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Note: This page contains sample records for the topic "molecular dynamics simulation" from the National Library of EnergyBeta (NLEBeta).
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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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1

Fluctuations in molecular dynamics simulations  

Science Conference Proceedings (OSTI)

Statistical fluctuations of a system about its equilibrium state, monitored in a molecular dynamics simulation, are an effective means of computing the thermodynamic and kinetic properties of interfaces in metals and alloys. In this work, three applications ... Keywords: Fluctuations, Grain boundaries, Interfaces, Interfacial free energy, Mobility, Molecular dynamics

J. J. Hoyt; Z. T. Trautt; M. Upmanyu

2010-03-01T23:59:59.000Z

2

A Molecular Dynamics Simulation  

Science Conference Proceedings (OSTI)

Ab Initio Local Energy and Local Stress Calculations: Applications to Materials ... Computational Fluid Dynamics and Experimental Results for the Horizontal .... Films and Applications to a New Generation of Multifunctional Devices/Systems.

3

Radiation in molecular dynamic simulations  

DOE Green Energy (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

LAMMPS Molecular Dynamics Simulator - TMS  

Science Conference Proceedings (OSTI)

Nov 8, 2007 ... LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, ...

5

Molecular Statics and Molecular Dynamics Simulations of the ...  

Science Conference Proceedings (OSTI)

Presentation Title, Molecular Statics and Molecular Dynamics Simulations of the Critical Stress for Motion of a/3 Screw Dislocations in a-Ti at Low ...

6

Phonostat: Thermostatting phonons in molecular dynamics simulations  

E-Print Network (OSTI)

Thermostat algorithms in a molecular dynamics simulation maintain an average temperature of a system by regulating the atomic velocities rather than the internal degrees of freedom. Herein, we present a “phonostat” algorithm ...

Raghunathan, Rajamani

7

Molecular dynamics simulations and drug discovery  

E-Print Network (OSTI)

JE: On the determination of molecular fields. II. From thescalability for parallel molecular dynamics. J Comput PhysKale L, Schulten K: Scalable molecular dynamics with NAMD. J

Durrant, Jacob D; McCammon, J Andrew

2011-01-01T23:59:59.000Z

8

Molecular dynamics simulations of ordered alkane chains physisorbed on graphite  

E-Print Network (OSTI)

Molecular dynamics simulations of ordered alkane chains physisorbed on graphite Reinhard Hentschke molecular axes oriented parallel to the substrate. Here we employ molecular dynamics (MD) simulations to obtain more details on the molecular order and dynamics within the alkane lamellae as a function

Peters, Achim

9

Molecular Dynamics Simulations of Thermoset Polymers for ...  

Science Conference Proceedings (OSTI)

Materials Genomics Past & Future: From CALPHAD to Flight · Modelling the Properties of Multi-Component Commercial Alloys · Molecular Dynamics ...

10

Molecular dynamics simulation of Li surface erosion and bubble formation  

E-Print Network (OSTI)

Molecular dynamics simulation of Li surface erosion and bubble formation Z. Insepov *, A. Hassanein Structure and dynamical properties of liquid Li containing He atoms were studied by the Molecular Dynamics devices. Molecular dynamics (MD) method is capable of studying important collision processes and providing

Harilal, S. S.

11

Molecular Dynamics Simulations of Microscale Fluid Transport  

E-Print Network (OSTI)

Recent advances in micro-science and technology, like Micro-ElectroMechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these nonequilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and address both scaling and modeling issues...

C. C. Wong; A. R. Lopez; M.J. Stevens; S. J. Plimpton; Category Uc; Like Micro-electro

1998-01-01T23:59:59.000Z

12

Molecular Dynamics Simulation of Cavitation in Metallic Glass  

Science Conference Proceedings (OSTI)

We have undertaken a series of molecular dynamics simulations of cavitation under hydrostatic tension in a binary metallic glass analog using pair-wise ...

13

Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters  

Science Conference Proceedings (OSTI)

We have developed a scalable hierarchical parallelization scheme for molecular dynamics (MD) simulation on multicore clusters. The scheme explores multilevel parallelism combining: (1) Internode parallelism using spatial decomposition via message passing; ... Keywords: Molecular dynamics simulation, Multicore cluster, Scalable hierarchical parallelization scheme, Single instruction multiple data

Liu Peng; Manaschai Kunaseth; Hikmet Dursun; Ken-Ichi Nomura; Weiqiang Wang; Rajiv K. Kalia; Aiichiro Nakano; Priya Vashishta

2011-07-01T23:59:59.000Z

14

Anton, a special-purpose machine for molecular dynamics simulation  

Science Conference Proceedings (OSTI)

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, ... Keywords: bioinformatics, biomolecular system simulation, computational biology, computational drug design, molecular dynamics, protein folding, protein structure, special-purpose machine

David E. Shaw; Martin M. Deneroff; Ron O. Dror; Jeffrey S. Kuskin; Richard H. Larson; John K. Salmon; Cliff Young; Brannon Batson; Kevin J. Bowers; Jack C. Chao; Michael P. Eastwood; Joseph Gagliardo; J. P. Grossman; C. Richard Ho; Douglas J. Ierardi; István Kolossváry; John L. Klepeis; Timothy Layman; Christine McLeavey; Mark A. Moraes; Rolf Mueller; Edward C. Priest; Yibing Shan; Jochen Spengler; Michael Theobald; Brian Towles; Stanley C. Wang

2007-06-01T23:59:59.000Z

15

Molecular Dynamics Simulations of Vacancy and Oxygen Diffusion ...  

Science Conference Proceedings (OSTI)

A Tale of Two States and More: Modeling of New Generation of Lattice Stability from Zero ... Analysis of Nano Fluid Using CFD-A Hybrid Approach for Cooling Purpose ... Molecular Dynamics Simulations of Grain Boundary Free Energy and

16

Millisecond-scale molecular dynamics simulations on Anton  

Science Conference Proceedings (OSTI)

Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware dramatically increases the speed of MD calculations, making possible for the first ...

David E. Shaw; Ron O. Dror; John K. Salmon; J. P. Grossman; Kenneth M. Mackenzie; Joseph A. Bank; Cliff Young; Martin M. Deneroff; Brannon Batson; Kevin J. Bowers; Edmond Chow; Michael P. Eastwood; Douglas J. Ierardi; John L. Klepeis; Jeffrey S. Kuskin; Richard H. Larson; Kresten Lindorff-Larsen; Paul Maragakis; Mark A. Moraes; Stefano Piana; Yibing Shan; Brian Towles

2009-11-01T23:59:59.000Z

17

Anton, a special-purpose machine for molecular dynamics simulation  

Science Conference Proceedings (OSTI)

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro-molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, ...

David E. Shaw; Martin M. Deneroff; Ron O. Dror; Jeffrey S. Kuskin; Richard H. Larson; John K. Salmon; Cliff Young; Brannon Batson; Kevin J. Bowers; Jack C. Chao; Michael P. Eastwood; Joseph Gagliardo; J. P. Grossman; C. Richard Ho; Douglas J. Ierardi; István Kolossváry; John L. Klepeis; Timothy Layman; Christine McLeavey; Mark A. Moraes; Rolf Mueller; Edward C. Priest; Yibing Shan; Jochen Spengler; Michael Theobald; Brian Towles; Stanley C. Wang

2008-07-01T23:59:59.000Z

18

Molecular Dynamics Simulation of Thermoset Fracture with ...  

Science Conference Proceedings (OSTI)

The effects of resin chain extensibility and dilution on fracture behavior are studied by testing a variety of molecular systems. The molecular bases for precursors ...

19

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

DOE Data Explorer (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

20

Molecular dynamics simulation of deuterium trapping and bubble formation in tungsten  

E-Print Network (OSTI)

Molecular dynamics simulation of deuterium trapping and bubble formation in tungsten Xue Yang using classical molecular dynamic methods. " Low energy deuterium atoms tend to affix to high environment. The deuterium bombardment of monocrystalline tungsten was modeled by molecular dynamics

Harilal, S. S.

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


21

Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems  

Science Conference Proceedings (OSTI)

The acceleration of molecular dynamics (MD) simulations using high-performance reconfigurable computing (HPRC) has been much studied. Given the intense competition from multicore and GPUs, there is now a question whether MD on HPRC can be competitive. ... Keywords: FPGA-based coprocessors, application acceleration, bioinformatics, biological sequence alignment, high performance reconfigurable computing

Matt Chiu; Martin C. Herbordt

2010-11-01T23:59:59.000Z

22

Phase-field Simulations/Molecular Dynamics  

Science Conference Proceedings (OSTI)

The sharp interface model was used to determine the SLI free energy and its anisotropy by fitting to the MD data. Finally, the MD simulation of the B2 growth ...

23

Transforming molecular biology research through extreme acceleration of AMBER molecular dynamics simulations: sampling for the 99%  

Science Conference Proceedings (OSTI)

This talk will cover recent developments in the acceleration of Molecular Dynamics Simulations using NVIDIA Graphics Processing units with the AMBER software package. In particular it will focus on recent algorithmic improvements aimed at accelerating ...

Ross C. Walker; Levi Pierce; Romelia Salomon

2012-07-01T23:59:59.000Z

24

Prototyping Bio-Nanorobots using Molecular Dynamics Simulation  

E-Print Network (OSTI)

This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can design and characterize through physical simulation and 3-D visualization the behavior of Bio-NanoRobotic components and structures. The main novelty of the proposed simulations is based on the characterization of stiffness performances of passive joints-based deca-alanine protein molecule and active joints-based viral protein motor (VPL) in their native environment. Their use as elementary Bio-NanoRobotic components (1 dof platform) are also simulated and the results discussed.

Hamdi, Mustapha; Ferreira, A; Mavroidis, Constantinos

2007-01-01T23:59:59.000Z

25

Molecular dynamics simulation of displacement cascades in FeCr alloys  

E-Print Network (OSTI)

Molecular dynamics simulation of displacement cascades in Fe­Cr alloys L. Malerba a,*, D. Terentyev by displacement cascades in the relevant material. Molecular dynamics (MD) is well known to be the simulation tool

26

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine  

E-Print Network (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.

Rapaport, D C

2009-01-01T23:59:59.000Z

27

Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit  

E-Print Network (OSTI)

Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further speedup the computations.

Ji Xu; Ying Ren; Wei Ge; Xiang Yu; Xiaozhen Yang; Jinghai Li

2010-01-21T23:59:59.000Z

28

The molecular dynamics simulation of ion-induced ripple growth  

Science Conference Proceedings (OSTI)

The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength ({lambda}) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths ({lambda}35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in {lambda} long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for {lambda}>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.

Suele, P. [Research Institute for Technical Physics and Materials Science, Konkoly Thege u. 29-33, 1125 Budapest (Hungary); Heinig, K.-H. [Institute of Ion Beam Physics and Materials Research, Forschungszentrum Dresden-Rossendorf, P.O. Box 51 01 19, 01314 Dresden (Germany)

2009-11-28T23:59:59.000Z

29

Molecular Dynamics Simulations to Compute the Bulk Response of Amorphous PMMA  

E-Print Network (OSTI)

Molecular Dynamics Simulations to Compute the Bulk Response of Amorphous PMMA S.B. Sane* , T. Cagin of molecular dynamics computations and corresponding values of laboratory measurements are compared to assess computational methods has offered the potential for "molecular dynamics" simulations to predict the mechanical

Goddard III, William A.

30

Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen  

DOE Green Energy (OSTI)

The temperature equilibration rate in dense hydrogen (for both T{sub i} > T{sub e} and T{sub i} < T{sub e}) has been calculated with large-scale molecular dynamics simulations for temperatures between 10 and 300 eV and densities between 10{sup 20}/cc to 10{sup 24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L {approx}> 1, Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] with the sub-leading corrections and the fit of Gericke-Murillo-Schlanges [Gericke et al., PRE 65, 036418 (2003)] to the T-matrix evaluation of the collision operator, agrees with the MD data to within the error bars of the simulation. For more strongly-coupled plasmas where L {approx}< 1, our numerical results are consistent with the fit of Gericke-Murillo-Schlanges.

Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M; Benedict, L; Hau-Riege, S; Langdon, A; London, R

2008-02-14T23:59:59.000Z

31

Lightweight computational steering of very large scale molecular dynamics simulations  

Science Conference Proceedings (OSTI)

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.

Beazley, D.M. [Univ. of Utah, Salt Lake City, UT (United States). Dept. of Computer Science; Lomdahl, P.S. [Los Alamos National Lab., NM (United States)

1996-09-01T23:59:59.000Z

32

Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite  

E-Print Network (OSTI)

Abstract. Hydrogen adsorption by graphite is examined by classical molecular dynamics simulation using a modified Brenner REBO potential. Such interactions are typical in chemical sputtering experiments, and knowledge of the fundamental behavior of hydrogen and graphene in collisional conditions is essential for modeling the sputtering mechanism. The hydrogen adsorption rate is found to be dependent on the incident hydrogen energy and not on graphene temperature. Rather than destroying the graphene, hydrogen incidence at energies of less than 100 eV can be classified into three regimes of adsorption, reflection and penetration through one or more graphene layers. Incidence at the lowest energies is shown to distort the graphene structure. 1.

unknown authors

2005-01-01T23:59:59.000Z

33

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.

34

Structural Modeling and Molecular Dynamics Simulation of the Actin Filament  

DOE Green Energy (OSTI)

Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

Splettstoesser, Thomas [University of Heidelberg; Holmes, Kenneth [Max Planck Institute, Heidelberg, Germany; Noe, Frank [DFG Research Center Matheon, FU Berlin, Germany; Smith, Jeremy C [ORNL

2011-01-01T23:59:59.000Z

35

Force spectroscopy of polymer desorption: Theory and Molecular Dynamics simulation  

E-Print Network (OSTI)

Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics (MD) simulations with Langevin thermostat. The suggested approach makes it possible to go beyond the limitations of the conventional Bell-Evans model. We observe a series of characteristic force spikes when the pulling force is measured against the cantilever displacement during detachment at constant velocity $v_c$ (displacement control mode) and find that the average magnitude of this force increases as $v_c$ grows. The probability distributions of the pulling force and the end-monomer distance from the surface at the moment of final detachment are investigated for different adsorption energy $\\epsilon$ and pulling velocity $v_c$. Our extensive MD-simulations validate and support the main theoretical findings. Moreover, the simulation reveals a novel behavior: for a strong-friction and massive cantilever the force spikes pattern is smeared out at large $v_c$. As a challenging task for experimental bio-polymers sequencing in future we suggest the fabrication of stiff, super-light, nanometer-sized AFM probe.

J. Paturej; J. L. A. Dubbeldam; V. G. Rostiashvili; A. Milchev; T. A. Vilgis

2013-10-14T23:59:59.000Z

36

The implementation of polarizable and flexible models in molecular dynamics simulations  

Science Conference Proceedings (OSTI)

We discuss a new methodology for implementing polarizable and flexible molecular models - the fluctuating charge and intramolecular potential (fCINTRA) method - in Molecular Dynamics (MD) simulations. An example has been provided for ethanol. In these ... Keywords: message passing interface, molecular dynamics simulation, polarizable and flexible model

Shihao Wang; Natalie M. Cann

2009-06-01T23:59:59.000Z

37

A Complexity O(1) priority queue for event driven molecular dynamics simulations  

Science Conference Proceedings (OSTI)

We propose and implement a priority queue suitable for use in event driven molecular dynamics simulations. All operations on the queue take on average O(1) time per collision. In comparison, previously studied queues for event driven molecular dynamics ... Keywords: Molecular dynamics, Priority queue

Gerald Paul

2007-02-01T23:59:59.000Z

38

Enhanced molecular dynamics for simulating porous interphase layers in batteries.  

DOE Green Energy (OSTI)

Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.

Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan (Rice University, Houston, TX)

2009-10-01T23:59:59.000Z

39

Surface detection, meshing and analysis during large molecular dynamics simulations  

SciTech Connect

New techniques are presented for the detection and analysis of surfaces and interfaces in atomistic simulations of solids. Atomistic and other particle-based simulations have no inherent notion of a surface, only atomic positions and interactions. The algorithms we introduce here provide an unambiguous means to determine which atoms constitute the surface, and the list of surface atoms and a tessellation (meshing) of the surface are determined simultaneously. The algorithms have been implemented and demonstrated to run automatically (on the fly) in a large-scale parallel molecular dynamics (MD) code on a supercomputer. We demonstrate the validity of the method in three applications in which the surfaces and interfaces evolve: void surfaces in ductile fracture, the surface morphology due to significant plastic deformation of a nanoscale metal plate, and the interfaces (grain boundaries) and void surfaces in a nanoscale polycrystalline system undergoing ductile failure. The technique is found to be quite robust, even when the topology of the surfaces changes as in the case of void coalescence where two surfaces merge into one. It is found to add negligible computational overhead to an MD code, and is much less expensive than other techniques such as the solvent-accessible surface.

Dupuy, L M; Rudd, R E

2005-08-01T23:59:59.000Z

40

A scalable parallel algorithm for dynamic range-limited n-tuple computation in many-body molecular dynamics simulation  

Science Conference Proceedings (OSTI)

Recent advancements in reactive molecular dynamics (MD) simulations based on many-body interatomic potentials necessitate efficient dynamic n-tuple computation, where a set of atomic n-tuples within a given spatial range is constructed ... Keywords: dynamic range-limited n-tuple computation, molecular dynamics, parallel computing

Manaschai Kunaseth, Rajiv K. Kalia, Aiichiro Nakano, Ken-ichi Nomura, Priya Vashishta

2013-11-01T23:59:59.000Z

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

Order parameter prediction from molecular dynamics simulations in proteins  

E-Print Network (OSTI)

A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy barriers and within a complex energy landscape. This makes it very difficult to reliably connect, for example by all-atom molecular dynamics calculations, the states, their energies and the pathways between them. A major issue needed to improve sampling on the intermediate states is an order parameter -- a reduced descriptor for the major subset of degrees of freedom -- that can be used to aid sampling for the large conformational change. We present a novel way to combine information from molecular dynamics using non-linear time series and dimensionality reduction, in order to quantitatively determine an order parameter connecting two large-scale conformationally distinct protein states. This new method suggests an implementation for molecular dynamics calculations that ma...

Perilla, Juan R

2011-01-01T23:59:59.000Z

42

Nanoaggregation and solubility of crude oil asphaltenes from molecular dynamics simulations  

Science Conference Proceedings (OSTI)

The aggregation and solubility of asphaltenes are studied by classical molecular dynamics simulations. Average three-dimensional atomistic models are built on the basis of experimental data for the asphaltenes from a series of crude oil samples. The ... Keywords: Hildebrand, aggregation, asphaltene, forcefield, molecular dynamics, oil, simulation, solubility, solvent

Francesco Frigerio

2009-12-01T23:59:59.000Z

43

Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films  

E-Print Network (OSTI)

Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the wall-fluid interface. In order to properly simulate the flow and heat transfer in nano-scale channels, an interactive thermal wall model is developed. Using this model, the Fourier’s law of heat conduction is verified in a 3.24 nm height channel, where linear temperature profiles with constant thermal conductivity is obtained. The thermal conductivity is verified using the predictions of Green-Kubo theory. MD simulations at different wall wettability ( ??f /? ) and crystal bonding stiffness values (K) have shown temperature jumps at the liquid/solid interface, corresponding to the well known Kapitza resistance. Using systematic studies, the thermal resistance length at the interface is characterized as a function of the surface wettability, thermal oscillation frequency, wall temperature and thermal gradient. An empirical model for the thermal resistance length, which could be used as the jump-coefficient of a Navier boundary condition, is developed. Temperature distributions in the nano-channels are predicted using analytical solution of the continuum heat conduction equation subjected to the new temperature jump condition, and validated using the MD results. Momentum and heat transfer in shear driven nanochannel flows are also investigated. Work done by the viscous stresses heats the fluid, which is dissipated through the channel walls, maintained at isothermal conditions. Spatial variations in the fluid density, kinematic viscosity, shear- and energy dissipation rates are presented. The energy dissipation rate is almost a constant for ??f /? < 0.6, which results in parabolic temperature profiles in the domain with temperature jumps due to the Kapitza resistance at the liquid/solid interfaces. Using the energy dissipation rates predicted by MD simulations and the continuum energy equation subjected to the temperature jump boundary conditions developed in this study, the analytical solutions are obtained for the temperature profiles, which agree well with the MD results.

Kim, Bo Hung

2009-05-01T23:59:59.000Z

44

Performance analysis and optimization of molecular dynamics simulation on Godson-T many-core processor  

Science Conference Proceedings (OSTI)

Molecular dynamics (MD) simulation has broad applications, but its irregular memory-access pattern makes performance optimization a challenge. This paper presents a joint application/architecture study to enhance on-chip parallelism of MD on Godson-T ...

Liu Peng; Aiichiro Nakano; Guangming Tan; Priya Vashishta; Dongrui Fan; Hao Zhang; Rajiv K. Kalia; Fenglong Song

2011-05-01T23:59:59.000Z

45

A molecular dynamics simulation study of elastic properties of HMX Thomas D. Sewell and Ralph Menikoff  

E-Print Network (OSTI)

. (1989a,b) from a molecular dynamics simulation of the measured structure factor results of Susman et al., and BOLLER,A.,1994, Thermochim. Acta, 238, 227. ZHANG,M., and BOOLCHAND,P.,1994, Science, 266, 1355. 1772

Utah, University of

46

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

SciTech Connect

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

Molecular dynamics simulation of strongly coupled QCD plasmas  

E-Print Network (OSTI)

The properties of a strongly interacting quark plasma are investigated by molecular dynamics method including non-abelian quark-quark potential. Our main goal is to study the thermalization process in this system. We find an interesting resonance-like behaviour: at a characteristic time close to the inverse plasma frequency the quark plasma is heated up substantially via energy transfer from quark potential energy into one particle kinetic energy. Color rotation mechanism enhances the effectivity of this heating process, leading to a very fast thermalization with high temperature.

P. Hartmann; Z. Donko; P. Levai; G. J. Kalman

2006-01-06T23:59:59.000Z

48

Processed Splitting Algorithms for Rigid-Body Molecular Dynamics Simulations  

E-Print Network (OSTI)

A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and orientational coordinates are decoded by processing transformations. This allows to overcome the barrier on the order of precision of the integration at a given number of force-torque evaluations per time step. Testing in dynamics of water versus previous methods shows that the obtained algorithms significantly improve the accuracy of the simulations without extra computational costs.

Igor P. Omelyan

2008-05-15T23:59:59.000Z

49

Molecular dynamics simulation of UO2 nanocrystals melting  

E-Print Network (OSTI)

In this article we study melting of uranium dioxide (UO2) nanocrystals (NC) isolated in vacuum (i.e. non-periodic boundary conditions) using molecular dynamics (MD) in the approximation of pair potentials and rigid ions. We calculate the size dependence of the temperature and heat of melting, the density jump for crystals of cubic shape and volumes up to 1000 nm^3 (50000 particles). Linear and parabolic extrapolations of these dependences to macroscopic (infinite) size are considered, the parabolic is found to be better suited for the analysis of data on the temperature and the heat of melting. The closest to the modern experimental data estimates of the melting temperature of macrocrystals are obtained using the interaction potentials Goel-08 (2969K), Yakub-09 (3105K) and MOX-07 (3291K). The density jump at melting is well reproduced by Yakub-09 (8.66%) and MOX-07 (7.97%). The heat of fusion for all sets of the potentials considered is found to be underestimated by 50-75%, possibly because of the excluded he...

Boyarchenkov, A S; Nekrasov, K A; Kupryazhkin, A Ya

2011-01-01T23:59:59.000Z

50

A molecular dynamics simulation of the melting points and glass transition temperatures of myo-and neo-inositol  

E-Print Network (OSTI)

A molecular dynamics simulation of the melting points and glass transition temperatures of myo molecular potentials for atomistic simulation studies COMPASS H. Sun, J. Phys. Chem. B 102, 7338 1998 force field and molecular dynamics techniques. Our results show that the calculated heats of sublimation

de Gispert, Adrià

51

Molecular dynamics simulation of erosion and surface evolution of tungsten due to bombardment with deuterium and carbon in  

E-Print Network (OSTI)

Molecular dynamics simulation of erosion and surface evolution of tungsten due to bombardment Available online 24 May 2013 Keywords: Molecular dynamic simulation Carbon irradiation on tungsten t The behavior of tungsten as plasma facing material in fusion environment is investigated using molecular

Harilal, S. S.

52

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

NLE Websites -- All DOE Office Websites (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

53

I12: Quantum Chemical Molecular Dynamics Simulations on ...  

Science Conference Proceedings (OSTI)

To achieve the fabrication with less defects, the dynamic behaviors of ions and radicals with chemical reactions should be clarified. Then, we investigate the ...

54

Equation of state of dense plasmas by ab initio simulations: Bridging the gap between quantum molecular dynamics and orbital-free molecular dynamics at high temperature  

SciTech Connect

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 the Thomas-Fermi semiclassical approximation and possibly on a gradient correction, is the only simulation method currently available at high temperature. We show in the case of a dense boron plasma that the two approaches give pressures differing by a few percent even at temperatures as high as a few tens of electron-volts. We indicate how the pressures obtained by orbital-free molecular dynamics can be corrected in order to appear as a limit of the quantum molecular dynamics results as temperature increases. We thus obtain a method to calculate the equation of state of a dense plasma up to high temperatures where quantum molecular dynamics cannot be directly implemented.

Danel, J.-F.; Kazandjian, L.; Zerah, G. [CEA, DAM, DIF, F-91297 Arpajon (France)

2012-12-15T23:59:59.000Z

55

Molecular dynamics simulation of hydrogen diffusion in titanium  

National Nuclear Security Administration (NNSA)

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...

56

Research article: Fine grained sampling of residue characteristics using molecular dynamics simulation  

Science Conference Proceedings (OSTI)

In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ... Keywords: Backbone conformation, Dynameome, Molecular dynamics simulation, Ramachandran plot, Residue volume, Rotamer, Side-chain packing

Hyun Joo; Xiaotao Qu; Rosemarie Swanson; C. Michael McCallum; Jerry Tsai

2010-06-01T23:59:59.000Z

57

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 have been analyzed. Elastic moduli and thermal coefficient of expansion are calculated and their variation with diameter and length is investigated. In particular, the nanotubes are modeled using 3D elastic beam finite elements with six degrees of freedom at each node. The difficulty in modeling multi walled nanotubes is the van der Waal's forces between adjacent layers which are geometrically non linear in nature. These forces are modeled using truss elements. The nanotube-polymer interface in a nano-composite is modeled on a similar basis. While performing the molecular dynamic simulations, the geometric optimization is performed initially to obtain the minimized configuration and then the desired temperature is attained by rescaling the velocities of carbon atoms in the nanotube. Results show that the Young's modulus increases with tube diameter in molecular mechanics whereas decreases in molecular dynamics since the inter-atomic potential due to chemical reactions between the atoms is taken into consideration in molecular dynamics unlike in molecular mechanics.

Gaddamanugu, Dhatri

2009-05-01T23:59:59.000Z

58

Modeling ramp compression experiments using large-scale molecular dynamics simulation.  

Science Conference Proceedings (OSTI)

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01T23:59:59.000Z

59

A Molecular Dynamics  

Science Conference Proceedings (OSTI)

A Tale of Two States and More: Modeling of New Generation of Lattice Stability from Zero ... Analysis of Nano Fluid Using CFD-A Hybrid Approach for Cooling Purpose ... Molecular Dynamics Simulations of Grain Boundary Free Energy and

60

A Molecular Dynamic Study  

Science Conference Proceedings (OSTI)

A Tale of Two States and More: Modeling of New Generation of Lattice Stability from Zero ... Analysis of Nano Fluid Using CFD-A Hybrid Approach for Cooling Purpose ... Molecular Dynamics Simulations of Grain Boundary Free Energy and

Note: This page contains sample records for the topic "molecular dynamics simulation" 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 high strain-rate void nucleation and growth in copper  

Science Conference Proceedings (OSTI)

Isotropic tension is simulated in nanoscale polycrystalline copper with 10 nm grain size using large-scale molecular dynamics. The nanocrystalline copper is fabricated on the computer by growing randomly oriented grains from seed sites in simulations cell. Constant volume strain rates of 10-8 to 10-10 are considered for systems ranging from 10-5 to 10-6 atoms using EAM interatomic potential for copper. The spacing between voids for room temperature single crystal simulations is found to scale approximately as l{approximately}0. 005 Cs/gamma, where Cs is the sound speed and gamma is the strain rate. Below strain rates of about 10-9, only one void is observed to nucleate and grow in the 10 nm polycrystalline simulation cell. The growth of small voids is simulated by cutting a void out of the simulation cell and repeating the isotropic expansion.

Belak, J.

1997-07-01T23:59:59.000Z

62

Interactions between Ether Phospholipids and Cholesterol as Determined by Scattering and Molecular Dynamics Simulations  

SciTech Connect

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol s molecular interactions with ether lipids as determined using a combination of small-angle neutron and Xray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

Pan, Jianjun [ORNL; Cheng, Xiaolin [ORNL; Heberle, Frederick A [ORNL; Mostofian, Barmak [ORNL; Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Drazba, Paul [ORNL; Katsaras, John [ORNL

2012-01-01T23:59:59.000Z

63

Bayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing framework  

Science Conference Proceedings (OSTI)

We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures. Furthermore

Panagiotis Angelikopoulos; Costas Papadimitriou; Petros Koumoutsakos

2012-01-01T23:59:59.000Z

64

Energy of one-dimensional diatomic elastic granular gas: Theory and molecular dynamics Simulation  

E-Print Network (OSTI)

One-dimensional ideal diatomic gas is simulated through possible types of motion of a molecule. Energy of each type of its motion is calculated from theory and numerical method. Calculation of kinetic energy of an atom in translational-vibrational motion is not analytically simple, but it can be solved by numerical method of molecular dynamic simulation. This paper justifies that kinetic energy of a diatomic molecule can be determined by two different approaches. The first is the sum of kinetic energy of each atom and second is the sum of kinetic energy of translational motion and vibrational motion.

Khotimah, Siti Nurul; Widayani,; Waris, Abdul

2011-01-01T23:59:59.000Z

65

Large-scale molecular dynamics simulations of shock-induced plasticity, phase transformations, and detonation  

SciTech Connect

Modern computers enable routine multimillion-atom molecular dynamics simulations of shock propagation in solids using realistic interatomic potentials, and offer a direct insight into the atomistic processes underlying plasticity, phase transformations, and the detonation of energetic materials. Past, present, and prospects for future simulations will be discussed in the context of prototypical systems for each of these three classes of problems. Initial samples ranging from perfect single crystals, to those with specific isolated defects, to full-fledged polycrystalline materials will be considered.

Germann, T. C. (Timothy C.)

2001-06-01T23:59:59.000Z

66

A new battery-charging method suggested by molecular dynamics simulations  

E-Print Network (OSTI)

Based on large-scale molecular dynamics simulations, we propose a new charging method that should be capable of charging a Lithium-ion battery in a fraction of the time needed when using traditional methods. This charging method uses an additional applied oscillatory electric field. Our simulation results show that this charging method offers a great reduction in the average intercalation time for Li+ ions, which dominates the charging time. The oscillating field not only increases the diffusion rate of Li+ ions in the electrolyte but, more importantly, also enhances intercalation by lowering the corresponding overall energy barrier.

Hamad, Ibrahim Abou; Wipf, D; Rikvold, P A; 10.1039/b920970k

2010-01-01T23:59:59.000Z

67

Adaptive-boost molecular dynamics simulation of carbon diffusion in iron  

E-Print Network (OSTI)

We have developed an accelerated molecular dynamics (MD) method to model atomic-scale rare events. In this method, a smooth histogram of collective variables is first estimated by canonical ensemble molecular dynamics ...

Ishii, Akio

68

Substructured multibody molecular dynamics.  

SciTech Connect

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

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

2006-11-01T23:59:59.000Z

69

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

70

A multi-scale approach to molecular dynamics simulations of shock waves  

DOE Green Energy (OSTI)

Study of the propagation of shock waves in condensed matter has led to new discoveries ranging from new metastable states of carbon [1] to the metallic conductivity of hydrogen in Jupiter, [2] but progress in understanding the microscopic details of shocked materials has been extremely difficult. Complications can include the unexpected formation of metastable states of matter that determine the structure, instabilities, and time-evolution of the shock wave. [1,3] The formation of these metastable states can depend on the time-dependent thermodynamic pathway that the material follows behind the shock front. Furthermore, the states of matter observed in the shock wave can depend on the timescale on which observation is made. [4,1] Significant progress in understanding these microscopic details has been made through molecular dynamics simulations using the popular non-equilibrium molecular dynamics (NEMD) approach to atomistic simulation of shock compression. [5] The NEMD method involves creating a shock at one edge of a large system by assigning some atoms at the edge a fixed velocity. The shock propagates across the computational cell to the opposite side. The computational work required by NEMD scales at least quadratically in the evolution time because larger systems are needed for longer simulations to prevent the shock wave from reflecting from the edge of the computational cell and propagating back into the cell. When quantum mechanical methods with poor scaling of computational effort with system size are employed, this approach to shock simulations rapidly becomes impossible.

Reed, E J; Fried, L E; Manaa, M R; Joannopoulos, J D

2004-09-03T23:59:59.000Z

71

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

DOE Green Energy (OSTI)

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

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

2008-11-01T23:59:59.000Z

72

Molecular dynamics simulations of swift heavy ion induced defect recovery in SiC  

SciTech Connect

Swift heavy ions induce a high density of electronic excitations that can cause the formation of amorphous ion tracks in insulators. No ion tracks have been observed in the semiconductor SiC, but recent experimental work suggests that irradiation damaged SiC can undergo defect recovery under swift heavy ion irradiation. It is believed that local heating of the lattice due to the electronic energy deposition can anneal, and thereby recover, some of the disordered structure. We simulate the local heating due to the ions by the inelastic thermal spike model and perform molecular dynamics simulations of dierent model damage states to study the defect recovery on an atomistic level. We find significant recovery of point defects and a disordered layer, as well as recrystallization at the amorphous-to-crystalline interface of an amorphous layer. The simulation results support the swift heavy ion annealing hypothesis.Swift heavy ions induce a high density of electronic excitations that can cause the formation of amorphous ion tracks in insulators. No ion tracks have been observed in the semiconductor SiC, but recent experimental work suggests that irradiation damaged SiC can undergo defect recovery under swift heavy ion irradiation. It is believed that local heating of the lattice due to the electronic energy deposition can anneal, and thereby recover, some of the disordered structure. We simulate the local heating due to the ions by the inelastic thermal spike model and perform molecular dynamics simulations of dierent model damage states to study the defect recovery on an atomistic level. We find significant recovery of point defects and a disordered layer, as well as recrystallization at the amorphous-to-crystalline interface of an amorphous layer. The simulation results support the swift heavy ion annealing hypothesis.

