory results.

Peng, N.; Xiong, L. Y.; Dong, B.; Liu, L. Q. [State Key Laboratory of Technologies in Space Cryogenic Propellants, Technical Institute of Physics and Chemistry, CAS, Beijing, 100190 (China); Lei, L. L.; Tang, J. C. [State Key Laboratory of Technologies in Space Cryogenic Propellants, Technical Institute of Physics and Chemistry, CAS, Beijing, 100190 China and Graduate University of Chinese Academy of Sciences, Beijing, 100190 (China)

2014-01-29T23:59:59.000Z

204

Dynamic simulation of polyester mooring lines  

E-Print Network [OSTI]

A numerical scheme, known as CABLE3D, originally developed for the simulation of dynamics of steel chain-wire mooring lines is extended to allow for the large elongation in a mooring line, the dependence of the modulus on tension, and energy...

Kim, Min Suk

2004-09-30T23:59:59.000Z

205

Dynamic simulation , 1.1 INTRODUCTION  

E-Print Network [OSTI]

storage tank to prevent flashing in the line. 1.2.2 Propane Storage System Product propane from either receipt as well as product loading. Each of the storage tanks is equipped with one circulation pump Compressor Control system . Dynamic simulation , , , . STEADY STATE

Hong, Deog Ki

206

dMCS: distributed molecular communication simulator  

Science Journals Connector (OSTI)

Nanonetworking is a new research field in which nanotechnology and communication engineering disciplines are employed to explore the possible communication mechanisms at nanoscale. Inspired by living organisms, molecular communication is one of the alternatives ...

Ali Akkaya; Tuna Tugcu

2013-09-01T23:59:59.000Z

207

Quantum Monte Carlo Simulation of the High-Pressure Molecular-Atomic Crossover in Fluid Hydrogen  

Science Journals Connector (OSTI)

A first-order liquid-liquid phase transition in high-pressure hydrogen between molecular and atomic fluid phases has been predicted in computer simulations using ab initio molecular dynamics approaches. However, experiments indicate that molecular dissociation may occur through a continuous crossover rather than a first-order transition. Here we study the nature of molecular dissociation in fluid hydrogen using an alternative simulation technique in which electronic correlation is computed within quantum Monte Carlo methods, the so-called coupled electron-ion Monte Carlo method. We find no evidence for a first-order liquid-liquid phase transition.

Kris T. Delaney; Carlo Pierleoni; D. M. Ceperley

2006-12-06T23:59:59.000Z

208

Evaluation of a locus of azeotropes by molecular simulation  

SciTech Connect (OSTI)

The technique proposed here for the evaluation of azeotrope lines by molecular simulation builds on ideas used to devise the Gibbs-Duhem integration (GDI) technique for evaluating phase equilibria by molecular simulation. Beginning with a known azeotropic state point, the method integrates a differential equation for the locus of azeotropes with a single semigrand-ensemble molecular simulation performed at each integration state point. Unlike the standard GDI method, fluctuation quantities are needed to conduct the integration. Although these quantities are measured less precisely than simple ensemble averages, the integration is not adversely affected by this difficulty. The method is demonstrated by applying to three model Lennard-Hones binaries. Among these mixtures in one in which the molecular diameter o one species is varied along the azeotrope line. This application shows how details of the intermolecular interactions affect azeotropic behavior. Such an understanding might be useful in formulating additives to break an azeotrope.

Pandit, S.P.; Kofke, D.A.

1999-10-01T23:59:59.000Z

209

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

210

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

211

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

212

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

213

Physics results from dynamical overlap fermion simulations  

E-Print Network [OSTI]

I summarize the physics results obtained from large-scale dynamical overlap fermion simulations by the JLQCD and TWQCD collaborations. The numerical simulations are performed at a fixed global topological sector; the physics results in the theta-vacuum is reconstructed by correcting the finite volume effect, for which the measurement of the topological susceptibility is crucial. Physics applications we studied so far include a calculation of chiral condensate, pion mass, decay constant, form factors, as well as (vector and axial-vector) vacuum polarization functions and nucleon sigma term.

Shoji Hashimoto

2008-11-08T23:59:59.000Z

214

IGCC Dynamic Simulator and Training Center  

SciTech Connect (OSTI)

Integrated Gasification Combined Cycle (IGCC) is emerging as the technology of choice for providing clean, low-cost electricity for the next generation of coal-fired power plants and will play a central role in the development of high-efficiency, zero-emissions power plants such as FutureGen. Several major utilities and developers recently announced plans to build IGCC plants and other major utilities are evaluating IGCC’s suitability for base-load capacity additions. This recent surge of attention to IGCC power generation is creating a growing demand for experience with the analysis, operation, and control of commercial-scale IGCC plants. To meet this need, the National Energy Technology Laboratory (NETL) has launched a project to develop a generic, full-scope, IGCC dynamic plant simulator for use in establishing a state-of-the-art simulator training center at West Virginia University’s (WVU) National Research Center for Coal and Energy (NRCCE). The IGCC Dynamic Simulator & Training (DS&T) Center will be established under the auspices of the Collaboratory for Process & Dynamic Systems Modeling (“Collaboratory”) organized between NETL, WVU, the University of Pittsburgh, and Carnegie Mellon University.

Zitney, S.E.; Erbes, M.R. (Enginomix, LLC)

2006-10-01T23:59:59.000Z

215

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.

216

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

217

Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties  

SciTech Connect (OSTI)

The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments.

Mereghetti, Paolo; Gabdoulline, Razif; Wade, Rebecca C.

2010-12-01T23:59:59.000Z

218

Molecular Simulation of Hydrogen Storage in SWNT ? Shigeo MARUYAMAa  

E-Print Network [OSTI]

Molecular Simulation of Hydrogen Storage in SWNT ? Shigeo MARUYAMAa , Tatsuto KIMURAb a Eng. Res efficiency storage of hydrogen with single walled nanotubes (SWNTs) by Dillon et al. [1], experimental determinations of the storage capacity and mechanism of storage have been extensively studied. Hydrogen storage

Maruyama, Shigeo

219

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

220

Simulation of systems with dynamically varying model structure  

Science Journals Connector (OSTI)

Hybrid systems are dynamical systems composed of components with discrete and continuous behavior. Some systems change their structure during simulation, or their components behavior is essentially changing. This ''structural dynamics'' can be described ... Keywords: Discrete-continuous simulation, Hybrid systems, Modelica, Structural dynamics, VHDL-AMS

Peter Schwarz

2008-12-01T23:59:59.000Z

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

A New Motorcycle Simulator Platform: Mechatronics Design, Dynamics Modeling  

E-Print Network [OSTI]

A New Motorcycle Simulator Platform: Mechatronics Design, Dynamics Modeling and Control L. Nehaoua of these techniques to other simulators (cars and motorcycles) is possible but not direct. Indeed, the dynamics motorcycle driving simulators were build. The first prototype was developed by Honda in 1988

Paris-Sud XI, Université de

222

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

223

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

224

2005-3-21 1 Dynamic Equipment and Process Simulation  

E-Print Network [OSTI]

, reduced order) Simulation-based technology, manufacturing and ESH Metrics Current physical and chemical understanding Simulation ToolDynamic behavior through process cycle Verification Guidelines for equipment) · Gas phase transport · Reactant adsorption and byproduct desorption · Surface

Rubloff, Gary W.

225

A Quasi-Dynamic HVAC and Building Simulation Methodology  

E-Print Network [OSTI]

This thesis introduces a quasi-dynamic building simulation methodology which complements existing building simulators by allowing transient models of HVAC (heating, ventilating and air-conditioning) systems to be created in an analogous way...

Davis, Clinton Paul

2012-07-16T23:59:59.000Z

226

Avestar® - Integrated Gasification Combined Cycle (IGCC) Dynamic Simulator  

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

Integrated Gasification Combined Cycle (IGCC) Dynamic Simulator Integrated Gasification Combined Cycle (IGCC) Dynamic Simulator The AVESTAR® center offers courses using the Integrated Gasification Combined Cycle (IGCC) Dynamic Simulator. The IGCC simulator builds on and reaches beyond existing combined-cycle and conventional-coal power plant simulators to combine--for the first time--a Gasification with CO2 Capture process simulator with a Combined-Cycle power simulator together in a single dynamic simulation framework. The AVESTAR® center IGCC courses provide unique, comprehensive training on all aspects of an IGCC plant, illustrating the high-efficiency aspects of the gasifier, gas turbine, and steam turbine integration. IGCC Operator training station HMI display for overview of IGCC Plant - Train A Reference:

227

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

228

Molecular simulation as a tool for studying lignin  

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

Simulation Simulation as a Tool for Studying Lignin Amandeep K. Sangha, a,b Loukas Petridis, a,b Jeremy C. Smith, a,b,c Angela Ziebell, d,e and Jerry M. Parks a,b a UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6309; parksjm@ornl.gov (for correspondence) b BioEnergy Science Center, Oak Ridge, TN c Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 d National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401-3393; angela.ziebell@nrel.gov (for correspondence) e BioEnergy Science Center, Golden, CO Published online 30 December 2011 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/ep.10628 Lignocellulosic biomass provides a sustainable source of sugars for biofuel and biomaterial production.

229

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

230

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

231

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

232

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

233

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

234

AVESTAR® - Natural Gas Combined Cycle (NGCC) Dynamic Simulator  

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

Natural Gas Combined Cycle (NGCC) Dynamic Simulator Natural Gas Combined Cycle (NGCC) Dynamic Simulator A simulator that can provide future engineers with realistic, hands-on experience for operating advanced natural gas combined cycle (NGCC) power plants will soon be available at an innovative U.S. Department of Energy training center. Under a new cooperative research and development agreement signed by the Office of Fossil Energy's National Energy Technology Laboratory (NETL) and Invensys Operations Management, the partners will develop, test, and deploy a dynamic simulator and operator training system (OTS) for a generic NGCC power plant equipped for use with post-combustion carbon capture. NETL will operate the new dynamic simulator/OTS at the AVESTAR (Advanced Virtual Energy Simulation Training and Research) Center in Morgantown, W.Va.

235

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

236

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

237

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

238

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

239

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

240

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

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

Avestar® - Syngas-Fired Combined Cycle Dynamic Simulator  

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

Syngas-Fired Combined Cycle Dynamic Simulator Syngas-Fired Combined Cycle Dynamic Simulator The AVESTAR® center offers courses using the Combined Cycle Simulator, focusing on the power generation process after gasification. This simulator is well-suited for concentrated training on operation and control of the gas and steam turbines; condensate, feed water, and circulating water systems; heat recovery steam generator; and selective catalytic reduction (SCR) unit. Combined cycle simulator startup operations include bringing up the gas turbine to rated speed on natural gas and then switching over to the firing of synthesis gas. Key capabilities of the Combined Cycle Simulator include: Combined Cycle Simulator Operator training station HMI display for overview of Gas Turbine - Train A Normal base load operation

242

Use of High Dynamic Range Images for Improved Medical Simulations  

Science Journals Connector (OSTI)

Here we describe the use of high-dynamic range lighting techniques to improve the rendering quality of real-time medical simulation systems. Specifically we show our method of extracting the lighting information ...

Meagan Leflar; Omar Hesham; Chris Joslin

2009-01-01T23:59:59.000Z

243

Modelica® Library for Dynamic Simulation of Thermoelectric Generators  

Science Journals Connector (OSTI)

The contribution presents a new modeling library for the dynamic simulation of thermoelectric generators (TEG) in 1D spatial resolution. The core of the library is a model of the thermoelectric legs (TEL), which ...

M. Nesarajah; L. Exel; G. Frey

2014-01-01T23:59:59.000Z

244

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...

245

Detonation shock dynamics and comparisons with direct numerical simulation  

E-Print Network [OSTI]

Detonation shock dynamics and comparisons with direct numerical simulation Tariq D. Aslam # , and D­ nation and detonation shock dynamics (DSD) is made. The theory of DSD defines the motion of the detonation shock in terms of intrinsic geometry of the shock surface, in particular for condensed phase ex

Aslam, Tariq

246

Detonation shock dynamics and comparisons with direct numerical simulation  

E-Print Network [OSTI]

Detonation shock dynamics and comparisons with direct numerical simulation Tariq D. Aslam , and D- nation and detonation shock dynamics (DSD) is made. The theory of DSD defines the motion of the detonation shock in terms of intrinsic geometry of the shock surface, in particular for condensed phase ex

Aslam, Tariq

247

Patch dynamics: macroscopic simulation of multiscale systems , Y. Kevrekidis2  

E-Print Network [OSTI]

Patch dynamics: macroscopic simulation of multiscale systems G. Samaey1 , Y. Kevrekidis2 , D. Rose1-called "equation-free" framework, based on the idea of a so-called coarse-grained time-stepper. The patch dynamics microscopic model in small portions of the space-time domain (the patches). We present some theoretical

Gorban, Alexander N.

248

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

249

Parallel Transient Dynamics Simulations: Algorithms for Contact Detection  

E-Print Network [OSTI]

February 5, 1998 Abstract Transient dynamics simulations are commonly used to model phenomena such as car and deform with the objects as they undergo stress. Fluids (gasoline, water) or fluid­ like materials (soil is a natural candidate for the power of parallel computers. Unfortunately, these kinds of simulations have

Plimpton, Steve

250

Molecular simulation as a tool for studying lignin  

SciTech Connect (OSTI)

Lignocellulosic biomass provides a sustainable source of sugars for biofuel and biomaterial production. However, biomass resistance to degradation imposes difficulties for economical conversion of plant carbohydrates to fermentable sugars. One of the key contributors to recalcitrance is lignin. Understanding the properties of lignin macromolecules in the cell wall matrix is useful for manipulating biomass structure to generate more easily degradable biomass. Along with experimental techniques such as 2D-NMR and mass spectrometry, computational techniques can be useful for characterizing the structural and energetic properties of the biomass assembly and its individual constituents. Here, we provide a brief introduction to lignin, review some of the recent, relevant scientific literature, and give our perspectives on the role of molecular simulation in understanding lignin structure.