Backman, Marie [University of Tennessee, Knoxville (UTK); Toulemonde, Marcel [CEA-CNRS-ENSICAEN-University of Caen, FRANCE; Pakarinen, Olli H [University of Helsinki; Juslin, Niklas [University of Tennessee, Knoxville (UTK); Djurabekova, Flyura [University of Helsinki; Nordlund, Kai [University of Helsinki; Debelle, Aurelien [Universite Paris Sud, Orsay, France; Weber, William J [ORNL

2013-01-01T23:59:59.000Z

73

An Event-Driven Hybrid Molecular Dynamics and Direct Simulation Monte Carlo Algorithm  

Science Conference Proceedings (OSTI)

A novel algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with the solvent particles with hard core potentials. The algorithm uses event-driven molecular dynamics (MD) for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in event-driven algorithms, rather, the momentum and energy exchange in the solvent is determined stochastically using the Direct Simulation Monte Carlo (DSMC) method. The coupling between the solvent and the solute is consistently represented at the particle level, however, unlike full MD simulations of both the solvent and the solute, the spatial structure of the solvent is ignored. The algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard wall subjected to uniform shear. The algorithm closely reproduces full MD simulations with two orders of magnitude greater efficiency. Results do not confirm the existence of periodic (cycling) motion of the polymer chain.

Donev, A; Garcia, A L; Alder, B J

2007-07-30T23:59:59.000Z

74

Visualization of parallel molecular dynamics simulation on a remote visualization platform  

SciTech Connect

Visualization requires high performance computers. In order to use these shared high performance computers located at national centers, the authors need an environment for remote visualization. Remote visualization is a special process that uses computing resources and data that are physically distributed over long distances. In their experimental environment, a parallel raytracer is designed for the rendering task. It allows one to efficiently visualize molecular dynamics simulations represented by three dimensional ball-and-stick models. Different issues encountered in creating their platform are discussed, such as I/O, load balancing, and data distribution.

Lee, T.Y.; Raghavendra, C.S. [Washington State Univ., Pullman, WA (United States); Nicholas, J.B. [Pacific Northwest Lab., Richland, WA (United States). Molecular Science Research Center

1994-09-01T23:59:59.000Z

75

Nonequilibrium molecular dynamics simulation of shear viscosity by a uniform momentum source-and-sink scheme  

Science Conference Proceedings (OSTI)

A uniform momentum source-and-sink scheme of nonequilibrium molecular dynamics (NEMD) is developed to calculate the shear viscosity of fluids in this paper. The uniform momentum source and sink are realized by momentum exchanges of individual atoms in ... Keywords: Molecular fluid, Nonequilibrium molecular dynamics, Shear viscosity, Uniform source-and-sink scheme

Bing-Yang Cao; Ruo-Yu Dong

2012-06-01T23:59:59.000Z

76

A combined Event-Driven/Time-Driven molecular dynamics algorithm for the simulation of shock waves in rarefied gases  

Science Conference Proceedings (OSTI)

A novel combined Event-Driven/Time-Driven (ED/TD) algorithm to speed-up the Molecular Dynamics simulation of rarefied gases using realistic spherically symmetric soft potentials is presented. Due to the low density regime, the proposed method correctly ... Keywords: 47.11.Mn, 47.40.Ki, 47.45.-n, 47.61.Cb, Event-Driven MD, Molecular Dynamics, Non-continuum effects, Shock Waves

Paolo Valentini; Thomas E. Schwartzentruber

2009-12-01T23:59:59.000Z

77

How trehalose protects DNA in the dry state: a molecular dynamics simulation  

E-Print Network (OSTI)

Molecular dynamics simulations were conducted on a system consisting of a decamer DNA solvated by trehalose and water (molecular ratio= 1:2), to mimic a relatively dry state for the DNA molecule. Simulations were performed at two different temperatures, 300 K and 450 K. The B-form DNA structure was shown to be stable at both temperatures. The analysis of hydrogen bonds between trehalose/water and DNA revealed that trehalose and backbone DNA formed the largest number of hydrogen bonds and thus constituted the major effect of structural protection for DNA. The number of hydrogen bonds formed by each OH group of trehalose with the backbone DNA was compared. Different types of trehalose-DNA interactions were analyzed, with no prevalent pattern recognized. Diffusion constants for trehalose and water were also calculated, suggesting a glassy/viscose state of the simulation system. It is believed that trehalose protects DNA in the dry state through the network of hydrogen bonds built by the sugars, which reduces the structural fluctuations of DNA and prevents its denaturation.

Fu, Xuebing

2008-08-01T23:59:59.000Z

78

High-precision molecular dynamics simulation of UO2-PuO2: pair potentials comparison  

E-Print Network (OSTI)

Our series of articles is devoted to high-precision molecular dynamics simulation of mixed actinide-oxide (MOX) fuel in the rigid ions approximation using high-performance graphics processors (GPU). In the first article we assess 10 most relevant interatomic sets of pair potentials (SPP) by reproduction of solid phase properties of uranium dioxide (UO2) - temperature dependences of the lattice constant, bulk modulus, enthalpy and heat capacity. Measurements were performed with 1K accuracy in a wide temperature range from 300K up to melting point. The best results are demonstrated by two recent SPPs MOX-07 and Yakub-09, which both had been fitted to the recommended thermal expansion in the range of temperatures 300-3100K. Compared with them, the widely used SPPs Basak-03 and Morelon-03 reproduce the experimental data noticeably worse at temperatures above 2500K.

Potashnikov, S I; Nekrasov, K A; Kupryazhkin, A Ya

2011-01-01T23:59:59.000Z

79

Molecular dynamics simulation of interaction of H with vacancy in W  

DOE Green Energy (OSTI)

Molecular dynamics simulations were performed to investigate the interaction between H and vacancy in W using an analytical bond-order potential to describe the interactions between W-W, W-H and H-H. The most stable configuration for H in W is the tetrahedron interstitial site. We calculated the binding energies of an H and a vacancy to an H-vacancy cluster (HnVm) in W, respectively, where n and m ranged from 0 to 10. The binding energy was almost unchanged. The binding energy of a vacancy to H-vacancy cluster is about 0.4eV, which is higher than the binding energy of an H to H-vacancy cluster. Vacancy is much easier to binding with H-vacancy cluster than H. And H is easier to stay in the tetrahedron interstitial site or octahedron interstitial site in bcc W.

Li, Xiaochun; Gao, Fei; Lu, Guang-Hong

2009-09-15T23:59:59.000Z

80

Molecular dynamics simulations of ion range profiles for heavy ions in light targets  

SciTech Connect

The determination of stopping powers for slow heavy ions in targets containing light elements is important to accurately describe ion–solid interactions, evaluate ion irradiation effects and predict ion ranges for device fabrication and nuclear applications. Recently, discrepancies of up to 40% between the experimental results and SRIM (Stopping and Range of Ions in Matter) predictions of ion ranges for heavy ions with medium and low energies (molecular dynamics simulation scheme is developed to calculate the ion ranges of heavy ions in light elemental targets. Electronic stopping powers generated from both a reciprocity approach and the SRIM code are used to investigate the influence of electronic stopping on ion range profiles. The ion range profiles for Au and Pb ions in SiC and Er ions in Si, with energies between 20 and 5250 keV, are simulated. The simulation results show that the depth profiles of implanted ions are deeper and in better agreement with the experiments when using the electronic stopping power values derived from the reciprocity approach. These results indicate that the origin of the discrepancy in ion ranges between experimental results and SRIM predictions in the low energy region may be an overestimation of the electronic stopping powers used in SRIM.

Lan, C.; Xue, J. M.; Zhang, Y.; Morris, J. R.; Zhu, Zh.; Gao, Yanfei; Wang, Y. G.; Yan, S.; Weber, William

2012-01-01T23:59:59.000Z

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

Molecular dynamics simulations of ion range profiles for heavy ions in light targets  

SciTech Connect

The determination of stopping powers for slow heavy ions in targets containing light elements is important to accurately describe ion-solid interactions, evaluate ion irradiation effects and predict ion ranges for device fabrication and nuclear applications. Recently, discrepancies of up to 40% between the experimental results and SRIM (Stopping and Range of Ions in Matter) predictions of ion ranges for heavy ions with medium and low energies (< {approx} 25 keV/nucleon) in light elemental targets have been reported. The longer experimental ion ranges indicate that the stopping powers used in the SRIM code are overestimated. Here, a molecular dynamics simulation scheme is developed to calculate the ion ranges of heavy ions in light elemental targets. Electronic stopping powers generated from both a reciprocity approach and the SRIM code are used to investigate the influence of electronic stopping on ion range profiles. The ion range profiles for Au and Pb ions in SiC and Er ions in Si, with energies between 20 and 5250 keV, are simulated. The simulation results show that the depth profiles of implanted ions are deeper and in better agreement with the experiments when using the electronic stopping power values derived from the reciprocity approach. These results indicate that the origin of the discrepancy in ion ranges between experimental results and SRIM predictions in the low energy region may be an overestimation of the electronic stopping powers used in SRIM.

Lan, Chune [Peking University; Xue, Jianming [Peking University; Zhang, Yanwen [ORNL; Morris, James R [ORNL; Zhu, Zihua [Pacific Northwest National Laboratory (PNNL); Gao, Yuan [Peking University; Wang, Yugang [Peking University; Yan, Sha [Peking University; Weber, William J [ORNL

2012-01-01T23:59:59.000Z

82

Molecular dynamics simulations of ion range profiles for heavy ions in light targets  

SciTech Connect

The determination of stopping powers for slow heavy ions in targets containing light elements is important to accurately describe ion-solid interactions, evaluate ion irradiation effects and predict ion ranges for device fabrication and nuclear applications. Recently, discrepancies of up to 40% between the experimental results and SRIM (Stopping and Range of Ions in Matter) predictions of ion ranges for heavy ions with medium and low energies (<25 keV/nucleon) in light elemental targets have been reported. The longer experimental ion ranges indicate that the stopping powers used in the SRIM code are overestimated. Here, a molecular dynamics simulation scheme is developed to calculate the ion ranges of heavy ions in light elemental targets. Electronic stopping powers generated from both a reciprocity approach and the SRIM code are used to investigate the influence of electronic stopping on ion range profiles. The ion range profiles for Au and Pb ions in SiC and Er ions in Si, with energies between 20 and 5250 keV, are simulated. The simulation results show that the depth profiles of implanted ions are deeper and in better agreement with the experiments when using the electronic stopping power values derived from the reciprocity approach. These results indicate that the origin of the discrepancy in ion ranges between experimental results and SRIM predictions in the low energy region may be an overestimation of the electronic stopping powers used in SRIM.

Lan, Chune; Xue, Jianming; Zhang, Yanwen; Morris, James R.; Zhu, Zihua; Gao, Yuan; Wang, Yugang; Yan, Sha; Weber, William J.

2012-09-01T23:59:59.000Z

83

Molecular Dynamics Simulation of the Transport Properties of Molten Transuranic Chloride Salts  

E-Print Network (OSTI)

The Accelerator Research Laboratory at Texas A&M is proposing a design for accelerator-driven subcritical fission in molten salt (ADSMS), a system that destroys the transuranic elements in used nuclear fuel. The transuranics (TRU) are the most enduring hazard of nuclear power. TRU contain high radiotoxicity and have half-lives of a thousand to a million years. The ADSMS core is fueled by a homogeneous chloride-based molten salt mixture containing TRUCl3 and NaCl. Certain thermodynamic properties are critical to modeling both the neutronics and heat transfer of an ADSMS system. There is a lack of experimental data on the density, heat capacity, electrical and thermal conductivities, and viscosity of TRUCl3 salt systems. Molecular dynamics simulations using a polarizable ion model (PIM) are employed to determine the density and heat capacity of these melts as a function of temperature. Green-Kubo methods are implemented to calculate the electrical conductivity, thermal conductivity, and viscosity of the salt using the outputs of the simulations. Results for pure molten salt systems are compared to experimental data when possible to validate the potentials used. Here I discuss chloride salt systems of interest, their calculated properties, and possible sources of error for our simulations.

Baty, Austin Alan

2013-05-01T23:59:59.000Z

84

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

E-Print Network (OSTI)

histogram analysis method (WHAM) [25, 8] and is shown inexchange simulation by WHAM with corresponding uncertaintiesat 302K, as determined by WHAM, and assigning ini- tial

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

2006-01-01T23:59:59.000Z

85

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

E-Print Network (OSTI)

Simulation of shock-induced melting of Ni using molecular dynamics coupled to a two-temperature and electron-phonon coupling, Pmelt and Tmelt change. For a given pressure, the temperature behind the shock conduction and electron-phonon coupling. The decrease in the temperature behind the shock front is enhanced

Zhigilei, Leonid V.

86

Molecular Dynamics Simulation of Phase-Change of Water inside a SWNT Shigeo Maruyama, Tatsuto Kimura and Yasuhiro Igarashi  

E-Print Network (OSTI)

, Bunkyo-ku, Tokyo 113-8656, Japan The phase change of liquid water to ice crystal inside a singleMolecular Dynamics Simulation of Phase-Change of Water inside a SWNT Shigeo Maruyama, Tatsuto, the carbon atoms were cooled at the constant heat-removal rate. The phase change phenomena with various rates

Maruyama, Shigeo

87

Molecular Dynamics Simulation of Tri-n-Butyl-Phophate Liquid: A Force Field Comparative Study  

SciTech Connect

Molecular dynamics (MD) simulations were conducted to compare the performance of four force fields in predicting thermophysical properties of tri-n-butyl-phosphate (TBP) in the liquid phase. The intramolecular force parameters used were from the Assisted Model Building with Energy Refinement (AMBER) force field model. The van der Waals parameters were based on either the AMBER or the Optimized Potential for Liquid Simulation (OPLS) force fields. The atomic partial charges were either assigned by performing quantum chemistry calculations or utilized previously published data, and were scaled to approximate the average experimental value of the electric dipole moment. Canonical ensemble computations based on the aforementioned parameters were performed near the atmospheric pressure and temperature to obtain the electric dipole moment, mass density, and self-diffusion coefficient. In addition, the microscopic structure of the liquid was characterized via pair correlation functions between selected atoms. It has been demonstrated that the electric dipole moment can be approximated within 1% of the average experimental value by virtue of scaled atomic partial charges. The liquid mass density can be predicted within 0.5-1% of its experimentally determined value when using the corresponding charge scaling. However, in all cases the predicted self- diffusion coefficient is significantly smaller than a commonly quoted experimental measurement; this result is qualified by the fact that the uncertainty of the experimental value was not available.

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

2012-01-01T23:59:59.000Z

88

Non-Fourier heat conduction in a single-walled carbon nanotube: Classical molecular dynamics simulations  

SciTech Connect

Nonstationary heat conduction in a single-walled carbon nanotube was investigated by applying a local heat pulse with duration of subpicoseconds. The investigation was based on classical molecular dynamics simulations, where the heat pulse was generated as coherent fluctuations by connecting a thermostat to the local cell for a short duration. The heat conduction through the nanotube was observed in terms of spatiotemporal temperature profiles. Results of the simulations exhibit non-Fourier heat conduction where a distinct amount of heat is transported in a wavelike form. The geometry of carbon nanotubes allows us to observe such a phenomenon in the actual scale of the material. The resulting spatiotemporal profile was compared with the available macroscopic equations, the so-called non-Fourier heat conduction equations, in order to investigate the applicability of the phenomenological models to a quasi-one-dimensional system. The conventional hyperbolic diffusion equation fails to predict the heat conduction due to the lack of local diffusion. It is shown that this can be remedied by adopting a model with dual relaxation time. Further modal analyses using wavelet transformations reveal a significant contribution of the optical phonon modes to the observed wavelike heat conduction. The result suggests that, in carbon nanotubes with finite length where the long-wavelength acoustic phonons behave ballistically, even optical phonons can play a major role in the non-Fourier heat conduction.

Shiomi, Junichiro; Maruyama, Shigeo [Department of Mechanical Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)

2006-05-15T23:59:59.000Z

89

MOLECULAR DYNAMICS STUDY OF THE THERMAL CONDUCTIVITY OF AMORPHOUS NANOPOROUS SILICA  

E-Print Network (OSTI)

Domain size effects in molecular dynamics simulation ofC. H. , 2010. “Size effects in molecular dynamics thermaland nanowires using molecular dynamics simulations”.

Coquil, Thomas; Fang, Jin; Pilon, Laurent

2011-01-01T23:59:59.000Z

90

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 constant at 1g/cc. Results at 298 K show the formation of a well-ordered structure constituted by water layers parallel to the graphite surfaces. The water molecules in the layers in contact with the surface have a tendency to orient their dipole parallel to the surface. Such ice-like structures may have different structural and dynamic properties than those of ice. The calculated mean square displacement reveals that the mobilities of the confined water at a separation of 8 Å become similar to that of low-temperature water (213 K) at the same density, although the structures of water are very different. The temperature at which the mobility of water confined at the separation of 7 Å would become similar to that of bulk low-temperature water was found to be 373K. With respect to the dynamics of confined water, a significant blue shift is observed in the intermolecular vibrational modes associated with the O×××O×××O bending and O×××O stretching of molecules linked by hydrogen bonds. The analysis of the geometry of water clusters confined between two graphite surfaces has been performed using ab initio methods. The ab initio calculations yield two preferential orientations of water molecules which are; 1) one O-H bond points to the surface and the other is parallel; 2) both O-H bonds are parallel to the surface. These orientations agree with those found in our MD simulation results. The calculated energy barriers for proton transfer of the confined H3O+-(H2O) complexes between two graphite model surfaces suggest that the confinement enhances the proton transfer at the separation 6-14.5 Å. When the confinement is high, at a separation of 4 Å, the barrier energies are extremely large. The confinement does not enhance proton transfer when the H3O+-(H2O) complexes are located further from the surfaces by more than 8 Å. As a result, the barrier energies start to increase at the separation of 20 Å.

Hirunsit, Pussana

2007-05-01T23:59:59.000Z

91

A comparison of crystalline and molten structures of zirconolite (CaZrTi?O?), a potential plutonium wasteform medium, by molecular dynamics simulation and topological analysis  

E-Print Network (OSTI)

Molecular dynamics simulations of the ceramic compound zirconolite (CaZrTi?O?), a potential crystalline wasteform host for plutonium, were carried out for ideal and experimental crystalline forms and a simulated molten ...

Rich, Sarah Celeste

2008-01-01T23:59:59.000Z

92

Stochastic Event-Driven Molecular Dynamics  

Science Conference Proceedings (OSTI)

A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. ... Keywords: Complex flow, DSMC, Event-driven molecular dynamics, Polymer suspension

Aleksandar Donev; Alejandro L. Garcia; Berni J. Alder

2008-02-01T23:59:59.000Z

93

Modification of Defect Structures in Graphene by Electron Irradiation: Ab Initio Molecular Dynamics Simulations  

SciTech Connect

Defects play an important role on the unique properties of the sp2-bonded materials, such as graphene. The creation and evolution of mono-vacancy, di-vacancy, Stone-Wales (SW) and grain boundaries (GBs) under irradiation in graphene are investigated using density functional theory and time-dependent density functional theory molecular dynamics simulations. It is of great interest to note that the patterns of these defects can be controlled through electron irradiation. The SW defects can be created by electron irradiation with energy of above the displacement threshold energy (Td, {approx}19 eV) and can be healed with an energy (14-18 eV) lower than Td. The transformation between four types of divacancies, V2(5-8-5), V2(555-777), V2(5555-6-7777), and V2(55-77) can be realized through bond rotation induced by electron irradiation. The migrations of divancancies, SW defects, and GBs can also be controlled by electron irradiation. Thus, electron irradiation can serve as an important tool to modify morphology in a controllable manner, and to tailor the physical properties of graphene.

Wang, Zhiguo; Zhou, Yungang; Bang, Junhyeok; Prange, Micah P.; Zhang, Shengbai; Gao, Fei

2012-08-02T23:59:59.000Z

94

Modified Nose-Hoover thermostat for solid state for constant temperature molecular dynamics simulation  

SciTech Connect

Nose-Hoover (NH) thermostat methods incorporated with molecular dynamics (MD) simulation have been widely used to simulate the instantaneous system temperature and feedback energy in a canonical ensemble. The method simply relates the kinetic energy to the system temperature via the particles' momenta based on the ideal gas law. However, when used in a tightly bound system such as solids, the method may suffer from deriving a lower system temperature and potentially inducing early breaking of atomic bonds at relatively high temperature due to the neglect of the effect of the potential energy of atoms based on solid state physics. In this paper, a modified NH thermostat method is proposed for solid system. The method takes into account the contribution of phonons by virtue of the vibrational energy of lattice and the zero-point energy, derived based on the Debye theory. Proof of the equivalence of the method and the canonical ensemble is first made. The modified NH thermostat is tested on different gold nanocrystals to characterize their melting point and constant volume specific heat, and also their size and temperature dependence. Results show that the modified NH method can give much more comparable results to both the literature experimental and theoretical data than the standard NH. Most importantly, the present model is the only one, among the six thermostat algorithms under comparison, that can accurately reproduce the experimental data and also the T{sup 3}-law at temperature below the Debye temperature, where the specific heat of a solid at constant volume is proportional to the cube of temperature.

Chen, Wen-Hwa, E-mail: whchen@pme.nthu.edu.tw [Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China); National Applied Research Laboratories, Taipei 10622, Taiwan, ROC (China); Wu, Chun-Hung [Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Cheng, Hsien-Chie [Department of Aerospace and Systems Engineering, Feng Chia University, Taichung 40724, Taiwan (China)

2011-07-10T23:59:59.000Z

95

Molecular dynamics simulation of montmorillonite and mechanical and thermodynamic properties calculations  

E-Print Network (OSTI)

Nanocomposites refer to the materials in which the defining characteristic size of inclusions is in the order of 10-100nm. There are several types of nanoparticle inclusions with different structures: metal clusters, fullerenes particles and molybdenum selenide, Our research focus is on polymer nanocomposites with inorganic clay particles as inclusions, in particular we used sodium montmorillonite polymer nanocomposite. In our study, modeling and simulations of sodium montmorillonite (Na+-MMT) is currently being investigated as an inorganic nanocomposite material. Na+-MMT clay consists of platelets, one nanometer thick with large lateral dimensions, which can be used to achieve efficient reinforcement of polymer matrices. This nanocomposite has different applications such as a binder of animal feed, a plasticizing agent in cement, brick and ceramic, and a thickener and stabilizer of latex and rubber adhesives. In this study, sodium montmorillonite called Na+-MMT structure is built with the bulk system and the layered system which includes from 1 to 12 layers by using Crystal Builder of Cerius2. An isothermal and isobaric ensemble is used for calculation of thermodynamic properties such as specific heat capacities and isothermal expansion coefficients of Na+-MMT. A canonical ensemble which holds a fixed temperature, volume and number of molecules is used for defining exfoliation kinetics of layered structures and surface formation energies for Na+-MMT layered structures are calculated by using a canonical ensemble. Mechanical properties are used to help characterize and identify the Na+-MMT structure. Several elastic properties such as compliance and stiffness matrices, Young's, shear, and bulk modulus, volume compressibility, Poisson's ratios, Lamé constants, and velocities of sound are calculated in specified directions. Another calculation method is the Vienna Ab-initio Simulation Package (VASP). VASP is a complex package for performing ab-initio quantum-mechanical calculations and molecular dynamic (MD) simulations using pseudopotentials and a plane wave basis set. Cut off energy is optimized for the unit cell of Na+-MMT by using different cut off energy values. Experimental and theoretical cell parameters are compared by using cell shape and volume optimization and root mean square (RMS) coordinate difference is calculated for variation of cell parameters. Cell shape and volume optimization are done for calculating optimum expansion or compression constant.

Atilhan, Selma

2007-05-01T23:59:59.000Z

96

DL_POLY Molecular Simulation Package  

Science Conference Proceedings (OSTI)

Jan 8, 2008 ... DL_POLY is a general purpose serial and parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith, ...

97

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.  

Science Conference Proceedings (OSTI)

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1{prime}-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1{micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline{prime}-1-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.

De Hatten, Xavier [University of Bordeaux; Cournia, Zoe [Yale University; Smith, Jeremy C [ORNL; Metzler-Nolte, Nils [University of Bochum, Germany

2007-08-01T23:59:59.000Z

98

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics  

Science Conference Proceedings (OSTI)

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C{sub 2}-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 {micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 {micro}s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.

De Hatten, Xavier [University of Bordeaux; Cournia, Zoe [Yale University; Smith, Jeremy C [ORNL; Huc, I [University of Bochum, Germany; Metzler-Nolte, Nils [University of Bochum, Germany

2007-08-01T23:59:59.000Z

99

A Molecular Simulation Study  

Science Conference Proceedings (OSTI)

Presentation Title, Enhanced CO2 Adsorption in Ti-exchanged Zirconium Organic Frameworks – A Molecular Simulation Study. Author(s), Ravichandar Babarao ...

100

Assessment of Molecular Modeling & Simulation  

Science Conference Proceedings (OSTI)

This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.

None

2002-01-03T23:59:59.000Z

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101

Neighbor List Collision-Driven Molecular Dynamics Simulation for Nonspherical Particles. I. Algorithmic Details II. Applications to Ellipses and Ellipsoids  

E-Print Network (OSTI)

In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or hard-wall boundary conditions. The algorithm extends previous event-driven molecular dynamics algorithms for spheres. We present a novel partial-update near-neighbor list (NNL) algorithm that is superior to previous algorithms at high densities, without compromising the correctness of the algorithm. This efficiency of the algorithm is further increased for systems of very aspherical particles by using bounding sphere complexes (BSC). In the second part of this series of papers we apply the algorithm presented in the first part of this series of papers to systems of hard ellipses and ellipsoids. The theoretical machinery needed to treat such particles, including the overlap potentials, is developed in full detail. We describe an algorithm for predicting the time of collision for tw...

Donev, A; Stillinger, F H; Donev, Aleksandar; Torquato, Salvatore; Stillinger, Frank H.

2004-01-01T23:59:59.000Z

102

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

Science Conference Proceedings (OSTI)

Molecular dynamics simulations were performed to examine trends in trivalent lanthanide [Ln(III)] sorption to quartz surface SiOH0 and SiO- sites across the 4f period. Complementary laser induced fluorescence studies examined Eu(III) sorption to quartz at varying ionic strength such that the surface sorbed species could be extrapolated at zero ionic strength, the conditions under which the simulations are performed. This allowed for direct comparison of the data, enabling a molecular understanding of the surface sorbed species and the role of the ion surface charge density upon the interfacial reactivity. Thus, this combined theoretical and experimental approach aids in the prediction of the fate of trivalent radioactive contaminants at temporary and permanent nuclear waste storage sites. Potential of mean force molecular dynamics, as well as simulations of pre-sorbed Ln(III) species agrees with the spectroscopic study of Eu(III) sorption, indicating that strongly bound inner-sphere complexes are formed upon sorption to an SiO- site. The coordination shell of the ion contains 6-7 waters of hydration and it is predicted that surface OH groups dissociate from the quartz and bind within the inner coordination shell of Eu(III). Molecular simulations predict less-strongly bound inner2 sphere species in early lanthanides and more strongly bound species in late lanthanides, following trends in the ionic radius of the 4f ions. The participation of surface dissociated OHgroups within the inner coordination shell of the Ln(III) ion is, however, consistent across the series studied. Sorption to a fully protonated quartz surface is not predicted to be favorable by any Ln(III), except perhaps Lu.

Kuta, Jadwiga; Wander, Matthew C F.; Wang, Zheming; Jiang, Siduo; Wall, Nathalie; Clark, Aurora E.

2011-11-08T23:59:59.000Z

103

Molecular Dynamics Simulation of Smaller Granular Particles Deposition on a Larger One Due to Velocity Sequence Dependent Electrical Charge Distribution  

E-Print Network (OSTI)

Deposition of smaller granular particles on a larger nucleus particle has been simulated in two-dimension using molecular dynamics method. Variation of sequences of velocity of deposited particles is conducted and reported in this work. The sequences obey a normal distribution function of velocity with the same parameters. It has been observed that for velocity in range of 0 to 0.02 the densest deposited site (15-17 % number of grains) is located at about angle {\\pi}/4 where location of injection point is {\\pi}/4. And the less dense is about {\\pi}/4 + {\\pi}/2. Different sequences give similar result.

Euis Sustini; Siti Nurul Khotimah; Ferry Iskandar; Sparisoma Viridi

2011-07-11T23:59:59.000Z

104

Ab-Initio Molecular Dynamics  

E-Print Network (OSTI)

Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.

Kühne, Thomas D

2012-01-01T23:59:59.000Z

105

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 of dendritic surfactants, the confinement force profiles featuring oscillatory fashion at moderate layer separation of 10 to 25 Å were observed. Integration of the confinement forces led to free energy profiles, which, in turn, were used to determine the final morphology of the nanocomposite. From the free energy profiles, smaller and linear surfactants (G1 and G2L) are expected to intercalate into the clay comfortably, while larger surfactants (G2 and G3) are expected to form frustrated intercalated structures due to the location and depth of the free energy minima. This would agree with the previous observations. As primary steps to understand the Ab protein behavior under biological conditions, simulations of bulk water and hydrated lipids were performed and the results were compared with the literature. Hydrated lipids were simulated using a full atomistic model of lipids (dipalmitoylphosphatidylcholine) and water with a cvff force-field and it was found that structural properties such as the molecular head group area and membrane thickness were accurately produced with MD simulation. Systems of the protein Ab(1-42) in bulk water were simulated and some secondary structural change, with loss of part of the a-helical structure, occurred during the 1 ns of simulation time at 323K. The fragment Ab(31-42) with b-sheet conformation was also simulated in bulk water, and the extended b-sheet structure became a bent structure. Simulations of Ab(1- 42) or Ab(31-42) near lipid bilayers have been performed to investigate the structural property changes under biological conditions. The different nature of structural change was observed from the simulations of the protein or fragment in water and near lipid bilayers due to the different solvent environment. The protein has close contacts with the membrane surface. It was impossible to observe the conformational change to b-sheet and protein entrance into the lipid bilayer within 1 ns simulations.

Han, Kunwoo

2006-08-01T23:59:59.000Z

106

369 TFlop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer  

Science Conference Proceedings (OSTI)

The authors present timing and performance numbers for a short-range parallel molecular dynamics (MD) code, SPaSM, that has been rewritten for the heterogeneous Roadrunner supercomputer. Each Roadrunner compute node consists of two AMD Opteron dual-core microprocessors and four PowerXCell 8i enhanced Cell microprocessors, so that there are four MPI ranks per node, each with one Opteron and one Cell. The interatomic forces are computed on the Cells (each with one PPU and eight SPU cores), while the Opterons are used to direct inter-rank communication and perform I/O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard-Jones pair potential benchmark reached a peak of 369 Tflop/s double-precision floating-point performance on the full Roadrunner system (27.7% of peak), corresponding to 124 MFlop/Watt/s at a price of approximately 3.69 MFlops/dollar. They demonstrate an initial target application, the jetting and ejection of material from a shocked surface.

Swaminarayan, Sriram [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Kadau, Kai [Los Alamos National Laboratory; Fossum, Gordon C [IBM CORPORATION

2008-01-01T23:59:59.000Z

107

Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations.  

DOE Green Energy (OSTI)

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Hairpin loop structures are common motifs in folded nucleic acids. The 59-GCGCAGC sequence in DNA forms a characteristic and stable trinucleotide hairpin loop flanked by a two basepair stem helix. To better understand the structure formation of this hairpin loop motif in atomic detail, we employed replica-exchange molecular dynamics (RexMD) simulations starting from a single-stranded DNA conformation. In two independent 36 ns RexMD simulations, conformations in very close agreement with the experimental hairpin structure were sampled as dominant conformations (lowest free energy state) during the final phase of the RexMDs (;35% at the lowest temperature replica). Simultaneous compaction and accumulation of folded structures were observed. Comparison of the GCA trinucleotides from early stages of the simulations with the folded topology indicated a variety of central loop conformations, but arrangements close to experiment that are sampled before the fully folded structure also appeared. Most of these intermediates included a stacking of the C2 and G3 bases, which was further stabilized by hydrogen bonding to the A5 base and a strongly bound water molecule bridging the C2 and A5 in the DNA minor groove. The simulations suggest a folding mechanism where these intermediates can rapidly proceed toward the fully folded hairpin and emphasize the importance of loop and stem nucleotide interactions for hairpin folding. In one simulation, a loop motif with G3 in syn conformation (dihedral flip at N-glycosidic bond) accumulated, resulting in a misfolded hairpin. Such conformations may correspond to long-lived trapped states that have been postulated to account for the folding kinetics of nucleic acid hairpins that are slower than expected for a semiflexible polymer of the same size.

Kannan, Srinivasaraghavan; Zacharias, Martin W.

2007-11-01T23:59:59.000Z

108

Ab initio molecular dynamics simulations of low energy recoil events in ceramics  

SciTech Connect

The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.