Sangha, Amandeep K [ORNL; Petridis, Loukas [ORNL; Smith, Jeremy C [ORNL; Ziebell, Angela L [ORNL; Parks, Jerry M [ORNL

2012-01-01T23:59:59.000Z

251

MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS  

SciTech Connect (OSTI)

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

Athanassios Z. Panagiotopoulos

2009-09-09T23:59:59.000Z

252

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

253

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

254

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

255

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

256

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation  

Science Journals Connector (OSTI)

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110 ...

Pengyu Ren; Jay W. Ponder

2003-05-24T23:59:59.000Z

257

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

258

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

259

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...

260

Dynamic Ball & Socket Joint Force Simulator  

E-Print Network [OSTI]

................................................. 137 Appendix F Results ............................................................................................... 144 vi LIST OF FIGURES Figure 1. Autodesk rendering of the DBSJFS mounted inside the 858 Mini Bionix Machine... the perpendicular axes. Additionally, Figure 1 on the following page is an Autodesk rending of the DBSJFS that shows the orientation of the X’, Y’, and Z axes on the simulator. 15 Figure 1. Autodesk rendering of the DBSJFS mounted inside the 858 Mini Bionix...

Farmer, Ryan Neal

2011-07-26T23:59:59.000Z

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

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

262

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

263

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

264

Dynamic Simulation of DFIG Wind Turbines on FPGA Boards  

E-Print Network [OSTI]

Dynamic Simulation of DFIG Wind Turbines on FPGA Boards Hao Chen, Student Member, IEEE, Song Sun is a friction coefficient. The wind turbine model is based on the relation between the upstream wind speed V w + 1 where p is the air density; Rw is the wind turbine radius; cp (A, (3) is the performance

Zambreno, Joseph A.

265

Interactive visual simulation of dynamic ink diffusion effects  

Science Journals Connector (OSTI)

This paper presents an effective method that simulates the ink diffusion process with visual plausible effects and real-time performance. Our algorithm updates the dynamic ink volume with a hybrid grid-particle representation: the fluid velocity field ... Keywords: industrial animation, ink diffusion, interaction, motion blur

Shibiao Xu; Xing Mei; Weiming Dong; Zhiyi Zhang; Xiaopeng Zhang

2011-12-01T23:59:59.000Z

266

DOE/NETL IGCC Dynamic Simulator Research and Training Center  

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

NETL IGCC Dynamic Simulator NETL IGCC Dynamic Simulator Research and Training Center 01 Aug 2008 Volume 2: IGCC Process Descriptions DOE/NETL-2008/1324 NETL Collaboratory for Process & Dynamic Systems Research Disclaimer This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference therein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement,

267

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

268

Simulating Field-Scale Soil Organic Carbon Dynamics Using EPIC  

SciTech Connect (OSTI)

Simulation models integrate our knowledge of soil organic C (SOC) dynamics and are useful tools for evaluating impacts of crop management on soil C sequestration; yet, they require local calibration. Our objectives were to calibrate the Environmental Policy Integrated Climate (EPIC) model, and evaluate its performance for simulating SOC fractions as affected by soil landscape and management. An automated parameter optimization procedure was used to calibrate the model for a site-specific experiment in the Coastal Plain of central Alabama. The ability of EPIC to predict corn (Zea mays L.) and cotton (Gossypium hirsutum L.) yields and SOC dynamics on different soil landscape positions (summit, sideslope and drainageway) during the initial period of conservation tillage adoption (5 years) was evaluated using regression and mean squared deviations. Simulated yield explained 88% of measured yield variation, with greatest disagreement on the sideslope position and highest agreement in the drainageway. Simulations explained approximately 1, 34 and 40% of the total variation in microbial biomass C (MBC), particulate organic C (POC) and total organic C (TOC), respectively. Lowest errors on TOC simulations (0-20 cm) were found on the sideslope and summit. We conclude that the automated parameterization was generally successful, although further work is needed to refine the MBC and POC fractions, and to improve EPIC predictions of SOC dynamics with depth. Overall, EPIC was sensitive to spatial differences in C fractions that resulted from differing soil landscape positions. The model needs additional refinement for accurate simulations of field-scale SOC dynamics affected by short-term management decisions.

Causarano, Hector J.; Shaw, Joey N.; Franzluebbers, A. J.; reeves, D. W.; Raper, Randy L.; Balkcom, Kipling S.; Norfleet, M. L.; Izaurralde, R Cesar

2007-07-01T23:59:59.000Z

269

Development of a ReaxFF Reactive Force Field for Ettringite and Study of its Mechanical Failure Modes from Reactive Dynamics Simulations  

Science Journals Connector (OSTI)

Development of a ReaxFF Reactive Force Field for Ettringite and Study of its Mechanical Failure Modes from Reactive Dynamics Simulations ... Ettringite is a hexacalcium aluminate trisulfate hydrate mineral that forms during Portland cement hydration. ... Here, we report on the development of this ReaxFF force field and on its validation and application using reactive molecular dynamics (RMD) simulations to characterize and understand the elastic, plastic, and failure response of ettringite at the atomic scale. ...

Lianchi Liu; Andres Jaramillo-Botero; William A. Goddard; III; Huai Sun

2012-03-13T23:59:59.000Z

270

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

271

Visualizations and Simulations from the Center for Simulation of Dynamic Response of Materials (ASC/ASAP)  

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

In Phase 1 of the ASC/ASAP program, The Caltech Center for Simulation of Dynamic Response of Materials developed a proof of concept for a Virtual shock physics Test Facility (VTF) in which the full three-dimensional response of a variety of target materials can be simulated for a wide range of compressive, tensional, and shear loadings, including those produced by detonation of energetic materials. The VTF is being applied to a series of integrated multiphysics simulations each with direct relevance to fundamental scientific issues in the dynamic response of materials that in turn are directly connected to proposed and existing experiments. New generations of multiscale models and terascale simulations are being created. The ASC/ASAP Gallery provides access to visualizations in the areas of materials, fluids, solids, and those related to the VTF. A section of tools and resources is available, as well as the full text of a long list of graphics-rich publications.

272

COMPUTATIONAL ANALYSIS AND SIMULATION OF BACTERIAL MOLECULAR NETWORKS  

SciTech Connect (OSTI)

The project examined a number of aspects of complex bacterial networks, their architecture, topology, dynamics and design principles.

Andrey Rzhetsky; Dimitris Anastassiou

2009-12-03T23:59:59.000Z

273

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

274

Petascale Simulations of Self-Healing Nanomaterials | Argonne...  

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

simulation of the oxidation of a fractured alumina matrix embedded with silicon carbide nanoparticles Reactive molecular dynamics simulation of the oxidation of a fractured alumina...

275

Survey of Dynamic Simulation Programs for Nuclear Fuel Reprocessing  

SciTech Connect (OSTI)

The absence of any industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other industries. Modeling programs to simulate the dynamic behavior of nuclear fuel separations and processing were originally developed to support the US government’s mission of weapons production and defense fuel recovery. Consequently there has been little effort is the US devoted towards improving this specific process simulation capability during the last two or three decades. More recent work has been focused on elucidating chemical thermodynamics and developing better models of predicting equilibrium in actinide solvent extraction systems. These equilibrium models have been used to augment flowsheet development and testing primarily at laboratory scales. The development of more robust and complete process models has not kept pace with the vast improvements in computational power and user interface and is significantly behind simulation capability in other chemical processing and separation fields.

Troy J. Tranter; Daryl R. Haefner

2008-06-01T23:59:59.000Z

276

Computer Simulation of Quantum Dynamics in a Classical Spin Environment  

E-Print Network [OSTI]

In this paper a formalism for studying the dynamics of quantum systems coupled to classical spin environments is reviewed. The theory is based on generalized antisymmetric brackets and naturally predicts open-path off-diagonal geometric phases in the evolution of the density matrix. It is shown that such geometric phases must also be considered in the quantum-classical Liouville equation for a classical bath with canonical phase space coordinates; this occurs whenever the adiabatics basis is complex (as in the case of a magnetic field coupled to the quantum subsystem). When the quantum subsystem is weakly coupled to the spin environment, non-adiabatic transitions can be neglected and one can construct an effective non-Markovian computer simulation scheme for open quantum system dynamics in classical spin environments. In order to tackle this case, integration algorithms based on the symmetric Trotter factorization of the classical-like spin propagator are derived. Such algorithms are applied to a model comprising a quantum two-level system coupled to a single classical spin in an external magnetic field. Starting from an excited state, the population difference and the coherences of this two-state model are simulated in time while the dynamics of the classical spin is monitored in detail. It is the author's opinion that the numerical evidence provided in this paper is a first step toward developing the simulation of quantum dynamics in classical spin environments into an effective tool. In turn, the ability to simulate such a dynamics can have a positive impact on various fields, among which, for example, nano-science.

Alessandro Sergi

2014-04-24T23:59:59.000Z

277

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

278

Library for modeling and simulating the thermal dynamics of buildings  

Science Journals Connector (OSTI)

Today's buildings consume more energy than any other sector of the U.S. economy, including transportation and industry; a similar importance can be expected in most European countries. Due to the increased interest in saving energy in buildings, new dynamic thermal models that describe transient response in more flexible modeling languages become necessary. Traditional building simulation software (e.g. TRNSYS or Energy Plus) are based on almost intractable simulation codes, difficult to maintain and modify, that predict system quantities at fixed time intervals. More clear code, properly separated from the simulation environment, with variable time step solvers would be necessary for the assessment of HVAC system performance with quicker dynamics. Following some ideas from a previous building thermal behavior library, a new enhanced Modelica library for modeling buildings is presented. The library basically consists of a combination of lumped parameter models and one-dimensional distributed parameter models that interconnects with each other through a set of common interfaces. Object-oriented features like class parameters and multiple-inheritance are used to improve the library structure making it easy to read and use. Complex building topologies can be built-up from component blocks that result in physically correct compound models that can be efficiently simulated and studied in any Modelica simulation environment.

Juan I. Videla; Bernt Lie

2006-01-01T23:59:59.000Z

279

A Groundwater Dynamic Simulation Model: Application to the Upper San Pedro Basin  

E-Print Network [OSTI]

A Groundwater Dynamic Simulation Model: Application to the Upper San Pedro Basin Report Prepared by using tools such as tracers to determine groundwater travel times and this dynamic simulation modeling

Fay, Noah

280

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 simulations" 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

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

282

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

283

Study of Porous Adsorbents for Carbon Capture via Molecular Simulation  

E-Print Network [OSTI]

1.5 Porous adsorbents . . . . . . . 2 Evaluating mixtureStudy of Porous Adsorbents for Carbon Capture via MolecularFall 2012 Study of Porous Adsorbents for Carbon Capture via

Swisher, Joseph Andrew

2012-01-01T23:59:59.000Z

284

Simulating Soil Carbon Dynamics, Erosion and Tillage with EPIC  

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

Simulating Soil Carbon Dynamics, Erosion Simulating Soil Carbon Dynamics, Erosion and Tillage with EPIC 1 R. C. Izaurralde (cesar.izaurralde@pnl.gov; 202-646-5227) Joint Global Change Research Institute (JGCRI) Pacific Northwest Nat'l Lab. - Univ. of Maryland 901 D St. S.W., Suite 900 Washington, DC 20024-2115 J. R. Williams (williams@brc.tamus.edu; 254-774-6124) Texas A&M University Blackland Research Center 808 East Blackland Road Temple, TX 76502 W. B. McGill (mcgill@unbc.ca) Faculty of Science and Management University of Northern British Columbia 3333 University Way, Prince George, BC V2N 4Z9 N. J. Rosenberg (nj.rosenberg@pnl.gov; 202-646-5029) Joint Global Change Research Institute (JGCRI) Pacific Northwest Nat'l Lab. - Univ. of Maryland 901 D St. S.W., Suite 900 Washington, DC 20024-2115

285

AVESTAR® - Oxy-Coal Carbon Capture (OCCC) Dynamic Simulator  

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

Oxy-Coal Carbon Capture (OCCC) Dynamic Simulator Oxy-Coal Carbon Capture (OCCC) Dynamic Simulator FutureGen 2.0 is a first-of-its-kind, near-zero emissions coal-fueled power plant using oxy-combustion technology to capture the plant's carbon emissions. To help meet the Nation's ever growing demand for clean energy, the FutureGen Industrial Alliance (Alliance) was formed to test and commercialize advanced coal-based systems fully integrated with carbon capture and geologic storage technologies. In cooperation with the U.S. Department of Energy (DOE), the Alliance and its project partners AirLiquide and Babcock & Wilcox, will upgrade an existing power plant in Meredosia, Illinois with oxy-coal carbon capture (OCCC) technology to capture and permanantly store approximately 1.0 million tonnes of CO2 each year.

286

Cellular-automaton-based simulation of 2D polymer dynamics  

Science Journals Connector (OSTI)

A cellular-automaton-based model that simulates flexible polymers in good solvents is constructed. Excluded-volume effects as well as hydrodynamic interactions are incorporated in this model in a very natural way. The center-of-mass velocity autocorrelation function of a single polymer chain in a 2D solution is found to obey a dynamic scaling relation which violates the nondraining concept.

J. M. Vianney A. Koelman

1990-04-16T23:59:59.000Z

287

Molecular Simulations of Electrolytes and Electrolyte/Electrode...  

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

Simulations of Electrolytes and ElectrolyteElectrode Interfaces Grant D. Smith and Oleg Borodin Department of Materials Science & Engineering University of Utah 02182008 "This...

288

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

289

MODELING PLANT COMPETITION WITH THE GAPS OBJECT-ORIENTED DYNAMIC SIMULATION MODEL  

E-Print Network [OSTI]

MODELING PLANT COMPETITION WITH THE GAPS OBJECT-ORIENTED DYNAMIC SIMULATION MODEL David G. Rossiter of Agronomy, Inc. #12;MODELING PLANT COMPETITION WITH THE GAPS OBJECT-ORIENTED DYNAMIC SIMULATION MODEL Abstract Modeling inter-species competition is a natural application for dynamic simulation models

Rossiter, D G "David"

290

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

291

Structural models of bioactive glasses from molecular dynamics simulations  

Science Journals Connector (OSTI)

...an excellent reference to support new fundamental investigations, whose conclusions will...bone-bonding ability of bioactive materials, fundamental investigations only need to focus on...bioactive glass-ceramic prostheses. In Handbook of bioactive ceramics: 1. Bioactive...

2009-01-01T23:59:59.000Z

292

MOLECULAR DYNAMICS SIMULATIONS OF HMX CRYSTAL POLYMORPHS USING  

E-Print Network [OSTI]

Dmitry Bedrov1 , Grant D. Smith1 , and Thomas D. Sewell2 1 Department of Materials Science & Engineering Plastic-bonded explosives (PBXs) are composites of high-explosive crystallites held together without modification in the present study with the exception that partial atomic charges were increased

Utah, University of

293

Mechanical Properties of Glassy Polyethylene Nanofibers via Molecular Dynamics Simulations  

E-Print Network [OSTI]

The extent to which the intrinsic mechanical properties of polymer fibers depend on physical size has been a matter of dispute that is relevant to most nanofiber applications. Here, we report the elastic and plastic ...

Buell, Sezen

294

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes  

Science Journals Connector (OSTI)

...Y.-T. Yu, M. A. Shapiro, E. Olson, and C. O. Rock 1998 Broad spectrum...Li, G. E. Roland, and C. O. Rock 2000 Inhibition...4654 ) 33 Villalain, J. , C. R. Mateo, F. J. Aranda, S. Shapiro, and V. Micol 2001 Membranotropic...

2011-01-01T23:59:59.000Z

295

Ab initio Molecular Dynamics Simulations of Structural Transformations in Silicon  

Science Journals Connector (OSTI)

......1985) A31. 1695[APS] . 3) Car R. , Parrinello M. Phys...combined with the conventional Car- Parrinello method. 3) The...by excluding an interstitial defective particle. The bcc structure...A31 (1985), 1695. 3) R. Car and M. Parrinello, Phys......

Tetsuya Morishita; Shuichi Nosé

2000-04-01T23:59:59.000Z

296

Molecular dynamics simulation of thermal conductivity of nanocrystalline composite films  

E-Print Network [OSTI]

October 2008 Available online 30 December 2008 a b s t r a c t The efficiency of a thermoelectric material that result in significant improvements in thermoelectric performance [1]. In particular, these materials show material, then the thermoelectric performance will increase by a factor of 2 over that of the homogeneous

Walker, D. Greg

297

Nonequilibrium Molecular Dynamics Simulation of Electric Conduction Tatsuro YUGE  

E-Print Network [OSTI]

that the system reaches a nonequilibrium steady state in the presence of an external electric field. The electrical conductivity is almost independent of the impurity distribution and the system size-Jones systems, exhibit the Fourier- type heat conduction in three dimensions, although anom- alous behaviors

Shimizu, Akira

298

A special purpose computer for ab initio molecular dynamics simulations  

E-Print Network [OSTI]

III. PARALLELIZATION SCHEME AND COMPUTER ARCHITECTURE In ourdesign of the computer architecture, and a direct anda machine, and the best computer architecture to realize our

Wang, Lin-Wang

2008-01-01T23:59:59.000Z

299

A special purpose computer for ab initio molecular dynamics simulations  

E-Print Network [OSTI]

algorithms for electronic structure calculations”, LBNLtheory electronic structure calculations” (unpublished). [processors in electronic structure calculations [21]. But

Wang, Lin-Wang

2008-01-01T23:59:59.000Z

300

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

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

intio studies of electrolytes and electrolyteelectrode interfaces Grant D. Smith and Oleg Borodin University of Utah May 11, 2011 This presentation does not contain any...

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


301

Molecular dynamics simulation studies of electrolytes and electrolyte...  

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

May 21, 2009 Project ID es40smith This presentation does not contain any proprietary, confidential, or otherwise restricted information 2 Overview * Start 20108 * Complete 1...

302

Brittle and ductile fracture of semiconductor nanowires --molecular dynamics simulations  

E-Print Network [OSTI]

potentials . . . . . . . . . . . . . . . . . . . . 7 2.4 Fundamental questions], and with their electronic properties tunable by doping [2], NWs can be used to construct nano-scale electronic devices function of these NWs is usually not to bear loads. NWs are attractive systems for studying the fundamental

Cai, Wei

303

Molecular dynamics simulation of nanoporous graphene for selective gas separation  

E-Print Network [OSTI]

Graphene with sub-nanometer sized pores has the potential to act as a filter for gas separation with considerable efficiency gains compared to traditional technologies. Nanoporous graphene membranes are expected to yield ...

Au, Harold (Harold S.)

2012-01-01T23:59:59.000Z

304

Neutron Powder Diffraction and Molecular Simulation Study of...  

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

leading to the rotation of the B-N bond parallel to the c-axis. The structural phase transition at 225 K is marked by dramatic change in the dynamics of both the amine and borane...

305

Molecular Simulation Study of Diverting Materials Used in Matrix Acidizing  

E-Print Network [OSTI]

of metal acetate, metal hydrate and square valency divided by ionic radius of the cation .............................. 224 Figure C.4 3D optimized molecular structure with Ca?O and hydrogen bond (OH?O) are connected for All calculated using B3LYP/6...

Sultan, Abdullah S.

2010-10-12T23:59:59.000Z

306

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

307

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

308

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.

309

Molecular Dynamics Simulation ofMolecular Dynamics Simulation of Asperity Shear in AluminumAsperity Shear in Aluminum  

E-Print Network [OSTI]

Hualiang Yu Science and Engineering of Materials Program, Arizona State University James B. Adams Company of America, Pa, USA #12;Motivation: Wear processes cost the US overMotivation: Wear processes costGoal: Understand deformation during indentation and wear.indentation and wear. F F V Indentation Asperity

Adams, James B

310

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

311

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

312

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

313

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

314

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

315

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

316

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

317

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

318

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

319

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.

320

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.

Note: This page contains sample records for the topic "molecular dynamics simulations" 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
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321

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

322

Modeling dilute sediment suspension using large-eddy simulation with a dynamic mixed model  

E-Print Network [OSTI]

Modeling dilute sediment suspension using large-eddy simulation with a dynamic mixed model Yi Transport of suspended sediment in high Reynolds number channel flows Re=O 600 000 is simulated using large-eddy simulation along with a dynamic-mixed model DMM . Because the modeled sediment concentration is low

Fringer, Oliver B.

323

Static and Dynamic Simulation of Steam Methane Reformers  

Science Journals Connector (OSTI)

The steam-methane reaction is an essential step for many processing plants. Hydrogen, ammonia and methanol are mostly produced by means of methane steam reforming. Since hydrogen is essential for any refinery employing hydrotreating, the performance monitoring of the hydrogen plant is highly desirable. The use of models or simulation is now a standard practice in most chemical plants and refineries. However, reliable models are still lacking for speciality reactors like the methane steam reformer. This paper describes steady-state and dynamic models for the reactions involved in reforming methane and higher hydrocarbon gases. The performance of the reformer is then illustrated by sensitivity analysis to various input disturbances like inlet pressure, temperature, feed concentration and rate, fuel rate and density and steam to carbon ratio. The effect of these disturbances on exit temperature and conversion is studied and analyzed. Catalyst deactivation effects are also discussed and it is shown by sample calculations that the simulator can give insight into catalyst performance and assist in monitoring catalyst deactivation. The transient effects are also reported and dynamic elements like gains and response time are discussed. Such information should give insight into controller design and effects of various parameters.

I.M. Alatiqi; A.M. Meziou; G.A. Gasmelseed

1989-01-01T23:59:59.000Z

324

Object-oriented modelling and simulation for the ALFRED dynamics  

Science Journals Connector (OSTI)

Abstract In this paper, a control-oriented modelling and simulation tool for the study of the Advanced Lead-cooled Fast Reactor European Demonstrator (ALFRED) plant dynamics is presented. It has been developed in order to perform design-basis transient analyses aimed at providing essential feedbacks for the system design finalization. The simulator has been meant to be modular, open and efficient. In this perspective, an object-oriented modelling approach has been adopted, by employing the reliable, tested and well-documented Modelica language. Simulation of core behaviour is based on point kinetics for neutronics and one-dimensional heat transfer models for thermal-hydraulics, coherently with ALFRED specifications. An effort has been spent to model the bayonet-tube Steam Generator (SG) foreseen to be installed within the reactor vessel. The primary loop model has been built by connecting the above-mentioned components (taking into account suitable time delays) and by incorporating the cold pool, which has revealed to be fundamental for an accurate definition of the time constants characteristic of the system because of its large thermal inertia. The description of the overall plant has been finalized by connecting standard turbine, condenser and other components of the balance of plant. Afterwards, the reactor responses to three typical transient initiators have been simulated (i.e., reduction of feedwater mass flow rate, variation of the turbine admission valve coefficient and transient of overpower). Simulation outcomes confirm the strong coupling between core and SG, besides showing the characteristic time constants of the various component responses. Results of the present study constitute a starting point in the definition of plant control strategies, laying the basis for investigation and development of a model-based control-system design.

Roberto Ponciroli; Andrea Bigoni; Antonio Cammi; Stefano Lorenzi; Lelio Luzzi

2014-01-01T23:59:59.000Z

325

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

326

Molecular Simulation of CO2 Solubility and Its Effect on Octane Swelling  

Science Journals Connector (OSTI)

Molecular Simulation of CO2 Solubility and Its Effect on Octane Swelling ... Carbon dioxide (CO2) flooding is one of the very important industrial processes for enhanced hydrocarbon recovery. ... In this study, CO2 solubility in octane and its effect on octane (n-octane) swelling are investigated by performing configurational-bias Monte Carlo simulations in the osmotic ensemble at two temperatures of 323 and 353 K and a pressure range of 2–10 MPa. ...

Junfang Zhang; Zhejun Pan; Keyu Liu; Nick Burke

2013-04-08T23:59:59.000Z

327

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

328

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

329

Linear interfacial polymerization: Theory and simulations with dissipative particle dynamics  

Science Journals Connector (OSTI)

Step-growth alternating interfacial polymerization between two miscible or immiscible monomer melts is investigated theoretically and by dissipative particle dynamics simulations. In both cases the kinetics for an initially bilayer system passes from the reaction to diffusion control. The polymer composed of immiscible monomers precipitates at the interface forming a film of nearly uniform density. It is demonstrated that the reaction proceeds in a narrow zone which expands much slower than the whole film so that newly formed polymer is extruded from the reaction zone. This concept of “reactive extrusion” is used to analytically predict the degree of polymerization and distribution of all components (monomers polymer and end groups) within the film in close agreement with the simulations. Increasing the comonomer incompatibility leads to thinner and more uniform films with the higher average degree of polymerization. The final product is considerably more polydisperse than expected for the homogeneous step-growth polymerization. The results extend the previous theoretical reports on interfacial polymerization and provide new insights into the internal film structure and polymer characteristics which are important for membrane preparation microencapsulation and 3D printing technologies. A systematic way of mapping the simulation data onto laboratory scales is discussed.

2014-01-01T23:59:59.000Z

330

VISION - Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics  

SciTech Connect (OSTI)

The U.S. DOE Advanced Fuel Cycle Initiative’s (AFCI) fundamental objective is to provide technology options that - if implemented - would enable long-term growth of nuclear power while improving sustainability and energy security. The AFCI organization structure consists of four areas; Systems Analysis, Fuels, Separations and Transmutations. The Systems Analysis Working Group is tasked with bridging the program technical areas and providing the models, tools, and analyses required to assess the feasibility of design and deployment options and inform key decision makers. An integral part of the Systems Analysis tool set is the development of a system level model that can be used to examine the implications of the different mixes of reactors, implications of fuel reprocessing, impact of deployment technologies, as well as potential "exit" or "off ramp" approaches to phase out technologies, waste management issues and long-term repository needs. The Verifiable Fuel Cycle Simulation Model (VISION) is a computer-based simulation model that allows performing dynamic simulations of fuel cycles to quantify infrastructure requirements and identify key trade-offs between alternatives. It is based on the current AFCI system analysis tool "DYMOND-US" functionalities in addition to economics, isotopic decay, and other new functionalities. VISION is intended to serve as a broad systems analysis and study tool applicable to work conducted as part of the AFCI and Generation IV reactor development studies.

Steven J. Piet; A. M. Yacout; J. J. Jacobson; C. Laws; G. E. Matthern; D. E. Shropshire

2006-02-01T23:59:59.000Z

331

Nitrogen-Doped Mesoporous Carbon for Carbon Capture – A Molecular Simulation Study  

Science Journals Connector (OSTI)

Using molecular simulation, we investigate the effect of nitrogen doping on adsorption capacity and selectivity of CO2 versus N2 in model mesoporous carbon. We show that nitrogen doping greatly enhances CO2 adsorption capacity; with a 7 wt % dopant ...