Gao, Fei [Pacific Northwest National Laboratory (PNNL); Xiao, Haiyan [ORNL; Weber, William J [ORNL

2011-01-01T23:59:59.000Z

109

Ab initio molecular dynamics simulations of low energy recoil events in ceramics  

SciTech Connect

The recent progress in the use of large-scale ab initio molecular dynamics (AIMD) to investigate low energy recoil events and determine threshold displacement energies, Ed, in ceramics is reviewed. In general, Ed shows a significant dependence on recoil direction and atom. In 3C-SiC, the minimum Ed for both C and Si atoms is found along the <100> direction, with a value of 20 and 49 eV, respectively. The results demonstrate that significant charge transfer occurs during the dynamics process, and defects can enhance charge transfer to surrounding atoms, which provides important insights into the formation of charged defects. It is found that the C vacancy is a positively charged defect, whereas the Si vacancy is in its neutral state. The minimum Ed in GaN is determined to be 17 and 39 eV for N and Ga atoms, respectively, both along the direction. The average Ed for N atoms (32.4 eV) is smaller than that for Ga atoms (73.2 eV). It is of interest to note that the N defects created along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed. In Y2Ti2O7 prochlore, the minimum Ed for Y atoms is determined to be 27 eV for a recoil along the <100> direction, 31.5 eV for Ti atoms along the <100> direction, 14.5 eV for O48f atoms along the <110> direction and 13 eV for O8b atoms along the <111> direction. The average Ed values determined are 32.7, 34.2, 14.2 and 16.1 eV for yttrium, titanium, O48f and O8b atoms, respectively. Cation interstitials at vacant 8a sites, which are generally occupied by oxygen anions, and at the bridge sites between two neighboring cations along the <010> direction are observed after low energy recoil events.

Gao, Fei; Xiao, Haiyan Y.; Weber, William J.

2011-07-15T23:59:59.000Z

110

Molecular-dynamics simulation of clustering processes in sea-ice floes  

E-Print Network (OSTI)

In seasonally ice-covered seas and along the margins of perennial ice pack, i.e. in regions with medium ice concentrations, the ice cover typically consists of separate floes interacting with each other by inelastic collisions. In this paper, hitherto unexplored analogies between this type of ice cover and two-dimensional granular gases are used to formulate a model of ice dynamics at the floe level. The model consists of: (i) momentum equations for floe motion between collisions, formulated in the form of a Stokes-flow problem, with floe-size dependent time constant and equilibrium velocity, and (ii) hard-disk collision model. The numerical algorithm developed is suitable for simulating particle-laden flow of $N$ disk-shaped floes with arbitrary size distribution. The model is applied to study clustering phenomena in sea ice with power-law floe-size distribution. In particular, the influence of the average ice concentration $\\bar{A}$ on the formation and characteristics of clusters is analyzed in detail. The...

Herman, Agnieszka

2011-01-01T23:59:59.000Z

111

Free energy of solvation from molecular dynamics simulation applying Voronoi-Delaunay triangulation to the cavity creation  

Science Conference Proceedings (OSTI)

The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostaticfree energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene

Paulo F. B. Goncalves; Hubert Stassen

2005-01-01T23:59:59.000Z

112

High-precision molecular dynamics simulation of UO2-PuO2: superionic transition in uranium dioxide  

E-Print Network (OSTI)

Our series of articles is devoted to high-precision molecular dynamics simulation of mixed actinide-oxide (MOX) fuel in the rigid ions approximation using high-performance graphics processors (GPU). In this article we assess the 10 most relevant interatomic sets of pair potential (SPP) by reproduction of the Bredig superionic phase transition (anion sublattice premelting) in uranium dioxide. The measurements carried out in a wide temperature range from 300K up to melting point with 1K accuracy allowed reliable detection of this phase transition with each SPP. The {\\lambda}-peaks obtained are smoother and wider than it was assumed previously. In addition, for the first time a pressure dependence of the {\\lambda}-peak characteristics was measured, in a range from -5 GPa to 5 GPa its amplitudes had parabolic plot and temperatures had linear (that is similar to the Clausius-Clapeyron equation for melting temperature).

Potashnikov, S I; Nekrasov, K A; Kupryazhkin, A Ya

2011-01-01T23:59:59.000Z

113

Molecular Dynamics Simulation of Solidification in Cu50Zr50 Alloy  

Science Conference Proceedings (OSTI)

Next, MD simulation of melting B2 phase surrounded by liquid was .... Thermochemical Models and Phase Equilibria of Urania Rare Earth Fluorite Phases.

114

Gas-phase and Solution-phase Peptide Conformations Studied by Ion Mobility-mass Spectrometry and Molecular Dynamics Simulations  

E-Print Network (OSTI)

Ion mobility spectrometry (IMS) separates ions on the basis of ion-neutral collision cross-sections (CCS, [omega]), which are determined by the geometry or conformation of the ions. The size-based IM separation can be extended to distinguish conformers that have different shapes in cases where shape differences influence the accessible surface area of the molecule. In recent years, IM has rapidly evolved as a structural characterization technique, which has applied on various structural biology problems. In this work, IMS is combined with molecular dynamics simulation (MDS), specially the integrated tempering sampling molecular dynamics simulation (ITS-MDS) to explore the gas-phase conformation space of two molecular systems (i) protonated tryptophan zipper 1 (trpzip1) ions and its six derivatives (ii) alkali metal ion (Na, K and Cs) adducts of gramicidin A (GA). The structural distributions obtained from ITS-MDS are compared well with results obtained from matrix-assisted laser desorption ionization-ion mobility-mass spectrometry (MALDI-IM-MS) for trpzip 1 series and electrospray ionization-ion mobility-mass spectrometry (ESI-IM-MS) for alkali metal ion adducts of GA. Furthermore, the solvent dependence on conformational preferences of the GA dimer is investigated using a combination of mass spectrometry techniques, viz. ESI-IM-MS and hydrogen/deuterium exchange (HDX)-MS, and MDS. The IM experiments reveal three distinct gramicidin A species, detected as the sodium ion adduct ions, [2GA + 2Na]²?, and the equilibrium abundances of the dimer ions varies with solvent polarity. The solution phase conformations are assigned as the parallel and anti-parallel [beta]-helix dimer, and the anti-parallel dimer is the preferred conformation in non-polar organic solvent. The calculated CCS profiles by ITS-MDS agree very well with the experimentally measured CCS profiles, which underscore the utility of the method for determining candidate structures as well as the relative abundances of the candidate structures. The benefit of combining ion mobility measurements with solution-phase H/D exchange is allowing identifications and detail analysis of the solution-phase subgroup conformations, which cannot be uncovered by one method alone.

Chen, Liuxi

2012-08-01T23:59:59.000Z

115

Molecular Dynamics Study of Nucleation during Crystallization  

Science Conference Proceedings (OSTI)

A Tale of Two States and More: Modeling of New Generation of Lattice Stability from Zero ... Analysis of Nano Fluid Using CFD-A Hybrid Approach for Cooling Purpose ... Molecular Dynamics Simulations of Grain Boundary Free Energy and

116

OpenAtom -- Ab initio molecular dynamics package  

Science Conference Proceedings (OSTI)

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

Roberto Car Mark E. Tuckerman Glenn J. Martyna Nick Nystrom Michael Klein Josep Torrellas Klaus Schulten Jack Dongarra Eric Bohm Abhinav Bhatele Laxmikant Kale Sameer Kumar Anshu Arya Ramprasad Venkataraman

2008-01-01T23:59:59.000Z

117

Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations  

Science Conference Proceedings (OSTI)

We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)-O pair correlation function exhibits a satellite peak at 2.15 A associated with the shorter U(IV)-(OH{sup -}) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.

Leung, Kevin; Nenoff, Tina M. [Sandia National Laboratories, MS 1415, Albuquerque, New Mexico 87185 (United States)

2012-08-21T23:59:59.000Z

118

Mass Transport Properties of LiD-U Mixtures from Orbital Free Molecular Dynamics Simulations and a Pressure-Matching Mixing Rule  

SciTech Connect

Mass transport properties for LiD-U mixtures were calculated using a pressure matching mixture rule for the mixing of LiD and of U properties simulated with Orbital Free Molecular Dynamics (OFMD). The mixing rule was checked against benchmark OFMD simulations for the fully interacting three-component (Li, D, U) system. To obtain transport coefficients for LiD-U mixtures of different (LiD){sub x}U{sub (1-x)} compositions as functions of temperature and mixture density is a tedious task. Quantum molecular dynamics (MD) simulations can be employed, as in the case LiD or U. However, due to the presence of the heavy constituent U, such simulations proceed so slowly that only a limited number of numerical data points in the (x, {rho}, T) phase space can be obtained. To finesse this difficulty, transport coefficients for a mixture can be obtained using a pressure-matching mixing rule discussed. For both LiD and U, the corresponding transport coefficients were obtained earlier from quantum molecular dynamics simulations. In these simulations, the quantum behavior of the electrons was represented using an orbital free (OF) version of density functional theory, and ions were advanced in time using classical molecular dynamics. The total pressure of the system, P = nk{sub B}T/V + P{sub e}, is the sum of the ideal gas pressure of the ions plus the electron pressure. The mass self-diffusion coefficient for species {alpha}, D{sub {alpha}}, the mutual diffusion coefficient for species {alpha} and {beta}, D{alpha}{beta}, and the shear viscosity, {eta}, are computed from the appropriate autocorrelation function. The details of similar QMD calculations on LiH are described in Ref. [1] for 0.5 eV < T < 3 eV, and in Ref. [2] for 2 eV < T < 6 eV.

Burakovsky, Leonid [Los Alamos National Laboratory; Kress, Joel D. [Los Alamos National Laboratory; Collins, Lee A. [Los Alamos National Laboratory

2012-05-31T23:59:59.000Z

119

Structure and Dynamics of N, N-diethyl-N-methylammonium Triflate Ionic Liquid, Neat and with Water, from Molecular Dynamics Simulations  

DOE Green Energy (OSTI)

We investigated by means of molecular dynamics simulations the properties (structure, thermodynamics, ion transport, and dynamics) of the protic ionic liquid N,N-diethyl-N-methyl-ammonium triflate (dema:Tfl) and of selected aqueous mixtures of dema:Tfl. This ionic liquid, a good candidate for a water-free proton exchange membrane, is shown to exhibit high ion mobility and conductivity. For bulk melts in the temperature range of 303-453K, both liquid densities and enthalpies of vaporization are found to decrease roughly linearly with increasing temperature. The radial distribution functions reveal a significant long-range structural correlation. The ammonium cations [dema]+ are found to diffuse slightly faster than the triflate anions [Tfl]-, and both types of ions exhibit enhanced mobility at higher temperatures, leading to higher ionic conductivity of these ionic liquids. Analysis of the dynamics of ion pairing clearly points to the existence of long-lived contact ion pairs in this ionic liquid. We also examined the effects of water on the ionic properties of dema:Tfl-water mixtures. From the structural analysis it was found that water molecules tend to replace counter ions in the coordination shell and hydrogen bond to both ions, thus weakening their mutual association. As water concentration increases, water molecules start to connect with each other and eventually form a large network that percolates through the system. It is also found that water has a strong influence on the ion dynamics in the mixtures. As the concentration of water increases, both translational and rotational motion of [dema]+ and [Tfl]- are significantly enhanced. As a result, higher ionic conductivity is observed with increased hydration level. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

Chang, Tsun-Mei; Dang, Liem X.; Devanathan, Ramaswami; Dupuis, Michel

2010-12-09T23:59:59.000Z

120

Molecular Dynamics Simulations II  

Science Conference Proceedings (OSTI)

Mar 5, 2013... NIST; Dongwon Shin, Oak Ridge National Laboratory; Zi Kui Liu, .... and finite activation energies were accounted for by introducing statistics ...

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121

Molecular Dynamics Simulations I  

Science Conference Proceedings (OSTI)

Mar 5, 2013... NIST; Dongwon Shin, Oak Ridge National Laboratory; Zi Kui Liu, Penn .... Manufacturing Eng.; 2Ames Laboratory; 3Massachusetts Institute of ...

122

Introduction to Accelerated Molecular Dynamics  

SciTech Connect

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

Perez, Danny [Los Alamos National Laboratory

2012-07-10T23:59:59.000Z

123

Introduction to Accelerated Molecular Dynamics  

SciTech Connect

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

Perez, Danny [Los Alamos National Laboratory

2012-07-10T23:59:59.000Z

124

Molecular-dynamics simulation of the heat capacity for nickel and copper clusters: Shape and size effects  

SciTech Connect

We have investigated the heat capacity of ideal Cu and Ni fcc clusters with diameters from 2 to 6 nm in the temperature range 200-800 K by the molecular-dynamics method using a modified tight-binding potential. Our analysis has shown consistency with the experimental results at temperatures of 200-300 K. The data obtained are also indicative of several regularities that are in agreement with the analytical calculations. We have concluded from the results of our computer simulations that the heat capacity in the case of isolated free clusters can exceed that of a bulk material, with this difference decreasing as the nanoparticle grows proportionally to the reduction in the fraction of surface atoms. The excess of the heat capacity for ideal copper and nickel nanoclusters with D = 6 nm at T = 200 K has been found to be 10% and 13%, respectively. Consequently, the large heat capacities of copper and nickel nanostructures observed in some real experiments cannot be related to the characteristics of free clusters. We hypothesize that these properties of a nanomaterial depend on the degree of agglomeration of its constituent particles, i.e., the surfaces and interphase boundaries of interconnected nanoclusters can have a strong effect. To test this hypothesis, we took nickel and copper clusters of various sizes (4000-7200 atoms) produced through the simulation of condensation from the gas phase. At high temperatures, we failed to adequately assess the role of the interphase boundaries in calculating the heat capacity of nanoparticles. The reason was the mass diffusion of Ni or Cu atoms to impart an energetically more favorable shape and structure to the synthesized clusters. At low temperatures, the heat capacity of such clusters exceeded that of clusters with an ideal shape and structure by a value from 3.2% to 10.6%. We have concluded that the Ni and Cu clusters produced in real experiments cannot be applied in devices using the thermal energy of such clusters without a preliminary optimization stage, because their external shape and interior structure are nonideal.

Gafner, S. L.; Redel, L. V.; Gafner, Yu. Ya., E-mail: ygafner@khsu.ru [Katanov Khakassian State University (Russian Federation)

2012-03-15T23:59:59.000Z

125

Optimization of density functional tight-binding and classical reactive molecular dynamics for high-throughput simulations of carbon materials  

Science Conference Proceedings (OSTI)

Carbon materials and nanostructures (fullerenes, nanotubes) are promising building blocks of nanotechnology. Potential applications include optical and electronic devices, sensors, and nano-scale machines. The multiscale character of processes related ... Keywords: ACM proceedings, BLAS, Cray XT5, LAPACK, advanced materials, density-functional tight binding, high-throughput, linear algebra, material science, molecular dynamics, multiscale-modeling, quantum chemistry, scientific libraries, scientific-computing

Jacek Jakowski; Bilel Hadri; Steven J. Stuart; Predrag Krstic; Stephan Irle; Dulma Nugawela; Sophya Garashchuk

2012-07-01T23:59:59.000Z

126

Ab initio Molecular Dynamics Simulations of the Initial Stages of Solid-electrolyte Interphase Formation on Lithium Ion Battery Graphitic Anodes  

E-Print Network (OSTI)

The decomposition of ethylene carbonate (EC) during the initial growth of solid-electrolyte interphase (SEI) films at the solvent-graphitic anode interface is critical to lithium ion battery operations. Ab initio molecular dynamics simulations of explicit liquid EC/graphite interfaces are conducted to study these electrochemical reactions. We show that carbon edge terminations are crucial at this stage, and that achievable experimental conditions can lead to surprisingly fast EC breakdown mechanisms, yielding decomposition products seen in experiments but not previously predicted.

Leung, Kevin; 10.1039/B925853A

2010-01-01T23:59:59.000Z

127

Gas-Phase Molecular Dynamics  

NLE Websites -- All DOE Office Websites (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,"

128

Langevin molecular dynamics derived from Ehrenfest dynamics  

E-Print Network (OSTI)

Stochastic Langevin molecular dynamics for nuclei is derived from quantum classical molecular dynamics, also called Ehrenfest dynamics, at positive temperature, assuming that the molecular bulk system is in equilibrium and that the initial data for the electrons is stochastically perturbed from the ground state. The initial electron probability distribution is derived from the Liouville equilibrium solution generated by the nuclei acting as a heat bath for the electrons. The diffusion and friction coefficients in the Langevin equation satisfy Einstein's fluctuation-dissipation relation. The fluctuating initial data yields, in addition to the fluctuating diffusion terms, also a contribution to the drift, modifying the standard ab initio Born-Oppenheimer solution at zero temperature, where the electrons are in their ground state for the current nuclear configuration. The dissipative friction mechanism comes from the evolution of the electron ground state, due to slow dynamics of the nuclei, while the modified d...

Szepessy, Anders

2007-01-01T23:59:59.000Z

129

Molecular Simulation Study of Alkyl Monolayers on Si(111) Luzheng Zhang  

E-Print Network (OSTI)

Molecular Simulation Study of Alkyl Monolayers on Si(111) Luzheng Zhang Department of Chemical of Washington, Seattle, Washington 98195 Received April 30, 2001 Molecular mechanics and molecular dynamics) surface. The optimal molecular packing was found basedontheconsiderationofthreemajorfactors

Zhang, Luzheng

130

In Silico Design, Extended Molecular Dynamic Simulations and Binding Energy Calculations for a New Series of Dually Acting Inhibitors against EGFR and HER2  

E-Print Network (OSTI)

Starting from the lead structure we have identified in our previous works, we are extending our insight understanding of its potential inhibitory effect against both EGFR and HER2 receptors. Herein and using extended molecular dynamic simulations and different scoring techniques, we are providing plausible explanations for the observed inhibitory effect. Also, we are comparing the binding mechanism in addition to the dynamics of binding with two other approved inhibitors against EGFR (Lapatinib) and HER2 (SYR). Based on this information, we are also designing and in silico screening new potential inhibitors sharing the same scaffold of the lead structure. We have chosen the best scoring inhibitor for additional in silico investigation against both the wild-type and T790M mutant strain of EGFR. It seems that certain substitution pattern guarantees the binding to the conserved water molecule commonly observed with kinase crystal structures. Also, the new inhibitors seem to form a stable interaction with the mut...

Ahmed, Marawan; Abouzid, Khaled A; Wang, Feng

2013-01-01T23:59:59.000Z

131

Molecular dynamics simulation of electron transfer in proteins. Theory and application to Q sub A yields Q sub B transfer in the photosynthetic reaction center  

Science Conference Proceedings (OSTI)

Electron transfer (ET) from the primary menaquinone Q{sub A} to the secondary ubiquinone Q{sub B}, i.e., Q{sub A}{sup {minus}}Q{sub B} {yields} Q{sub A}Q{sub B}{sup {minus}}, in the photosynthetic reaction center of Rhodopseudomonas viridis has been simulated by using the method of molecular dynamics accounting for the classical motion of a protein's nuclear degrees of freedom, the redistribution of charge accompanying electron transfer being described quantum chemically. We outline the role of classical nuclear degrees of freedom in electron transfer, identifying the essential dynamic properties that should be determined from molecular dynamics simulations in order to characterize electron transfer. These quantities, all related to the energy difference {Delta}E(t) = E{sub p}(t) - E{sub R}O(t) of virtual forward (electron tries to jump forward before ET) and backward (electron tries to jump backward after ET) electron transfer, R and P denoting the states Q{sub A}{sup {minus}}Q{sub B} and Q{sub A}Q{sub B}{sup {minus}}, respectively, are as follows: the variance of {Delta}E(t) and the average value of {Delta}E(t) before and after transfer, i.e., {Sigma}{sub R} (6.9 kcal/mol), {sub R} (22 kcal/mol) and {Sigma}{sub p} (8.8 kcal/mol), {sub p} ({minus}25 kcal/mol), respectively; the relaxation time of the energy-energy correlation function {sub R})({Delta}E(0) - {sub R})>{sub R} (120 fs); the time describing the relaxation of {Delta}E(t) from an average value {sub R} to an average value {sub p} immediately after electron transfer (200 fs). The quantities in brackets are the respective simulation results.

Nonella, M.; Schulten, K. (Univ. of Illinois, Urbana (USA))

1991-03-07T23:59:59.000Z

132

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

133

Accelerated Molecular Dynamics Methods  

NLE Websites -- All DOE Office Websites (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

134

Stochastic Event-Driven Molecular Dynamics  

Science Conference Proceedings (OSTI)

A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in EDMD, rather, the momentum and energy exchange in the solvent is determined stochastically using DSMC. The coupling between the solvent and the solute is consistently represented at the particle level retaining hydrodynamic interactions and thermodynamic fluctuations. However, unlike full MD simulations of both the solvent and the solute, in SEDMD the spatial structure of the solvent is ignored. The SEDMD algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard-wall subjected to uniform shear. SEDMD closely reproduces results obtained using traditional EDMD simulations with two orders of magnitude greater efficiency. Results question the existence of periodic (cycling) motion of the polymer chain.

Donev, Aleksandar [Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-9900 (United States)], E-mail: aleks.donev@gmail.com; Garcia, Alejandro L. [Department of Physics, San Jose State University, San Jose, CA 95192 (United States); Alder, Berni J. [Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-9900 (United States)

2008-02-01T23:59:59.000Z

135

Gas Phase Molecular Dynamics  

Science Conference Proceedings (OSTI)

The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.

Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.

1999-05-21T23:59:59.000Z

136

GAS PHASE MOLECULAR DYNAMICS  

SciTech Connect

The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution, high-sensitivity, laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule. The work of group members Fockenberg and Muckerman is described in separate abstracts of this volume.

SEARS,T.J.; HALL,G.E.; PRESES,J.M.; WESTON,R.E.,JR.

1999-06-09T23:59:59.000Z

137

Can Dynamic Contact Angle Be Measured Using Molecular Modeling?  

E-Print Network (OSTI)

A method is presented for determining the dynamic contact angle at the three-phase contact between a solid, a liquid, and a vapor under an applied force, using molecular simulation. The method is demonstrated using a ...

Malani, Ateeque A. A. G.

138

Application of Ab-Initio Quantum and Classical Molecular Dynamics...  

NLE Websites -- All DOE Office Websites (Extended Search)

Ab-Initio Quantum and Classical Molecular Dynamics Simulations to Study Clustered DNA Damage J.H. Miller 1 , M.B. Ernst 2 , M. Haranczyh 3 , L. Douali 2 , M. Gutowski 2 , and...

139

Langevin molecular dynamics derived from Ehrenfest dynamics  

E-Print Network (OSTI)

Stochastic Langevin molecular dynamics for nuclei is derived from the Ehrenfest Hamiltonian system (also called quantum classical molecular dynamics) in a Kac-Zwanzig setting, with the initial data for the electrons stochastically perturbed from the ground state and the ratio, $M$, of nuclei and electron mass tending to infinity. The Ehrenfest nuclei dynamics is approximated by the Langevin dynamics with accuracy $o(M^{-1/2})$ on bounded time intervals and by $o(1)$ on unbounded time intervals, which makes the small $\\mathcal{O}(M^{-1/2})$ friction and $o(M^{-1/2})$ diffusion terms visible. The initial electron probability distribution is a Gibbs density at low temperture, derived by a stability and consistency argument: starting with any equilibrium measure of the Ehrenfest Hamiltonian system, the initial electron distribution is sampled from the equilibrium measure conditioned on the nuclei positions, which after long time leads to the nuclei positions in a Gibbs distribution (i.e. asymptotic stability); by consistency the original equilibrium measure is then a Gibbs measure.The diffusion and friction coefficients in the Langevin equation satisfy the Einstein's fluctuation-dissipation relation.

Anders Szepessy

2007-12-21T23:59:59.000Z

140

Molecular Simulation of Nanofluids Mark J. Biggs  

E-Print Network (OSTI)

Molecular Simulation of Nanofluids Mark J. Biggs School of Chemical Engineering, The University. As the molecules and interactions between them are explicitly modelled in these `molecular simulations', they may the volumes and timescales accessible to molecular simulation are small on the macroscale, they are ideally

Adler, Joan

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

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

Science Conference Proceedings (OSTI)

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

Wang, X. J.; Xiao, Haiyan Y.; Zu, Xiaotao; Zhang, Yanwen; Weber, William J.

2012-12-21T23:59:59.000Z

142

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

SciTech Connect

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

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

2013-01-01T23:59:59.000Z

143

New and interesting prepolymers based on the molecular dynamics computer simulation of binary systems to be utilized in the clean-up technologies of off-shore oil spills  

Science Conference Proceedings (OSTI)

New emerging technologies for the clean-up of off-shore oil spills have been reported. Several research groups are currently working on various ways to develop new urethane prepolymers that will foam upon contact with water and encapsulate the oil droplets ... Keywords: computer simulation, hydrophobic, miscibility, molecular dynamics, oil spill, urethane prepolymer

Rasha A. Azzam; Tarek M. Madkour

2008-12-01T23:59:59.000Z

144

Hydration, Swelling, Interlayer Structure, and Hydrogen Bonding in Organolayered Double Hydroxides: Insights from Molecular Dynamics Simulation of Citrate-Intercalated  

E-Print Network (OSTI)

citrate, C6H5O7 3- , as the charge balancing interlayer anion provides new molecular scale insight hydration levels, in contrast to the preferred low hydration states of most LDHs intercalated with small. Introduction Layered double hydroxides (LDHs), also known as hydro- talcite-like compounds, form an important

Kalinichev, Andrey G.

145

Structure and Phase Transitions of Monolayers of Intermediate-length n-alkanes on Graphite Studied by Neutron Diffraction and Molecular Dynamics Simulation  

Science Conference Proceedings (OSTI)

We present evidence from neutron diffraction measurements and molecular dynamics (MD) simulations of three different monolayer phases of the intermediate-length alkanes tetracosane (n-C(24)H(50) denoted as C24) and dotriacontane (n-C(32)H(66) denoted as C32) adsorbed on a graphite basal-plane surface. Our measurements indicate that the two monolayer films differ principally in the transition temperatures between phases. At the lowest temperatures, both C24 and C32 form a crystalline monolayer phase with a rectangular-centered (RC) structure. The two sublattices of the RC structure each consists of parallel rows of molecules in their all-trans conformation aligned with their long axis parallel to the surface and forming so-called lamellas of width approximately equal to the all-trans length of the molecule. The RC structure is uniaxially commensurate with the graphite surface in its [110] direction such that the distance between molecular rows in a lamella is 4.26 A=sqrt[3a(g)], where a(g)=2.46 A is the lattice constant of the graphite basal plane. Molecules in adjacent rows of a lamella alternate in orientation between the carbon skeletal plane being parallel and perpendicular to the graphite surface. Upon heating, the crystalline monolayers transform to a 'smectic' phase in which the inter-row spacing within a lamella expands by approximately 10% and the molecules are predominantly oriented with the carbon skeletal plane parallel to the graphite surface. In the smectic phase, the MD simulations show evidence of broadening of the lamella boundaries as a result of molecules diffusing parallel to their long axis. At still higher temperatures, they indicate that the introduction of gauche defects into the alkane chains drives a melting transition to a monolayer fluid phase as reported previously.

Taub, H. [University of Missouri, Columbia; Hansen, F.Y. [Technical University of Denmark; Diama, Amand [National University of the Ivory Coast; Matthies, Blake [Goodyear Tire and Rubber Company, The; Criswell, Leah [University of Missouri, Columbia; Mo, Haiding [Advanced Optowave Corporation; Bai, M [University of Missouri, Columbia; Herwig, Kenneth W [ORNL

2009-01-01T23:59:59.000Z

146

Phase separation of an asymmetric binary fluid mixture confined in a nanoscopic slit pore: Molecular-dynamics simulations  

E-Print Network (OSTI)

As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones interactions for the carbon dioxide molecules. In previous work, it has been shown that this model reproduces the real phase diagram reasonable well, and also the initial stages of spinodal decomposition in the bulk following a sudden expansion of the system could be studied. Using the parallelized simulation package ESPResSo on a multiprocessor supercomputer, phase separation of thin fluid films confined between parallel walls that are repulsive for both types of molecules are simulated in a rather large system (1356 x 1356 x 67.8 A^3, corresponding to about 3.2 million atoms). Following the sudden system expansion, a complicated interplay between phase separation in the directions perpendicular and parallel to the walls is found: in the early stages the hexadecane molecules accumulate mostly in the center of the slit pore, but as the coarsening of the structure in the parallel direction proceeds, the inhomogeneity in the perpendicular direction gets much reduced. Studying then the structure factors and correlation functions at fixed distances from the wall, the densities are essentially not conserved at these distances, and hence the behavior differs strongly from spinodal decomposition in the bulk. Some of the characteristic lengths show a nonmonotonic variation with time, and simple coarsening described by power-law growth is only observed if the domain sizes are much larger than the film thickness.

K. Bucior; L. Yelash; K. Binder

2008-04-09T23:59:59.000Z

147

A thread calculus with molecular dynamics  

Science Conference Proceedings (OSTI)

We present a theory of threads, interleaving of threads, and interaction between threads and services with features of molecular dynamics, a model of computation that bears on computations in which dynamic data structures are involved. Threads can interact ... Keywords: Molecular dynamics, Projective limit model, Restriction, Thread algebra, Thread calculus

J. A. Bergstra; C. A. Middelburg

2010-07-01T23:59:59.000Z

148

Application of optimal prediction to molecular dynamics  

SciTech Connect

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

Barber IV, John Letherman

2004-12-01T23:59:59.000Z

149

Dynamic Infrared Simulation.  

E-Print Network (OSTI)

?? The increased usage of infrared sensors by pilots has created a growing demand for simulated environments based on infrared radiation. This has led to… (more)

Dehlin, Jonas

2006-01-01T23:59:59.000Z

150

AVESTAR® - Gasification Dynamic Simulator  

NLE Websites -- All DOE Office Websites (Extended Search)

Meet Our Partners Simulators IGCC Gasification Combined Cycle NGCC SCOT Oxy-coal Shale Gas 3D Virtual IGCC Training How to Register for Training IGCC Gasification Combined...

151

Molecular Dynamics Study of a Surfactant-Mediated Decane-Water Interface: Effect of Molecular Architecture of Alkyl Benzene Sulfonate  

E-Print Network (OSTI)

Molecular Dynamics Study of a Surfactant-Mediated Decane-Water Interface: Effect of Molecular; In Final Form: May 25, 2004 The effect of molecular architecture of a surfactant, particularly and molecular alignment at the interface, than other surfactants simulated in this study. Furthermore

Goddard III, William A.

152

Molecular Dynamics of Martenstic Phase Transitions  

Science Conference Proceedings (OSTI)

Presentation Title, Kinetics of martensitic phase transformation: Molecular Dynamics of Martenstic ... A Comparison of Coulombic and Plastic Shear Faults in Ice.

153

Car-Parrinello Molecular Dynamics With A Sinusoidal Time-Dependent Potential Field  

E-Print Network (OSTI)

A sinusoidal external field is applied in Car-Parrinello molecular dynamics simulations. We present an implementation and discuss first test applications to electron and ion transfers in complex molecular systems.

Alznauer, Tobias

2012-01-01T23:59:59.000Z

154

System dynamics simulation of the telecom industry  

E-Print Network (OSTI)

The primary goal of this research effort was to integrate several pieces of relatively simple dynamics simulations into a full blown system dynamics simulation of the telecom industry. The economic simulation model was ...

Shapira, Gil, 1971-

2004-01-01T23:59:59.000Z

155

Thermostatted molecular dynamics: How to avoid the Toda demon hidden in Nose-Hoover dynamics  

SciTech Connect

The Nose-Hoover thermostat, which is often used in the hope of modifying molecular dynamics trajectories in order to achieve canonical-ensemble averages, has hidden in it a Toda ``demon,`` which can give rise to unwanted, noncanonical undulations in the instantaneous kinetic temperature. We show how these long-lived oscillations arise from insufficient coupling of the thermostat to the atoms, and give straightforward, practical procedures for avoiding this weak-coupling pathology in isothermal molecular dynamics simulations.

Holian, B.L.; Voter, A.F. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Ravelo, R. [Department of Physics, University of Texas, El Paso, Texas 79968 (United States)

1995-09-01T23:59:59.000Z

156

Molecular Dynamics of Surface-Moving Thermally Driven Alexei V. Akimov,,  

E-Print Network (OSTI)

Molecular Dynamics of Surface-Moving Thermally Driven Nanocars Alexei V. Akimov,,§ Alexander V Abstract: We developed molecular models describing the thermally initiated motion of nanocars, nanosized-grained-type molecular dynamics simulations were carried out for the species "Trimer" and "Nanotruck", the simplified

157

Molecular dynamics study of nanoparticle evolution in a background gas under laser ablation conditions  

E-Print Network (OSTI)

Molecular dynamics study of nanoparticle evolution in a background gas under laser ablation,7] are used to explain the evaporation­condensation process. Molecular dynamics (MD) method [4,5,8,9] directly simulates molecular movement and interactions and can be used to investigate the evaporation process

Zhigilei, Leonid V.

158

Molecular Dynamic Studies of Viral-Protein Based Nano-Actuators Constantinos Mavroidis (PI)  

E-Print Network (OSTI)

1 Molecular Dynamic Studies of Viral-Protein Based Nano-Actuators Constantinos Mavroidis (PI: In this paper, we perform molecular simulations on novel viral protein linear nanoactuators. The main challenge changes, is the limitation on computational time. A modified molecular dynamic approach known as Targeted

Mavroidis, Constantinos

159

Molecular Dynamics Study of Krypton Isotopes Physisorbed on Graphite  

E-Print Network (OSTI)

Equations of Motion in Molecular Dynamics” Lecture Notes,OF CALIFORNIA RIVERSIDE Molecular Dynamics Study of Krypton2.5 Choice of Time step in Molecular Dynamics 2.6 Desorption

Bader, Karson

2012-01-01T23:59:59.000Z

160

DFT-based molecular dynamics as a new tool for computational biology: first applications and perspective  

Science Conference Proceedings (OSTI)

Static and molecular dynamics (MD) calculations based on density-functional theory (DFT) are emerging as a valuable means for simulations in the field of biology, especially when coupled with classical simulations. In this contribution, we point out ...

W. Andreoni; A. Curioni; T. Mordasini

2001-05-01T23:59:59.000Z

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


161

Understanding Cellulose Through Molecular Simulation and Electron Tomography  

SciTech Connect

High-resolution cellulose crystal structures have been determined from diffraction experiments using large diameter microfibrils as the sample material. However, cellulose microfibrils in plants are much smaller in diameter, and are more difficult to directly examine experimentally. Molecular dynamics simulation combined with quantum chemical calculations can help to elucidate the structure and dynamics of small diameter cellulose microfibrils. These simulation techniques also aid in the interpretation of electron tomography volumetric structural data from maize cell walls, where pretreatment with dilute acid or ammonia reveals microfibril geometry.