Ravichandar Babarao; Sheng Dai; De-en Jiang

2012-02-29T23:59:59.000Z

332

Molecular simulations of Hugoniots of detonation products mixtures at chemical equilibrium: Microscopic calculation  

E-Print Network [OSTI]

Molecular simulations of Hugoniots of detonation products mixtures at chemical equilibrium and chemical equilibrium of mixtures of detonation products on the Hugoniot curve. The ReMC method (W. R. Smith the system to satisfy the Hugoniot relation. Once the Hugoniot curve of the detonation products mixture

Paris-Sud XI, Université de

333

Haptic molecular simulation based on force control Aude Bolopion, Barthelemy Cagneau, Stephane Redon and Stephane Regnier  

E-Print Network [OSTI]

to manipulate the molecules, with major stability concerns. These two control modes are compared in terms of adequacy with the molecular simulator. Stability with respect to the scaling coefficients introduced of the haptic handle), to the Bubble technique (combination of position and rate control) [5]. As an alternative

Paris-Sud XI, Université de

334

Prediction of the PC-SAFT Associating Parameters by Molecular Simulation  

Science Journals Connector (OSTI)

Prediction of the PC-SAFT Associating Parameters by Molecular Simulation ... In this work, we propose a new methodology to determine association scheme and association parameters (energy and volume) of a SAFT-type EoS for hydrogen-bonding molecules. ... A new set of parameters for 1-alkanol for the PPC-SAFT equation of state has been proposed following this methodology. ...

Nicolas Ferrando; Jean-Charles de Hemptinne; Pascal Mougin; Jean-Philippe Passarello

2011-11-29T23:59:59.000Z

335

Computational fluid dynamics (CFD) simulations of aerosol in a u-shaped steam generator tube  

E-Print Network [OSTI]

as the physical model replicated for numerical simulation. Realizable k-? and standard k-? turbulence models were selected from the computational fluid dynamics (CFD) code, FLUENT, to provide the Eulerian description of the gaseous phase. Flow field simulation...

Longmire, Pamela

2009-05-15T23:59:59.000Z

336

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

337

INVESTIGATION OF SYSTEM DYNAMICS APPLIED TO BUILDING SIMULATION FOR ANTI-TERRORISM RESOURCE ALLOCATION  

E-Print Network [OSTI]

INVESTIGATION OF SYSTEM DYNAMICS APPLIED TO BUILDING SIMULATION FOR ANTI-TERRORISM RESOURCE ............................................................................. 26 2.8 Terrorism-Resistant Design

Bank, Lawrence C.

338

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

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

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

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

Localized dynamic subgrid closure for simulation of magnetohydrodynamic turbulence  

SciTech Connect (OSTI)

A local dynamic kinetic energy model (LDKM) for large-eddy simulation (LES) of magnetohydrodynamic (MHD) turbulence is proposed. The proposed MHD turbulence model evaluates all model coefficients locally and dynamically without any ad hoc averaging. This model also does not assume low magnetic Reynolds numbers. The turbulent residual-helicity effect ({alpha}-effect) appearing in the magnetic induction equation is successfully modeled. For validation, high-Re decaying isotropic decay turbulence with and without a mean magnetic field are studied using LES. The effect of rotation is also studied. For the case without rotation, it is observed that the energy spectrum follows a k{sup -5/3} law. For the case with rotation, it is shown that two mechanisms, phase scrambling due to frame rotation and Joule dissipation, are competing, and two distinct regimes with respect to rotation rate are observed. There is a critical rotation rate at which the energy decays most in MHD turbulence. It is also shown that this MHD-LDKM model is applicable to wide variety of high/low magnetic Reynolds number applications.

Miki, Kenji; Menon, Suresh [Georgia Institute of Technology, School of Aerospace Engineering, Atlanta, Georgia 30332-0150 (United States)

2008-07-15T23:59:59.000Z

342

Calibrated Langevin-dynamics simulations of intrinsically disordered proteins  

Science Journals Connector (OSTI)

We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the interresidue separations for 36 pairs of residues in five IDPs: ??, ??, and ?-synuclein, the microtubule-associated protein ?, and prothymosin ?. We find that our CG model is able to recapitulate the average interresidue separations regardless of the choice of the hydrophobicity scale, which shows that our calibrated model can robustly capture the conformational dynamics of IDPs. We then employ our model to study the scaling of the radius of gyration with chemical distance in 11 known IDPs. We identify a strong correlation between the distance to the dividing line between folded proteins and IDPs in the mean charge and hydrophobicity space and the scaling exponent of the radius of gyration with chemical distance along the protein.

W. Wendell Smith; Po-Yi Ho; Corey S. O'Hern

2014-10-13T23:59:59.000Z

343

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

344

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

345

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

346

Unexpectedly high pressure for molecular dissociation in liquid hydrogen by a reliable electronic simulation  

E-Print Network [OSTI]

The study of the high pressure phase diagram of hydrogen has continued with renewed effort for about one century as it remains a fundamental challenge for experimental and theoretical techniques. Here we employ an efficient molecular dynamics based on the quantum Monte Carlo method, which can describe accurately the electronic correlation and treat a large number of hydrogen atoms, allowing a realistic and reliable prediction of thermodynamic roperties. We find that the molecular liquid phase is unexpectedly stable and the transition towards a fully atomic liquid phase occurs at much higher pressure than previously believed. The old standing problem of low temperature atomization is, therefore, still far from experimental reach.

Mazzola, Guglielmo; Sorella, Sandro

2014-01-01T23:59:59.000Z

347

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

348

Fully-Coupled Simulations of the Rotorcraft / Ship Dynamic Interface Emre Alpman  

E-Print Network [OSTI]

representation of the effect of ship deck on the rotor wake (simplified ground effectFully-Coupled Simulations of the Rotorcraft / Ship Dynamic Interface Emre Alpman exa152@psu A fully- coupled simulation tool has been developed to analyze the rotorcraft/ship dynamic interface

349

A Numerical Model for the Dynamic Simulation of a Recirculation Single-Effect Absorption Chiller  

E-Print Network [OSTI]

A Numerical Model for the Dynamic Simulation of a Recirculation Single- Effect Absorption Chiller A dynamic model for the simulation of a new single-effect water/lithium bromide absorption chiller. Keywords: absorption; chiller; modelling; transient; water-lithium bromide; falling film hal-00713904

Paris-Sud XI, Université de

350

Effect of Hydrodynamic Interactions on DNA Dynamics in Extensional Flow: Simulation and Single Molecule Experiment  

E-Print Network [OSTI]

a combination of single molecule experimental techniques and Brownian dynamics (BD) simulation to investigate, and chain stretch in strong flows. More recently, the advent of single molecule visualizations using. A careful coupling of single molecule visualization and Brownian dynamics simulation of polymer chains

Shaqfeh, Eric

351

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

352

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

353

An Energy-Aware Simulation Model and Transaction Protocol for Dynamic Workload Distribution in Mobile Ad Hoc Networks1  

E-Print Network [OSTI]

An Energy-Aware Simulation Model and Transaction Protocol for Dynamic Workload Distribution California {tari, prong, pedram}@usc.edu Abstract This paper introduces a network simulation model

Pedram, Massoud

354

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

355

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

356

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

357

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

358

Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures  

E-Print Network [OSTI]

Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures and shrink. In this paper we present a simulation algorithm that combines single molecule simula- tions in three-dimensional space with single molecule simulations on one-dimensional structures of arbitrary

Flener, Pierre

359

The Optimal Golf Swing An exercise in simulation of dynamic systems  

E-Print Network [OSTI]

correct handling is critical. Examples are flight-simulators and the training of operators in large power Dynamic systems have many applications, and simulators may be used for training personnel in cases where of true feeling the operators experience during the simulator training d the efficiency and accuracy

Mosegaard, Klaus

360

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

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

362

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

363

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

364

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

365

Molecular size characterization of heavy oil fractions in vacuum and solution by molecular dynamic simulation  

Science Journals Connector (OSTI)

Two kinds of heavy oils were fractionated into eight fractions by Liquid-Solid Adsorption Chromatography, respectively, and samples were collected to measure properties. According to the elemental analysis, mo...

Wenpo Ren; Honggang Chen; Chaohe Yang…

2010-09-01T23:59:59.000Z

366

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

367

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

368

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

369

Dyna-CLUE Model Improvement Based on Exponential Smoothing Method and Land Use Dynamic Simulation  

Science Journals Connector (OSTI)

Response variables and their driving factors often vary with time in the process of land use dynamic simulation; however, there are few existing literatures mentioned it.In order to evaluate the impact of time fa...

Minghao Liu; Yaoxing Wang; Donghong Li…

2013-01-01T23:59:59.000Z

370

Lattice Boltzmann simulation to study multiple bubble dynamics Amit Gupta, Ranganathan Kumar *  

E-Print Network [OSTI]

Lattice Boltzmann simulation to study multiple bubble dynamics Amit Gupta, Ranganathan Kumar Keywords: Lattice Boltzmann Bubble Two-phase Coalescence a b s t r a c t Lattice Boltzmann method (LBM) has

Gupta, Amit

371

Research on propeller dynamic load simulation system of electric propulsion ship  

Science Journals Connector (OSTI)

A dynamic marine propeller simulation system was developed, which is ... requirement of theory research and engineering design of marine electric propulsion system. By applying an actual ship parameter...J? ? K ...

Hui Huang ? ?; Ai-di Shen ???; Jian-xin Chu ???

2013-04-01T23:59:59.000Z

372

Developing an integrated building design tool by coupling building energy simulation and computational fluid dynamics programs  

E-Print Network [OSTI]

Building energy simulation (ES) and computational fluid dynamics (CFD) can play important roles in building design by providing essential information to help design energy-efficient, thermally comfortable and healthy ...

Zhai, Zhiqiang, 1971-

2003-01-01T23:59:59.000Z

373

Parallel Simulation of Subsonic Fluid Dynamics on a Cluster of Workstations  

E-Print Network [OSTI]

An effective approach of simulating fluid dynamics on a cluster of non- dedicated workstations is presented. The approach uses local interaction algorithms, small communication capacity, and automatic migration of parallel ...

Skordos, Panayotis A.

1995-12-01T23:59:59.000Z

374

Dynamic simulation on collision between ship and offshore wind turbine  

Science Journals Connector (OSTI)

By using ABAQUS/Explicit, the dynamic process of an offshore wind turbine(OWT) stricken by a ship of 5000DWT...

Hongyan Ding ???; Qi Zhu ? ?; Puyang Zhang ???

2014-02-01T23:59:59.000Z

375

Experimental characterization of energetic material dynamics for multiphase blast simulation.  

SciTech Connect (OSTI)

Currently there is a substantial lack of data for interactions of shock waves with particle fields having volume fractions residing between the dilute and granular regimes, which creates one of the largest sources of uncertainty in the simulation of energetic material detonation. To close this gap, a novel Multiphase Shock Tube has been constructed to drive a planar shock wave into a dense gas-solid field of particles. A nearly spatially isotropic field of particles is generated in the test section by a gravity-fed method that results in a spanwise curtain of spherical 100-micron particles having a volume fraction of about 19%. Interactions with incident shock Mach numbers of 1.66, 1.92, and 2.02 were achieved. High-speed schlieren imaging simultaneous with high-frequency wall pressure measurements are used to reveal the complex wave structure associated with the interaction. Following incident shock impingement, transmitted and reflected shocks are observed, which lead to differences in particle drag across the streamwise dimension of the curtain. Shortly thereafter, the particle field begins to propagate downstream and spread. For all three Mach numbers tested, the energy and momentum fluxes in the induced flow far downstream are reduced about 30-40% by the presence of the particle field. X-Ray diagnostics have been developed to penetrate the opacity of the flow, revealing the concentrations throughout the particle field as it expands and spreads downstream with time. Furthermore, an X-Ray particle tracking velocimetry diagnostic has been demonstrated to be feasible for this flow, which can be used to follow the trajectory of tracer particles seeded into the curtain. Additional experiments on single spherical particles accelerated behind an incident shock wave have shown that elevated particle drag coefficients can be attributed to increased compressibility rather than flow unsteadiness, clarifying confusing results from the historical database of shock tube experiments. The development of the Multiphase Shock Tube and associated diagnostic capabilities offers experimental capability to a previously inaccessible regime, which can provide unprecedented data concerning particle dynamics of dense gas-solid flows.

Beresh, Steven Jay; Wagner, Justin L.; Kearney, Sean Patrick; Wright, Elton K.; Baer, Melvin R.; Pruett, Brian Owen Matthew

2011-09-01T23:59:59.000Z

376

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...

377

Simulation of fluid flows in the nanometer: kinetic approach and molecular dynamic simulation  

E-Print Network [OSTI]

ZHAOLI GUO{, T. S. ZHAO*, CHAO XU and YOUNG SHI National Laboratory of Coal Combustion, Huazhong fundamental researches and practical applications in material science, chemistry, microengineering and biology

Zhao, Tianshou

378

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

379

Atomic detail brownian dynamics simulations of concentrated protein...  

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

method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation,...

380

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

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

BEAM DYNAMICS SIMULATIONS FOR A DC GUN BASED INJECTOR F.Zhou 1,2,  

E-Print Network [OSTI]

BEAM DYNAMICS SIMULATIONS FOR A DC GUN BASED INJECTOR FOR PERL* F.Zhou 1,2, , I.Ben-Zvi2 , X for this machine are being extensively investigated at BNL. One of the possible options is photocathode DC gun. The schematic layout of a PERL DC gun based injector and its preliminary beam dynamics are presented

Brookhaven National Laboratory

382

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.