Matthews, J.

2013-01-01T23:59:59.000Z

162

Molecular dynamics calculation of free energy  

Science Conference Proceedings (OSTI)

The results of a systematic study of a recently proposed method by Frenkel and Ladd for calculating free energies via molecular dynamics are reported. Internal measures of the error

J. F. Lutsko; D. Wolf; S. Yip

1988-01-01T23:59:59.000Z

163

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

164

Mesoscale Molecular Dynamics with LAMMPS  

Science Conference Proceedings (OSTI)

Tendency of Cooperative Grain Boundary Sliding in Nanocrystalline Materials · Ultra-Large Scale Simulations of Deformation and Failure of Biological Protein ...

165

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations  

E-Print Network (OSTI)

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change

de Groot, Bert

166

Molecular dynamics simulations of the electrical double layer on smectite surfaces contacting concentrated mixed electrolyte (NaCl-CaCl2)  

SciTech Connect

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

167

Instructional JAVA modules based on molecular simulation - TMS  

Science Conference Proceedings (OSTI)

Nov 9, 2007 ... This website contains a selection of instructional JAVA modules designed to increase understanding of molecular simulations and molecular ...

168

Thermal interface conductance in Si/Ge superlattices by equilibrium molecular dynamics  

E-Print Network (OSTI)

We provide a derivation allowing the calculation of thermal conductance at interfaces by equilibrium molecular dynamics simulations and illustrate our approach by studying thermal conduction mechanisms in Si/Ge superlattices. ...

Esfarjani, Keivan

169

Molecular mechanism of gas adsorption into ionic liquids: A molecular dynamics study  

Science Conference Proceedings (OSTI)

Room temperature ionic liquids (RTILs) have been shown to be versatile and tunable solvents that can be used in many chemical applications. In this study, we developed a dynamical, molecular-scale picture of the gas dissolution and interfacial processes in RTILs using molecular simulations. These simulations can provide the free energies associated with transporting a gas solute across various RTIL interfaces and physical insights into the interfacial properties and transport molecular mechanism of gas sorption processes. For CO2 sorption, the features in the potential of mean force (PMF) of CO2 using both polarizable and non-polarizable force fields are similar qualitatively. However, we observed some quantitative differences, and we describe the causes of these differences in this paper. We also show the significant impact of ionic-liquid chemical structures on the gas sorption process, and we discuss their influence on the H2O transport mechanism.

Dang, Liem X.; Chang, Tsun-Mei

2012-01-19T23:59:59.000Z

170

Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron  

E-Print Network (OSTI)

novel measurements of chemical dynamics for clusters, Chemical Dynamics, Molecular Energetics, and Kinetics at theUniversity of California Chemical Sciences Division,

Leone, Stephen R.

2010-01-01T23:59:59.000Z

171

Molecular Simulations of the Effect of Cholesterol on Membrane-Mediated Protein-Protein Interactions  

E-Print Network (OSTI)

5 Molecular Simulation of the Effect of Cholesterol Protein-Properties . . . . . . . . iii 3 Molecular Simulation StudyProtein-Protein In- 4 Molecular Simulation Study of the

de Meyer, Frédérick Jean-Marie

2010-01-01T23:59:59.000Z

172

Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within the eMinerals escience  

E-Print Network (OSTI)

Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within the e how molecular-scale simulations can be performed using grid computing. The potential for running many gained by the UK eMinerals project [1] in developing grid computing methods for molecular simulations

Cambridge, University of

173

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

E-Print Network (OSTI)

We present an efficient general approach to first principles molecular dynamics simulations based on extended Lagrangian Born-Oppenheimer molecular dynamics 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 longterm energy drift. The optimization-free first principles molecular dynamics requires only one single diagonalization per time step and yields 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 a robust and efficient formulation of a new generation first principles quantum mechanical molecular dynamics simulation schemes.

Souvatzis, Petros

2013-01-01T23:59:59.000Z

174

Better HMC integrators for dynamical simulations  

SciTech Connect

We show how to improve the molecular dynamics step of Hybrid Monte Carlo, both by tuning the integrator using Poisson brackets measurements and by the use of force gradient integrators. We present results for moderate lattice sizes.

M.A. Clark, Balint Joo, A.D. Kennedy, P.J. Silva

2010-06-01T23:59:59.000Z

175

Large-scale Excited Electron Molecular Mechanics/Dynamics  

Science Conference Proceedings (OSTI)

Abstract Scope, To simulate large electronically excited systems, we have developed [at the Materials and Process Simulation Center at Caltech] a molecular ...

176

Molecular Dynamics Simulation of the alpha-Helix to beta-Sheet Transition in Coiled Protein Filaments: Evidence for a Critical Filament Length Scale  

E-Print Network (OSTI)

The alpha-helix to beta-sheet transition (?-? transition) is a universal deformation mechanism in alpha-helix rich protein materials such as wool, hair, hoof, and cellular proteins. Through a combination of molecular and ...

Buehler, Markus J.

177

Molecular to fluid dynamics: The consequences of stochastic molecular motion Stefan Heinz*  

E-Print Network (OSTI)

Molecular to fluid dynamics: The consequences of stochastic molecular motion Stefan Heinz) The derivation of fluid dynamic equations from molecular equations is considered. This is done on the basis of a stochastic model for the molecular motion which can be obtained by a projection of underlying determin- istic

Heinz, Stefan

178

Molecular dynamics studies of interfacial water at the alumina surface.  

DOE Green Energy (OSTI)

Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bond network within the first few hydration layers illustrates the significance of water?water interactions on the structural properties at the interface.

Argyris, Dr. Dimitrios [University of Oklahoma; Ho, Thomas [ORNL; Cole, David [Ohio State University

2011-01-01T23:59:59.000Z

179

DYNAMICAL ANALYSIS OF HIGHLY EXCITED MOLECULAR SPECTRA  

SciTech Connect

Spectra and internal dynamics of highly excited molecules are essential to understanding processes of fundamental importance for combustion, including intramolecular energy transfer and isomerization reactions. The goal of our program is to develop new theoretical tools to unravel information about intramolecular dynamics encoded in highly excited experimental spectra. We want to understand the formations of ''new vibrational modes'' when the ordinary normal modes picture breaks down in highly excited vibrations. We use bifurcation analysis of semiclassical versions of the effective Hamiltonians used by spectroscopists to fit complex experimental spectra. Specific molecular systems are of interest for their relevance to combustion and the availability of high-quality experimental data. Because of its immense importance in combustion, the isomerizing acetylene/vinylidene system has been the object of long-standing experimental and theoretical research. We have made significant progress in systematically understanding the bending dynamics of the acetylene system. We have begun to make progress on extending our methodology to the full bend-stretch vibrational degrees of freedom, including dynamics with multiple wells and above barrier motion, and time-dependent dynamics. For this, development of our previous methods using spectroscopic fitting Hamiltonians is needed, for example, for systems with multiple barriers.

Michael E. Kellman

2005-06-17T23:59:59.000Z

180

Dynamic Properties of Molecular Motors in Burnt-Bridge Models  

E-Print Network (OSTI)

Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed as an effective diffusion along one-dimensional lattices with periodically distributed weak links. When an unbiased random walker passes the weak link it can be destroyed (``burned'') with probability p, providing a bias in the motion of the molecular motor. A new theoretical approach that allows one to calculate exactly all dynamic properties of motor proteins, such as velocity and dispersion, at general conditions is presented. It is found that dispersion is a decreasing function of the concentration of bridges, while the dependence of dispersion on the burning probability is more complex. Our calculations also show a gap in dispersion for very low concentrations of weak links which indicates a dynamic phase transition between unbiased and biased diffusion regimes. Theoretical findings are supported by Monte Carlo computer simulations.

Maxim N. Artyomov; Alexander Yu. Morozov; Ekaterina Pronina; Anatoly B. Kolomeisky

2007-05-04T23:59:59.000Z

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

Molecular simulation of nano-dispersed fluid phases  

E-Print Network (OSTI)

Fluid phase equilibria involving nano-dispersed phases, where at least one of the coexisting phases is confined to a small volume, are investigated by molecular dynamics simulation. Complementing previous studies on nanoscopic droplets, simulation volumes containing a nanoscopic gas bubble surrounded by a subsaturated liquid phase under tension, i.e. at negative pressure, are conducted in the canonical ensemble. The boundary conditions are chosen such that the phase equilibrium at the curved interface is thermodynamically stable. Two distinct size-dependent effects are found: Curvature induces a subsaturation of the system, leading to a smaller liquid density. For the gas in the centre of the bubble, the small diameter has an additional obverse effect, increasing its density. The curvature dependence of the surface tension is discussed by evaluating average radial density profiles to obtain the excess equimolar radius, which is found to be positive, corresponding to a negative Tolman length.

Martin Horsch; Hans Hasse

2013-07-22T23:59:59.000Z

182

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

2006-10-19T23:59:59.000Z

183

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

184

Charge transport through bio-molecular wires in a solvent: Bridging molecular dynamics and model Hamiltonian approaches  

E-Print Network (OSTI)

We present a hybrid method based on a combination of quantum/classical molecular dynamics (MD) simulations and a mod el Hamiltonian approach to describe charge transport through bio-molecular wires with variable lengths in presence o f a solvent. The core of our approach consists in a mapping of the bio-molecular electronic structure, as obtained f rom density-functional based tight-binding calculations of molecular structures along MD trajectories, onto a low di mensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuat ion effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the c ase of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

R. Gutierrez; R. Caetano; P. B. Woiczikowski; T. Kubar; M. Elstner; G. Cuniberti

2009-01-22T23:59:59.000Z

185

Molecular Dynamics Method in Microscale Heat Transfer Shigeo Maruyama  

E-Print Network (OSTI)

1 Molecular Dynamics Method in Microscale Heat Transfer Shigeo Maruyama Department of Mechanical://www.photon.t.u-tokyo.ac.jp/~maruyama/ 1. INTRODUCTION Molecular level understandings are becoming more important and molecular based to take account of nuclei in size of molecular clusters. The effect of the surfactant on the heat and mass

Maruyama, Shigeo

186

Massively Parallel Molecular Statics Simulations of the Percolation ...  

Science Conference Proceedings (OSTI)

Presentation Title, Massively Parallel Molecular Statics Simulations of the Percolation of Dislocations through a Random Array of Forest Dislocation Obstacles in ...

187

Molecular simulation of crystal growth in alkane and polyethylene melts  

E-Print Network (OSTI)

Molecular simulation has become a very powerful tool for understanding the process of polymer crystallization. By using carefully constructed simulations, one can independently observe the two phenomena responsible for ...

Waheed, Numan

2005-01-01T23:59:59.000Z

188

Dynamics Simulation in a Wave Environment  

NLE Websites -- All DOE Office Websites (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

189

GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES  

SciTech Connect

The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

MUCKERMAN,J.T.

1999-06-09T23:59:59.000Z

190

Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules  

SciTech Connect

The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometic sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

Muckerman, J.T.

1999-05-21T23:59:59.000Z

191

Dynamic simulation recalls condensate piping event  

Science Conference Proceedings (OSTI)

This article describes how experience gained from simulating and reconstructing a condensate piping event will be used by Consolidated Edison to analyze control system problems. A cooperative effort by Con Edison and the Chemical Engineering Department at Polytechnic University used modular modeling system to investigate the probable cause of a Con Edison condensate piping event. Con Edison commissioned the work to serve as a case study for the more general problem of control systems analysis using dynamic simulation and MMS.

Farrell, R.J.; Reneberg, K.O. (Polytechnic Univ., Brooklyn, NY (United States)); Moy, H.C. (Consolidated Edison Co., New York, NY (United States))

1994-05-01T23:59:59.000Z

192

Molecular Simulation Study of Diverting Materials Used in Matrix Acidizing  

E-Print Network (OSTI)

Recently there has been a great deal of attention in the oilfield industry focused on the phenomenal properties of viscoelastic surfactants (VES). The interest is motivated by their applications as switchable smart fluids, their surface tension, and their thickening and rheology enhancement in aqueous solution. Surfactant molecules in solution are known for their ability to assemble spontaneously into complex structures. Under certain thermodynamic conditions, temperature and electrolyte concentrations, wormlike micelles are formed. These micelles share similar equilibrium and dynamic properties with polymer solutions, However, micellar chains can break and recombine spontaneously which make them part of the more general class of living polymers. It is vital to understand the properties of viscoelastic wormlike micelles with regard to their flow in porous media. The overall objective of this study is to establish a better understanding of counterion effect on behavior of VES. The dependence of macroscopic properties on intermolecular interactions of complex fluid systems such as VES is an enormous challenge. To achieve our objective, we use first-principle calculations and molecular dynamics (MD) simulations to resolve the full chemical details in order to study how the structure of the micellar and solution properties depends on the chemical structure of the surfactant head group (HG) and type of counterion. In particular, we run simulations for different structures in gas-phase and aqueous solutions together with their salt counterions at room temperature and atmospheric pressure. For this purpose, we consider four types of surfactant HG (anionic, cationic, betaine and amidoamine oxide) together with the most common ions present in the acidizing fluid of a carbonate reservoir such as Ca2+, Mg2+, Fe2+, Fe3+, Mn2+ and Zn2+, Cl-, OH- and HS-. Hydration of ions as well as interactions with surfactant the HG are studied using density functional theory (DFT). The results give important insight into the links between molecular details of VES HG structure and observed solution properties. This study proposes for the first time the possible mechanisms that explain the exotic behavior of VES at high Fe(III) concentration. Also, our MD simulation suggests that distribution of chloride ion around surfactant molecules is responsible for their viscosity behavior in HCl solution. We believe that our results are an important step to develop more systematic procedures for the molecular design and formulation of more effective and efficient VES systems.

Sultan, Abdullah S.

2009-08-01T23:59:59.000Z

193

Nonequilibrium Molecular Dynamics Simulations of the Rheology...  

NLE Websites -- All DOE Office Websites (Extended Search)

the relevant conditions Complexity examples for system size: * 100x100x100 nm box of water molecules would have 4 x 10 5 H 2 O molecules * Neutral pH requires 10 7 H 2 O...

194

Reactive Molecular Dynamics Simulations of Switching in ...  

Science Conference Proceedings (OSTI)

Abstract Scope, In the search of new memory devices, conductive bridge random .... Ultra-long and Noble Copper Nanowires Tailored by Various Structure ...

195

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

Science Conference Proceedings (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

196

EI7153_Praktikum_Simulation_and_Characterization_of_Molecular_Devices.xls Allgemeine Daten  

E-Print Network (OSTI)

EI7153_Praktikum_Simulation_and_Characterization_of_Molecular_Devices.xls Allgemeine Daten: Modulnummer: EI7153 Modulbezeichnung (dt.): Praktikum Simulation and Characterization of Molecular Devices Modulbezeichnung (en.): Praktikum Simulation and Characterization of Molecular Devices Modulniveau: MSc Kürzel

Kuehnlenz, Kolja

197

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

Science Conference Proceedings (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

198

Development of models and methods for the molecular simulation of large systems and molecules  

E-Print Network (OSTI)

The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new models for carbon dioxide and cyclohexanolare discussed and a new method for the model development is introduced. Force fields and models for the simulation of PNIPAAm hydrogel in pure water and sodium chloride solution are tested and verified and applied to the simulation of nucleation processes.

Walter, Jonathan; Horsch, Martin; Vrabec, Jadran; Hasse, Hans

2010-01-01T23:59:59.000Z

199

Final report [Molecular simulations of complex fluids in confined geometrics  

SciTech Connect

This award supports collaborative research between Kansas State University and Sandia National Laboratories on the topic ''Molecular simulations of complex fluids in confined geometries.'' The objectives of this work are to develop new methodologies for fast and accurate simulations, and to apply simulations to various problems of interest to DOE. The success of this work will address several deficiencies in Sandia's capabilities in the area of molecular simulations. In addition, it provides educational opportunities for students and will enhance the science and technology capabilities at Kansas State through partnership with the national laboratories.

Gehrke, Stevin H.; Jiang, Shaoyi

2002-07-22T23:59:59.000Z

200

Fast plane wave density functional theory molecular dynamics calculations on multi-GPU machines  

Science Conference Proceedings (OSTI)

Plane wave pseudopotential (PWP) density functional theory (DFT) calculation is the most widely used method for material simulations, but its absolute speed stagnated due to the inability to use large scale CPU based computers. By a drastic redesign ... Keywords: Density functional theory, Electronic structure, First-principles, GPU, Molecular dynamics, Plane wave pseudopotential

Weile Jia, Jiyun Fu, Zongyan Cao, Long Wang, Xuebin Chi, Weiguo Gao, Lin-Wang Wang

2013-10-01T23:59:59.000Z

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201

Nitrogen Adsorption in Carbon Aerogels: A Molecular Simulation Study  

E-Print Network (OSTI)

Nitrogen Adsorption in Carbon Aerogels: A Molecular Simulation Study S. Gavalda, K. E. Gubbins,*, Y a molecular model for carbon aerogel in which the mesopore space is represented by carbon spheres-ray diffraction. The resulting model aerogel had a surface area, porosity, and pore size distribution that closely

202

Dynamic Simulation of a Helium Liquefier  

SciTech Connect

Dynamic behavior of a helium liquefier has been studied in detail with a Cryogenic Process REal-time SimulaTor (C-PREST) at the National Institute for Fusion Science (NIFS). The C-PREST is being developed to integrate large-scale helium cryogenic plant design, operation and maintenance for optimum process establishment. As a first step of simulations of cooldown to 4.5 K with the helium liquefier model is conducted, which provides a plant-process validation platform. The helium liquefier consists of seven heat exchangers, a liquid-nitrogen (LN2) precooler, two expansion turbines and a liquid-helium (LHe) reservoir. Process simulations are fulfilled with sequence programs, which were implemented with C-PREST based on an existing liquefier operation. The interactions of a JT valve, a JT-bypass valve and a reservoir-return valve have been dynamically simulated. The paper discusses various aspects of refrigeration process simulation, including its difficulties such as a balance between complexity of the adopted models and CPU time.

Maekawa, R.; Ooba, K.; Mito, T. [National Institute for Fusion Science, Toki, Gifu, 509-5292 (Japan); Nobutoki, M. [Nippon Sanso Co., Kawasaki, Kanagawa, 210-0861 (Japan)

2004-06-23T23:59:59.000Z

203

Molecular simulation of adsorbed natural gas  

SciTech Connect

Absorbed natural gas is being investigated as a substitute for gasoline., The most important factor in engineering studies is the maximum storage capacity of adsorbents for natural gas. Monte Carlo calculations were performed to simulate the adsorption of natural gas on activated carbon. Adsorption isotherms, storage capacities, and isoteric heats were determined from simulations and compared with experimental data. Simulations predict a maximum storage capacity of 244 V/V at 35 atm.

Matranga, K.R.; Stella, A.; Myers, A.L.; Glandt, E.D. (Univ. of Pennsylvania, Philadelphia (United States))

1992-11-01T23:59:59.000Z

204

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

205

IGCC Dynamic Simulator and Training Center  

SciTech Connect

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

206

Ab Initio Molecular Dynamics Bull. Korean Chem. Soc. 2003, Vol. 24, No. 6 1 Ab Initio Molecular Dynamics with Born-Oppenheimer and Extended  

E-Print Network (OSTI)

Ab Initio Molecular Dynamics Bull. Korean Chem. Soc. 2003, Vol. 24, No. 6 1 Ab Initio Molecular February 25, 2003 In ab initio molecular dynamics, whenever information about the potential energy surface advances for both approaches are discussed. Key Words : Ab initio molecular dynamics, Direct classical

Schlegel, H. Bernhard

207

Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps  

E-Print Network (OSTI)

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

Volkovich, Roie

2010-01-01T23:59:59.000Z

208

Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps  

E-Print Network (OSTI)

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

Roie Volkovich; Uri Peskin

2010-12-01T23:59:59.000Z

209

Interlayer Structure and Dynamics of Cl-Bearing Hydrotalcite: Far Infrared Spectroscopy and Molecular Dynamics Modeling  

SciTech Connect

Comparison of the observed far-infrared (FIR) spectrum of Cl--containing hydrotalcite, [Mg3Al(OH)8]Cl?3H2O, with its power spectrum calculated using molecular dynamics (MD) computer simulation provides greatly increased understanding of the structure and vibrational dynamics in the interlayers of layered double hydroxides. The simulation model assumes an ordered Mg3Al arrangement in the octahedral layer and no constraints on the movement of any atoms or on the geometry and symmetry of the simulation supercell. Calculated anisotropic components of the individual atomic power spectra in combination with computed animations of the vibrational modes from normal mode analysis allow for reliable interpretations of the observed spectral bands. For the vibrations related to octahedral cation motions, bands near 145, 180 and 250 cm-1 are due dominantly to Mg vibration in the z direction (perpendicular to the hydroxide layers), Al vibration in the z direction and Mg and Al vibrations in the x-y plane (parallel to the hydroxide layers), respectively. The low frequency vibrational motions of the interlayer are controlled by a network of hydrogen bonds formed among interlayer water molecules, Cl- ions, and the OH groups of the main hydroxide layers. The bands near 40-70 cm-1 are related to the translational motions of interlayer Cl- and H2O in the x-y plane, and the bands near 120 cm-1 and 210 cm-1 are due largely to translational motions of the interlayer species in the z direction. The three librational modes of interlayer water molecules near 390, 450 and 540 cm-1 correspond to twisting, rocking and wagging hindered rotations, respectively. The spectral components of the interlayer Cl- motions are remarkably similar to those of bulk aqueous chloride solutions, reflecting the structural and dynamic similarity of the nearest-neighbor Cl- environments in the interlayer and in solution.

Wang, Jianwei; Kalinichev, Andrey G.; Amonette, James E.; Kirkpatrick, Robert J.

2003-02-01T23:59:59.000Z

210

Modeling Molecular Hydrogen and Star Formation in Cosmological Simulations  

DOE Green Energy (OSTI)

We describe a phenomenological model for molecular hydrogen formation suited for applications in galaxy formation simulations, which includes on-equilibrium formation of molecular hydrogen on dust and approximate treatment of both its self-shielding and shielding by dust from the dissociating UV radiation. The model is applicable in simulations in which individual star forming regions--the giant molecular complexes--can be identified (resolution of tens of pc) and their mean internal density estimated reliably, even if internal structure is not resolved. In agreement with previous studies, calculations based on our model show that the transition from atomic to fully molecular phase depends primarily on the metallicity, which we assume is directly related to the dust abundance, and clumpiness of the interstellar medium. The clumpiness simply boosts the formation rate of molecular hydrogen, while dust serves both as a catalyst of molecular hydrogen formation and as an additional shielding from dissociating UV radiation. The upshot is that it is difficult to form fully-shielded giant molecular clouds while gas metallicity is low. However, once the gas is enriched to Z {approx} 0.01-0.1 solar, the subsequent star formation and enrichment can proceed at a much faster rate. This may keep star formation efficiency in the low-mass, low-metallicity progenitors of galaxies very low for a certain period of time with the effect similar to a strong 'feedback' mechanism.

Gnedin, Nickolay Y.; /Fermilab /KICP, Chicago /Chicago U., Astron. Astrophys. Ctr.; Tassis, Konstantinos; /Chicago U., Astron. Astrophys. Ctr. /KICP, Chicago; Kravtsov, Andrey V.; /KICP, Chicago /Chicago U., Astron. Astrophys. Ctr. /Chicago U., EFI

2008-10-01T23:59:59.000Z

211

Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices  

Science Conference Proceedings (OSTI)

Highlights: {yields} Molecular Dynamics codes implemented on GPUs have achieved two-order of magnitude computational accelerations. {yields} Brownian Dynamics and Dissipative Particle Dynamics simulations require a large number of random numbers per time step. {yields} We introduce a method for generating small batches of pseudorandom numbers distributed over many threads of calculations. {yields} With this method, Dissipative Particle Dynamics is implemented on a GPU device without requiring thread-to-thread communication. - Abstract: Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat requires a pseudo-random number generator (PRNG) to generate the stochastic force applied to each particle or pair of neighboring particles during each time step in the integration of Newton's equations of motion. In a Single-Instruction-Multiple-Thread (SIMT) GPU parallel computing environment, small batches of random numbers must be generated over thousands of threads and millions of kernel calls. In this communication we introduce a one-PRNG-per-kernel-call-per-thread scheme, in which a micro-stream of pseudorandom numbers is generated in each thread and kernel call. These high quality, statistically robust micro-streams require no global memory for state storage, are more computationally efficient than other PRNG schemes in memory-bound kernels, and uniquely enable the DPD simulation method without requiring communication between threads.

Phillips, Carolyn L. [Applied Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States); Anderson, Joshua A. [Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109 (United States); Glotzer, Sharon C., E-mail: sglotzer@umich.edu [Applied Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States); Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109 (United States); Material Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109 (United States)

2011-08-10T23:59:59.000Z

212

Iterative Energy Minimization for Quantum Molecular Dynamics  

E-Print Network (OSTI)

for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California Email: anakano: · Example 1: · Example 2: E = dr E f (r) f (r) E f (r)[ ] = dr f (r)( )2 E f (r) = 2 f (r) E (r

Southern California, University of

213

Kinetic Simulations of Fusion Energy Dynamics at the Extreme...  

NLE Websites -- All DOE Office Websites (Extended Search)

Kinetic Simulations of Fusion Energy Dynamics at the Extreme Scale PI Name: William Tang PI Email: tang@pppl.gov Institution: Princeton Plasma Physics Laboratory Allocation...

214

Computational Fluid Dynamic Simulations of a Regenerative Process...  

NLE Websites -- All DOE Office Websites (Extended Search)

Fluid Dynamic Simulations of a Regenerative Process for Carbon Dioxide Capture in Advanced Gasification Based Power Systems Background The Department of Energy (DOE) National...

215

Dynamic Simulation of Cell Voltage Resonance Effect in Aluminum ...  

Science Conference Proceedings (OSTI)

Dubal Cell Voltage Drop Initiatives towards Low Energy High Amperage Cells · Dynamic Simulation of Cell Voltage Resonance Effect in Aluminum Electrolysis ...

216

Two-Dimensional Computational Fluid Dynamics and Conduction Simulation...  

NLE Websites -- All DOE Office Websites (Extended Search)

Two-Dimensional Computational Fluid Dynamics and Conduction Simulations of Heat Transfer in Horizontal Window Frames with Internal Cavities Title Two-Dimensional Computational...

217

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

NLE Websites -- All DOE Office Websites (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:

218

New amorphous forms of solid CO2 from ab initio molecular dynamics  

E-Print Network (OSTI)

By employing ab initio molecular dynamics simulations at constant pressure, we investigated behavior of amorphous carbon dioxide between 0-100 GPa and 200-500 K and found several new amorphous forms. We focused on evolution of the high-pressure tetrahedral amorphous form known as a-carbonia on its way down to zero pressure, where it eventually converts into a molecular amorphous solid. During decompression, two nonmolecular amorphous forms with different proportion of three and four-coordinated carbons and two mixed molecular-nonmolecular forms were observed. Transformation from a-carbonia to the molecular state appears to proceed discontinuously via several intermediate stages. This suggests that solid CO2 might belong to the group of materials exhibiting polyamorphism. We also studied relations of the amorphous forms to their crystalline counterparts. The predominantly four-coordinated a-carbonia is related to phase V according to their structural properties, while existence of the mixed forms may reflect h...

Plašienka, Dušan

2013-01-01T23:59:59.000Z

219

Size dependence of the nonlinear elastic softening of nanoscale graphene monolayers under plane-strain bulge tests: a molecular dynamics study  

Science Conference Proceedings (OSTI)

The pressure bulge test is an experimental technique to characterize the mechanical properties of microscale thin films. Here, we perform constant-temperature molecular dynamics simulations of the plane-strain cylindrical bulge test of nanosized monolayer ...

Sukky Jun; Tenzin Tashi; Harold S. Park

2011-01-01T23:59:59.000Z

220

Molecular simulation as a tool for studying lignin  

NLE Websites -- All DOE Office Websites (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.

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

Design of an Enterprise Dynamic Performance Simulation and Analysis System  

Science Conference Proceedings (OSTI)

Many problems in enterprise running faced by managers can be resolved by simulation of the corresponding system dynamics model. It is often desirable to forecasting enterprise running in the next period. And managers hope to find the reason quickly if ... Keywords: dynamic performance, simulation, sensitivity, diagnose, performance optimization

Zheng Li; Yueting Chai; Yi Liu

2011-04-01T23:59:59.000Z

222

83.10.Mj – Molecular dynamics, Brownian dynamics  

E-Print Network (OSTI)

Abstract –Westudycomplexfrictionalstick-sliposcillationsbyformulatinganovelfirst-passage time problem whose solutions are used to compute distributions of stick-slip oscillation periods, displacements, and slip durations for a generic family of stochastic friction models. Approximate solutions are developed using a level-crossing expansion due to Rice and Stratonovich. Sample results for a minimal Langevin sliding friction model agree with simulations over a range of system parameters, and reproduce qualitative features of prior experimental studies of stick-slip motion. The analysis also reveals a complex oscillatory regime near the transition from stick-slip to continuous sliding, in which additional transient modes are excited through boundary-noise interactions. Copyright c ? EPLA, 2011 Stick-slip oscillations, an important source of vibration and acoustic emissions in natural and man-made mechanical systems, are observed in many frictional settings: during macroscopic sliding between unlubricated solid surfaces, such as vehicle brakes [1]; in the bowing of a violin

Y. Visell (a

2011-01-01T23:59:59.000Z

223

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

NLE Websites -- All DOE Office Websites (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.

224

Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron  

SciTech Connect

Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

2010-03-14T23:59:59.000Z

225

Quantum dynamics of bio-molecular systems in noisy environments  

E-Print Network (OSTI)

We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.

M. B. Plenio; S. F. Huelga

2012-02-05T23:59:59.000Z

226

Structure and dynamics of water adsorbed in carbon nanotubes : a joint neutron scattering and molecular-dynamics study.  

DOE Green Energy (OSTI)

The advent of nanocarbons, from single- and multiple-walled nanotubes to nanohorns, avails model studies of confined molecules on the nanoscale. Water encapsulated inside the quasi-one-dimensional channels of these materials is expected to exhibit anomalous behavior due to the unique geometry of nanotubes and the weak interaction between the water molecules and the carbon atoms. We have employed neutron small-to-wide angle diffraction, quasielastic and inelastic scattering in conjunction with molecular-dynamics simulations to characterize the structures and dynamics of water adsorbed in open-ended single- and double-walled nanotubes over a wide range of spatial and temporal scales. We find that a square-ice sheet wrapped next to the inner nanotube wall and a water chain in the interior are the key structural elements of nanotube-confined water/ice. This configuration results in a hydrogen-bond connectivity that markedly differs from that in bulk water. This significantly softened hydrogen-bond network manifests in strong energy shifts of the observed and simulated inter- and intra-molecular vibrations. The very large mean-square displacement of hydrogen atoms observed experimentally and the strong anharmonicity inferred from simulations explain the fluid-like behavior at temperatures far below the freezing point of normal water.

de Souza, N. R.; Kolesnikov, A. I.; Loong, C.-K.; Moravsky, A. P.; Loutfy, R. O.; Burnham, C. J.; Intense Pulsed Neutron Source; MER Corp.; Univ. of Utah

2004-01-01T23:59:59.000Z

227

Molecular dynamics study of sodium using a model pseudopotential  

Science Conference Proceedings (OSTI)

The dynamics of sodium is investigated using the coulomb and Born-Mayer interaction augmented by a model pseudopotential to represent the electron interactions including screening, exchange, and correlation. The model parameters were previously determined and have been shown to accurately reproduce experimental equation-of-state, lattice vibration, and crystal phase properties of sodium in the harmonic limit. In this paper the equation-of-state and structural properties are examined in molecular dynamics calculations. The long range effects of the potential are included. Typically, each particle interacts with about 500 neighbors. The calculated equation of state of sodium in the hcp, bcc, and liquid structures is discussed.

Swanson, R.E.; Straub, G.K.; Holian, B.L.

1981-01-01T23:59:59.000Z

228

Simulation of chemical reaction dynamics on an NMR quantum computer  

E-Print Network (OSTI)

Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging quantum chemistry problems. Here we report an experimental demonstration that a small nuclear-magnetic-resonance (NMR) quantum computer is already able to simulate the dynamics of a prototype chemical reaction. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.

Dawei Lu; Nanyang Xu; Ruixue Xu; Hongwei Chen; Jiangbin Gong; Xinhua Peng; Jiangfeng Du

2011-05-21T23:59:59.000Z

229

Atomistic simulation of damage production by atomic and molecular ion irradiation in GaN  

Science Conference Proceedings (OSTI)

We have studied defect production during single atomic and molecular ion irradiation having an energy of 50 eV/amu in GaN by molecular dynamics simulations. Enhanced defect recombination is found in GaN, in accordance with experimental data. Instantaneous damage shows non-linearity with different molecular projectile and increasing molecular mass. Number of instantaneous defects produced by the PF{sub 4} molecule close to target surface is four times higher than that for PF{sub 2} molecule and three times higher than that calculated as a sum of the damage produced by one P and four F ion irradiation (P+4 Multiplication-Sign F). We explain this non-linearity by energy spike due to molecular effects. On the contrary, final damage created by PF{sub 4} and PF{sub 2} shows a linear pattern when the sample cools down. Total numbers of defects produced by Ag and PF{sub 4} having similar atomic masses are comparable. However, defect-depth distributions produced by these species are quite different, also indicating molecular effect.

Ullah, M. W.; Kuronen, A.; Nordlund, K.; Djurabekova, F. [Department of Physics, University of Helsinki, P.O. Box 64, FIN-00014 Helsinki (Finland); Karaseov, P. A.; Titov, A. I. [St. Petersburg State Polytechnic University, 195251 St. Petersburg (Russian Federation)

2012-08-15T23:59:59.000Z

230

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

SciTech Connect

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

231

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

SciTech Connect

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.; Goncharov, V.

2012-05-29T23:59:59.000Z

232

Computer Simulations of Protein Dynamics and Thermodynamics  

Science Conference Proceedings (OSTI)

The computational challenges of producing realistic biomedical simulations are reviewed. Techniques for applying classical mechanics simulation methods to proteins and ways to solve Newton's equations are discussed. Two recent applications of these methods ...

David Case

1993-10-01T23:59:59.000Z

233

On the Importance of Zero-Point Effects in Molecular Level Classical Simulations of Water  

DOE Green Energy (OSTI)

We discuss the fundamental difficulties involved in comparing energetic results obtained via classical simulations of bulk water with the observed values. Emphasis is placed on the difference between quantum and classical dynamics and correction techniques, which can be used to emulate quantum effects in a classical system, are investigated. We present molecular dynamics simulation results for liquid water using the ''Thole-type'' all atom polarizable water model, which has previously been shown to give reasonable results for both ice Ih and small water clusters. We employ expressions for the density of states power spectrum in the liquid in either atomic or rigid-body coordinates that are appropriate for rigid molecule simulations. It is demonstrated that the atomic power spectra can be written as a linear combination of the center of mass and rotational power spectra via the use of the ''coupling matrix'' of linear coefficients. This approach allows us to introduce the concept of ''fractional degrees of freedom'' for nuclei in rigid molecule simulation. Within this framework, it is illustrated that, in a rigid water molecule, the Oxygen and Hydrogen atoms have 2.82 and 1.59 degrees of freedom, respectively (for the TIP4P geometry). Within our suggested approach, we finally demonstrate that Debye-Waller factors can be obtained from the coupling matrix and show that quantum corrections to the structure can be accounted for by raising the temperature of the system in a classical simulation by around 500, a result consistent with previous suggestions.

Burnham, Christian J.; Xantheas, Sotiris S.

2004-03-15T23:59:59.000Z

234

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

SciTech Connect

This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.

Hall,G.E.; Sears, T.J.

2009-04-03T23:59:59.000Z

235

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

Science Conference Proceedings (OSTI)

The structural behavior of perdeuterated, 11B-enriched ammonia borane, ND311BD3, was investigated by neutron powder diffraction measurements collected over the temperature range from 15 to 340 K and by molecular dynamics simulation. In the low temperature orthorhombic phase, the progressive displacement of the borane group under the amine group was observed 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 group that is problematic to extract from the metrics provided by Rietveld analysis of the NPD data alone but is evident in the molecular dynamics simulation and other spectroscopic evidence. This study highlights the valued added by complimentary experimental approaches and coupled computational studies.

Hess, Nancy J.; Schenter, Gregory K.; Hartman, Michael R.; Daemen, Luke L.; Proffen, Thomas E.; Kathmann, Shawn M.; Mundy, Christopher J.; Hartl, Monika A.; Heldebrant, David J.; Stowe, Ashley C.; Autrey, Thomas

2009-04-17T23:59:59.000Z

236

Avestar® - Syngas-Fired Combined Cycle Dynamic Simulator  

NLE Websites -- All DOE Office Websites (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

237

Physics issues in simulations with dynamical overlap fermions  

E-Print Network (OSTI)

We discuss the impact of various improvements on simulations of dynamical overlap fermions using the Hybrid Monte Carlo algorithm. We focus on the usage of fat links and multiple pseudo-fermion fields.

Thomas DeGrand; Stefan Schaefer

2004-12-01T23:59:59.000Z

238

Simulated Convective Lines with Leading Precipitation. Part I: Governing Dynamics  

Science Conference Proceedings (OSTI)

This article, the first of two describing a study in which the authors used idealized numerical simulations to investigate convective lines with leading precipitation, addresses the dynamics governing the systems' structures and individual air ...

Matthew D. Parker; Richard H. Johnson

2004-07-01T23:59:59.000Z

239

Dynamical Effects of Aerosol Perturbations on Simulated Idealized Squall Lines  

Science Conference Proceedings (OSTI)

The dynamical effects of increased aerosol loading on the strength and structure of numerically simulated squall lines are explored. Results are explained in the context of RKW theory. Changes in aerosol loading lead to changes in rain drop size ...

Zachary J. Lebo; Hugh Morrison

240

Simulation of the dynamic response of a damped taught string  

E-Print Network (OSTI)

Marine pipeline are facing new issues involved by the increase of the depth of exploited oil and gas reservoirs. This thesis discusses the changes in the dynamic behavior of marine pipelines and proposes a simple simulation ...

Favennec, Hervé

2007-01-01T23:59:59.000Z

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

Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics  

Science Conference Proceedings (OSTI)

The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

Yu H. G.; Muckerman, J.T.

2012-05-29T23:59:59.000Z

242

Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics  

SciTech Connect

The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

Yu, H.G.; Muckerman, J.T.

2010-06-01T23:59:59.000Z

243

Large-Scale Hybrid Dynamic Simulation Employing Field Measurements  

Science Conference Proceedings (OSTI)

Simulation and measurements are two primary ways for power engineers to gain understanding of system behaviors and thus accomplish tasks in system planning and operation. Many well-developed simulation tools are available in today's market. On the other hand, large amount of measured data can be obtained from traditional SCADA systems and currently fast growing phasor networks. However, simulation and measurement are still two separate worlds. There is a need to combine the advantages of simulation and measurements. In view of this, this paper proposes the concept of hybrid dynamic simulation which opens up traditional simulation by providing entries for measurements. A method is presented to implement hybrid simulation with PSLF/PSDS. Test studies show the validity of the proposed hybrid simulation method. Applications of such hybrid simulation include system event playback, model validation, and software validation.

Huang, Zhenyu; Guttromson, Ross T.; Hauer, John F.

2004-06-30T23:59:59.000Z

244

Numerical study: Iron corrosion-resistance in lead-bismuth eutectic coolant by molecular dynamics method  

Science Conference Proceedings (OSTI)

In this present work, we report numerical results of iron (cladding) corrosion study in interaction with lead-bismuth eutectic coolant of advanced nuclear reactors. The goal of this work is to study how the oxygen can be used to reduce the corrosion rate of cladding. The molecular dynamics method was applied to simulate corrosion process. By evaluating the diffusion coefficients, RDF functions, MSD curves of the iron and also observed the crystal structure of iron before and after oxygen injection to the coolant then we concluded that a significant and effective reduction can be achieved by issuing about 2% number of oxygen atoms to lead-bismuth eutectic coolant.

Arkundato, Artoto; Su'ud, Zaki; Abdullah, Mikrajuddin; Widayani,; Celino, Massimo [Nuclear Physics and Biophysics Research Division, Physics Department Institut Teknologi Bandung, Jl. Ganesha 10, Bandung Physics Department, Faculty of Mathematical and Natural Sciences Universitas (Indonesia); Nuclear Physics and Biophysics Research Division, Physics Department Institut Teknologi Bandung, Jl. Ganesha 10, Bandung (Indonesia); ENEA, CR Cassacia, Via Anguillarese 301, Roma (Italy)

2012-06-06T23:59:59.000Z

245

Dynamic electrothermal simulation of integrated resistors at device level  

Science Conference Proceedings (OSTI)

This paper presents the dynamic electrothermal simulation of a rectangular resistor integrated on a semi-conductor substrate. Due to the temperature dependence of the electrical conductivity of the resistive sheet, self-heating provokes a coupling between ... Keywords: Electrothermal simulation, Nonlinearity, Structure functions, Thermal impedance, Transient

B. Vermeersch; G. De Mey

2009-09-01T23:59:59.000Z

246

A multiscale Molecular Dynamics approach to Contact Mechanics  

E-Print Network (OSTI)

The friction and adhesion between elastic bodies are strongly influenced by the roughness of the surfaces in contact. Here we develop a multiscale molecular dynamics approach to contact mechanics, which can be used also when the surfaces have roughness on many different length-scales, e.g., for self affine fractal surfaces. As an illustration we consider the contact between randomly rough surfaces, and show that the contact area varies linearly with the load for small load. We also analyze the contact morphology and the pressure distribution at different magnification, both with and without adhesion. The calculations are compared with analytical contact mechanics models based on continuum mechanics.

C. Yang; U. Tartaglino; B. N. J. Persson

2005-08-10T23:59:59.000Z

247

Molecular Dynamics Model of Ultraviolet Matrix-Assisted Laser Desorption/Ionization Including Ionization Processes  

E-Print Network (OSTI)

Molecular Dynamics Model of Ultraviolet Matrix-Assisted Laser Desorption/Ionization Including A molecular dynamics model of UV-MALDI including ionization processes is presented. In addition/desorption of molecular systems, it includes radiative and nonradiative decay, exciton hopping, two pooling processes

Zhigilei, Leonid V.

248

Molecular C dynamics downstream: The biochemical decomposition sequence and its impact on soil organic  

E-Print Network (OSTI)

Molecular C dynamics downstream: The biochemical decomposition sequence and its impact on soil chemistry. As a result, the molecular characteristics of soil C are now known for a range of ecosystems research. Here we present a conceptual model of molecular soil C dynamics to stimulate inter- disciplinary

Neff, Jason

249

Programmable quantum simulation by dynamic Hamiltonian engineering  

E-Print Network (OSTI)

Quantum simulation is a promising near term application for mesoscale quantum information processors, with the potential to solve computationally intractable problems at the scale of just a few dozen interacting quantum systems. Recent experiments in a range of technical platforms have demonstrated the basic functionality of quantum simulation applied to quantum magnetism, quantum phase transitions, and relativistic quantum mechanics. In all cases, the underlying hardware platforms restrict the achievable inter-particle interaction, forming a serious constraint on the ability to realize a versatile, programmable, quantum simulator. In this work, we address this problem by developing novel sequences of unitary operations that engineer desired effective Hamiltonians in the time-domain. The result is a hybrid programmable analog simulator permitting a broad class of interacting spin-lattice models to be generated starting only with an arbitrary native inter-particle interaction and single-qubit addressing. Building on previous work proving that universal simulation is possible using both entangling gates and single-qubit unitaries, we show how determining the relevant hardware "program" of unitary pulses to implement an arbitrary spin Hamiltonian on such a simulator can be formulated as a linear program that runs in polynomial time and scales efficiently in hardware resources. Our analysis extends from circuit model quantum information to adiabatic quantum evolutions, where our approach allows for the creation of non-native ground state solutions to a computation.

David L. Hayes; Steven T. Flammia; Michael J. Biercuk

2013-09-26T23:59:59.000Z

250

Simulating the dynamics of auroral phenomena  

Science Conference Proceedings (OSTI)

Simulating natural phenomena has always been a focal point for computer graphics research. Its importance goes beyond the production of appealing presentations, since research in this area can contribute to the scientific understanding of complex natural ... Keywords: Atmospheric effects, natural phenomena, plasma phenomena, rendering

Gladimir V. G. Baranoski; Justin Wan; Jon G. Rokne; Ian Bell

2005-01-01T23:59:59.000Z

251

Molecular simulation analysis of structural variations in lipoplexes  

E-Print Network (OSTI)

We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting structures through direct visualization of the molecular arrangements and through calculations of the corresponding scattering plots. The latter approach provides a means for comparison with published data from X-ray scattering experiments. Consistent with experimental results, we find that upon increasing the stiffness of the lipid material, the system tends to form lamellar structures. Two characteristic distances can be extracted from the scattering plots of lamellar complexes - the lamellar (interlayer) spacing and the DNA-spacing within each layer. We find a remarkable agreement between the computed values of these two quantities and the experimental data [J. O. R\\"{a}dler, I. Koltover, T. Salditt and C. R. Safinya, Science Vol. 275, 810 (1997)] over the entire range of mole fractions of charged lipids (CLs) studied experimentally. A visual inspection of the simulated systems reveals that, for very high fractions of CLs, disordered structures consisting of DNA molecules bound to small membrane fragments are spontaneously formed. The diffraction plots of these non-lamellar disordered complexes appear very similar to that of the lamellar structure, which makes the interpretation of the X-ray data ambiguous. The loss of lamellar order may be the origin of the observed increase in the efficiency of lipoplexes as gene delivery vectors at high charge densities.

Oded Farago; Niels Grønbech-Jensen

2011-03-03T23:59:59.000Z

252

Carbon nanotubes and graphene in aqueous surfactant solutions : molecular simulations and theoretical modeling  

E-Print Network (OSTI)

This thesis describes combined molecular simulations and theoretical modeling studies, supported by experimental observations, on properties and applications of carbon nanotubes (CNTs) and graphene sheets dispersed in ...

Lin, Shangchao

2012-01-01T23:59:59.000Z

253

Ensemble Simulations with Coupled Atmospheric Dynamic and Dispersion Models: Illustrating Uncertainties in Dosage Simulations  

Science Conference Proceedings (OSTI)

Ensemble simulations made using a coupled atmospheric dynamic model and a probabilistic Lagrangian puff dispersion model were employed in a forensic analysis of the transport and dispersion of a toxic gas that may have been released near Al ...

Thomas T. Warner; Rong-Shyang Sheu; James F. Bowers; R. Ian Sykes; Gregory C. Dodd; Douglas S. Henn

2002-05-01T23:59:59.000Z

254

Molecular hydrogen regulated star formation in cosmological SPH simulations  

E-Print Network (OSTI)

It has been shown observationally that star formation (SF) correlates tightly with the presence of molecular hydrogen (H2). Therefore it would be important to investigate its implication on galaxy formation in a cosmological context. In the present work, we track the H2 mass fraction within our cosmological smoothed particle hydrodynamics (SPH) code GADGET-3 using an equilibrium analytic model by Krumholz et al. This model allows us to regulate the star formation in our simulation by the local abundance of H2 rather than the total cold gas density, and naturally introduce the dependence of star formation on metallicity. We investigate implications of the equilibrium H2-based SF model on galaxy population properties, such as the stellar-to-halo mass ratio (SHMR), baryon fraction, cosmic star formation rate density (SFRD), galaxy specific SFR, galaxy stellar mass functions (GSMF), and Kennicutt-Schmidt (KS) relationship. The advantage of our work over the previous ones is having a large sample of simulated gala...

Thompson, Robert; Jaacks, Jason; Choi, Jun-Hwan

2013-01-01T23:59:59.000Z

255

Modeling and simulation of consumer response to dynamic pricing.  

Science Conference Proceedings (OSTI)

Assessing the impacts of dynamic-pricing under the smart grid concept is becoming extremely important for deciding its full deployment. In this paper, we develop a model that represents the response of consumers to dynamic pricing. In the model, consumers use forecasted day-ahead prices to shift daily energy consumption from hours when the price is expected to be high to hours when the price is expected to be low while maintaining the total energy consumption as unchanged. We integrate the consumer response model into the Electricity Market Complex Adaptive System (EMCAS). EMCAS is an agent-based model that simulates restructured electricity markets. We explore the impacts of dynamic-pricing on price spikes, peak demand, consumer energy bills, power supplier profits, and congestion costs. A simulation of an 11-node test network that includes eight generation companies and five aggregated consumers is performed for a period of 1 month. In addition, we simulate the Korean power system.

Valenzuela, J.; Thimmapuram, P.; Kim, J (Decision and Information Sciences); (Auburn Univ.)

2012-08-01T23:59:59.000Z

256

Lessons Learned From Dynamic Simulations of Advanced Fuel Cycles  

SciTech Connect

Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe “lessons learned” from dynamic simulations but attempt to answer the “so what” question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.

Steven J. Piet; Brent W. Dixon; Jacob J. Jacobson; Gretchen E. Matthern; David E. Shropshire

2009-04-01T23:59:59.000Z

257

LINAC BEAM DYNAMICS SIMULATIONS WITH PY-ORBIT  

Science Conference Proceedings (OSTI)

Linac dynamics simulation capabilities of the PyORBIT code are discussed. PyORBIT is an open source code and a further development of the original ORBIT code that was created and used for design, studies, and commissioning of the SNS ring. The PyORBIT code, like the original one, has a two-layer structure. C++ is used to perform time-consuming computations, and the program flow is controlled from a Python language shell. The flexible structure makes it possible to use PyORBIT also for linac dynamics simulations. A benchmark of PyORBIT with Parmila and the XAL Online model is presented.

Shishlo, Andrei P [ORNL

2012-01-01T23:59:59.000Z

258

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

Science Conference Proceedings (OSTI)

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

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

2009-12-14T23:59:59.000Z

259

Molecular Dynamics Studies on the Effects of Water Speciation on Interfacial Structure and Dynamics in Silica-Filled PDMS Composites  

DOE Green Energy (OSTI)

Significant changes in materials properties of siloxane based polymers can be obtained by the addition of inorganic fillers. In silica-filled polydimethylsiloxane (PDMS) based composites the mechanism of this reinforcing behavior is presumably hydrogen bonding between surface hydroxyls and backbone siloxane species. We have chosen to investigate in detail the effect of chemisorbed and physisorbed water on the interfacial structure and dynamics in silica-filled PDMS based composites. Toward this end, we have combined molecular dynamics simulations and experimental studies employing DMA and Nh4R analysis. Our results suggest that the polymer-silica contact distance and the mobility of interfacial polymer chains significantly decreased as the hydration level at the interface was reduced. The reduced mobility of the PDMS chains in the interfacial domain reduced the overall, bulk, motional properties of the polymer, thus causing an effective ''stiffening'' of the polymer matrix. The role of the long-ranged Coulombic interactions on the structural features and chain dynamics of the polymer were also examined. Both are found to be strongly influenced by the electrostatic interactions as identified by the bond orientation time correlation function and local density distribution functions. These results have important implications for the design of nanocomposite silica-siloxane materials.

Gee, R H; Maxwell, R S; Dinh, L N; Balazs, B

2001-11-21T23:59:59.000Z

260

Atomistic modeling of metal surfaces under electric fields: direct coupling of electric fields to a molecular dynamics algorithm  

E-Print Network (OSTI)

The effect of electric fields on metal surfaces is fairly well studied, resulting in numerous analytical models developed to understand the mechanisms of ionization of surface atoms observed at very high electric fields, as well as the general behavior of a metal surface in this condition. However, the derivation of analytical models does not include explicitly the structural properties of metals, missing the link between the instantaneous effects owing to the applied field and the consequent response observed in the metal surface as a result of an extended application of an electric field. In the present work, we have developed a concurrent electrodynamic–molecular dynamic model for the dynamical simulation of an electric-field effect and subsequent modification of a metal surface in the framework of an atomistic molecular dynamics (MD) approach. The partial charge induced on the surface atoms by the electric field is assessed by applying the classical Gauss law. The electric forces acting on the partially...

Djurabekova, Flyura; Pohjonen, Aarne; Nordlund, Kai

2011-01-01T23:59:59.000Z

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

Molecular Computation Models in ACL2: a Simulation of Lipton's Experiment Solving SAT.  

E-Print Network (OSTI)

Molecular Computation Models in ACL2: a Simulation of Lipton's Experiment Solving SAT. F.J. Mart Abstract In this paper we present an ACL2 formalization of a molecular computing model: Adle- man to build a prototype of a molecular computer. In 1995, R.J. Lipton [7] solved an instance

Alonso, José A.

262

A fully dynamical simulation of central nuclear collisions  

E-Print Network (OSTI)

We present a fully dynamical simulation of central nuclear collisions around mid-rapidity at LHC energies. Unlike previous treatments, we simulate all phases of the collision, including the equilibration of the system. For the simulation, we use numerical relativity solutions to AdS/CFT for the pre-equilibrium stage, viscous hydrodynamics for the plasma equilibrium stage and kinetic theory for the low density hadronic stage. Our pre-equilibrium stage provides initial conditions for hydrodynamics and our results are insensitive to the AdS/hydro switching time. The resulting light particle spectra reproduce the measurements from the ALICE experiment at all transverse momenta.

van der Schee, Wilke; Pratt, Scott

2013-01-01T23:59:59.000Z

263

Simulation of Dynamic Characteristic for Passive Hydraulic Mount  

Science Conference Proceedings (OSTI)

Dynamic modeling of Passive Hydraulic Engine Mounts (PHEM) is developed with inertia track, decoupler and throttle. Mathematically, the state equations governing vibration isolation behaviors of the PHEMs are presented and solved by means of the lumped ... Keywords: passive hydraulic mount, simulation, test

Zhang Yunxia; Fang Zuhua

2009-08-01T23:59:59.000Z

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

DOE/NETL IGCC Dynamic Simulator Research and Training Center  

NLE Websites -- All DOE Office Websites (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,

266

BP205 Molecular Dynamics of the Cell 10 weeks / 2 lectures per week  

E-Print Network (OSTI)

BP205 Molecular Dynamics of the Cell 10 weeks / 2 lectures per week Room S204 Genentech Hall page / form of a journal letter SYLLABUS January 6: Class Overview Molecular Motions in the Cell: Molecular Motions in the Cell B · Fick's Law and the diffusion equation · Steady-state and time

Voigt, Chris

267

Hydrodynamic slip boundary condition at chemically patterned surfaces: A continuum deduction from molecular dynamics  

E-Print Network (OSTI)

We investigate the slip boundary condition for single-phase flow past a chemically patterned surface. Molecular dynamics (MD) simulations show that modulation of fluid-solid interaction along a chemically patterned surface induces a lateral structure in the fluid molecular organization near the surface. Consequently, various forces and stresses in the fluid vary along the patterned surface. Given the presence of these lateral variations, a general scheme is developed to extract hydrodynamic information from MD data. With the help of this scheme, the validity of the Navier slip boundary condition is verified for the chemically patterned surface, where a local slip length can be defined. Based on the MD results, a continuum hydrodynamic model is formulated using the Navier-Stokes equation and the Navier boundary condition, with a slip length varying along the patterned surface. Steady-state velocity fields from continuum calculations are in quantitative agreement with those from MD simulations. It is shown that, when the pattern period is sufficiently small, the solid surface appears to be homogeneous, with an effective slip length that can be controlled by surface patterning. Such a tunable slip length may have important applications in nanofluidics.

Tiezheng Qian; Xiao-Ping Wang; Ping Sheng

2005-02-26T23:59:59.000Z

268

Probing the hydration structure of polarizable halides: a multi-edge XAFS and molecular dynamics study of the iodide anion.  

DOE Green Energy (OSTI)

A comprehensive analysis of the H2O structure about aqueous iodide (I-) is reported from molecular dynamics (MD) simulation and x-ray absorption fine structure (XAFS) measurements. XAFS spectra from the iodide K-, L1-, and L3- edges were co-refined to establish the complete structure of the first hydration shell about aqueous I-. The results show approximately 6.3 water molecules located at I-H and I-O distances of 2.65 Å and 3.50 Å, respectively. Whereas the I-O bond is moderately disordered (Debye Waller factor, ?2 = 0.017 Å2) due to the relatively low charge-to-ion radius ratio, the I-H interaction shows even higher disorder (?2 = 0.036 Å2) due to the variable angular orientation of water at the ion surface. Molecular dynamics simulations employing both DFT (+dispersion) and classical potentials generate quite similar structures and they both agree to a large extent with the structure from the experimental XAFS. However the DFT-MD simulations provide a description of molecular structure that is more consistent with the XAFS experiment data. We employ a molecular anaylsis in which we incrementally evaluate the structural contributions from each of the nearest-neighbor water molecules about the iodide to provide a clear picture of the hydrated structure. For the DFT description of molecular interaction, a water molecule in the first shell has more freedom to rotate about the O atom when compared to motions resulting from a classical potential. Further, the hydrogen bonding of first-shell water with the second shell water establishes an strong ordering of the water about I- surface leading to characteristic O-I-O angles of 79 and 142°. This ordering, in addition to the higher coordination number leads to a more symmetric solvation from the DFT-MD configurations relative to the classical potential simulation.

Fulton, John L.; Schenter, Gregory K.; Baer, Marcel; Mundy, Christopher J.; Dang, Liem X.; Balasubramanian, Mahalingam

2010-10-14T23:59:59.000Z

269

Structural dynamics test simulation and optimization for aerospace components  

SciTech Connect

This paper initially describes an innovative approach to product realization called Knowledge Based Testing (KBT). This research program integrates test simulation and optimization software, rapid fabrication techniques and computational model validation to support a new experimentally-based design concept. This design concept implements well defined tests earlier in the design cycle enabling the realization of highly reliable aerospace components. A test simulation and optimization software environment provides engineers with an essential tool needed to support this KBT approach. This software environment, called the Virtual Environment for Test Optimization (VETO), integrates analysis and test based models to support optimal structural dynamic test design. A goal in developing this software tool is to provide test and analysis engineers with a capability of mathematically simulating the complete structural dynamics test environment within a computer. A developed computational model of an aerospace component can be combined with analytical and/or experimentally derived models of typical structural dynamic test instrumentation within the VETO to determine an optimal test design. The VETO provides the user with a unique analysis and visualization environment to evaluate new and existing test methods in addition to simulating specific experiments designed to maximize test based information needed to validate computational models. The results of both a modal and a vibration test design are presented for a reentry vehicle and a space truss structure.

Klenke, S.E.; Baca, T.J.

1996-06-01T23:59:59.000Z

270

Climate Simulations with an Isentropic Finite Volume Dynamical Core  

SciTech Connect

This paper discusses the impact of changing the vertical coordinate from a hybrid pressure to a hybrid-isentropic coordinate within the finite volume dynamical core of the Community Atmosphere Model (CAM). Results from a 20-year climate simulation using the new model coordinate configuration are compared to control simulations produced by the Eulerian spectral and FV dynamical cores of CAM which both use a pressure-based ({sigma}-p) coordinate. The same physical parameterization package is employed in all three dynamical cores. The isentropic modeling framework significantly alters the simulated climatology and has several desirable features. The revised model produces a better representation of heat transport processes in the atmosphere leading to much improved atmospheric temperatures. We show that the isentropic model is very effective in reducing the long standing cold temperature bias in the upper troposphere and lower stratosphere, a deficiency shared among most climate models. The warmer upper troposphere and stratosphere seen in the isentropic model reduces the global coverage of high clouds which is in better agreement with observations. The isentropic model also shows improvements in the simulated wintertime mean sea-level pressure field in the northern hemisphere.

Chen, Chih-Chieh; Rasch, Philip J.

2012-04-15T23:59:59.000Z

271

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 to their design and simulated in a computationally efficient manner. The methodology represents a system as interconnected, object-oriented sub-models known as components. Fluids and their local properties are modeled using discrete, incompressible objects known as packets. System wide pressure and flow rates are modeled similar to electrical circuit models. Transferring packets between components emulates fluid flow, while the system wide fluid circuit formed by the components' interconnections determines system wide pressures and flow rates. A tool named PAQS, after the PAacketized Quasi-dynamic Simulation methodology, was built to demonstrate the described methodology. Validation tests of PAQS found that its steady state energy use predictions differed less than 3% from a comparable steady state model. PAQS was also able to correctly model the transient behavior of a dynamic linear analytical system.

Davis, Clinton Paul

2012-05-01T23:59:59.000Z

272

Ad Hoc Distributed Dynamic Data-Driven Simulations of Surface Transportation Systems  

Science Conference Proceedings (OSTI)

An ad hoc distributed dynamic data-driven simulation is a collection of autonomous online simulations brought together to model an operational system. They offer the potential of increased accuracy, responsiveness, and robustness compared to centralized ... Keywords: ad hoc distributed simulation, dynamic data-driven application system, microscopic simulation model, online simulation

Michael Hunter; Hoe Kyoung Kim; Wonho Suh; Richard Fujimoto; Jason Sirichoke; Mahesh Palekar

2009-04-01T23:59:59.000Z

273

Advanced beam-dynamics simulation tools for RIA.  

Science Conference Proceedings (OSTI)

We are developing multi-particle beam-dynamics simulation codes for RIA driver-linac simulations extending from the low-energy beam transport (LEBT) line to the end of the linac. These codes run on the NERSC parallel supercomputing platforms at LBNL, which allow us to run simulations with large numbers of macroparticles. The codes have the physics capabilities needed for RIA, including transport and acceleration of multiple-charge-state beams, beam-line elements such as high-voltage platforms within the linac, interdigital accelerating structures, charge-stripper foils, and capabilities for handling the effects of machine errors and other off-normal conditions. This year will mark the end of our project. In this paper we present the status of the work, describe some recent additions to the codes, and show some preliminary simulation results.

Garnett, R. W.; Wangler, T. P.; Billen, J. H.; Qiang, J.; Ryne, R.; Crandall, K. R.; Ostroumov, P.; York, R.; Zhao, Q.; Physics; LANL; LBNL; Tech Source; Michigan State Univ.

2005-01-01T23:59:59.000Z

274

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase  

Science Conference Proceedings (OSTI)

Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexible in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.

Smith, Dayle MA; Xiong, Yijia; Straatsma, TP; Rosso, Kevin M.; Squier, Thomas C.

2012-05-09T23:59:59.000Z

275

Simulating Soil Carbon Dynamics, Erosion and Tillage with EPIC  

NLE Websites -- All DOE Office Websites (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

276

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

NLE Websites -- All DOE Office Websites (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.

277

Dynamic Simulation and Training for IGCC Power Plants  

SciTech Connect

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.

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

2006-09-01T23:59:59.000Z

278

Dynamic simulation for IGCC process and control design  

Science Conference Proceedings (OSTI)

Detailed dynamic simulation analysis is a valuable tool that increases the understanding of unit interactions and control system performance in a complex integrated gasification combined-cycle (IGCC) plant. The Sarlux integrated gasification combined cycle (IGCC) plant must simultaneously satisfy electrical power and refinery hydrogen and steam demands (trigeneration gasification). The plant`s gasifier, heat recovery, sulfur removal, hydrogen recovery and steam power generation units are highly integrated and require coordinated control. In this study, dynamic simulation provides insights into the behavior of the process and combined cycle units during normal and upset conditions. The dynamic simulation is used to design a control system that drives the gasifiers to satisfy power, steam and hydrogen demands before a load change or upset is detected by the syngas pressure controller. At the study conclusion, the model will demonstrate how the IGCC plant will respond to the contractual maximum load change rate and process upsets. The study tests the basic process and control system design during the project engineering phase to minimize startup troubleshooting and expensive field changes.

Depew, C.; Martinez, A. [Fluor Daniel, Irvine, CA (United States); Collodi, G.; Meloni, R. [Snamprogetti, Milan (Italy)

1998-01-01T23:59:59.000Z

279

A simple and effective Verlet-type algorithm for simulating Langevin dynamics  

E-Print Network (OSTI)

We present a revision to the well known Stormer-Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate that the new algorithm correctly reproduces diffusive behavior of a particle in a flat potential. For a harmonic oscillator, our algorithm provides the exact Boltzmann distribution for any value of damping, frequency, and time step for both underdamped and over damped behavior within the usual the stability limit of the Verlet algorithm. Given the structure and simplicity of the method we conclude this approach can trivially be adapted for contemporary applications, including molecular dynamics with extensions such as molecular constraints.

Grønbech-Jensen, Niels

2013-01-01T23:59:59.000Z

280

A simple and effective Verlet-type algorithm for simulating Langevin dynamics  

E-Print Network (OSTI)

We present a revision to the well known Stormer-Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate that the new algorithm correctly reproduces diffusive behavior of a particle in a flat potential. For a harmonic oscillator, our algorithm provides the exact Boltzmann distribution for any value of damping, frequency, and time step for both underdamped and over damped behavior within the usual the stability limit of the Verlet algorithm. Given the structure and simplicity of the method we conclude this approach can trivially be adapted for contemporary applications, including molecular dynamics with extensions such as molecular constraints.

Niels Grønbech-Jensen; Oded Farago

2012-12-06T23:59:59.000Z

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

Simulation: Thermodynamic  

E-Print Network (OSTI)

(by selectively reflecting), so system energy stays constant. -- Heat is generated by viscous action corresponds to vortex generation in similar fluid mechanical situations. But the high flow speed#12; ' & $ % Coupling Continuum to Molecular Dynamics Simulation: Reflecting Particle Method

Li, Ju

282

Contents 1 Molecular Dynamics Simulation of Argon 1  

E-Print Network (OSTI)

1.1 Simple model of interacting Argon atoms........................... 2 2 A simple MD program 4 2.1 Newton’s Equations of Motion................................ 6

unknown authors

2010-01-01T23:59:59.000Z

283

Molecular Dynamics Simulation on the Surface Melting and ...  

Science Conference Proceedings (OSTI)

Abstract Scope, Thermal and non-thermal ultra-fast laser induced surface melting and nanojoining of Ag nanoparticles and nanowires were investigated ...

284

Metallic Cluster Coalescence: Molecular Dynamics Simulations of Boundary Formation  

E-Print Network (OSTI)

During the evaporative deposition of polycrystalline thin films, the development of a tensile stress at small film thicknesses is associated with island coalescence. Several continuum models exist to describe the magnitude ...

Takahashi, A. R.

285

Molecular dynamics simulation of thermal energy transport in polydimethylsiloxane (PDMS)  

E-Print Network (OSTI)

Heat transfer across thermal interface materials is a critical issue for microelectronics thermal management. Polydimethylsiloxane (PDMS), one of the most important components of thermal interface materials presents a large ...

Luo, Tengfei

286

Molecular Dynamics Simulation of Al Oxide Stress Corrosion Cracking  

Science Conference Proceedings (OSTI)

About this Abstract. Meeting, Materials Science & Technology 2013. Symposium, Structure – Property Relationships in Low-Dimensional Metallic Nanostructures.

287

Molecular Dynamics Simulation of Reactions Forming Ni-Al ...  

Science Conference Proceedings (OSTI)

Abstract Scope, Alloying reactions of a Ni-coated Al nanoparticle, Al-coated ... Atomistic Modeling of Screw Dislocation Mobility in Alpha-Fe ... Mesoscale Polycrystal Calculations of Damage Histories in Shock Loaded Metals ... Multi- time Scale Modeling of the Annealing of Radiation-Induced Defects at Tilt Grain Boundaries.

288

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

289

Molecular Dynamics Simulations of Grain Boundary Free Energy ...  

Science Conference Proceedings (OSTI)

A Tale of Two States and More: Modeling of New Generation of Lattice Stability ... Analysis of Nano Fluid Using CFD-A Hybrid Approach for Cooling Purpose.