383

GIANT MOLECULAR CLOUD FORMATION IN DISK GALAXIES: CHARACTERIZING SIMULATED VERSUS OBSERVED CLOUD CATALOGS  

SciTech Connect (OSTI)

We present the results of a study of simulated giant molecular clouds (GMCs) formed in a Milky Way-type galactic disk with a flat rotation curve. This simulation, which does not include star formation or feedback, produces clouds with masses ranging between 10{sup 4} M{sub ?} and 10{sup 7} M{sub ?}. We compare our simulated cloud population to two observational surveys: the Boston University-Five College Radio Astronomy Observatory Galactic Ring Survey and the BIMA All-Disk Survey of M33. An analysis of the global cloud properties as well as a comparison of Larson's scaling relations is carried out. We find that simulated cloud properties agree well with the observed cloud properties, with the closest agreement occurring between the clouds at comparable resolution in M33. Our clouds are highly filamentary—a property that derives both from their formation due to gravitational instability in the sheared galactic environment, as well as to cloud-cloud gravitational encounters. We also find that the rate at which potentially star-forming gas accumulates within dense regions—wherein n{sub thresh} ? 10{sup 4} cm{sup –3}—is 3% per 10 Myr, in clouds of roughly 10{sup 6} M{sub ?}. This suggests that star formation rates in observed clouds are related to the rates at which gas can be accumulated into dense subregions within GMCs via filamentary flows. The most internally well-resolved clouds are chosen for listing in a catalog of simulated GMCs—the first of its kind. The cataloged clouds are available as an extracted data set from the global simulation.

Benincasa, Samantha M.; Pudritz, Ralph E.; Wadsley, James [Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1 (Canada); Tasker, Elizabeth J. [Department of Physics, Faculty of Science, Hokkaido University, Kita-ku, Sapporo 060-0810 (Japan)

2013-10-10T23:59:59.000Z

384

A Virtual Test Facility for the Simulation of Dynamic Response in Materials  

Science Journals Connector (OSTI)

The Center for Simulating Dynamic Response of Materials at the California Institute of Technology is constructing a virtual shock physics facility for studying the response of various target materials to very strong shocks. The Virtual Test Facility ... Keywords: parallel computing, shock physics simulation

Julian Cummings; Michael Aivazis; Ravi Samtaney; Raul Radovitzky; Sean Mauch; Dan Meiron

2002-08-01T23:59:59.000Z

385

Proper Orthogonal Decomposition-Based Modeling, Analysis, and Simulation of Dynamic Wind Load  

E-Print Network [OSTI]

Proper Orthogonal Decomposition-Based Modeling, Analysis, and Simulation of Dynamic Wind Load.1061/ ASCE 0733-9399 2005 131:4 325 CE Database subject headings: Simulation; Wind loads; Buildings; Random on the decomposition of the covariance and XPSD matrices is presented. A physically meaningful linkage between the wind

Chen, Xinzhong

386

On the self-similarity assumption in dynamic models for large eddy simulations  

E-Print Network [OSTI]

that the present formulation of the DP is usually incompatible with its under- lying self-similarity assumption SSAOn the self-similarity assumption in dynamic models for large eddy simulations Daniele Carati eddy simulations and their underlying self-similarity assumption is discussed. The interpretation

Van Den Eijnden, Eric

387

Building design and thermal renovation measures proposal by means of regression models issued from dynamic simulations  

E-Print Network [OSTI]

comparison between different energy reduction strategies, like improving the insulation levels or increasing the thermal inertia. An example of their use and a data comparison with a dynamic simulation is shown in last;Nowadays, the most reliable solutions to calculate the energy demand are the simulation energy tools

Boyer, Edmond

388

Integrating Models and Simulations of Continuous Dynamics into SysML  

E-Print Network [OSTI]

and the corresponding Modelica models; and the integration of simulation experiments with other SysML constructsIntegrating Models and Simulations of Continuous Dynamics into SysML Thomas Johnson1 Christiaan J.J. Paredis1 Roger Burkhart2 1 Systems Realization Laboratory The G. W. Woodruff School of Mechanical

389

Climate Dynamics Diagnosis of the Marine Low Cloud Simulation in the NCAR Community Earth System  

E-Print Network [OSTI]

-of-the-art coupled atmosphere-ocean models: the NCAR Community Earth System Model (CESM) and the NCEP Global of the Marine Low Cloud Simulation in the NCAR1 Community Earth System Model (CESM) and the NCEP Global2Climate Dynamics Diagnosis of the Marine Low Cloud Simulation in the NCAR Community Earth System

Bretherton, Chris

390

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

391

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

392

Coupled displacive and orderdisorder dynamics in LiNbO3 by molecular-dynamics simulation  

E-Print Network [OSTI]

transition. We find that this phase transition is a two-stage process involving a displacive transition, in the paraelectric phase each Nb ion sits at the center of a cage of six oxygen ions; in the ferroelectric structure phase the Li ions are actually displaced from the oxygen plane. Due to electrostatic repulsion, the Li

Gopalan, Venkatraman

393

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

394

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

395

Multiplatform Dynamic System Simulation of a DC-DC Converter.  

E-Print Network [OSTI]

??The work presented in this paper focuses on the usability testing for the Open-Modelica. The modeling and simulation of the BMR450 DC-DC converter is also… (more)

Song, Wenpeng

2012-01-01T23:59:59.000Z

396

Investigating dynamic underground coal fires by means of numerical simulation  

Science Journals Connector (OSTI)

......is the key to successful prediction of various combustion processes (Hjertager 1986). Ten years ago, limited computer...Blasi C.D. ,1993. Modeling and simulation of combustion processes of charring and non-charring solid fuels, Prog......

S. Wessling; W. Kessels; M. Schmidt; U. Krause

2008-01-01T23:59:59.000Z

397

An Analysis Tool for Flight Dynamics Monte Carlo Simulations  

E-Print Network [OSTI]

and analysis work to understand vehicle operating limits and identify circumstances that lead to mission failure. A Monte Carlo simulation approach that varies a wide range of physical parameters is typically used to generate thousands of test cases...

Restrepo, Carolina 1982-

2011-05-20T23:59:59.000Z

398

Dynamic Human Reliability Analysis: Benefits and Challenges of Simulating Human Performance  

SciTech Connect (OSTI)

To date, there has been considerable work on dynamic event trees and other areas related to dynamic probabilistic safety assessment (PSA). The counterpart to these efforts in human reliability analysis (HRA) has centered on the development of specific methods to account for the dynamic nature of human performance. In this paper, the author posits that the key to dynamic HRA is not in the development of specific methods but in the utilization of cognitive modeling and simulation to produce a framework of data that may be used in quantifying the likelihood of human error. This paper provides an overview of simulation approaches to HRA; reviews differences between first, second, and dynamic generation HRA; and outlines potential benefits and challenges of this approach.

R. L. Boring

2007-06-01T23:59:59.000Z

399

Computational Fluid Dynamics Simulation of Open-Channel Flows Over Bridge-Decks Under Various Flooding Conditions  

E-Print Network [OSTI]

. This study simulates limited scaled experimental data conducted elsewhere for bridge flooding in open channel simulation, Computational fluid dynamics, Flooding flows, Turbulence modeling, VOF modeling. 1. IntroductionComputational Fluid Dynamics Simulation of Open-Channel Flows Over Bridge-Decks Under Various

Kostic, Milivoje M.

400

A dynamic process model of a natural gas combined cycle -- Model development with startup and shutdown simulations  

SciTech Connect (OSTI)

Research in dynamic process simulation for integrated gasification combined cycles (IGCC) with carbon capture has been ongoing at the National Energy Technology Laboratory (NETL), culminating in a full operator training simulator (OTS) and immersive training simulator (ITS) for use in both operator training and research. A derivative work of the IGCC dynamic simulator has been a modification of the combined cycle section to more closely represent a typical natural gas fired combined cycle (NGCC). This paper describes the NGCC dynamic process model and highlights some of the simulator’s current capabilities through a particular startup and shutdown scenario.

Liese, Eric [U.S. DOE; Zitney, Stephen E. [U.S. DOE

2013-01-01T23:59:59.000Z

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

AMIP Simulation with the CAM4 Spectral Element Dynamical Core  

SciTech Connect (OSTI)

We evaluate the climate produced by the Community Earth System Model, version 1, running with the new spectral-element atmospheric dynamical core option. The spectral-element method is congured to use a cubed-sphere grid, providing quasi-uniform resolution over the sphere, increased parallel scalability and removing the need for polar filters. It uses a fourth order accurate spatial discretization which locally conserves mass and moist total energy. Using the Atmosphere Model Intercomparison Project protocol, we compare the results from the spectral-element dy- namical core with those produced by the default nite-volume dynamical core and with observations.

Evans, Katherine J [ORNL; Lauritzen, Peter [National Center for Atmospheric Research (NCAR); Mishra, Saroj [National Center for Atmospheric Research (NCAR); Neale, Rich [National Center for Atmospheric Research (NCAR); Taylor, Mark [Sandia National Laboratories (SNL); Tribbia, Joe [National Center for Atmospheric Research (NCAR)

2013-01-01T23:59:59.000Z

402

Ion and Electron Dynamics in Nonlinear PIC Simulations  

SciTech Connect (OSTI)

ITG and ETG turbulence is investigated with the nonlinear global PIC code ORB5. The large variety of numerical schemes and simulations domains used has sometimes lead to important discrepancies in the transport predictions. In order to discuss these disagreements, emphasis must be put on ways to check the numerical accuracy, such as energy conservation and numerical noise measurement. This paper therefore presents benchmarks, new algorithms and a noise diagnostic. After having demonstrated the numerical quality of our simulations, 2 topics are visited: the unclear role of the parallel nonlinearity and the transport level in ETG turbulence, for which predictions differing by one order of magnitude had been made elsewhere.

Jolliet, S.; Angelino, P.; Tran, T. M.; McMillan, B. F.; Sauter, O.; Villard, L. [Ecole Polytechnique Federale de Lausanne, Centre de Recherches en Physique des Plasmas, Association Euratom-Confederation Suisse, CH-1015 Lausanne (Switzerland); Bottino, A.; Peeters, A. G.; Poli, E. [Max Planck Institut fuer Plasmaphysik, IPP-EURATOM Association, Garching (Germany); Hatzky, R. [Computer Center of the Max-Planck-Gesellschaft, D 85748 Garching (Germany)

2006-11-30T23:59:59.000Z

403

Integrated Dynamic Simulation for Process Optimization and Control  

E-Print Network [OSTI]

wherever possible ­ Radiative heat transfer ­ Mass balance ­ Boundary layer transport ­ Surface adsorption;Schematics of Polysilicon RT-CVD Reactor MFC gas cylinder heating lamps RTP reactor RTP pumps 1st stage 2nd-level description ­ Reduced-order models to represent high complexity (e.g., reactor fluid dynamics, heat transfer

Rubloff, Gary W.

404

Darlington tritium removal facility and station upgrading plant dynamic process simulation  

SciTech Connect (OSTI)

Ontario Power Generation Nuclear (OPGN) has a 4 x 880 MWe CANDU nuclear station at its Darlington Nuclear Div. located in Bowmanville. The station has been operating a Tritium Removal Facility (TRF) and a D{sub 2}O station Upgrading Plant (SUP) since 1989. Both facilities were designed with a Distributed Control System (DCS) and programmable logic controllers (PLC) for process control. This control system was replaced with a DCS only, in 1998. A dynamic plant simulator was developed for the Darlington TRF (DTRF) and the SUP, as part of the computer control system replacement. The simulator was used to test the new software, required to eliminate the PLCs. The simulator is now used for operator training and testing of process control software changes prior to field installation. Dynamic simulation will be essential for the ITER isotope separation system, where the process is more dynamic than the relatively steady-state DTRF process. This paper describes the development and application of the DTRF and SUP dynamic simulator, its benefits, architecture, and the operational experience with the simulator. (authors)

Busigin, A. [NITEK USA, Inc., 6405 NW 77 PL, Parkland, FL 33067 (United States); Williams, G. I. D.; Wong, T. C. W.; Kulczynski, D.; Reid, A. [Ontario Power Generation Nuclear, Box 4000, Bowmanville, ON L1C 3Z8 (Canada)

2008-07-15T23:59:59.000Z

405

Dynamic simulation method for transmission and distribution planning  

Science Journals Connector (OSTI)

Under the conditions of liberalised market development optimisation role is not to be decreasing but even increasing. Basic definitions and model structure of optimisation system under market conditions is discussed in a paper, as well the experience ... Keywords: development optimisation, liberalised electricity market, power generation, power system planning, power system simulation, power transmission, risk analysis, uncertainty

Z. Krishans; I. Oleinikova; A. Mutule; J. Runcs

2006-12-01T23:59:59.000Z

406

Dynamic Deployment of Executing and Simulating Software Components  

E-Print Network [OSTI]

can reduce its processor power to conserve energy when its energy supply (i.e., battery) is low in the past, simulation merely mimicked some real-world behav- ior, we argue that in the future it will become necessary to intertwine the model world with the real world. This will be essential but not limited to cases

Egyed, Alexander

407

Periodic Boundary Conditions for Dislocation Dynamics Simulations in Three Dimensions  

E-Print Network [OSTI]

, the choice of initial configurations compatible with PBC and a consistent treatment of image stress of PBC for large-scale DD simulations in 3D. INTRODUCTION Treatment of boundary conditions or external interface (surface, crack, grain or phase boundary, etc.), it is necessary to account for stress

Cai, Wei

408

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

409

Kinetics of enzymatic starch liquefaction: simulation of the high molecular weight product distribution  

SciTech Connect (OSTI)

Enzymatic corn starch liquefaction with alpha-amylase was carried out. Molecular weight distributions of the resulting hydrolysates are presented using aqueous size exclusion chromatographic techniques. It is demonstrated that despite the fact that the enzyme employed reacts in a random endoacting manner, the product distributions are nonrandom. The results are explained in part by a multimerization process whereby the polymeric substrate molecules preferentially associate, forming intermolecular aggregates. These aggregates are either a consequence of the manner in which the material is deposited into the native granular structure of starch or due to intrinsic physical chemical properties of the polysaccharide. In the latter case, the results are shown to correspond to known multimerized amylose, although complete characterization of the polysaccharide is currently not available. The results presented are used to develop a simplified kinetic model of starch liquefaction and shown to simulate the product distributions accurately. 44 references.