290

Molecular dynamics simulations of threshold displacement energies in Fe  

E-Print Network (OSTI)

, Finland b Department of Nuclear and Reactor Physics, Royal Institute of Technology, Stockholm, Sweden c Department of Neutron Research, Uppsala University, Uppsala, Sweden d Reactor Materials Research Unit, SCK of the Frenkel pair (in total about 25 eV). Since then it has played a key role in radiation damage theory

Nordlund, Kai

291

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine  

E-Print Network (OSTI)

FIX COPY ORNL/Sub/84-00205/1 SEROEDGEY EQVE C= Status of Free Piston Stirling Engine Driven Heat STIRLING ENGINE DRIVEN HEAT PUMPS-DEVELOPMENT, ISSUES, AND OPTIONS FINAL REPORT Date Published- April 1986 the results of a program to review the recent experience with free piston Stirling engine (FPSE) driven beat

Rapaport, Dennis C.

292

Molecular Dynamics Simulation of Crack Propagation in Silicon ...  

Science Conference Proceedings (OSTI)

Abstract Scope, Lithium ion batteries (LIBs) are widely used as power devices for .... The Electrochemical Flow Capacitor for Efficient Grid-Scale Energy Storage.

293

Simulation of Tailrace Hydrodynamics Using Computational Fluid Dynamics Models  

DOE Green Energy (OSTI)

This report investigates the feasibility of using computational fluid dynamics (CFD) tools to investigate hydrodynamic flow fields surrounding the tailrace zone below large hydraulic structures. Previous and ongoing studies using CFD tools to simulate gradually varied flow with multiple constituents and forebay/intake hydrodynamics have shown that CFD tools can provide valuable information for hydraulic and biological evaluation of fish passage near hydraulic structures. These studies however are incapable of simulating the rapidly varying flow fields that involving breakup of the free-surface, such as those through and below high flow outfalls and spillways. Although the use of CFD tools for these types of flow are still an active area of research, initial applications discussed in this report show that these tools are capable of simulating the primary features of these highly transient flow fields.

Cook, Chris B; Richmond, Marshall C

2001-05-01T23:59:59.000Z

294

Constraint-Based Simulation of Biological Systems Described by Molecular Interaction Maps  

Science Conference Proceedings (OSTI)

We present a method to simulate biochemical networks described by the graphical notation of Molecular Inter- action Maps within stochastic Concurrent Constraint Pro- gramming. Such maps are compact, as they represent im- plicitly a wide set of reactions, ...

Luca Bortolussi; Simone Fonda; Alberto Policriti

2007-11-01T23:59:59.000Z

295

Visualization of Folktales on a Map by Coupling Dynamic DEVS Simulation within Google Earth  

E-Print Network (OSTI)

Visualization of Folktales on a Map by Coupling Dynamic DEVS Simulation within Google Earth, Google Earth API, Dynamic variable structures Abstract: This paper deals with dynamic visualization of folktales on a map. The visualization is performed using a coupling of dynamic simulation with the google

Paris-Sud XI, Université de

296

Development of directional capabilities to an ultradeep water dynamic kill simulator and simulations runs  

E-Print Network (OSTI)

The world is dependent on the production of oil and gas, and every day the demand increases. Technologies have to keep up with the demand of this resource to keep the world running. Since hydrocarbons are finite and will eventually run out, the increasing demand of oil and gas is the impetus to search for oil in more difficult and challenging areas. One challenging area is offshore in ultradeep water, with water depths greater than 5000 ft. This is the new arena for drilling technology. Unfortunately with greater challenges there are greater risks of losing control and blowing out a well. A dynamic kill simulator was developed in late 2004 to model initial conditions of a blowout in ultradeep water and to calculate the minimum kill rate required to kill a blowing well using the dynamic kill method. The simulator was simple and efficient, but had limitations; only vertical wells could be simulated. To keep up with technology, modifications were made to the simulator to model directional wells. COMASim (Cherokee, Offshore Technology Research Center, Minerals Management Service, Texas A&M Simulator) is the name of the dynamic kill simulator. The new version, COMASim1.0, has the ability to model almost any type of wellbore geometry when provided the measured and vertical depths of the well. Eighteen models with varying wellbore geometry were simulated to examine the effects of wellbore geometry on the minimum kill rate requirement. The main observation was that lower kill rate requirement was needed in wells with larger measured depth. COMASim 1.0 cannot determine whether the inputs provided by the user are practical; COMASim 1.0 can only determine if the inputs are incorrect, inconsistent or cannot be computed. If unreasonable drilling scenarios are input, unreasonable outputs will result. COMASim1.0 adds greater functionality to the previous version while maintaining the original framework and simplicity of calculations and usage.

Meier, Hector Ulysses

2005-08-01T23:59:59.000Z

297

Preliminary analysis of the dynamic heliosphere by MHD simulations  

SciTech Connect

A preliminary analysis of the dynamic heliosphere to estimate the termination shock (TS) distance from the sun around the time when Voyager 1 passed the termination shock at December 16, 2004 is performed by using MHD simulations. For input to this simulation, we use the Voyager 2 solar-wind data. We first find a stationary solution of the 3-D outer heliosphere by assigning a set of LISM parameters as our outer boundary conditions and then the dynamical analysis is performed. The model TS crossing is within 6 months of the observed date. The TS is pushed outward every time a high ram-pressure solar wind pulse arrives. After the end of the high ram-pressure wind, the TS shock shrinks inward. When the last Halloween event passed through the TS at DOY 250, 2004, the TS began to shrink inward very quickly and the TS crossed V1. The highest inward speed of the TS is over 400 km/s. The high ram-pressure solar wind transmitted through the TS becomes a high thermal-pressure plasma in the heliosheath, acting to push the TS inward. This suggests that the position of the TS is determined not only by the steady-state pressure balance condition between the solar wind ram-pressure and the LISM pressure, but by the dynamical ram pressure too. The period when the high ram-pressure solar wind arrives at the TS shock seems to correspond to the period of the TS particle event (Stone et al, 2005, Decker et al., 2005). The TS crossing date will be revised in future simulations using a more appropriate set of parameters for the LISM. This will enable us to undertake a detailed comparison of the simulation results with the TS particle events.

Washimi, H.; Zank, G. P. [Institute of Geophysics and Planetary Physics (IGPP), University of California, Riverside, CA 92521 (United States); Tanaka, T. [Faculty of Science, Kyushu University, Hakozaki, Fukuoka 812-8581 (Japan)

2006-09-26T23:59:59.000Z

298

Infrared Spectroscopy and Hydrogen-Bond Dynamics of Liquid Water from Centroid Molecular Dynamics with an Ab Initio-Based Force Field  

DOE Green Energy (OSTI)

A molecular-level description of the unique properties of hydrogen-bond networks is critical for understanding many fundamental physico-chemical processes in aqueous environments. In this article a novel simulation approach, combining an ab-initio based force field for water with a quantum treatment of the nuclear motion, is applied to investigate hydrogen-bond dynamics in liquid water with a specific focus on the relationship of these dynamics to vibrational spectroscopy. Linear and nonlinear infrared (IR) spectra are calculated for liquid water, HOD in D2O and HOD in H2O and discussed in the context of the results obtained using other approaches that have been employed in studies of water dynamics. A comparison between the calculated spectra and the available experimental data yields an overall good agreement, indicating the accuracy of the present simulation approach in describing the properties of liquid water at ambient conditions. Possible improvements on the representation of the underlying water interactions as well as the treatment of the molecular motion at the quantum-mechanical level are also discussed. This research was supported by the Division of Chemical Sciences, Biosciences and Geosciences, US Department of Energy. Battelle operates the Pacific Northwest National Laboratory for the US Department of Energy.

Paesani, Francesco; Xantheas, Sotiris S.; Voth, Gregory A.

2009-10-01T23:59:59.000Z

299

Molecular dynamics analysis of PVA-AgnP composites by dielectric spectroscopy  

Science Conference Proceedings (OSTI)

The molecular dynamics of PVA/AgnP composites were studied by dielectric spectroscopy (DS) in the 20-300°C temperature range. Improper water elimination leads to misinterpretation of thermal relaxations in PVA composites in agreement with the previous ...

J. Betzabe González-Campos; Evgen Prokhorov; Isaac C. Sanchez; J. Gabriel Luna-Bárcenas; Alejandro Manzano-Ramírez; Jesús González-Hernández; Yliana López-Castro; Rosa E. del Río

2012-01-01T23:59:59.000Z

300

The Performance of Different Communication Mechanisms and Algorithms Used for Parallelization of Molecular Dynamics Code  

Science Conference Proceedings (OSTI)

Communication performance appears to have the most important influence on parallelization efficiency of large scientific applications. Different communication algorithms and communication mechanisms were used in parallelization of molecular dynamics ...

Rafal Metkowski; Piotr Bala; Terry W. Clark

2001-09-01T23:59:59.000Z

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

Simulation I - Programmaster.org  

Science Conference Proceedings (OSTI)

Feb 15, 2010 ... Molecular dynamics Simulation of Nucleation Process: Ramanarayan Hariharaputran1; David Wu1; 1Institute of High Performance Computing, ...

302

Modifying the molecular dynamics action to increase topological tunnelling rate for dynamical overlap fermions  

E-Print Network (OSTI)

We describe a new Hybrid Monte Carlo (HMC) algorithm for dynamical overlap fermions, which improves the rate of topological index changes by adding an additional (intensive) term to the action for the molecular dynamics part of the algorithm. The metropolis step still uses the exact action, so that the Monte Carlo algorithm still generates the correct ensemble. By tuning this new term, we hope to be able to balance the acceptance rate of the HMC algorithm and the rate of topological index changes. We also describe how suppressing, but not eliminating, the small eigenvalues of the kernel operator may improve the volume scaling of the cost per trajectory for overlap HMC while still allowing topological index changes. We test this operator on small lattices, comparing our new algorithm with an old overlap HMC algorithm with a slower rate of topological charge changes, and an overlap HMC algorithm which fixes the topology. Our new HMC algorithm more than doubles the rate of topological index changes compared to the previous state of the art, while maintaining the same metropolis acceptance rate. We investigate the effect of topological index changes on the local topological charge density, measured using an improved field theoretic operator after heavy smearing. We find that the creation and annihilation of large lumps of topological charge is increased with the new algorithm.

Nigel Cundy; Weonjong Lee

2011-10-10T23:59:59.000Z

303

Electron, Photon, and Positron Scattering Dynamics of Complex Molecular Targets  

E-Print Network (OSTI)

Electron scattering cross sections have been computed for pyridine and pyrimidine using the static-exchange approximation with model potential to account for dynamic electron correlation. To obtain well-converged orbitals, we have expanded all partial waves to a maximum angular momentum of l = 60 for both targets. We have obtained total cross sections for electron scattering energies to 20 eV. Both targets display similar features, namely a dipole-induced increase in the integrated cross section at scattering energies below 5 eV, and peaks corresponding to resonances in b1, a2, and b1 symmetries. These resonances were investigated through a Siegert eigenstate analysis and Breit-Wigner fit of the SECP eigenphase sums. They were also compared to the virtual orbitals obtained from a minimum basis set Hartree-Fock calculation on both targets. We consider electron scattering resonances from cis-diamminedichloroplatinum, [Pt(NH3)2Cl2], the ligand molecular species Cl2 (1Sigma+g ), and the isolated transition metal center Pt in a nondegenerate atomic state (1S) at the SECP level of theory. As a rigorous comparison to the single-state, single-configuration SECP level results of these smaller, yet electron dense targets, we have also considered scattering from ground state Cl2 and Pt in the 1S and 3D states in the multichannel configuration-interaction (MCCI) approximation originally developed for photoionization for scattering up to 10 eV. Photoionization cross sections and angular distributions in the recoil frame (RFPAD) and molecular frame (MFPAD) have been computed for inner-shell C 1s and Cl 2p ionization from the chloroalkanes chloromethane and chloroethane, with ionization leading to a variety of ionic fragment states. We have also computed valence level ionization from the nitro molecule nitromethane CH3NO2 leading to the dissociation of the CN bond. All of these calculations were performed in the frozen-core Hartree-Fock approximation. Even at this level of theory, we obtain computed results that compare well to the photoelectronphotoion coincidence measurements. The fullerene C20 is the smallest fullerene predicted to exist, with most relevant structural calculations suggesting the reduction of the icosahedral symmetry into one in which the target species possesses at maximum only a dihedral axis. We have computed positron scattering cross sections for the molecule in two low-symmetry structural isomers Ci and C2, within the HF approximation. Density functional expressions were used to incorporate important positron-electron interactions within the calculation. We have found similar cross sections and resonance features for both isomers, including a positron scattering resonance whose density is found within the framework of the fullerene cluster.

Carey, Ralph

2012-05-01T23:59:59.000Z

304

Crossed molecular beam studies of atmospheric chemical reaction dynamics  

SciTech Connect

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

305

Dynamic Simulation and Optimization of Nuclear Hydrogen Production Systems  

DOE Green Energy (OSTI)

This project is part of a research effort to design a hydrogen plant and its interface with a nuclear reactor. This project developed a dynamic modeling, simulation and optimization environment for nuclear hydrogen production systems. A hybrid discrete/continuous model captures both the continuous dynamics of the nuclear plant, the hydrogen plant, and their interface, along with discrete events such as major upsets. This hybrid model makes us of accurate thermodynamic sub-models for the description of phase and reaction equilibria in the thermochemical reactor. Use of the detailed thermodynamic models will allow researchers to examine the process in detail and have confidence in the accurary of the property package they use.

Paul I. Barton; Mujid S. Kaximi; Georgios Bollas; Patricio Ramirez Munoz

2009-07-31T23:59:59.000Z

306

Mesoscale Structures at Complex Fluid-Fluid Interfaces: a Novel Lattice Boltzmann / Molecular Dynamics Coupling  

E-Print Network (OSTI)

Complex fluid-fluid interfaces featuring mesoscale structures with adsorbed particles are key components of newly designed materials which are continuously enriching the field of soft matter. Simulation tools which are able to cope with the different scales characterizing these systems are a fundamental requirement for efficient theoretical investigations. In this paper we present a novel simulation method, based on the approach of Ahlrichs and D\\"unweg [Ahlrichs and D\\"unweg, Int. J. Mod. Phys. C, 1998, 9, 1429], that couples the "Shan-Chen" multicomponent Lattice Boltzmann technique to off-lattice molecular dynamics. We demonstrate how this approach can be used to solve a wide class of challenging problems. Several examples are given, with an accent on bicontinuous phases formation in polyelectrolyte solutions and ferrofluid emulsions. We show also that the introduction of solvation free energies in the particle-fluid interaction unveils the hidden, multiscale nature of the particle-fluid coupling, allowing to treat symmetrically (and interchangeably) the on-lattice and off-lattice components of the system.

Marcello Sega; Mauro Sbragaglia; Sofia Sergeevna Kantorovich; Alexey Olegovich Ivanov

2013-06-04T23:59:59.000Z

307

Simulating dislocation loop internal dynamics and collective diffusion using stochastic differential equations  

Science Conference Proceedings (OSTI)

Nanoscale prismatic loops are modeled via a partial stochastic differential equation that describes an overdamped continuum elastic string, with a view to describing both the internal and collective dynamics of the loop as a function of temperature. Within the framework of the Langevin equation, expressions are derived that relate the empirical parameters of the model, the friction per unit length, and the elastic stiffness per unit length, to observables that can be obtained directly via molecular-dynamics simulations of interstitial or vacancy prismatic loop mobility. The resulting expressions naturally exhibit the properties that the collective diffusion coefficient of the loop (i) scales inversely with the square root of the number of interstitials, a feature that has been observed in both atomistic simulation and in situ TEM investigations of loop mobility, and (ii) the collective diffusion coefficient is not at all dependent on the internal interactions within the loop, thus qualitatively rationalizing past simulation results showing that the characteristic migration energy barrier is comparable to that of a single interstitial, and cluster migration is a result of individual (but correlated) interstitial activity.

Derlet, P. M.; Gilbert, M. R.; Dudarev, S. L. [Condensed Matter Theory Group, Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); EURATOM/CCFE Fusion Association, Culham Centre for Fusion Energy, Oxfordshire OX14 3DB (United Kingdom)

2011-10-01T23:59:59.000Z

308

Dynamic computer simulation of the Fort St. Vrain steam turbines  

SciTech Connect

A computer simulation is described for the dynamic response of the Fort St. Vrain nuclear reactor regenerative intermediate- and low-pressure steam turbines. The fundamental computer-modeling assumptions for the turbines and feedwater heaters are developed. A turbine heat balance specifying steam and feedwater conditions at a given generator load and the volumes of the feedwater heaters are all that are necessary as descriptive input parameters. Actual plant data for a generator load reduction from 100 to 50% power (which occurred as part of a plant transient on November 9, 1981) are compared with computer-generated predictions, with reasonably good agreement.

Conklin, J.C.

1983-01-01T23:59:59.000Z

309

Dynamics  

NLE Websites -- All DOE Office Websites (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

310

Dynamic simulation and performance evaluation of fossil power plants  

Science Conference Proceedings (OSTI)

A dynamic performance model of a standard fossil-fired power plant has been developed. The model contains major components in a plant, including pulverizer, boiler, superheaters, reheaters, economizer, attemperators, pumps, valves, pipings, condenser, turbines, deaerator and low/high pressure feedwater heaters. The EPRI Modular Modeling System (MMS) and Boeing Computer Services' Engineering Analysis System (EASY5) simulation language were used in the analysis. A system control model also developed to simulate the plant control and perform the necessary control functions. The plant model has a general structure and can readily be modified to simulate a specific power plant. To demonstrate the utility of the model, simulation calculations were carried out for a standard coal-fired power plant of the Middle South Services (MSS) during steady state and transient modes of operation. The results were obtained for full load and reduced loads down to 35 percent. In general, good agreement was obtained with the plant heat balance data. 15 refs., 35 figs., 11 tabs.

Hashemi, A.; Lin, C.S.; Munis, A.; Lee, S. (Science Applications International Corp., Hermosa Beach, CA (USA))

1988-12-01T23:59:59.000Z

311

RIAPMTQ/Impact : beam-dynamics simulation tool for RIA.  

Science Conference Proceedings (OSTI)

We have developed a pair of multiparticle beam dynamics codes for end-to-end computer simulations of the proposed RIA heavy-ion driver linac. The two codes are: (1) an adaptation of PARMTEQ called RIAPMTQ for the normal-conducting-linac front end, and (2) IMPACT for the superconducting linac. The codes run on a PC as well as on parallel supercomputing platforms such as NERSC at LBNL. The parallel capability allows us to run simulations with large numbers of macroparticles for the computation of beam halo and beam-losses. The codes are being benchmarked for rms beam properties against previously existing codes at ANL and MSU. The work is being performed by a collaboration including LANL, LBNL, ANL, and Michigan State University (MSU). In this paper we present an overview, the status of the work, comparison of simulation results from RIAPMTQ and the ANL code TRACK for the ANL front-end design, and the first RIAPMTQ/IMPACT end-to-end multiprocessor simulation for the MSU design.

Wangler, T. P.; Billen, J. H.; Garnett, R. W.; Qiang, J.; Ryne, R.; Crandall, K. R.; Ostroumov, P.; Aseev, V. N.; Mustapha, B.; York, R. C.; Wu, X.; Zhao, Q.; Gorelov, D.; Doleans, M.; Physics; LANL; Tech Source; Michigan State Univ.

2006-01-01T23:59:59.000Z

312

Molecular dynamics on distributed-memory MIMD computers with load balancing  

Science Conference Proceedings (OSTI)

We report two aspects of a computational molecular dynamics study of large-scale problems on a distributed-memory MIMD parallel computer: (1) efficiency and scalability results on Intel Paragon parallel computers with up to 512 nodes and (2) a new method for dynamic load balancing.

Deng, Y.; McCoy, R.A. [State Univ. of New York, Stony Brook, NY (United States). Research Foundation; Marr, R.B.; Peierls, R.F. [Brookhaven National Lab., Upton, NY (United States); Yasar, O. [Brookhaven National Lab., Upton, NY (United States)

1994-12-31T23:59:59.000Z

313

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

314

A Dissipative-Particle-Dynamics Model for Simulating Dynamics of Charged Colloid  

E-Print Network (OSTI)

A mesoscopic colloid model is developed in which a spherical colloid is represented by many interacting sites on its surface. The hydrodynamic interactions with thermal fluctuations are taken accounts in full using Dissipative Particle Dynamics, and the electrostatic interactions are simulated using Particle-Particle-Particle Mesh method. This new model is applied to investigate the electrophoretic mobility of a charged colloid under an external electric field, and the influence of salt concentration and colloid charge are systematically studied. The simulation results show good agreement with predictions from the electrokinetic theory.

Jiajia Zhou; Friederike Schmid

2013-11-05T23:59:59.000Z

315

Implementing Molecular Dynamics on Hybrid High Performance Computers - Three-Body Potentials  

SciTech Connect

The use of coprocessors or accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power re- quirements. Hybrid high-performance computers, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. Although there has been extensive research into methods to efficiently use accelerators to improve the performance of molecular dynamics (MD) employing pairwise potential energy models, little is reported in the literature for models that include many-body effects. 3-body terms are required for many popular potentials such as MEAM, Tersoff, REBO, AIREBO, Stillinger-Weber, Bond-Order Potentials, and others. Because the per-atom simulation times are much higher for models incorporating 3-body terms, there is a clear need for efficient algo- rithms usable on hybrid high performance computers. Here, we report a shared-memory force-decomposition for 3-body potentials that avoids memory conflicts to allow for a deterministic code with substantial performance improvements on hybrid machines. We describe modifications necessary for use in distributed memory MD codes and show results for the simulation of water with Stillinger-Weber on the hybrid Titan supercomputer. We compare performance of the 3-body model to the SPC/E water model when using accelerators. Finally, we demonstrate that our approach can attain a speedup of 5.1 with acceleration on Titan for production simulations to study water droplet freezing on a surface.

Brown, W Michael [ORNL] [ORNL; Yamada, Masako [GE Global Research] [GE Global Research

2013-01-01T23:59:59.000Z

316

The application of discrete event simulation and system dynamics in the logistics and supply chain context  

Science Conference Proceedings (OSTI)

Discrete event simulation (DES) and system dynamics (SD) are two modelling approaches widely used as decision support tools in logistics and supply chain management (LSCM). A widely held belief exists that SD is mostly used to model problems at a strategic ... Keywords: Comparison of methods, Discrete-event simulation, Logistics and supply chain management, Simulation modelling, System dynamics

Antuela A. Tako; Stewart Robinson

2012-03-01T23:59:59.000Z

317

Ion dynamics at supercritical quasi-parallel shocks: Hybrid simulations  

Science Conference Proceedings (OSTI)

By separating the incident ions into directly transmitted, downstream thermalized, and diffuse ions, we perform one-dimensional (1D) hybrid simulations to investigate ion dynamics at a supercritical quasi-parallel shock. In the simulations, the angle between the upstream magnetic field and shock nominal direction is {theta}{sub Bn}=30 Degree-Sign , and the Alfven Mach number is M{sub A}{approx}5.5. The shock exhibits a periodic reformation process. The ion reflection occurs at the beginning of the reformation cycle. Part of the reflected ions is trapped between the old and new shock fronts for an extended time period. These particles eventually form superthermal diffuse ions after they escape to the upstream of the new shock front at the end of the reformation cycle. The other reflected ions may return to the shock immediately or be trapped between the old and new shock fronts for a short time period. When the amplitude of the new shock front exceeds that of the old shock front and the reformation cycle is finished, these ions become thermalized ions in the downstream. No noticeable heating can be found in the directly transmitted ions. The relevance of our simulations to the satellite observations is also discussed in the paper.

Su Yanqing; Lu Quanming; Gao Xinliang; Huang Can; Wang Shui [CAS Key Laboratory of Basic Plasma Physics, Department of Geophysics and Planetary Science, University of Science and Technology of China, Hefei 230026 (China)

2012-09-15T23:59:59.000Z

318

Dynamic High Pressure Measurements and Molecular Dynamics Simulations of Phase Changes and Vibrational Dynamics in Molecular Solids  

E-Print Network (OSTI)

rate on the phase transitions of Ice VI 17,18 and Ice VII.for the phase transitions of water ? Ice VI and Ice VI ? Iceobserve the phase transitions of water ? Ice VI and Ice VI ?

Rice, Andrew Patrick

2011-01-01T23:59:59.000Z

319

Water at a hydrophilic solid surface probed by ab-initio molecular dynamics: inhomogeneous thin layers of dense fluid  

DOE Green Energy (OSTI)

We present a microscopic model of the interface between liquid water and a hydrophilic, solid surface, as obtained from ab-initio molecular dynamics simulations. In particular, we focused on the (100)surface of cubic SiC, a leading candidate semiconductor for bio-compatible devices. Our results show that, in the liquid in contact with the clean substrate, molecular dissociation occurs in a manner unexpectedly similar to that observed in the gas phase. After full hydroxylation takes place, the formation of a thin ({approx}3 {angstrom})interfacial layer is observed, which has higher density than bulk water and forms stable hydrogen bonds with the substrate. The liquid does not uniformly wet the surface, rather molecules preferably bind along directions parallel to the Si dimer rows. Our calculations also predict that one dimensional confinement between two hydrophilic surfaces at about 1.3 nm distance does not affect the structural and electronic properties of the whole water sample.

Cicero, G; Grossman, J; Galli, G; Catellani, A

2005-01-28T23:59:59.000Z

320

Homogeneous ice nucleation at moderate supercooling from molecular simulation  

E-Print Network (OSTI)

Among all the freezing transitions, that of water into ice is probably the most relevant to biology, physics, geology or atmospheric science. In this work we investigate homogeneous ice nucleation by means of computer simulations. We evaluate the size of the critical cluster and the nucleation rate for temperatures ranging between 15K and 35K below melting. We use the TIP4P/2005 and the TIP4P/Ice water models. Both give similar results when compared at the same temperature difference with the model's melting temperature. The size of the critical cluster varies from $\\sim$8000 molecules (radius$ = 4$nm) at 15K below melting to $\\sim$600 molecules (radius$ = 1.7$nm) at 35K below melting. We use Classical Nucleation Theory (CNT) to estimate the ice-water interfacial free energy and the nucleation free energy barrier. We obtain an interfacial free energy of 29(3)mN/m from an extrapolation of our results to the melting temperature. This value is in good agreement both with experimental measurements and with previous estimates from computer simulations of TIP4P-like models. Moreover, we obtain estimates of the nucleation rate from simulations of the critical cluster at the barrier top. The values we get for both models agree within statistical error with experimental measurements. At temperatures higher than 20K below melting we get nucleation rates slower than the appearance of a critical cluster in all the water of the hydrosphere in the age of the universe. Therefore, our simulations predict that water freezing above this temperature must necessarily be heterogeneous.

E. Sanz; C. Vega; J. R. Espinosa; R. Caballero-Bernal; J. L. F. Abascal; C. Valeriani

2013-12-03T23:59:59.000Z

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


321

A First Principles Molecular Dynamics Study Of Calcium Ion In Water  

SciTech Connect

In this work we report on Car-Parrinello simulations of the divalent calcium ion in water, aimed at understanding the structure of the hydration shell and at comparing theoretical results with a series of recent experiments. Our paper shows some of the progress in the investigation of aqueous solutions brought about by the advent of ab initio molecular dynamics and highlights the importance of accessing subtle details of ion-water interactions from first-principles. Calcium plays a vital role in many biological systems, including signal transduction, blood clotting and cell division. In particular, calcium ions are known to interact strongly with proteins as they tend to bind well to both negatively charged (e.g. in aspartate and glutamate) and uncharged oxygens (e.g. in main-chain carbonyls). The ability of calcium to coordinate multiple ligands (from 6 to 8 oxygen atoms) with an asymmetric coordination shell enables it to cross-link different segments of a protein and induce large conformational changes. The great biochemical importance of the calcium ion has led to a number of studies to determine its hydration shell and its preferred coordination number in water. Experimental studies have used a variety of techniques, including XRD, EXAFS, and neutron diffraction to elucidate the coordination of Ca{sup 2+} in water. The range of coordination numbers (n{sub C}) inferred by X-ray diffraction studies varies from 6 to 8, and is consistent with that reported in EXAFS experiments (8 and 7.2). A wider range of values (6 to 10) was found in early neutron diffraction studies, depending on concentration, while a more recent measurement by Badyal, et al. reports a value close to 7. In addition to experimental measurements, many theoretical studies have been carried out to investigate the solvation of Ca{sup 2+} in water and have also reported a wide range of coordination numbers. Most of the classical molecular dynamics (MD) and QM/MM simulations report n{sub C} in the range of 8 to 10; in general, n{sub C} appears to be highly sensitive to the choice of the ion-water potential used in the calculations. Even ab initio MD simulations have so far obtained conflicting values for n{sub C}. For the structure of the first salvation shell Naor, et al. found n{sub C} = 7 to 8 and a Ca{sup 2+} - oxygen average distance (r{sub Ca-O}) of 2.64 {angstrom}, while Bako, et al. found n{sub C} = 6 and r{sub Ca-O} = 2.45 {angstrom}. In view of the existing controversies, we have carried out extensive Car-Parrinello simulations of Ca{sup 2+} solvation in water, using both a rigid and a flexible water model, up to time scales of 40 ps. Our simulations show variations of coordination numbers from 6, 7 and 8 occurring over intervals of {approx} 0.3/0.4 exchanges/ps, and yielding average coordination numbers of 6.2 and 7 for flexible and rigid water models, respectively. These results are consistent with those reported in recent EXAFS and neutron diffraction experiments. In addition, our calculations show an asymmetric coordination of Ca{sup 2+} to oxygen, similar to the case of Mg{sup 2+}.

Lightstone, F; Schwegler, E; Allesch, M; Gygi, F; Galli, G

2005-01-28T23:59:59.000Z

322

A Dynamic Wind Turbine Simulator of the Wind Turbine Generator System  

Science Conference Proceedings (OSTI)

To study dynamic performances of wind turbine generator system (WTGS), and to determine the control structures in laboratory. The dynamic torque generated by wind turbine (WT) must be simulated. In there paper, a dynamic wind turbine emulator (WTE) is ... Keywords: dynamic wind turbine emulation, wind shear, tower shadow, torque compensation

Lei Lu; Zhen Xie; Xing Zhang; Shuying Yang; Renxian Cao

2012-01-01T23:59:59.000Z

323

Dynamic Coherence in Excitonic Molecular Complexes under Various Excitation Conditions  

E-Print Network (OSTI)

In this paper, we investigate the relevance of dynamic electronic coherence under conditions natural to light-harvesting systems. We formulate the results of a quantum mechanical treatment of a weak light-matter interaction in terms of experimental observable, such as the incident light spectrum and the absorption spectrum of the material, and we derive the description of the incoherent F\\"orster type energy transfer fully from the wave function formalism. We demonstrate that excitation of a coherent superposition of electronic eigenstates of natural light-harvesting complexes by sunlight or by excitation transfer from a neighboring antenna is unlikely and that dynamical coherence therefore cannot play any significant role in natural photosynthesis, regardless of their life time. Dynamical coherence as a transient phenomenon must be strictly distinguished from the effect of excited state delocalization (also termed quantum coherence in the literature) which is established by interaction between the pigments a...

Chenu, Aurélia; Mancal, Tomáš

2013-01-01T23:59:59.000Z

324

Superconducting Circuits for Quantum Simulation of Dynamical Gauge Fields  

E-Print Network (OSTI)

We describe a superconducting-circuit lattice design for the implementation and simulation of dynamical lattice gauge theories. We illustrate our proposal by analyzing a one-dimensional U(1) quantum-link model, where superconducting qubits play the role of matter fields on the lattice sites and the gauge fields are represented by two coupled microwave resonators on each link between neighboring sites. A detailed analysis of a minimal experimental protocol for probing the physics related to string breaking effects shows that despite the presence of decoherence in these systems, distinctive phenomena from condensed-matter and high-energy physics can be visualized with state-of-the-art technology in small superconducting-circuit arrays.

D. Marcos; P. Rabl; E. Rico; P. Zoller

2013-06-07T23:59:59.000Z

325

Video of Simulation of the Dynamics of a Wind-Driven Fire in a ...  

Science Conference Proceedings (OSTI)

Simulation of the Dynamics of a Wind-Driven Fire in a Ranch-Style House – Texas. Wind Driven Fire in Home, Texas, 2009. ...

2013-06-28T23:59:59.000Z

326

Web-based simulation 2: performance prediction of dynamic component substitutions  

Science Conference Proceedings (OSTI)

The Web-based Environment for Systems Engineering (wese) is a web-based modeling and simulation environment in which the level of abstraction of a model can be configured statically (prior to simulation) or dynamically (during ...

Dhananjai M. Rao; Philip A. Wilsey

2002-12-01T23:59:59.000Z

327

Dynamic parameterization to simulate DIN export due to gypsy moth defoliation  

Science Conference Proceedings (OSTI)

A module of dynamic parameterization is added into the HSPF watershed software for simulation of dissolved inorganic nitrogen (DIN) export from forest associated with gypsy moth defoliation. It simulates a changing ecosystem following the breakout of ...

Ping Wang; Lewis C. Linker; Keith N. Eshleman

2003-06-01T23:59:59.000Z

328

Consequences of Urban Stability Conditions for Computational Fluid Dynamics Simulations of Urban Dispersion  

Science Conference Proceedings (OSTI)

The validity of omitting stability considerations when simulating transport and dispersion in the urban environment is explored using observations from the Joint Urban 2003 field experiment and computational fluid dynamics simulations of that ...

Julie K. Lundquist; Stevens T. Chan

2007-07-01T23:59:59.000Z

329

Time-domain non-Monte Carlo noise simulation for nonlinear dynamic circuits with arbitrary excitations  

Science Conference Proceedings (OSTI)

A new, time-domain, non-Monte Carlo method for computer simulation of electrical noise in nonlinear dynamic circuits with arbitrary excitations is presented. This time-domain noise simulation ...