Rollings, J.E.; Thompson, R.W.

1984-12-01T23:59:59.000Z

410

Molecular modelling and simulation of the surface tension of real quadrupolar fluids  

E-Print Network [OSTI]

Molecular modelling and simulation of the surface tension of fluids with force fields is discussed. 29 real fluids are studied, including nitrogen, oxygen, carbon dioxide, carbon monoxide, fluorine, chlorine, bromine, iodine, ethane, ethylene, acetylene, propyne, propylene, propadiene, carbon disulfide, sulfur hexafluoride, and many refrigerants. The fluids are represented by two-centre Lennard-Jones plus point quadrupole models from the literature. These models were adjusted only to experimental data of the vapour pressure and saturated liquid density so that the results for the surface tension are predictions. The deviations between the predictions and experimental data for the surface tension are of the order of 20 percent. The surface tension is usually overestimated by the models. For further improvements, data on the surface tension can be included in the model development. A suitable strategy for this is multi-criteria optimization based on Pareto sets. This is demonstrated using the model for carbon d...

Werth, Stephan; Klein, Peter; Küfer, Karl-Heinz; Horsch, Martin; Hasse, Hans

2014-01-01T23:59:59.000Z

411

Molecular modelling and simulation of the surface tension of real quadrupolar fluids  

E-Print Network [OSTI]

Molecular modelling and simulation of the surface tension of fluids with force fields is discussed. 29 real fluids are studied, including nitrogen, oxygen, carbon dioxide, carbon monoxide, fluorine, chlorine, bromine, iodine, ethane, ethylene, acetylene, propyne, propylene, propadiene, carbon disulfide, sulfur hexafluoride, and many refrigerants. The fluids are represented by two-centre Lennard-Jones plus point quadrupole models from the literature. These models were adjusted only to experimental data of the vapour pressure and saturated liquid density so that the results for the surface tension are predictions. The deviations between the predictions and experimental data for the surface tension are of the order of 20 percent. The surface tension is usually overestimated by the models. For further improvements, data on the surface tension can be included in the model development. A suitable strategy for this is multi-criteria optimization based on Pareto sets. This is demonstrated using the model for carbon dioxide as an example.

Stephan Werth; Katrin Stöbener; Peter Klein; Karl-Heinz Küfer; Martin Horsch; Hans Hasse

2014-08-21T23:59:59.000Z

412

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

413

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

414

Helmet Streamers with Triple Structures: Simulations of resistive dynamics  

E-Print Network [OSTI]

Recent observations of the solar corona with the LASCO coronagraph on board of the SOHO spacecraft have revealed the occurrence of triple helmet streamers even during solar minimum, which occasionally go unstable and give rise to large coronal mass ejections. There are also indications that the slow solar wind is either a combination of a quasi-stationary flow and a highly fluctuating component or may even be caused completely by many small eruptions or instabilities. As a first step we recently presented an analytical method to calculate simple two-dimensional stationary models of triple helmet streamer configurations. In the present contribution we use the equations of time- dependent resistive magnetohydrodynamics to investigate the stability and the dynamical behaviour of these configurations. We particularly focus on the possible differences between the dynamics of single isolated streamers and triple streamers and on the way in which magnetic reconnection initiates both small scale and large scale dynamical behaviour of the streamers. Our results indicate that small eruptions at the helmet streamer cusp may incessantly accelerate small amounts of plasma without significant changes of the equilibrium configuration and might thus contribute to the non-stationary slow solar wind. On larger time and length scales, large coronal eruptions can occur as a consequence of large scale magnetic reconnection events inside the streamer configuration. Our results also show that triple streamers are usually more stable than a single streamer.

T. Wiegelmann; K. Schindler; T. Neukirch

2008-01-21T23:59:59.000Z

415

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

416

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

417

Dynamic Simulation of Startup in Ethyl tert-Butyl Ether Reactive Distillation with Input Multiplicity  

Science Journals Connector (OSTI)

Dynamic Simulation of Startup in Ethyl tert-Butyl Ether Reactive Distillation with Input Multiplicity ... However, smaller internal rates inside the column that result from lower reboiler and condenser duty could increase the potential risk of flooding in the column and reduce the availability of reactants in the reactive section. ... Column simulations performed using both Pro/II and SpeedUp showed excellent agreement with previously published exptl. ...

Budi H. Bisowarno; Moses O. Tadé

2000-05-09T23:59:59.000Z

418

Simulation of ultrafast heating induced structural dynamics using a one-dimensional spring model  

Science Journals Connector (OSTI)

We developed a one-dimensional spring model to study the dynamics of lattice motion upon ultrafast laser heating. Using this model, we simulated atomic positions as a function of time in a free-standing thin monoatomic metal film as well as in a thin film on a substrate. In particular, we studied how the electronic thermal stress influences lattice expansion after the ultrafast laser heating. The simulation results agree very well with experimental data obtained with femtosecond electron diffraction.

Junjie Li; Rick Clinite; Xuan Wang; Jianming Cao

2009-07-22T23:59:59.000Z

419

Simulation of transition dynamics to high confinement in fusion plasmas  

E-Print Network [OSTI]

The transition dynamics from the low (L) to the high (H) confinement mode in magnetically confined plasmas is investigated using a first-principles four-field fluid model. Numerical results are in close agreement with measurements from the Experimental Advanced Superconducting Tokamak - EAST. Particularly, the slow transition with an intermediate dithering phase is well reproduced by the numerical solutions. Additionally, the model reproduces the experimentally determined L-H transition power threshold scaling that the ion power threshold increases with increasing particle density. The results hold promise for developing predictive models of the transition, essential for understanding and optimizing future fusion power reactors.

Nielsen, A H; Madsen, J; Naulin, V; Rasmussen, J Juul; Wan, B N

2014-01-01T23:59:59.000Z

420

Vibrational Analysis of Brucite Surfaces and the Development of an Improved Force Field for Molecular Simulation of Interfaces  

Science Journals Connector (OSTI)

We introduce a nonbonded three-body harmonic potential energy term for Mg–O–H interactions for improved edge surface stability in molecular simulations. The new potential term is compatible with the Clayff force field and is applied here to brucite, a ...

Todd R. Zeitler; Jeffery A. Greathouse; Julian D. Gale; Randall T. Cygan

2014-03-21T23:59:59.000Z

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

Molecular-level Monte Carlo simulation at fixed entropy William R. Smith a,*, Martin Lisal b,c  

E-Print Network [OSTI]

Molecular-level Monte Carlo simulation at fixed entropy William R. Smith a,*, Martin Li´sal b.05.121 * Corresponding author. Fax: +1 905 721 3304. E-mail address: william.smith@uoit.ca (W.R. Smith). www

Lisal, Martin

422

Molecular Simulation of Henry's Constant at Vapor-Liquid and Liquid-Liquid Phase Richard J. Sadus  

E-Print Network [OSTI]

coexistence. 1. Introduction Henry's constant is a well-known measure of a solute's solubility in a particularMolecular Simulation of Henry's Constant at Vapor-Liquid and Liquid-Liquid Phase Boundaries Richard to determine Henry's constant from the residual chemical potential at infinite dilution at the vapor-liquid

423

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

424

Beam-dynamics Simulations for Channeling Radiation Electron Source  

Science Journals Connector (OSTI)

Abstract The intensity and the brilliance of the compact X-ray sources based on channeling radiation are strongly dependant on the electron beam quality. It was recently proposed to combine a field-emission electron source with channeling radiation through a diamond crystal to produce high-spectral-brilliance X-rays. There are two experiments in preparation at Fermilab to prove this technique. The beam energy in the two cases are 5-MeV and 40-MeV respectively. The field-emitted beams have emittance in the nanometer range when the microbunch is 25 ps long and the charge is about 2.5fC. RF guns operating at 1.3 GHz can produce trains of at least 2 × 105 microbunches. In this contribution we present beam-dymamics simulations of a the field-emission and subsequent accelerator up to the channeling-radiation target.

D. Mihalcea; C.A. Brau; B.K. Choi; W. Gabella; J.D. Jarvis; J.W. Lewellen; M. Mendenhall; P. Piot

2014-01-01T23:59:59.000Z

425

Impact of Resolution on Simulation of Closed Mesoscale Cellular Convection Identified by Dynamically Guided Watershed Segmentation  

SciTech Connect (OSTI)

Organized mesoscale cellular convection (MCC) is a common feature of marine stratocumulus that forms in response to a balance between mesoscale dynamics and smaller scale processes such as cloud radiative cooling and microphysics. We use the Weather Research and Forecasting model with chemistry (WRF-Chem) and fully coupled cloud-aerosol interactions to simulate marine low clouds during the VOCALS-REx campaign over the southeast Pacific. A suite of experiments with 3- and 9-km grid spacing indicates resolution-dependent behavior. The simulations with finer grid spacing have smaller liquid water paths and cloud fractions, while cloud tops are higher. The observed diurnal cycle is reasonably well simulated. To isolate organized MCC characteristics we develop a new automated method, which uses a variation of the watershed segmentation technique that combines the detection of cloud boundaries with a test for coincident vertical velocity characteristics. This ensures that the detected cloud fields are dynamically consistent for closed MCC, the most common MCC type over the VOCALS-REx region. We demonstrate that the 3-km simulation is able to reproduce the scaling between horizontal cell size and boundary layer height seen in satellite observations. However, the 9-km simulation is unable to resolve smaller circulations corresponding to shallower boundary layers, instead producing invariant MCC horizontal scale for all simulated boundary layers depths. The results imply that climate models with grid spacing of roughly 3 km or smaller may be needed to properly simulate the MCC structure in the marine stratocumulus regions.

Martini, Matus; Gustafson, William I.; Yang, Qing; Xiao, Heng

2014-11-27T23:59:59.000Z

426

The molecular basis of the adsorption of xylans on cellulose surface  

Science Journals Connector (OSTI)

In order to model the adsorption of xylan on cellulose, we have simulated, at ... level, the gas phase adsorption of small xylan fragments having 5 skeletal ? (1 ?...5...), using molecular dynamics simulations. A...

Karim Mazeau; Landry Charlier

2012-04-01T23:59:59.000Z

427

A Simple Interface to Computational Fluid Dynamics Programs for Building Environment Simulations  

E-Print Network [OSTI]

. SCI can be easily integrated into new CFD programs. Introduction Advanced building design requests and pressure distributions that are crucial for thermal comfort and building structure designs. TraditionallyA Simple Interface to Computational Fluid Dynamics Programs for Building Environment Simulations

Chen, Qingyan "Yan"

428

Two-Dimensional Computational Fluid Dynamics and Conduction Simulations of Heat Transfer in Window Frames  

E-Print Network [OSTI]

1 Two-Dimensional Computational Fluid Dynamics and Conduction Simulations of Heat Transfer Arasteh and Dragan Curcija ABSTRACT Accurately analyzing heat transfer in window frame cavities radiation heat-transfer effects.) We examine three representative complex cavity cross-section profiles

429

Accounting for patterns of collective behavior in crowd locomotor dynamics for realistic simulations  

Science Journals Connector (OSTI)

Do people in a crowd behave like a set of isolated individuals or like a cohesive group? Studies of crowd modeling usually consider pedestrian behavior either from the point of view of an isolated individual or from that of large swarms. We introduce ... Keywords: collective behavior, crowd simulation, locomotion dynamics

Stéphane Bonneaud; Kevin Rio; Pierre Chevaillier; William H. Warren

2012-01-01T23:59:59.000Z

430

Ecological Modelling 180 (2004) 135151 Simulating forest fuel and fire risk dynamics across  

E-Print Network [OSTI]

fuel module tracks fine fuel, coarse fuel and live fuel for each cell on a landscape. Fine fuel age (the oldest age cohorts) in combination with disturbance history. Live fuels, also called canopyEcological Modelling 180 (2004) 135­151 Simulating forest fuel and fire risk dynamics across

He, Hong S.

431

The robust dynamical contribution to precipitation extremes in idealized warming simulations  

E-Print Network [OSTI]

The robust dynamical contribution to precipitation extremes in idealized warming simulations across shift under climate warming on the distribution of precipitation extremes and the associated sensitivity in the frequency of the most extreme categories of the precipitation events at the poleward side of the midlatitude

Chen, Gang

432

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

433

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

434

Coupled multi-body dynamics and CFD for wind turbine simulation including explicit wind turbulence  

Science Journals Connector (OSTI)

Abstract A high fidelity approach for wind turbine aero-elastic simulations including explicit representation of the atmospheric wind turbulence is presented. The approach uses a dynamic overset computational fluid dynamics (CFD) code for the aerodynamics coupled with a multi-body dynamics (MBD) code for the motion responses to the aerodynamic loads. Mann's wind turbulence model was implemented into the CFD code as boundary and initial conditions. The wind turbulence model was validated by comparing the theoretical one-point spectrum for the three components of the velocity fluctuations, and by comparing the expected statistics from the CFD simulated wind turbulent field with the explicit wind turbulence inlet boundary from Mann model. Extensive simulations based on the proposed coupled approach were conducted with the conceptual NREL 5-MW offshore wind turbine in an increasing level of complexity, analyzing the turbine behavior as elasticity, wind shear and atmospheric wind turbulence are added to the simulations. Results are compared with the publicly available simulations results from OC3 participants, showing good agreement for the aerodynamic loads and blade tip deflections in time and frequency domains. Wind turbulence/turbine interaction was examined for the wake flow. It was found that explicit turbulence addition results in considerably increased wake diffusion. The coupled CFD/MBD approach can be extended to include multibody models of the shaft, bearings, gearbox and generator, resulting in a promising tool for wind turbine design under complex operational environments.

Y. Li; A.M. Castro; T. Sinokrot; W. Prescott; P.M. Carrica

2015-01-01T23:59:59.000Z

435

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

436

Quantum walks and quantum simulation of wavepacket dynamics with twisted photons  

E-Print Network [OSTI]

The "quantum walk" has emerged recently as a paradigmatic process for the dynamic simulation of complex quantum systems, entanglement production and quantum computation. Hitherto, photonic implementations of quantum walks have mainly been based on multi-path interferometric schemes in real space. Here, we report the experimental realization of a discrete quantum walk taking place in the orbital angular momentum space of light, both for a single photon and for two simultaneous photons. In contrast to previous implementations, the whole process develops in a single light beam, with no need of interferometers; it requires optical resources scaling linearly with the number of steps; and it allows flexible control of input and output superposition states. Exploiting the latter property, we also simulated the quantum dynamics of Gaussian wavepackets, exploring the system dispersion relation in momentum space and the associated spin-orbit topological features. Our demonstration introduces a novel versatile photonic platform for quantum simulations.

Filippo Cardano; Francesco Massa; Hammam Qassim; Ebrahim Karimi; Sergei Slussarenko; Domenico Paparo; Corrado de Lisio; Fabio Sciarrino; Enrico Santamato; Robert W. Boyd; Lorenzo Marrucci

2014-07-21T23:59:59.000Z

437

Meridional circulation dynamics from 3D MHD global simulations of solar convection  

E-Print Network [OSTI]

The form of the solar meridional circulation is a very important ingredient for mean field flux transport dynamo models. Yet a shroud of mystery still surrounds this large-scale flow, given that its measurement using current helioseismic techniques is challenging. In this work we use results from 3D global simulations of solar convection to infer the dynamical behavior of the established meridional circulation. We make a direct comparison between the meridional circulation that arises in these simulations and the latest observations. Based on our results we argue that there should be an equatorward flow at the base of the convection zone at mid latitudes, below the current maximum depth helioseismic measures can probe (0.75 R). We also provide physical arguments to justify this behaviour. The simulations indicate that the meridional circulation undergoes substantial changes in morphology as the magnetic cycle unfolds. We close by discussing the importance of these dynamical changes for current methods of obse...

Passos, Dario; Miesch, Mark

2015-01-01T23:59:59.000Z

438

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

439

Development of a dynamic simulator for a natural gas combined cycle (NGCC) power plant with post-combustion carbon capture  

SciTech Connect (OSTI)

The AVESTAR Center located at the U.S. Department of Energy’s National Energy Technology Laboratory and West Virginia University is a world-class research and training environment dedicated to using dynamic process simulation as a tool for advancing the safe, efficient and reliable operation of clean energy plants with CO{sub 2} capture. The AVESTAR Center was launched with a high-fidelity dynamic simulator for an Integrated Gasification Combined Cycle (IGCC) power plant with pre-combustion carbon capture. The IGCC dynamic simulator offers full-scope Operator Training Simulator (OTS) Human Machine Interface (HMI) graphics for realistic, real-time control room operation and is integrated with a 3D virtual Immersive Training Simulator (ITS), thus allowing joint control room and field operator training. The IGCC OTS/ITS solution combines a “gasification with CO{sub 2} capture” process simulator with a “combined cycle” power simulator into a single high-performance dynamic simulation framework. This presentation will describe progress on the development of a natural gas combined cycle (NGCC) dynamic simulator based on the syngas-fired combined cycle portion of AVESTAR’s IGCC dynamic simulator. The 574 MW gross NGCC power plant design consisting of two advanced F-class gas turbines, two heat recovery steam generators (HRSGs), and a steam turbine in a multi-shaft 2x2x1 configuration will be reviewed. Plans for integrating a post-combustion carbon capture system will also be discussed.

Liese, E.; Zitney, S.

2012-01-01T23:59:59.000Z

440

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

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441

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

442

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

443

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

444

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

445

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.

446

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

447

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.

448

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.

449

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

450

Beam dynamics simulations and measurements at the Project X Test Facility  

SciTech Connect (OSTI)

Project X, under study at Fermilab, is a multitask high-power superconducting RF proton beam facility, aiming to provide high intensity protons for rare processes experiments and nuclear physics at low energy, and simultaneously for the production of neutrinos, as well as muon beams in the long term. A beam test facility - former known as High Intensity Neutrino Source (HINS) - is under commissioning for testing critical components of the project, e.g. dynamics and diagnostics at low beam energies, broadband beam chopping, RF power generation and distribution. In this paper we describe the layout of the test facility and present beam dynamics simulations and measurements.

Gianfelice-Wendt, E.; Scarpine, V.E.; Webber, R.C.; /Fermilab

2011-03-01T23:59:59.000Z

451

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

452

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

453

Dynamic transport simulation code including plasma rotation and radial electric field  

Science Journals Connector (OSTI)

A new one-dimensional transport code named TASK/TX, which is able to describe dynamic behavior of tokamak plasmas, has been developed. It solves simultaneously a set of flux-surface averaged equations composed of Maxwell's equations, continuity equations, ... Keywords: 52.25.Fi, 52.30.-q, 52.55.Fa, 52.65.-y, Finite element method, Plasma rotation, Radial electric field, SUPG, Transport simulation

M. Honda; A. Fukuyama

2008-02-01T23:59:59.000Z

454

Ultrapdeep water blowouts: COMASim dynamic kill simulator validation and best practices recommendations  

E-Print Network [OSTI]

64 3 14 30 6 8 4 3 180 Total 26.7% 35.6% 1.7% 7.8% 16.7% 3.3% 4.4% 2.2% 1.7% 100.0% * External causes are typical; storm, military activity, ship collision, fire and earthquake. Fig. 1.10 clearly shows the most blowouts occur... 1 ULTRADEEP WATER BLOWOUTS: COMASIM DYNAMIC KILL SIMULATOR VALIDATION AND BEST PRACTICES RECOMMENDATIONS A Thesis by SAMUEL F. NOYNAERT...

Noynaert, Samuel F.

2005-02-17T23:59:59.000Z

455

A Gaussian process-based approach for handling uncertainty in vehicle dynamics simulation.  

SciTech Connect (OSTI)

Advances in vehicle modeling and simulation in recent years have led to designs that are safer, easier to handle, and less sensitive to external factors. Yet, the potential of simulation is adversely impacted by its limited ability to predict vehicle dynamics in the presence of uncertainty. A commonly occurring source of uncertainty in vehicle dynamics is the road-tire friction interaction, typically represented through a spatially distributed stochastic friction coefficient. The importance of its variation becomes apparent on roads with ice patches, where if the stochastic attributes of the friction coefficient are correctly factored into real time dynamics simulation, robust control strategies could be designed to improve transportation safety. This work concentrates on correctly accounting in the nonlinear dynamics of a car model for the inherent uncertainty in friction coefficient distribution at the road/tire interface. The outcome of this effort is the ability to quantify the effect of input uncertainty on a vehicle's trajectory and the associated escalation of risk in driving. By using a space-dependent Gaussian process, the statistical representation of the friction coefficient allows for consistent space dependence of randomness. The approach proposed allows for the incorporation of noise in the observed data and a nonzero mean for inhomogeneous distribution of the friction coefficient. Based on the statistical model considered, consistent friction coefficient sample distributions are generated over large spatial domains of interest. These samples are subsequently used to compute and characterize the statistics associated with the dynamics of a nonlinear vehicle model. The information concerning the state of the road and thus the friction coefficient is assumed available (measured) at a limited number of points by some sensing device that has a relatively homogeneous noise field (satellite picture or ground sensors, for instance). The methodology proposed can be modified to incorporate information that is sensed by each individual car as it advances along its trajectory.

Schmitt, K.; Madsen, J.; Anitescu, M.; Negrut, D.; Mathematics and Computer Science; Univ. of Wisconsin at Madison

2009-01-01T23:59:59.000Z

456

Dynamic modeling of steam power cycles: Part II – Simulation of a small simple Rankine cycle system  

Science Journals Connector (OSTI)

This paper presents the second part of the work concerning the dynamic simulation of small steam cycle plants for power generation. The work is part of the preliminary study for a 600 kWe biomass fired steam power plant for which the complete open-loop, lumped parameter dynamic model of the steam cycle has been developed using the SimECS software described in Part I of this work. For these low-power plants, a dynamic simulation tool is especially useful because these systems must be designed to operate in transient mode for most of the time. The plant model presented here consists of the following components: feedwater pump, economizer, evaporator, superheater, impulse turbine, electrical generator and condenser. The primary heat source is modeled as a flue gas flow and no combustion models are incorporated yet to model the furnace. A description of the various components forming the complete steam cycle is given to illustrate the capabilities and modularity of the developed modeling technique. The model is first validated quantitatively against steady-state values obtained using a well known, reliable steady-state process modeling software. Subsequently, the dynamic validation is presented. Results can only be discussed based on the qualitative assessment of the observed trends because measurements are not available, being the plant in the preliminary design phase. The qualitative validation is based on four dynamic simulations involving three small step disturbances of different magnitude imposed on the pump rotational speed and on the flue gas mass flow and a single large ramp disturbance on the flue gas mass flow.

H. van Putten; P. Colonna

2007-01-01T23:59:59.000Z

457

An object-oriented approach to simulation of IRIS dynamic response  

Science Journals Connector (OSTI)

In this paper the development of an adequate modelling and simulation tool for Dynamics and Control tasks is presented. The key features of the developed simulator are: “Modularity” – the system model is built by connecting the models of its components, which are written independently of their boundary conditions; “Openness” – the code of each component model is clearly readable and close to the original equations and easily customised by the experienced user; “Efficiency” – the simulation code is fast; “Tool support” – the simulation tool is based on reliable, tested and well-documented software. To achieve these objectives, the Modelica language was used as a basis for the development of the simulator. The Modelica language is the result of recent advances in the field of object-oriented, multi-physics, dynamic system modelling. The language definition is open-source and it has already been successfully adopted in several industrial fields. The test bed for the application of the object-oriented approach has been the new generation, integral type, IRIS nuclear reactor. IRIS (International Reactor Innovative and Secure) is a pressurized light water cooled, small/medium power (335 MWe) reactor reactor, under development by an international consortium of nineteen organizations from ten countries. The preliminary design has been completed and the pre-application licensing process with the US-Nuclear Regulatory Commission (NRC) is underway. To provide the required capabilities for the analysis, specific models for the nuclear reactor components have been developed, to be applied for the dynamic simulation of the IRIS integral reactor, albeit keeping general validity for PWR plants. The following Modelica models have been written to satisfy the IRIS modelling requirements and are presented in this paper: point reactor kinetic, fuel heat transfer, control rods model, and a once-through type steam generator, thus obtaining a specific library of nuclear models and components. As far as other classical power generation plant components are concerned, the Thermo Power open library, developed at Politecnico di Milano as well, has been adopted and is briefly presented in the paper. Originally conceived for conventional, fossil-fired plants, the highly modular approach allowed to effectively reuse the models of the balance of plant systems, which have been connected to the models of the nuclear power generation process, to obtain a system simulator for the IRIS reactor. Finally, preliminary results of the code validation process and the reactor dynamics are presented.

Antonio Cammi; Francesco Casella; Marco E. Ricotti; Francesco Schiavo

2011-01-01T23:59:59.000Z

458

Adsorption separation of CO2 from simulated flue gas mixtures by novel CO2 ''molecular basket'' adsorbents  

Science Journals Connector (OSTI)

Adsorption separation of CO2 from simulated flue gas mixtures containing CO2, O2, and N2 by using a novel CO2 ''molecular basket'' adsorbent was investigated in a flow adsorption separation system. The novel CO2 ''molecular basket'' adsorbents were developed by synthesising mesoporous molecular sieve MCM-41 and modifying it with polyethylenimine (PEI). The influence of operation conditions, including feed flow rate, temperature, feed CO2 concentration, and sweep gas flow rate, on the CO2 adsorption/desorption separation performance and CO2 breakthrough were examined. The CO2 adsorption capacity was 91.0 ml (STP)/g-PEI, which was 27 times higher than that of the MCM-41 alone. Further, the adsorbent showed separation selectivity of greater than 1000 for CO2/N2 ratio and approximately 180 for CO2/O2, which are significantly higher than those of the MCM-41, zeolites, and activated carbons. Cyclic adsorption/desorption measurements showed that the CO2 ''molecular basket'' adsorbent was stable at 75°C. However, the CO2 ''molecular basket'' adsorbent was not stable when the operation temperature was higher than 100°C.