Alper Demir; Edward W. Y. Liu; Alberto L. Sangiovanni-Vincentelli

1994-11-01T23:59:59.000Z

330

From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia  

E-Print Network (OSTI)

The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

2003-01-01T23:59:59.000Z

331

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

SciTech Connect

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

332

Fluidic Catalytic Cracking Power Recovery Dynamic Computer Simulation  

E-Print Network (OSTI)

Fluidic Cat Crackers (FCC) using the catalyst regeneration cycle are candidates for more power efficient operation by the use of high temperature dirty gas expanders. In a previous paper, a computer simulation was described for the steady state operation of the primary mechanical components, specifically the axial compressor and hot gas expander. The present work expands upon the steady state model to add the dynamic characteristics of these elements as well as the effects of the controlling process valves. In many applications the expander will develop more power than the axial compressor can absorb. A power absorbing source, specifically an electrical generator, converts the mechanical excess power into electrical energy. A review of the mechanical equipment and the electrical generator operating modes and controls is needed so that the process designer and operator will know how the system will respond if process upsets were to occur. The program code developed can simulate these elements for specific processes and demonstrate the logic control scheme proposed by the process designer. This information will therefore allow the process operator, process designer and mechanical equipment supplier an understanding of the interplay of the system control elements and define specific operating limits.

Samurin, N. A.

1980-01-01T23:59:59.000Z

333

Dynamic fluorescence imaging with molecular agents for cancer detection  

E-Print Network (OSTI)

Non-invasive dynamic optical imaging of small animals requires the development of a novel fluorescence imaging modality. Herein, fluorescence imaging is demonstrated with sub-second camera integration times using agents specifically targeted to disease markers, enabling rapid detection of cancerous regions. The continuous-wave fluorescence imaging acquires data with an intensified or an electronmultiplying charge-coupled device. The work presented in this dissertation (i) assessed dose-dependent uptake using dynamic fluorescence imaging and pharmacokinetic (PK) models, (ii) evaluated disease marker availability in two different xenograft tumors, (iii) compared the impact of autofluorescence in fluorescence imaging of near-infrared (NIR) vs. red light excitable fluorescent contrast agents, (iv) demonstrated dual-wavelength fluorescence imaging of angiogenic vessels and lymphatics associated with a xenograft tumor model, and (v) examined dynamic multi-wavelength, whole-body fluorescence imaging with two different fluorescent contrast agents. PK analysis showed that the uptake of Cy5.5-c(KRGDf) in xenograft tumor regions linearly increased with doses of Cy5.5-c(KRGDf) up to 1.5 nmol/mouse. Above 1.5 nmol/mouse, the uptake did not increase with doses, suggesting receptor saturation. Target to background ratio (TBR) and PK analysis for two different tumor cell lines showed that while Kaposi’s sarcoma (KS1767) exhibited early and rapid uptake of Cy5.5-c(KRGDf), human melanoma tumors (M21) had non-significant TBR differences and early uptake rates similar to the contralateral normal tissue regions. The differences may be due to different compartment location of the target. A comparison of fluorescence imaging with NIR vs. red light excitable fluorescent dyes demonstrates that NIR dyes are associated with less background signal, enabling rapid tumor detection. In contrast, animals injected with red light excitable fluorescent dyes showed high autofluorescence. Dual-wavelength fluorescence images were acquired using a targeted 111In- DTPA-K(IRDye800)-c(KRGDf) to selectively detect tumor angiogenesis and an untargeted Cy5.5 to image lymphatics. After acquiring the experimental data, fluorescence image-guided surgery was performed. Dynamic, multi-wavelength fluorescence imaging was accomplished using a liquid crystal tunable filter (LCTF). Excitation light was used for reflectance images with a LCTF transmitting a shorter wavelength than the peak in the excitation light spectrum. Therefore, images can be dynamically acquired alternating frame by frame between emission and excitation light, which should enable image-guided surgery.

Kwon, Sun Kuk

2006-12-01T23:59:59.000Z

334

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

E-Print Network (OSTI)

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by the dynamic reorganization of inter- and intra- molecular nuclear configuration modeled by a quantized nuclear degree of freedom [Cina et. al, J. Chem Phys. {118}, 46 (2003)]. The dynamics of the electronic population and nuclear coherence is analyzed by solving the chain of coupled differential equations for %mean coordinate, population inversion, electron-vibrational correlation, etc. [Prezhdo, Pereverzev, J. Chem. Phys. {113} 6557 (2000)]. Intriguing results are obtained in the approximation of a small change of the nuclear equilibrium upon photoexcitation. In the limiting case of resonance between the electronic energy gap and the frequency of the nuclear mode these results are justified by comparison to the exactly solvable Jaynes-Cummings model. It is found that the photoinduced processes in the model dimer are arranged according to their time scales: (i) fast scale of nuclear motion, (ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electron-nuclear correlation, (iii) slow scale of electronic population approach to the quasi-equilibrium distribution, decay of electron-nuclear correlation, and decrease of the amplitude of mean coordinate oscillation. The latter processes are accompanied by a noticeable growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. The demonstrated quantum relaxation features of the photoinduced vibronic dynamics in molecular dimers are obtained by a simple method, applicable to systems with many degrees of freedom.

Dmitri S. Kilin; Yuri V. Pereversev; Oleg V. Prezhdo

2004-03-13T23:59:59.000Z

335

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

Recanati, Catherine

336

Dynamic simulation model for non-supplementary firing triple-pressure heat recovery steam generator  

Science Conference Proceedings (OSTI)

By using the modular modeling method, a real-time dynamic simulation model for the non-supplementary tri-pressure reheat Heat Recovery Steam Generator (HRSG) is developed. On the basis of mass and energy conservation law, the paper discusses the model ... Keywords: HRSG, dynamic model, modular modelling, simulation

Ning Cui; Bing-Shu Wang; Xiang-Yang Gong; Jian-Qiang Gao

2007-10-01T23:59:59.000Z

337

Exploring the free-energy landscapes of biological systems with steered molecular dynamics  

E-Print Network (OSTI)

1 Exploring the free-energy landscapes of biological systems with steered molecular dynamics fluctuation-dissipation-theorem (BD -FDT) to accurately compute the free-energy profiles for several compute the free-energy profiles for all the afore-listed systems that represent various important aspects

Chen, Liao Y.

338

Molecular Dynamics Study of Phase Change of Water inside a Single-Walled Carbon Nanotube  

E-Print Network (OSTI)

The phase change of liquid water to ice crystal inside a single-walled carbon nanotube (SWNT) was studiedMolecular Dynamics Study of Phase Change of Water inside a Single-Walled Carbon Nanotube Shigeo phase change for various cooling rates in a SWNT with various chiralities were examined. With certain

Maruyama, Shigeo

339

Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids  

E-Print Network (OSTI)

Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids for calculating the absolute entropy, S, and free energy, F, by analyzing Boltzmann samples obtained by Monte. In this paper we remove the excluded volume EV restriction, replacing it by a "free volume" FV approach

Meirovitch, Hagai

340

Cocoa Butter and Related CompoundsChapter 5 Molecular Composition Dynamics and Structure of Cocoa Butter  

Science Conference Proceedings (OSTI)

Cocoa Butter and Related Compounds Chapter 5 Molecular Composition Dynamics and Structure of Cocoa Butter Food Science Health Nutrition eChapters Food Science & Technology Health - Nutrition - Biochemistry 84F5F2836D251770632F77CC72BA1E7

Note: This page contains sample records for the topic "molecular dynamics simulation" 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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341

Modelling transient heat conduction in solids at multiple length and time scales: A coupled non-equilibrium molecular dynamics/continuum approach  

SciTech Connect

A method for controlling the thermal boundary conditions of non-equilibrium molecular dynamics simulations is presented. The method is simple to implement into a conventional molecular dynamics code and independent of the atomistic model employed. It works by regulating the temperature in a thermostatted boundary region by feedback control to achieve the desired temperature at the edge of an inner region where the true atomistic dynamics are retained. This is necessary to avoid intrinsic boundary effects in non-equilibrium molecular dynamics simulations. Three thermostats are investigated: the global deterministic Nose-Hoover thermostat and two local stochastic thermostats, Langevin and stadium damping. The latter thermostat is introduced to avoid the adverse reflection of phonons that occurs at an abrupt interface. The method is then extended to allow atomistic/continuum models to be thermally coupled concurrently for the analysis of large steady state and transient heat conduction problems. The effectiveness of the algorithm is demonstrated for the example of heat flow down a three-dimensional atomistic rod of uniform cross-section subjected to a variety of boundary conditions.

Jolley, Kenny [Department of Engineering, University of Leicester, University Road, Leicester LE1 7RH (United Kingdom); Gill, Simon P.A. [Department of Engineering, University of Leicester, University Road, Leicester LE1 7RH (United Kingdom)], E-mail: spg3@le.ac.uk

2009-10-20T23:59:59.000Z

342

Crystal-melt interfacial Properties of HCP Metals by Molecular ...  

Science Conference Proceedings (OSTI)

Abstract Scope, Crystal-melt interfacial properties were studied by molecular dynamics simulations using different MEAM and EAM interatomic potentials for Mg, ...

343

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

SciTech Connect

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

344

Dynamic simulation of dual-speed wind turbine generation  

SciTech Connect

Induction generators have been used since the early development of utility-scale wind turbine generation. An induction generator is the generator of choice because of its ruggedness, and low cost. With an induction generator, the operating speed of the wind turbine is limited to a narrow range (almost constant speed). Dual- speed operation can be accomplished by using an induction generator with two different sets of winding configurations or by using two induction generators with two different rated speeds. With single- speed operation, the wind turbine operates at different power coefficients (Cp) as the wind speed varies. The operation at maximum Cp can occur only at a single wind speed. However, if the wind speed varies across a wider range, the operating Cp will vary significantly. Dual-speed operation has the advantage of enabling the wind turbine to operate at near maximum Cp over a wider range of wind-speeds. Thus, annual energy production can be increased. The dual-speed mode may generate less energy than a variable-speed mode; nevertheless, it offers an alternative to capture more energy than single-speed operation. In this paper, dual-speed operation of a wind turbine will be investigated. One type of control algorithm for dual- speed operation is proposed. Results from a dynamic simulation will be presented to show how the control algorithm works and how power, current and torque of the system vary as the wind turbine is exposed to varying wind speeds.

Muljadi, E.; Butterfield, C.P.

1996-10-01T23:59:59.000Z

345

Dynamic simulation solves process control problem in Oman  

Science Conference Proceedings (OSTI)

A dynamic simulation study solved the process control problems for a Saih Rawl, Oman, gas compressor station operated by Petroleum Development of Oman (PDO). PDO encountered persistent compressor failure that caused frequent facility shutdowns, oil production deferment, and gas flaring. It commissioned MSE (Consultants) Ltd., U.K., to find a solution for the problem. Saih Rawl, about 40 km from Qarn Alam, produces oil and associated gas from a large number of low and high-pressure wells. Oil and gas are separated in three separators. The oil is pumped to Qarn Alam for treatment and export. Associated gas is compressed in two parallel trains. Train K-1115 is a 350,000 standard cu m/day, four-stage reciprocating compressor driven by a fixed-speed electric motor. Train K-1120 is a 1 million standard cu m/day, four-stage reciprocating compressor driven by a fixed-speed electric motor. Train K-1120 is a 1 million standard cu m/day, four-stage centrifugal compressor driven by a variable-speed motor. The paper describes tripping and surging problems with the gas compressor and the control simplifications that solved the problem.

NONE

1998-11-16T23:59:59.000Z

346

Structure and energetics of solvated ferrous and ferric ions: Car-Parrinello molecular dynamics in the DFT+U formalism  

E-Print Network (OSTI)

We implemented a rotationally-invariant Hubbard U extension to density-functional theory in the Car-Parrinello molecular dynamics framework, with the goal of bringing the accuracy of the DFT+U approach to finite-temperature simulations, especially for liquids or solids containing transition-metal ions. First, we studied the effects on the Hubbard U on the static equilibrium structure of the hexa-aqua ferrous and ferric ions, and the inner-sphere reorganization energy for the electron-transfer reaction between aqueous ferrous and ferric ions. It is found that the reorganization energy is increased, mostly as a result of the Fe-O distance elongation in the hexa-aqua ferrous ion. Second, we performed a first-principles molecular dynamics study of the solvation structure of the two aqueous ferrous and ferric ions. The Hubbard term is found to change the Fe-O radial distribution function for the ferrous ion, while having a negligible effect on the aqueous ferric ion. Moreover, the frequencies of vibrations between Fe and oxygen atoms in the first-solvation shell are shown to be unaffected by the Hubbard corrections for both ferrous and ferric ions.

P. H. -L. Sit; Matteo Cococcioni; Nicola Marzari

2007-01-12T23:59:59.000Z

347

A parallel Lowe-Andersen thermostat for soft matter simulations  

Science Conference Proceedings (OSTI)

Simulating colloidal dynamics, with solvent mediated hydrodynamics interactions, is a challenging task. The traditional approach is to use Dissipative Particle Dynamics thermostat and soft interactions. However this can yield only low Schmidt number ... Keywords: MPI programing, molecular dynamics, thermostats

K. R. Prathyusha; P. B. Sunil Kumar

2012-05-01T23:59:59.000Z

348

Molecular Approaches to Understanding C & N Dynamics in MArine Sediments  

Science Conference Proceedings (OSTI)

Continental margin sediments constitute only about 10% of the total sediment surface area in the world’s oceans, nevertheless they are the dominant sites of nitrogen (N) cycling. Recent studies suggest that the oceanic nitrogen budget is unbalanced, primarily due to a higher nitrogen removal rate in contrast to the fixation rate, and it has been suggested that denitrification activity contributes significantly to this imbalance. Although denitrification in marine environments has been studied intensively at the process level, little is known about the species abundance, composition, distribution, and functional differences of the denitrifying population. Understanding the diversity of microbial populations in marine environments, their responses to various environmental factors such as NO3-, and how this impact the rate of denitrification is critical to predict global N dynamics. Environmental Microbiology has the prompt to study the influence of each microbial population on a biogeochemical process within a given ecosystem. Culture-dependent and –independent techniques using nucleic acid probes can access the identity and activity of cultured and uncultured microorganisms. Nucleic acid probes can target distintict genes which set phylogenetic relationships, such as rDNA 16S, DNA gyrase (gyrB) and RNA polymerase sigma 70 factor (rpoD). In the other hand, the genetic capabilities and their expression could be tracked using probes that target several functional genes, such as nirS, nirK, nosZ, and nifH, which are genes involved in denitrification. Selective detection of cells actively expressing functional genes within a community using In Situ Reverse Transcription-PCR (ISRT-PCR) could become a powerful culture-independent technique in microbial ecology. Here we describe an approach to study the expression of nirS genes in denitrifying bacteria. Pure cultures of Pseudomonas stutzeri and Paracoccus denitrificans, as well as co-cultures with non-denitrifying populations were used to optimize the ISRT-PCR protocol. Cells grown on nitrate broth were harvested and fixed at both logarithmic (24-48 h) and stationary phase (7 days). Fixed and RNA protectedTMcc cells were spotted on microscope slides to optimize cell wall permeabilization conditions with lyzozyme and proteinase K. Subsequently, ISRT-PCR was performed with NirS 1F and NirS 6R primers using the QIAGEN® OneStep RT-PCR Kit. Amplification products within the cell were detected by Fluorescent In Situ Hybridization (FISH) at 40ºC overnight using a Cy3 labeled internal probe, specifically designed to detect the nirS gene. After hybridization, the cells were counterstained with DAPI and examined by confocal fluorescence microscopy. P. stutzeri cells treated with RNase and Pseudomonas G179 (a nirK denitrifying strain) were used as negative controls. Optimal cell permeabilization was achieved using 1 mg ml-1 lyzozyme for 30 min and 2 µg ml-1 Proteinase K. RNase treated cells did not fluoresce after FISH, but were detectable by DAPI. Only nirS-type denitrifying cells in log phase (80-95% of total direct cell counts) were detected by this approach while fewer cells (5-10%) were detectable after 7 days in stationary phase. Co-cultures of P. denitrificans with a non-denitrifying isolate resulted in selective identification of target cells, thus supporting the potential use of this approach for gene expression analysis at the community level.

Arturo Massol; James Tiedje; Jizhong Zhou; Allan Devol

2007-05-16T23:59:59.000Z

349

Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase  

SciTech Connect

The confinement of the metalloenzyme organophosphorous hydrolase in functionalized mesoporous silica (FMS) enhances the stability and increases catalytic specific activity by 200% compared to the enzyme in solution. The mechanism by which these processes take place is not well understood. We have developed two coarse-grain models of confinement to provide insights into how the nanocage environment steers enzyme conformational dynamics towards enhanced stability and enzymatic activity. The structural dynamics of organophosphorous hydrolase under the two confinement models are very distinct from each other. Comparisons of the present simulations show that only one model leads to an accurate depiction of the internal dynamics of the enzyme.

Gomes, Diego Enry B.; Lins, Roberto D.; Pascutti, Pedro G.; Straatsma, TP; Soares, Thereza A.

2008-09-28T23:59:59.000Z

350

Dynamic component substitution in web-based simulation  

Science Conference Proceedings (OSTI)

Recent breakthroughs in communication and software engineering has resulted in significant growth of web-based computing. Web-based techniques have been employed for modeling, simulation, and analysis of systems. The models for simulation are usually ...

Dhananjai Madhava Rao; Philip A. Wilsey

2000-12-01T23:59:59.000Z

351

Numerical simulations of granular dynamics II. Particle dynamics in a shaken granular material  

E-Print Network (OSTI)

Surfaces of planets and small bodies of our Solar System are often covered by a layer of granular material that can range from a fine regolith to a gravel-like structure of varying depths. Therefore, the dynamics of granular materials are involved in many events occurring during planetary and small-body evolution thus contributing to their geological properties. We demonstrate that the new adaptation of the parallel N-body hard-sphere code pkdgrav has the capability to model accurately the key features of the collective motion of bidisperse granular materials in a dense regime as a result of shaking. As a stringent test of the numerical code we investigate the complex collective ordering and motion of granular material by direct comparison with laboratory experiments. We demonstrate that, as experimentally observed, the scale of the collective motion increases with increasing small-particle additive concentration. We then extend our investigations to assess how self-gravity and external gravity affect collective motion. In our reduced-gravity simulations both the gravitational conditions and the frequency of the vibrations roughly match the conditions on asteroids subjected to seismic shaking, though real regolith is likely to be much more heterogeneous and less ordered than in our idealised simulations. We also show that collective motion can occur in a granular material under a wide range of inter-particle gravity conditions and in the absence of an external gravitational field. These investigations demonstrate the great interest of being able to simulate conditions that are to relevant planetary science yet unreachable by Earth-based laboratory experiments.

Naomi Murdoch; Patrick Michel; Derek C. Richardson; Kerstin Nordstrom; Christian R. Berardi; Simon F. Green; Wolfgang Losert

2013-06-07T23:59:59.000Z

352

Abaqus Simulations of Rock Response to Dynamic Loading  

SciTech Connect

The LANL Geodynamics Team has been applying Abaqus modeling to achieve increasingly complex simulations. Advancements in Abaqus model building and simulation tools allows this progress. We use Lab-developed constitutive models, the fully coupled CEL Abaqus and general contact to simulate response of realistic sites to explosively driven shock.

Steedman, David W. [Los Alamos National Laboratory; Coblentz, David [Los Alamos National Laboratory

2012-08-15T23:59:59.000Z

353

Designing power system simulators for the smart grid: combining controls, communications, and electro-mechanical dynamics  

Science Conference Proceedings (OSTI)

Open source software has a leading role in research on simulation technology for electrical power systems. Research simulators demonstrate new features for which there is nascent but growing demand not yet provided for by commercial simulators. Of particular interest is the inclusion of models of software-intensive and communication-intensive controls in simulations of power system transients. This paper describes two features of the ORNL power system simulator that help it meet this need. First is its use of discrete event simulation for all aspects of the model: control, communication, and electro-mechanical dynamics. Second is an interoperability interface that enables the ORNL power system simulator to be integrated with existing, discrete event simulators of digital communication systems. The paper concludes with a brief discussion of how these aspects of the ORNL power system simulator might be inserted into production-grade simulation tools.

Nutaro, James J [ORNL

2011-01-01T23:59:59.000Z

354

Simulation of Rising Bubbles Dynamics Using the Lattice Boltzmann Method.  

E-Print Network (OSTI)

?? The main purpose of this thesis was to propose and test a new approach that captures the features of single and multiple bubbles dynamics… (more)

Ngachin, Merlin

2011-01-01T23:59:59.000Z

355

A Simulation-based Study of TCP Dynamics  

Science Conference Proceedings (OSTI)

... End Internet Dynamics", Ph.D. Thesis, LBNL-40319, UCB//CSD-97-945, University of California, Berkley. [20] WR Stevens ...

2009-02-03T23:59:59.000Z

356

Liquid-gas phase transition in finite nuclei within Fermionic Molecular Dynamics  

E-Print Network (OSTI)

Within Fermionic Molecular Dynamics (FMD) a quantal nuclear system with only 16 nucleons shows a clearly visible liquid-gas phase transition. The FMD model is an approximation to the many-body problem which describes the system by antisymmetrized many-body states in which each nucleon is occupying a Gaussian shaped time-dependent wave-packet. The statistical ensemble is obtained by time averaging.

H. Feldmeier; J. Schnack

1998-06-02T23:59:59.000Z

357

Qualitative simulation and related approaches for the analysis of dynamic systems  

Science Conference Proceedings (OSTI)

Methods for qualitative simulation allow predictions on the dynamics of a system to be made in the absence of quantitative information, by inferring the range of possible qualitative behaviors compatible with the structure of the system. This article ...

Hidde De Jong

2004-06-01T23:59:59.000Z

358

The Dynamics of an Explosively Developing Cyclone Simulated by a General Circulation Model  

Science Conference Proceedings (OSTI)

The synoptic structure and dynamics of an explosively developing winter extratropical cyclone simulated by NCAR’s CCM2 general circulation model is examined and compared with cyclones that have developed explosively in nature. The primary ...

Karen D. Walthorn; Phillip J. Smith

1998-11-01T23:59:59.000Z

359

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

360

The Effects of Different Climate Input Datasets on Simulated Carbon Dynamics in the Western Arctic  

Science Conference Proceedings (OSTI)

As part of the Western Arctic Linkage Experiment (WALE), simulations of carbon dynamics in the western Arctic (WALE region) were conducted during two recent decades by driving the Terrestrial Ecosystem Model (TEM) with three alternative climate ...

Joy Clein; A. David McGuire; Eugenie S. Euskirchen; Monika Calef

2007-08-01T23:59:59.000Z

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

Simulations of Dynamics and Transport during the September 2002 Antarctic Major Warming  

Science Conference Proceedings (OSTI)

A mechanistic model simulation initialized on 14 September 2002, forced by 100-hPa geopotential heights from Met Office analyses, reproduced the dynamical features of the 2002 Antarctic major warming. The vortex split on 25 September; recovery ...

Gloria L. Manney; Joseph L. Sabutis; Douglas R. Allen; William A. Lahoz; Adam A. Scaife; Cora E. Randall; Steven Pawson; Barbara Naujokat; Richard Swinbank

2005-03-01T23:59:59.000Z

362

Computational Fluid Dynamics (CFD) Simulation of Air Dense ...  

Science Conference Proceedings (OSTI)

In current study, the experimental results of coal beneficiation in a cylindrical bed are used to set up and evaluate the results of a CFD simulation software.

363

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

E-Print Network (OSTI)

will denote this approximation by EWF without the j subscript in the list of abbreviations used in the present in the l-labeled CS calculations EWF-l-CSA The l-labeled CS calculations with all vibrational wave computed using different basis functions. E cm 1 Ref. 7 Present calculationsa EWF-l-CSA EWFj-l-CSA 10 0

Zhao, Tianshou

364

The interplay between inter- and intra-molecular dynamics in a series of alkylcitrates  

Science Conference Proceedings (OSTI)

The inter- and intra-molecular dynamics in a series of glass-forming alkylcitrates is studied by a combination of Broadband Dielectric Spectroscopy (BDS), Pulsed Field Gradient Nuclear Magnetic Resonance (PFG NMR), Fourier-Transform Infrared (FTIR) spectroscopy and Differential Scanning Calorimetry (DSC). Analyzing the temperature dependencies of specific IR absorption bands in terms of their spectral position and the corresponding oscillator strengths enables one to unravel the intramolecular dynamics of specific molecular moieties and to compare them with the (primarily dielectrically) determined intermolecular dynamics. With decreasing temperature, the IR band positions of carbonyls (part of the core units) and H-bonded moieties of citrates show a red shift with a kink at the calorimetric glass transition temperature (Tg) while other moieties, whose dynamics are decoupled from those of the core units, exhibit a blue shift with nominal changes at Tg. The oscillator strength of all units in citrates depicts stronger temperature dependencies above Tg and in some, the ester linkage and H-bonded units show a change of slope at a temperature where structural and faster secondary relaxations merge. By that, a wealth of novel information is obtained proving the fundamental importance of intramolecular mobility in the process of glass formation, beyond coarse-grained descriptions.

Kipnusu, Wycliffe Kiprop [University of Leipzig, Germany; Kossack, Wilhelm [University of Leipzig, Germany; Iacob, Ciprian [University of Leipzig; Zeigermann, Philipp [University of Leipzig, Germany; Jasiurkowska, Malgorzata [University of Leipzig, Germany; Sangoro, Joshua R [ORNL; Valiullin, Rustem [University of Leipzig, Germany; Kremer, Friedrich [University of Leipzig

2013-01-01T23:59:59.000Z

365

Molecular simulation analysis and X-ray absorption measurement of Ca2+, K+, and Cl- ions in solution  

DOE Green Energy (OSTI)

Recent advances in the use of molecular simulations and Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy to understand solvated ions in aqueous solutions are described. We report and discuss the results of the EXAFS spectra, Debye-Waller factors and the related properties governing solvation processes of different ions in water, as well as in different solvents (methanol). Molecular dynamics (MD) trajectories are coupled to electron scattering simulations to generate the EXAFS spectra, which are found to be in very good agreement with the corresponding experimental measurements. From these spectra, both the ion-oxygen and the ion-hydrogen distances for the first hydration shell are predicted to be within 0.1-0.2 Å. The ionic species studied range from monovalent to divalent, positive and negative: K+, Ca2+ and Cl-. This work demonstrates that the combination of MD-EXAFS and the corresponding experiment measurement provides a powerful tool in the analysis of the solvation structure of aqueous ionic solutions. We also investigate the value of electronic structure analysis of small aqueous clusters as a benchmark to the empirical potentials. In a novel computational approach, we compute the Debye-Waller factors combining a harmonic analysis of data obtained from electronic structure calculations on finite ionwater clusters, and we present a direct comparison with results from a harmonic classical statistical mechanical analysis of an empirical potential. Work was supported by the Office of Science, Office of Basic Energy Sciences, Chemical Sciences Division of the U.S. Department of Energy (DOE). The Pacific Northwest National Laboratory is operated by Battelle for DOE.

Dang, Liem X.; Schenter, Gregory K.; Glezakou, Vanda A.; Fulton, John L.

2006-11-30T23:59:59.000Z

366

Simulation of the heat exchangers dynamics in MATLAB&simulink  

Science Conference Proceedings (OSTI)

Heat exchangers that transfer energy from flue gas to steam are important units of thermal power stations. Their inertias are often decisive for the design of the steam temperature control system. In this paper, the analysis and the simulation of the ... Keywords: MATLAB&simulink, S-functions, finite difference method, heat exchangers, partial differential equations, real-time, simulation, superheaters

Pavel Nevriva; Stepan Ozana; Ladislav Vilimec

2009-10-01T23:59:59.000Z

367

Cellulose Simulations Demystify High-Temperature Behavior (Fact...  

NLE Websites -- All DOE Office Websites (Extended Search)

easier to break down, which could lead to more efficient processing of cellulose into biofuel. Using molecular dynamics simulation, scientists at the National Renewable Energy...

368

The dynamic simulation of organic farming development scenarios - A case study in Slovenia  

Science Conference Proceedings (OSTI)

In this paper a system dynamics model for organic farming development to support government decision making is presented. The system incorporates relevant variables which affect organic farming development. The user seeks answers to strategic questions ... Keywords: Model, Organic farming, Simulation, System dynamics

Rtomir Rozman, Karmen Paek, Miroljub Kljaji?, Martina Bavec, Jernej Turk, Franc Bavec, Davorin Kofja?, Andrej ŠKraba

2013-08-01T23:59:59.000Z

369

Using system dynamics for simulation and optimization of one coal industry system under fuzzy environment  

Science Conference Proceedings (OSTI)

In this paper, we have developed a model that integrates system dynamics with fuzzy multiple objective programming (SD-FMOP). This model can be used to study the complex interactions in a industry system. In the process of confirming sensitive parameters ... Keywords: Coal industry planning, Fuzzy set theory, Multiple objective programming, Simulation, System dynamics

Jiuping Xu; Xiaofei Li

2011-09-01T23:59:59.000Z

370

Dynamical Subgrid-Scale Parameterizations from Direct Numerical Simulations  

Science Conference Proceedings (OSTI)

Dynamical subgrid-scale parameterizations of stochastic backscatter, eddy drain viscosity, and net eddy viscosity have been formulated and calculated for two-dimensional turbulent flows on the sphere based on the statistics of direct numerical ...

Jorgen S. Frederiksen; Steven M. Kepert

2006-11-01T23:59:59.000Z

371

ADAPT: abstraction hierarchies to better simulate teamwork under dynamics  

Science Conference Proceedings (OSTI)

In this paper we present a lightweight teamwork implementation by using abstraction hierarchies. The basis of this implementation is ADAPT, which supports Autonomous Dynamic Agent Planning for Teamwork. ADAPT's novelty ...

Meirav Hadad; Avi Rosenfeld

2011-05-01T23:59:59.000Z

372

AMIP Simulation with the CAM4 Spectral Element Dynamical Core  

Science Conference Proceedings (OSTI)

The authors evaluate the climate produced by the Community Climate System Model, version 4, running with the new spectral element atmospheric dynamical core option. The spectral element method is configured to use a cubed-sphere grid, providing ...

K. J. Evans; P. H. Lauritzen; S. K. Mishra; R. B. Neale; M. A. Taylor; J. J. Tribbia

2013-02-01T23:59:59.000Z

373

Dynamic Simulation of Lightning Attachment to Earthed Overhead Transmission Line Structures  

Science Conference Proceedings (OSTI)

In this paper a novel method is presented to investigate lightning stroke attachment to earthed overhead transmission line structures. This method is based on the dynamic simulation of lightning downward leader movement toward the ground in three dimensions. ... Keywords: charge simulation method, downward leader, lightning, transmission line, upward leader

Mohammad Reza Bank Tavakoli; Behrooz Vahidi

2010-07-01T23:59:59.000Z

374

A simulation-and-regression approach for stochastic dynamic programs with endogenous state variables  

Science Conference Proceedings (OSTI)

We investigate the optimum control of a stochastic system, in the presence of both exogenous (control-independent) stochastic state variables and endogenous (control-dependent) state variables. Our solution approach relies on simulations and regressions ... Keywords: Approximate dynamic programming, Hydropower management, Least-squares Monte Carlo, Simulation and regression, Stochastic control

Michel Denault, Jean-Guy Simonato, Lars Stentoft

2013-11-01T23:59:59.000Z

375

Multilevel Task Partition Algorithm for Parallel Simulation of Power System Dynamics  

Science Conference Proceedings (OSTI)

Nowadays task partition for parallel computing is becoming more and more important. Particular in power system dynamic simulation, it is critical to design an efficient partition algorithm to reduce the communication and balance the computation load ... Keywords: graph partition, parallel simulation, power system, task partition

Wei Xue; Shanxiang Qi

2007-05-01T23:59:59.000Z

376

Time-stepping numerical simulation of switched circuits within the nonsmooth dynamical systems approach  

Science Conference Proceedings (OSTI)

The numerical integration of switching circuits is known to be a tough issue when the number of switches is large, or when sliding modes exist. Then, classical analog simulators may behave poorly, or even fail. In this paper, it is shown on two examples ... Keywords: analog simulation, backward Euler algorithm, complementarity dynamical systems, complementarity problems, multivalued systems, power converters, switching circuits, unilateral state constraints

Vincent Acary; Olivier Bonnefon; Bernard Brogliato

2010-07-01T23:59:59.000Z

377

Dynamical Influences of Anvil Shading on Simulated Supercell Thunderstorms  

Science Conference Proceedings (OSTI)

Numerical simulations of supercell thunderstorms including parameterized radiative transfer and surface fluxes are performed using the Advanced Regional Prediction System (ARPS) model to investigate how low-level air temperature deficits within ...

Jeffrey Frame; Paul Markowski

2013-08-01T23:59:59.000Z

378

Dynamic Downscaling of Seasonal Simulations over South America  

Science Conference Proceedings (OSTI)

In this paper multiple atmospheric global circulation model (AGCM) integrations at T42 spectral truncation and prescribed sea surface temperature were used to drive regional spectral model (RSM) simulations at 80-km resolution for the austral ...

Vasubandhu Misra; Paul A. Dirmeyer; Ben P. Kirtman

2003-01-01T23:59:59.000Z

379

Solar Pilot Plant, Phase I. Preliminary design report. Volume II, Book 3. Dynamic simulation model and computer program descriptions. CDRL item 2. [SPP dynamics simulation program  

DOE Green Energy (OSTI)

The mathematical models and computer program comprising the SPP Dynamic Simulation are described. The SPP Dynamic Simulation is a computerized model representing the time-varying performance characteristics of the SPP. The model incorporates all the principal components of the pilot plant. Time-dependent direct normal solar insulation, as corrupted by simulated cloud passages, is transformed into absorbed radiant power by actions of the heliostat field and enclosed receiver cavity. The absorbed power then drives the steam generator model to produce superheated steam for the turbine and/or thermal storage subsystems. The thermal storage subsystem can, in turn, also produce steam for the turbine. The turbine using the steam flow energy produces the mechanical shaft power necessary for the generator to convert it to electrical power. This electrical power is subsequently transmitted to a transmission grid system. Exhaust steam from the turbine is condensed, reheated, deaerated, and pressurized by pumps for return as feedwater to the thermal storage and/or steam generator. A master control/instrumentation system is utilized to coordinate the various plant operations. The master controller reacts to plant operator demands and control settings to effect the desired output response. The SPP Dynamic Simulation Computer program is written in FORTRAN language. Various input options (e.g., insolation values, load demands, initial pressures/temperatures/flows) are permitted. Plant performance may be monitored via computer printout or computer generated plots. The remainder of this document describes the detailed pilot plant dynamic model, the basis for this simulation, and the utilization of this simulation to obtain analytical plant performance results.