Xiaochun Xu; Chunshan Song; John M. Andresen; Bruce G. Miller; Alan W. Scaroni

2004-01-01T23:59:59.000Z

459

Computer simulation study of surface wave dynamics at the crystal--melt interface  

E-Print Network [OSTI]

We study, by means of computer simulations, the crystal-melt interface of three different systems: hard-spheres, Lennard Jones and the TIP4P/2005 water model. In particular, we focus on the dynamics of surface waves. We observe that the processes involved in the relaxation of surface waves are characterized by distinct time scales: a slow one related to the continuous recrystallization and melting, that is governed by capillary forces; and a fast one which we suggest to be due to a combination of processes that quickly cause small perturbations to the shape of the interface (like e. g. Rayleigh waves, subdiffusion, or attachment/detachment of particles to/from the crystal). The relaxation of surface waves becomes dominated by the slow process as the wavelength increases. Moreover, we see that the slow relaxation is not influenced by the details of the microscopic dynamics. In a time scale characteristic for the diffusion of the liquid phase, the relaxation dynamics of the crystal-melt interface of water is around one order of magnitude slower than that of Lennard Jones or hard spheres, which we ascribe to the presence of orientational degrees of freedom in the water molecule. Finally, we estimate the rate of crystal growth from our analysis of the capillary wave dynamics and compare it with previous simulation studies and with experiments for the case of water.

Jorge Benet; Luis G. MacDowell; Eduardo Sanz

2014-10-01T23:59:59.000Z

460

The viscosity radius in dilute polymer solutions: Universal behaviour from DNA rheology and Brownian dynamics simulations  

E-Print Network [OSTI]

The swelling of the viscosity radius, $\\alpha_\\eta$, and the universal viscosity ratio, $U_{\\eta R}$, have been determined experimentally for linear DNA molecules in dilute solutions with excess salt, and numerically by Brownian dynamics simulations, as a function of the solvent quality. In the latter instance, asymptotic parameter free predictions have been obtained by extrapolating simulation data for finite chains to the long chain limit. Experiments and simulations show a universal crossover for $\\alpha_\\eta$ and $U_{\\eta R}$ from $\\theta$ to good solvents in line with earlier observations on synthetic polymer-solvent systems. The significant difference between the swelling of the dynamic viscosity radius from the observed swelling of the static radius of gyration, is shown to arise from the presence of hydrodynamic interactions in the non-draining limit. Simulated values of $\\alpha_\\eta$ and $U_{\\eta R}$ are in good agreement with experimental measurements in synthetic polymer solutions reported previously, and with the measurements in linear DNA solutions reported here.

Sharadwata Pan; D. Ahirwal; Duc At Nguyen; T. Sridhar; P. Sunthar; J. Ravi Prakash

2014-05-16T23:59:59.000Z

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461

An adaptively refined phase-space element method for cosmological simulations and collisionless dynamics  

E-Print Network [OSTI]

Dark matter numerical simulations and the N-body method are essential for understanding how structure forms and evolves in the Universe. However, the discrete nature of N-body simulations can affect its accuracy when modelling collisionless systems. We introduce a new approach to simulate the gravitational evolution of cold collisionless fluids by solving the Vlasov-Poisson equations in terms of adaptively refineable "Lagrangian phase space elements". These geometrical elements are piecewise smooth maps between three-dimensional Lagrangian space and six-dimensional Eulerian phase space and approximate the continuum structure of the distribution function. They allow for dynamical adaptive splitting to follow the evolution even in regions of very strong mixing. We discuss various test problems which demonstrate the correctness and performance of our method. We show that it has several advantages compared to standard N-body algorithms by i) explicitly tracking the fine-grained distribution function, ii) naturall...

Hahn, Oliver

2015-01-01T23:59:59.000Z

462

Simulation of polar stratospheric clouds in the specified dynamics version of the whole atmosphere community climate model  

E-Print Network [OSTI]

We evaluate the simulation of polar stratospheric clouds (PSCs) in the Specified Dynamics version of the Whole Atmosphere Community Climate Model for the Antarctic winter 2005. In this model, PSCs are assumed to form ...

Wegner, T.

463

Decision Support for Green Supply Chain Operations by Integrating Dynamic Simulation and LCA Indicators: Diaper Case Study  

Science Journals Connector (OSTI)

Decision Support for Green Supply Chain Operations by Integrating Dynamic Simulation and LCA Indicators: Diaper Case Study ... Lifecycle assessment (LCA) is widely used to measure the environmental consequences assignable to a product. ... This paper proposes a framework for green supply chain management by integrating a SC dynamic simulation and LCA indicators to evaluate both the economic and environmental impacts of various SC decisions such as inventories, distribution network configuration, and ordering policy. ...

Arief Adhitya; Iskandar Halim; Rajagopalan Srinivasan

2011-10-26T23:59:59.000Z

464

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

465

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

466

Dynamic modelling of MSF plants for automatic control and simulation purposes: a survey  

Science Journals Connector (OSTI)

The successful development of a control system requires an appropriate definition of the control structure (i.e., selection of output, input and disturbance variables) and an efficient dynamical model on which the design, analysis and evaluation can be carried out. Thus, the confidence in the obtained results depends on the validity of the control structure and of the model used. For multistage flash (MSF) desalination processes, several dynamical models can be found in the literature. However, most of them are not suitable for analysis and control design purposes because they bring too many variables into play. The variables, which are sharing in the control system, normally constitute a reduced subset of the total variables that can be defined in the process. Moreover, a dynamical model suitable for control is simpler than the model derived from the physics of the underlying process. Hence, the selection of variables and the model building from the point of view of control design presents a compromise between the indispensable information contained in the model and the mathematical complexity proper of the design. In this paper, different models from the literature are analysed. Their advantages and drawbacks are described taking into account simulation and automatic control purposes. Moreover, a set of wished modelling facilities from the control engineer point of view is highlighted. Finally, a block-oriented library for Matlab/Simulink is presented, so that different plant configurations can be implemented as block diagram to simulate the system and to test control algorithms.

Adrian Gambler; Essameddin Badreddin

2004-01-01T23:59:59.000Z

467

Modeling & Simulation publications  

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

Modeling & Simulation » Modeling & Simulation » Modeling & Simulation Publications Modeling & Simulation publications Research into alternative forms of energy, especially energy security, is one of the major national security imperatives of this century. Get Expertise David Harradine Physical Chemistry and Applied Spectroscopy Email Josh Smith Chemistry Email The inherent knowledge of transformation has beguiled sorcerers and scientists alike. D.A. Horner, F. Lambert, J.D. Kress, and L.A. Collins, "Transport properties of lithium hydride from quantum molecular dynamics and orbital-free molecular dynamics," Physical Review B - Condensed Matter and Materials Physics 80(2) (2009). J.D. Kress, D.A. Horner, and L.A. Collins, "Mixing rules for optical and transport properties of warm, dense matter," AIP Conference Proceedings 1195, 931-934 (2009).

468

Numerical Simulation of Squeeze Film Dampers and Study of the Effect of Central Groove on the Dynamic Pressure Distribution  

E-Print Network [OSTI]

. The behavior of dynamic pressure profiles at different operating conditions, and the effect of a central groove on dynamic pressure profiles were also studied. Simulation results of a 3D case which is similar to the one experimentally studied by Delgado were...

Boppa, Praneetha

2012-10-19T23:59:59.000Z

469

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

470

Direct Simulation of Magnetic Resonance Relaxation Rates and Line Shapes from Molecular Trajectories  

Science Journals Connector (OSTI)

The Sydney Opera House (SOPHE) method(54) for simulating randomly oriented powder spectra is used to set the initial angles for the N trajectories included in the simulations. ... A new method for simulating randomly oriented powder spectra in magnetic resonance: the Sydney Opera House (SOPHE) method ... A new method named the Sydney Opera House (SOPHE) method for computer reconstruction of randomly oriented powder spectra in magnetic resonance is presented. ...

David P. Rangel; Philippe C. Baveye; Bruce H. Robinson

2012-04-27T23:59:59.000Z

471

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

472

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

473

Canonicalization and symplectic simulation of the gyrocenter dynamics in time-independent magnetic fields  

SciTech Connect (OSTI)

The gyrocenter dynamics of charged particles in time-independent magnetic fields is a non-canonical Hamiltonian system. The canonical description of the gyrocenter has both theoretical and practical importance. We provide a general procedure of the gyrocenter canonicalization, which is expressed by the series of a small variable ? depending only on the parallel velocity u and can be expressed in a recursive manner. We prove that the truncation of the series to any given order generates a set of exact canonical coordinates for a system, whose Lagrangian approximates to that of the original gyrocenter system in the same order. If flux surfaces exist for the magnetic field, the series stops simply at the second order and an exact canonical form of the gyrocenter system is obtained. With the canonicalization schemes, the canonical symplectic simulation of gyrocenter dynamics is realized for the first time. The canonical symplectic algorithm has the advantage of good conservation properties and long-term numerical accuracy, while avoiding numerical instability. It is worth mentioning that explicitly expressing the canonical Hamiltonian in new coordinates is usually difficult and impractical. We give an iteration procedure that is easy to implement in the original coordinates associated with the coordinate transformation. This is crucial for modern large-scale simulation studies in plasma physics. The dynamics of gyrocenters in the dipole magnetic field and in the toroidal geometry are simulated using the canonical symplectic algorithm by comparison with the higher-order non symplectic Runge-Kutta scheme. The overwhelming superiorities of the symplectic method for the gyrocenter system are evidently exhibited.

Zhang, Ruili; Tang, Yifa; Zhu, Beibei [LSEC, ICMSEC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190 (China)] [LSEC, ICMSEC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190 (China); Liu, Jian, E-mail: jliuphy@ustc.edu.cn; Xiao, Jianyuan [Department of Modern Physics and Collaborative Innovation Center for Advanced Fusion Energy and Plasma Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China)] [Department of Modern Physics and Collaborative Innovation Center for Advanced Fusion Energy and Plasma Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China); Qin, Hong [Department of Modern Physics and Collaborative Innovation Center for Advanced Fusion Energy and Plasma Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China) [Department of Modern Physics and Collaborative Innovation Center for Advanced Fusion Energy and Plasma Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China); Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States)

2014-03-15T23:59:59.000Z

474

Numerical simulation of the stochastic dynamics of inclusions in biomembranes in presence of surface tension  

E-Print Network [OSTI]

The stochastic dynamics of inclusions in a randomly fluctuating biomembrane is simulated. These inclusions can represent the embedded proteins and the external particles arriving at a cell membrane. The energetics of the biomembrane is modelled via the Canham-Helfrich Hamiltonian. The contributions of both the bending elastic-curvature energy and the surface tension of the biomembrane are taken into account. The biomembrane is treated as a two-dimensional sheet whose height variations from a reference frame is treated as a stochastic Wiener process. The lateral diffusion parameter associated with this Wiener process coupled with the longitudinal diffusion parameter obtained from the standard Einsteinian diffusion theory completely determine the stochastic motion of the inclusions. It is shown that the presence of surface tension significantly affects the overall dynamics of the inclusions, particularly the rate of capture of the external inclusions, such as drug particles, at the site of the embedded inclusions, such as the embedded proteins.

H. Rafii-Tabar; H. R. Sepangi

2005-08-30T23:59:59.000Z

475

Analog and digital dynamic simulations of a rigid body aircraft in straight and level flight  

E-Print Network [OSTI]

. , Texas A&M University Directed by: Dr. Balusu M. Rao A study of the dynamic response characteristics of an aircraft at low approach speeds was conducted using both a digital and an analog computer to simulate a DeHavilland "Beaver" DHC-2 in flight... to produce more sideslip and yawing motions than the rudder with analytical solutions. The problem areas of the STOL aircraft at low approach speeds as a result of a study of the DeHavilland "Beaver" were in lateral stability. The aircraft's response...

Stroman, Morris Michael

2012-06-07T23:59:59.000Z

476

Design strategy for a Chemical Looping Combustion system using process simulation and Computational Fluid Dynamics  

Science Journals Connector (OSTI)

A strategy for design and optimisation of chemical processes involving multiple fluidised bed reactors is presented through a combination of standard design calculations, process simulation and Computational Fluid Dynamics (CFD). The strategy is demonstrated in designing a Chemical Looping Combustion (CLC) process that generates 12.5 kW of heat in the air reactor. The resulting design strategy will allow for very economical investigations into various design and optimisation considerations. It also offers a platform from which to conduct virtual prototyping investigations for new process concepts, which will lead to significant economic benefits when compared with a traditional experimental process development strategy.

Schalk Cloete; Shahriar Amini

2012-01-01T23:59:59.000Z

477

Use of Aria to simulate laser weld pool dynamics for neutron generator production.  

SciTech Connect (OSTI)

This report documents the results for the FY07 ASC Integrated Codes Level 2 Milestone number 2354. The description for this milestone is, 'Demonstrate level set free surface tracking capabilities in ARIA to simulate the dynamics of the formation and time evolution of a weld pool in laser welding applications for neutron generator production'. The specialized boundary conditions and material properties for the laser welding application were implemented and verified by comparison with existing, two-dimensional applications. Analyses of stationary spot welds and traveling line welds were performed and the accuracy of the three-dimensional (3D) level set algorithm is assessed by comparison with 3D moving mesh calculations.

Noble, David R.; Notz, Patrick K.; Martinez, Mario J.; Kraynik, Andrew Michael

2007-09-01T23:59:59.000Z

478

Cooling Energy Demand Evaluation by Meansof Regression Models Obtained From Dynamic Simulations  

E-Print Network [OSTI]

was calculated to be -8.78oC (Moscow in January) and maximum of 42.9 oC (Abu-Dhabi in August). The hourly values of outdoor air temperature and solar radiation were obtained using Trnsys (Trnsys, 2006) meteonorm files. b) Glazing surface and distribution... the ,,black-box,, function, dynamic simulations were conducted using Trnsys 16 software (Trnsys, 2005). The Trnsys building model, known as, Type 56, is compliant with general requirements of European Directive on the energy performance of buildings...

Catalina, T.; Virgone, J.

2011-01-01T23:59:59.000Z

479