None

1977-05-01T23:59:59.000Z

380

Use of computer simulation and molecular modeling techniques for the design of molecularly organized urea-urethane prototypes for thermal insulation  

Science Conference Proceedings (OSTI)

Polyurethane foams having densities as low as 120 kg/m3 are currently being used as thermal insulators. The closed-cell foam structure encompassing the air molecules prevents the thermal conductivity and enhances the efficiency of the used ... Keywords: Connolly surface, diffusion, free volume, molecular dynamics, polyurea-urethane foams, thermal insulators

Tarek M. Madkour

2008-12-01T23:59:59.000Z

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

AMIP Simulation with the CAM4 Spectral Element Dynamical Core  

SciTech Connect

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

382

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

Science Conference Proceedings (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

383

Adaptive Construction Modelling Within Whole Building Dynamic Simulation  

E-Print Network (OSTI)

............................ vii List of Symbols .......................... ix Chapter 1: Introduction ....................... 1 1.1 The need for building energy simulation ............... 1 1.2 The evolution of building energy simulation tools ............ 2 1.3 The need for accurate building fabric modelling ............ 4 1.4 Objective and outline of the present work ............... 5 Chapter 2: Review of Heat and Moisture Transport within Building Materials ...... 8 2.1 Building energy simulation ................... 8 2.1.1 Heat conduction .................... 8 2.1.2 Mass diffusion .................... 16 2.2 Adaptive gridding ...................... 18 2.3 Thermophysical properties ................... 23 2.4 Combined heat and moisture transport ................ 27 2.4.1 Moisture transport in porous building materials .......... 29 2.4.2 Differential equations for combined heat and moisture transport ..... 33 Chapter 3: Adaptive Building Fabric Gridding ................ 37 3.1 Math...

Abdullatif Nakhi Degree; Abdullatif E. Nakhi; Wife Masoumah

1995-01-01T23:59:59.000Z

384

System dynamics model for simulation of the software inspection process  

Science Conference Proceedings (OSTI)

Repairing a defect in the late phases of software development can be a hundred times more expensive than finding and fixing it during the requirements and design phase. Software inspection is a technique that may be used to aid in the identification ... Keywords: defect detection, software inspection, system dynamics

Jailton Jr. De Sousa Coelho, José Luis Braga, Bernardo Giori Ambrósio

2013-08-01T23:59:59.000Z

385

Numerical aspects in the dynamic simulation of geometrically exact rods  

Science Conference Proceedings (OSTI)

Classical geometrically exact Kirchhoff and Cosserat models are used to study the nonlinear deformation of rods. Extension, bending and torsion of the rod may be represented by the Kirchhoff model. The Cosserat model additionally takes into account shearing ... Keywords: Deformable bodies, Geometrically exact rods, Kirchhoff and Cosserat rods, Method of lines, Multibody dynamics, Partial differential algebraic equations, Time integration

Holger Lang; Martin Arnold

2012-10-01T23:59:59.000Z

386

Simulation of Dryline Misovortex Dynamics and Cumulus Formation  

Science Conference Proceedings (OSTI)

A dryline and misocyclones have been simulated in a cloud-resolving model by applying specified initial and time-dependent lateral boundary conditions obtained from analyses of the 22 May 2002 International H2O Project (IHOP_2002) dataset. The ...

Michael S. Buban; Conrad L. Ziegler; Edward R. Mansell; Yvette P. Richardson

2012-11-01T23:59:59.000Z

387

System dynamics simulation of the expansion of the Panama Canal  

Science Conference Proceedings (OSTI)

The expansion of the Panama Canal could be the largest project attempted by the Republic of Panama in its 100 years of existence. The objective of this simulation study is to use the Canal Expansion project to develop and demonstrate how more precise ...

Humberto R. Alvarez A.; Dario Solis; Arnoldo R. Cano S.; Serge Sala-Diakanda

2006-12-01T23:59:59.000Z

388

Nuclear liquid-gas phase transition studied with antisymmetrized molecular dynamics  

E-Print Network (OSTI)

The nuclear liquid-gas phase transition of the system in ideal thermal equilibrium is studied with antisymmetrized molecular dynamics. The time evolution of a many-nucleon system confined in a container is solved for a long time to get a microcanonical ensemble of a given energy and volume. The temperature and the pressure are extracted from this ensemble and the caloric curves are constructed. The present work is the first time that a microscopic dynamical model which describes nuclear multifragmentation reactions well is directly applied to get the nuclear caloric curve. The obtained constant pressure caloric curves clearly show the characteristic feature of the liquid-gas phase transition, namely negative heat capacity (backbending), which is expected for the phase transition in finite systems.

Takuya Furuta; Akira Ono

2003-05-19T23:59:59.000Z

389

Molecular dynamic studies on anisotropic explosion of laser irradiated Xe cluster  

Science Conference Proceedings (OSTI)

A three dimensional molecular dynamic model is used to investigate the dynamics of Xe clusters of various radii irradiated by laser of moderate intensities ({approx}10{sup 14}-10{sup 16}W/cm{sup 2}). The FWHM pulse duration of the laser is varied from few laser cycles to hundreds of femtosecond. For cluster of radius 50 A irradiated by a laser of 170 fs pulse duration, it is observed that ion yield is more along the direction of laser polarization than perpendicular to it. This trend reverses (more ions are emitted along the direction perpendicular to laser polarization than parallel to it) when laser pulses of few cycles are used. This reversal of anisotropy is explained on the basis of spatial shielding of ions due to the oscillating inner electron cloud along direction of laser electric field. The nature of anisotropy remains same with variations in laser intensity and cluster size.

Mishra, Gaurav; Gupta, N. K. [Theoretical Physics Division, Bhabha Atomic Research Centre, Mumabi-400085 (India)

2012-09-15T23:59:59.000Z

390

Stochastic Simulation of Nonadiabatic Dynamics at Long Time  

E-Print Network (OSTI)

Using a generalized energy-conserving transition probability, it is shown how nonadiabatic calculations, within the Wigner-Heisenberg representation of quantum mechanics, can be reliably extended to far longer times than those allowed by a primitive sampling scheme. Tackling the spin-boson model as a paradigmatic example, substantial numerical evidence is provided that effective integration of the dynamics can be achieved for a wide range of temperatures and friction.

Uken, Daniel A; Petruccione, Francesco

2010-01-01T23:59:59.000Z

391

Stochastic Simulation of Nonadiabatic Dynamics at Long Time  

E-Print Network (OSTI)

Using a generalized energy-conserving transition probability, it is shown how nonadiabatic calculations, within the Wigner-Heisenberg representation of quantum mechanics, can be reliably extended to far longer times than those allowed by a primitive sampling scheme. Tackling the spin-boson model as a paradigmatic example, substantial numerical evidence is provided that effective integration of the dynamics can be achieved for a wide range of temperatures and friction.

Daniel A. Uken; Alessandro Sergi; Francesco Petruccione

2010-03-16T23:59:59.000Z

392

Darlington tritium removal facility and station upgrading plant dynamic process simulation  

SciTech Connect

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

393

The optimizing-simulator: merging simulation and optimization using approximate dynamic programming  

Science Conference Proceedings (OSTI)

There is a wide range of simulation problems that involve making decisions during the simulation, where we would like to make the best decisions possible, taking into account not only what we know when we make the decision, but also the impact of the ...

Warren B. Powell

2007-12-01T23:59:59.000Z

394

Real-time dynamic simulator for the Topaz II reactor power system  

SciTech Connect

A dynamic simulator of the TOPAZ II reactor system has been developed for the Nuclear Electric Propulsion Space Test Program. The simulator is a self-contained IBM-PC compatible based system that executes at a speed faster than real-time. The simulator combines first-principle modeling and empirical correlations in its algorithm to attain the modeling accuracy and computational through-put that are required for real-time execution. The overall execution time of the simulator for each time step is 15 ms when no data is written to the disk, and 18 ms when nine double precision data points are written to the disk once in every time step. The simulation program has been tested and it is able to handle a step decrease of $8 worth of reactivity. It also provides simulation of fuel, emitter, collector, stainless steel, and ZrH moderator failures. Presented in this paper are the models used in the calculations, a sample simulation session, and a discussion of the performance and limitations of the simulator. The simulator has been found to provide realistic real-time dynamic response of the TOPAZ II reactor system under both normal and causality conditions.

Kwok, K.S.

1994-10-01T23:59:59.000Z

395

11/11/2002 1AVS 49th Int'l Symp. MS-MoA7 (Oct. 29, 2002) -Cho Dynamic Simulation and Optimization  

E-Print Network (OSTI)

'l Symp. MS-MoA7 (Oct. 29, 2002) - Cho Scope & Strategy Multilevel modeling & simulation incorporating dynamics &Multilevel modeling & simulation incorporating dynamics & stochasticsstochastics ESH fluctuations Incorporate capability in models for dynamics & stochastics Process & tool Fundamental science Si

Rubloff, Gary W.

396

Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh  

Science Conference Proceedings (OSTI)

The use of accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. In this paper, we present a continuation of previous work implementing algorithms for using accelerators into the LAMMPS molecular dynamics software for distributed memory parallel hybrid machines. In our previous work, we focused on acceleration for short-range models with an approach intended to harness the processing power of both the accelerator and (multi-core) CPUs. To augment the existing implementations, we present an efficient implementation of long-range electrostatic force calculation for molecular dynamics. Specifically, we present an implementation of the particle-particle particle-mesh method based on the work by Harvey and De Fabritiis. We present benchmark results on the Keeneland InfiniBand GPU cluster. We provide a performance comparison of the same kernels compiled with both CUDA and OpenCL. We discuss limitations to parallel efficiency and future directions for improving performance on hybrid or heterogeneous computers.

Brown, W Michael [ORNL; Kohlmeyer, Axel [Temple University; Plimpton, Steven J [ORNL; Tharrington, Arnold N [ORNL

2012-01-01T23:59:59.000Z

397

Design studies for the transmission simulator method of experimental dynamic substructuring.  

SciTech Connect

In recent years, a successful method for generating experimental dynamic substructures has been developed using an instrumented fixture, the transmission simulator. The transmission simulator method solves many of the problems associated with experimental substructuring. These solutions effectively address: (1) rotation and moment estimation at connection points; (2) providing substructure Ritz vectors that adequately span the connection motion space; and (3) adequately addressing multiple and continuous attachment locations. However, the transmission simulator method may fail if the transmission simulator is poorly designed. Four areas of the design addressed here are: (1) designating response sensor locations; (2) designating force input locations; (3) physical design of the transmission simulator; and (4) modal test design. In addition to the transmission simulator design investigations, a review of the theory with an example problem is presented.

Mayes, Randall Lee; Arviso, Michael

2010-05-01T23:59:59.000Z

398

Low Wind Speed Technology Phase II: Offshore Floating Wind Turbine Concepts: Fully Coupled Dynamic Response Simulations; Massachusetts Institute of Technology  

SciTech Connect

This fact sheet describes a subcontract with Massachusetts Institute of Technology to study dynamic response simulations to evaluate floating platform concepts for offshore wind turbines.

2006-03-01T23:59:59.000Z

399

Langevin dynamics simulations of biomolecules on graphics processors  

E-Print Network (OSTI)

Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging even for distributed computing systems. Graphics Processing Units (GPUs) are emerging as an alternative programming platform to the more traditional CPUs as they provide high raw computational power that can be utilized in a wide range of scientific applications. Using a coarse-grained Self Organized Polymer (SOP) model, we have developed and tested the GPU-based implementation of Langevin simulations for proteins (SOP-GPU program). Simultaneous calculation of forces for all particles is implemented using either the particle based or the interacting pair based parallelization, which leads to a ~30-fold acceleration compared to an optimized CPU version of the program. We assess the computational performance of an end-to-end application of the SOP-GPU program, where all steps of the algorithm are running on the GPU, by profiling the associated simulation time and memory usage for a number of small proteins, long protein fibers, and large-size protein assemblies. The SOP-GPU package can now be used in the theoretical exploration of the mechanical properties of large-size protein systems to generate the force-extension and force-indentation profiles under the experimental conditions of force application, and to relate the results of single-molecule experiments in vitro and in silico.

A. Zhmurov; R. I. Dima; Y. Kholodov; V. Barsegov

2010-03-04T23:59:59.000Z

400

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming  

Science Conference Proceedings (OSTI)

The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.

Levine, Benjamin G., E-mail: ben.levine@temple.ed [Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, PA (United States); Stone, John E., E-mail: johns@ks.uiuc.ed [Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL (United States); Kohlmeyer, Axel, E-mail: akohlmey@temple.ed [Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, PA (United States)

2011-05-01T23:59:59.000Z

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

Simulation studies of ion dynamic effects on dense plasma line shapes  

DOE Green Energy (OSTI)

Computer simulations have been widely used in studying dense plasma properties including the local field properties important in spectral line broadening calculations. We will review here a more recent use of simulation, possibly less familiar to this audience, where the time dependent ionic microfield generated by computer simulation of a plasma is used directly as a time dependent external potential for the evolution of the electronic structure of an ion. This permits calculation of the dipole correlation function and thus line shapes with the inclusion of ion dynamic effects. 12 refs., 7 figs.

Pollock, E.L.

1986-12-01T23:59:59.000Z

402

Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model  

E-Print Network (OSTI)

Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

Thorsten Erdmann; Philipp J. Albert; Ulrich S. Schwarz

2013-07-24T23:59:59.000Z

403

Dynamic Network Forecasting using SimGrid Simulations Matthieu Imbert and Eddy Caron  

E-Print Network (OSTI)

exists. Currently, the most widely-used approach for data management for distributed grid computation capacities, the network equipment capacities (line-cards or back-plane capacity), the interactions bothDynamic Network Forecasting using SimGrid Simulations Matthieu Imbert and Eddy Caron Université de

404

Simulant-material experimental investigation of flow dynamics in the CRBR Upper-Core Structure  

Science Conference Proceedings (OSTI)

The results of a simulant-material experimental investigation of flow dynamics in the Clinch River Breeder Reactor (CRBR) Upper Core Structure are described. The methodology used to design the experimental apparatus and select test conditions is detailed. Numerous comparisons between experimental data and SIMMER-II Code calculations are presented with both advantages and limitations of the SIMMER modeling features identified.

Wilhelm, D.; Starkovich, V.S.; Chapyak, E.J.

1982-09-01T23:59:59.000Z

405

A simulated annealing approach with probability matrix for semiconductor dynamic scheduling problem  

Science Conference Proceedings (OSTI)

The dynamic scheduling problem of semiconductor burn-in operations is studied in this paper. The burn-in oven is a batch-processing machine and the size of each job is independent of the oven's capacity. The processing time for each batch is represented ... Keywords: Deadlines, Heuristic, Simulated annealing, Total weighted completion time

Fuh-Der Chou; Hui-Mei Wang; Pei-Chann Chang

2008-11-01T23:59:59.000Z

406

DYNAMIC SIMULATION OF MONO-TUBE CAVITY RECEIVERS FOR DIRECT STEAM GENERATION  

E-Print Network (OSTI)

-tracing study of the heat flux distribution inside the steam receiver is used to spatially refine the modelDYNAMIC SIMULATION OF MONO-TUBE CAVITY RECEIVERS FOR DIRECT STEAM GENERATION José Zapata 1 , John dish has been in operation since 2010 with a mono-tube steam cavity receiver, the SG4 system

407

Dynamic Modeling and Simulation of Hybrid Power Systems Based on Renewable Energy  

Science Conference Proceedings (OSTI)

This paper describes dynamic modeling and simulation results of a renewable energy based hybrid power system. The paper focuses on the combination of solar cell (SC), wind turbine (WT), fuel cell (FC) and ultra-capacitor (UC) systems for power generation. ... Keywords: fuel cell, hybrid power system, renewable energy, solar cell, ultra-capacitor, wind turbine

Teng-Fa Tsao; Po-Hung Chen; Hung-Cheng Chen

2009-10-01T23:59:59.000Z

408

Corrosion Study of Fe in a Stagnant Liquid Pb by Molecular Dynamics Methods  

Science Conference Proceedings (OSTI)

It has been investigated theoretically the corrosion phenomena of iron (Fe) in liquid lead (Pb) by molecular dynamics methods. The corrosion phenomena was regarded as a diffusion process in which the Fe atoms of bulk material spreading into a liquid Pb. The D diffusion coefficient of the corrosion was calculated. We reported the self-diffusion coefficient of Fe in liquid Pb is D{sub MD} (750 deg.) = 2.59x10{sup -9}m{sup 2}/s. This is in the range of (1.31-5.75)x10{sup -9} m{sup 2}/s from literature and also closed to D{sub Robertson}(750 deg. C) = 2.74x10{sup -9} m{sup 2}/s based on the Robertson curve.

Arkundato, A. [Physics Dept, Faculty of Math. And Natural Sciences, Institut Teknologi Bandung, Indonesia Jl.Ganesha 10, Bandung 40132 (Indonesia); Physics Dept, Faculty of Math. And Natural Sciences, Universitas Jember (Indonesia); Suud, Zaki; Abdullah, Mikrajudin [Physics Dept, Faculty of Math. And Natural Sciences, Institut Teknologi Bandung, Indonesia Jl.Ganesha 10, Bandung 40132 (Indonesia)

2010-06-22T23:59:59.000Z

409

Particle dynamics in two-dimensional random energy landscapes - experiments and simulations  

E-Print Network (OSTI)

The dynamics of individual colloidal particles in random potential energy landscapes were investigated experimentally and by Monte Carlo simulations. The value of the potential at each point in the two-dimensional energy landscape follows a Gaussian distribution. The width of the distribution, and hence the degree of roughness of the energy landscape, was varied and its effect on the particle dynamics studied. This situation represents an example of Brownian dynamics in the presence of disorder. In the experiments, the energy landscapes were generated optically using a holographic set-up with a spatial light modulator, and the particle trajectories were followed by video microscopy. The dynamics are characterized using, e.g., the time-dependent diffusion coefficient, the mean squared displacement, the van Hove function and the non-Gaussian parameter. In both, experiments and simulations, the dynamics are initially diffusive, show an extended sub-diffusive regime at intermediate times before diffusive motion is recovered at very long times. The dependence of the long-time diffusion coefficient on the width of the Gaussian distribution agrees with theoretical predictions. Compared to the dynamics in a one-dimensional potential energy landscape, the localization at intermediate times is weaker and the diffusive regime at long times reached earlier, which is due to the possibility to avoid local maxima in two-dimensional energy landscapes.

Florian Evers; Christoph Zunke; Richard D. L. Hanes; Joerg Bewerunge; Imad Ladadwa; Andreas Heuer; Stefan U. Egelhaaf

2013-02-13T23:59:59.000Z

410

Numerical Simulation of Thunderstorm Outflow Dynamics. Part I: Outflow Sensitivity Experiments and Turbulence Dynamics  

Science Conference Proceedings (OSTI)

In this first paper of a two-part series, a two-dimensional numerical model is developed and used to investigate the dynamics of thunderstorm outflows. By focusing only on the outflow and using essentially inviscid equations and high spatial ...

Kelvin K. Droegemeier; Robert B. Wilhelmson

1987-04-01T23:59:59.000Z

411

Ultrafast probing of ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets  

SciTech Connect

The ejection dynamics of Rydberg atoms and molecular fragments from electronically excited helium nanodroplets are studied with time-resolved extreme ultraviolet ion imaging spectroscopy. At excitation energies of 23.6 {+-} 0.2 eV, Rydberg atoms in n= 3 and n= 4 states are ejected on different time scales and with significantly different kinetic energy distributions. Specifically, n= 3 Rydberg atoms are ejected with kinetic energies as high as 0.85 eV, but their appearance is delayed by approximately 200 fs. In contrast, n= 4 Rydberg atoms appear within the time resolution of the experiment with considerably lower kinetic energies. Major features in the Rydberg atom kinetic energy distributions for both principal quantum numbers can be described within a simple elastic scattering model of localized perturbed atomic Rydberg atoms that are expelled from the droplet due to their repulsive interaction with the surrounding helium bath. Time-dependent kinetic energy distributions of He{sub 2}{sup +} and He{sub 3}{sup +} ions are presented that support the formation of molecular ions in an indirect droplet ionization process and the ejection of neutral Rydberg dimers on a similar time scale as the n= 3 Rydberg atoms.

Buenermann, Oliver; Kornilov, Oleg; Neumark, Daniel M. [Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Department of Chemistry, University of California, Berkeley, California 94720 (United States); Haxton, Daniel J.; Gessner, Oliver [Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Leone, Stephen R. [Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Department of Chemistry, University of California, Berkeley, California 94720 (United States); Department of Physics, University of California, Berkeley, California 94720 (United States)

2012-12-07T23:59:59.000Z

412

A Combined 6,7Li NMR and Molecular Dynamics Study of Li Diffusion in Li2TiO3  

SciTech Connect

Understanding lithium diffusion properties in electrode materials is important for designing rechargeable lithium-ion batteries with improved performance. In this work, the lithium dynamics in layered Li2TiO3 were characterized using a combination of 6,7Li nuclear magnetic resonance (NMR) over a wide temperature range (150 to 500 K), and molecular dynamics (MD) simulations. The 7Li static NMR and stimulated echo experiments show slow and partial lithium diffusion in Li2TiO3. The high-field (21.1 T) 6Li magic angle spinning NMR shows a new tetrahedral lithium site along with the three crystallographic octahedral sites in Li2TiO3 sample. MD simulations predict that lithium can occupy a tetrahedral site if two or more vacancies exist in the vicinity, which may result, for example, from the presence of a Ti defect in the LiTi2 layer. 6Li two-dimensional (2D) exchange NMR experiments show evidence of lithium diffusion between the pure Li and LiTi2 layers along the c axis. Although the 2D exchange NMR data is not sensitive to lithium diffusion in the ab plane, MD simulations show that lithium diffusion in the pure Li layer is equally probable. Combining these results, a detailed picture of the lithium diffusion pathways in Li2TiO3 is presented.

Vijayakumar, M.; Kerisit, Sebastien N.; Yang, Zhenguo; Graff, Gordon L.; Liu, Jun; Sears, Jesse A.; Burton, Sarah D.; Rosso, Kevin M.; Hu, Jian Z.

2009-10-27T23:59:59.000Z

413

Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report â?? Phase I  

SciTech Connect

Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G} for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient parallel computation of particle and fluid dynamics simulations. These problems occur throughout DOE, military and commercial sectors: the potential payoff is high. We plan to license or sell the solution to contractors for military and domestic applications such as disaster simulation (aerodynamic and hydrodynamic), Government agencies (hydrological and environmental simulations), and medical applications (e.g., in tomographic image reconstruction). Keywords - High-performance Computing, Graphic Processing Unit, Fluid/Particle Simulation. Summary for Members of Congress - Department of Energy has many simulation codes that must compute faster, to be effective. The Phase I research parallelized particle/fluid simulations for rocket combustion, for high-performance computing systems.

Mark S. Schmalz

2011-07-24T23:59:59.000Z

414

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

Science Conference Proceedings (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

415

Modeling the Forest or Modeling the Trees A Comparison of System Dynamics and Agent-Based Simulation  

E-Print Network (OSTI)

System Dynamics and Agent-based Simulation are two approaches that use computer simulation for investigating non-linear social and socio-economic systems with a focus on the understanding and qualitative prediction of a system’s behavior. Although the two schools have a broad overlap in research topics they have been relatively unnoticed by each other so far. This paper contributes to the cross-study of System Dynamics and Agent-Based Simulation. It uncovers and contrasts the primary conceptual predispositions underlying the two approaches. Moreover, ideas about how the approaches could be integrated are presented. Key words: System Dynamics, Agent-based Simulation

Nadine Schieritz; Peter M. Milling

2003-01-01T23:59:59.000Z

416

A GAUSSIAN PROCESS BASED APPROACH FOR HANDLING UNCERTAINTY IN VEHICLE DYNAMICS SIMULATION  

E-Print Network (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 ? Address all correspondence to this author.

Kyle Schmitt; Justin Madsen; Mihai Anitescu; Dan Negrut

2008-01-01T23:59:59.000Z

417

Beam dynamics and wakefield simulations of the double grating accelerating structure  

Science Conference Proceedings (OSTI)

Laser-driven acceleration in dielectric structures can provide gradients on the order of GeV/m. The small transverse dimension and tiny feature sizes introduce challenges in design, fabrication, and simulation studies of these structures. In this paper we present the results of beam dynamic simulation and short range longitudinal wakefield simulation of the double grating structure. We show the linear trend of acceleration in a dielectric accelerator design and calculate the maximum achievable gradient equal to 0.47E{sub 0} where E0 is maximum electric field of the laser excitation. On the other hand, using wakefield simulations, we show that the loss factor of the structure with 400nm gap size will be 0.12GV/m for a 10fC, 100as electron bunch which is an order of magnitude less than expected gradient near damage threshold of the device.

Najafabadi, B. Montazeri; Byer, R. L.; Ng, C. K.; England, R. J.; Peralta, E. A.; Soong, K.; Noble, R.; Wu, Z. [Stanford University, Stanford, CA (United States); SLAC National Accelerator Laboratory, Menlo Park, CA (United States)

2012-12-21T23:59:59.000Z

418

Two-dimensional computational fluid dynamics and conduction simulations of heat transfer in window frames with internal cavities - Part 1: Cavities only  

E-Print Network (OSTI)

of heat fluxes from CFD and conduction simulations for theapproach to solve the conduction heat-transfer equation. TheFluid Dynamics and Conduction Simulations of Heat Transfer

Gustavsen, Arild; Kohler, Christian; Arasteh, Dariush; Curcija, Dragan

2003-01-01T23:59:59.000Z

419

Beam dynamics simulations and measurements at the Project X Test Facility  

Science Conference Proceedings (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

420

Final Report for Project Titled Nanoporous Materials: Experimental Studies and Molecular Simulations  

DOE Green Energy (OSTI)

In recent years significant research has been carried out aimed at developing a fundamental understanding of the phenomena involved in the transport of mixtures in nanoporous systems, such as adsorbents and membranes, which are crucial to many industrial separation processes. Carbon molecular-sieve membranes (CMSM) were the key focus early on in our DOE/BES-supported investigations. They are thought to be more stable and versatile than polymeric membranes, and capable of operating at higher temperatures, up to 300 C. In our research the emphasis was on understanding the factors determining the ability of the CMSM to separate mixtures based on differences in molecular mobility, and in affinity to the pore surface. Our study involved: (1) the preparation and characterization of the CMSM; (2) the computational modeling of their structure, and (3) the measurement and computer simulations of sorption and transport of mixtures through the membranes. The membranes developed are currently undergoing field-testing by Media & Process Technology (M & PT), our industrial collaborators in the project. In this research project we adopted the methodology and tools developed with the nanoporous CMSM to the preparation of novel membranes and films made of SiC. Our efforts were motivated here by the growing interest in the hydrogen economy, which has necessitated the development of robust nanoporous films that can be used as membranes and sensors in high-temperature and pressure processes related to H{sub 2} production. SiC is a promising material for these applications due to its many unique properties, such as high thermal conductivity, thermal shock resistance, biocompatibility, resistance in acidic and alkali environments, chemical inertness (e.g., towards steam, H{sub 2}S, NH{sub 3}, and HCl, of particular concern for H{sub 2} production from biomass and coal), and high mechanical strength. Though the CMSM exhibit many similar good properties, they are themselves unstable in the presence of O{sub 2} and steam at temperatures higher than 300 C (conditions typically encountered in reactive separations for H{sub 2} production). Other inorganic membranes, like ceramic (e.g., alumina, silica, and zeolite) and metal (Pd, Ag, and their alloys) membranes have, so far, also proven unstable, in such high-temperature applications in the presence of steam and H{sub 2}S. The preparation of SiC nanoporous membranes involves two important steps. First, the preparation of appropriate SiC porous supports, and second the deposition on these supports of crack- and pinhole-free, thin nanoporous SiC films. Our early research, in collaboration with M & PT, focused on the preparation of quality porous SiC substrates. Our recent efforts involved the deposition of thin nanoporous films on these substrates by the pyrolysis of pre-ceramic polymeric precursors. We have made substantial strides in this area (as discussed further in Section II) preparing hydrogen-selective membranes and films. The objective of the project was not only to advance the 'state-of-the-art' of preparing the SiC membranes and films, but also to significantly broaden our understanding of factors that determine the ability of the SiC materials to separate gas mixtures, based on differences in molecular mobility and molecule-pore surface interactions. It is only such an improved fundamental understanding that will lead to further substantial improvements in the techniques for preparing such materials. In our studies we proceeded along two paths: (1) the preparation and characterization of SiC membranes, and the computational modeling of their molecular structure, and (2) the measurement and simultaneous computer simulation of sorption and transport of mixtures through the membranes. Coupling experiments and simulations facilitated our efforts to relate the membrane's structure with its transport properties, and separation efficacy. This, in turn, enabled progress towards the long-term goal of first-principle molecular engineering and design of improved materials for adsorption and separati

Muhammad Sahimi and Theodore T. Tsotsis

2008-12-31T23:59:59.000Z

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421

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

Science Conference Proceedings (OSTI)

Using molecular simulation, we investigate the effect of nitrogen doping on adsorption capacity and selectivity of CO{sub 2} versus N{sub 2} in model mesoporous carbon. We show that nitrogen doping greatly enhances CO{sub 2} adsorption capacity; with a 7 wt % dopant concentration, the adsorption capacity at 1 bar and 298 K increases from 3 to 12 mmol/g (or 48% uptake by weight). This great enhancement is due to the preferred interaction between CO{sub 2} and the electronegative nitrogen. The nitrogen doping coupled with the mesoporosity also leads to a much higher working capacity for adsorption of the CO{sub 2}/N{sub 2} mixture in nitrogen-doped mesoporous carbon. In addition, the CO{sub 2}/N{sub 2} selectivity is almost 5 times greater than in nondoped carbon at ambient conditions. This work indicates that nitrogen doping is a promising strategy to create mesoporous carbons for high-capacity, selective carbon capture.

Babarao, Ravichandar [ORNL; Dai, Sheng [ORNL; Jiang, Deen [ORNL

2012-01-01T23:59:59.000Z

422

Molecular Science Research Center 1992 annual report  

Science Conference Proceedings (OSTI)

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

Knotek, M.L.

1994-01-01T23:59:59.000Z

423

Numerical simulation of high-speed penetration-perforation dynamics in layered armor shields  

E-Print Network (OSTI)

Penetration models and calculating algorithms are presented, describing the dynamics and fracture of composite armor shields penetrated by high-speed small arms. A shield considered consists of hard (metal or ceramic) facing and multilayered fabric backing. A simple formula is proved for the projectile residual velocity after perforation of a thin facing. A new plastic-flow jet model is proposed for calculating penetration dynamics in the case of a thick facing of ceramic or metal-ceramic FGM materials. By bringing together the developed models into a calculating algorithm, a computer tool is designed enabling simulations of penetration processes in the above-mentioned shields and analysis of optimization problems. Some results of computer simulation are presented. It is revealed in particular that strength proof of pliable backing can be better as compared with more rigid backing. Comparison of calculations and test data shows sufficient applicability of the models and the tool.

Ayzenberg-Stepanenko, Mark

2012-01-01T23:59:59.000Z

424

Numerical simulation of high-speed penetration-perforation dynamics in layered armor shields  

E-Print Network (OSTI)

Penetration models and calculating algorithms are presented, describing the dynamics and fracture of composite armor shields penetrated by high-speed small arms. A shield considered consists of hard (metal or ceramic) facing and multilayered fabric backing. A simple formula is proved for the projectile residual velocity after perforation of a thin facing. A new plastic-flow jet model is proposed for calculating penetration dynamics in the case of a thick facing of ceramic or metal-ceramic FGM materials. By bringing together the developed models into a calculating algorithm, a computer tool is designed enabling simulations of penetration processes in the above-mentioned shields and analysis of optimization problems. Some results of computer simulation are presented. It is revealed in particular that strength proof of pliable backing can be better as compared with more rigid backing. Comparison of calculations and test data shows sufficient applicability of the models and the tool.

Mark Ayzenberg-Stepanenko; Grigory Osharovich

2012-03-07T23:59:59.000Z

425

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

Science Conference Proceedings (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

426

Advanced beam-dynamics simulation tools for the RIA driver linac,Part I: Low energy beam transport and radiofrequency quadrupole  

Science Conference Proceedings (OSTI)

Advanced Beam-Dynamics Simulation Tools for the RIA Driver Linac; Low Energy Beam Transport and Radiofrequency Quadrupole.

Wangler, Thomas P.; Crandall, Kenneth R.; Garnett, Robert W.; Gorelov, Dmitry; Ostroumov, Petr; Qiang, Ji; Ryne, Robert; York, Richard

2003-08-26T23:59:59.000Z

427

GPU-accelerated molecular visualization on petascale supercomputing platforms  

Science Conference Proceedings (OSTI)

Petascale supercomputers create new opportunities for the study of the structure and function of large biomolecular complexes such as viruses and photosynthetic organelles, permitting all-atom molecular dynamics simulations of tens to hundreds of millions ... Keywords: GPU, many-core, molecular surface, molecular visualization, parallel rendering, ray tracing

John E. Stone, Kirby L. Vandivort, Klaus Schulten

2013-11-01T23:59:59.000Z

428

A dynamic object-oriented architecture approach to ecosystem modeling and simulation.  

SciTech Connect

Modeling and simulation in support of adaptive ecosystem management can be better accomplished through a dynamic, integrated, and flexible approach that incorporates scientific and technological components into a comprehensive ecosystem-modeling framework. The Integrated Dynamic Landscape Analysis and Modeling System (IDLAMS) integrates ecological models and decision support techniques, through a geographic information system (GIS)-based framework. The Strategic Environmental Research and Development Program (SERDP) sponsored the development of IDLAMS. Initially built upon a GIS framework, IDLAMS is migrating to an object-oriented (OO) architectural framework. An object-oriented architecture is more flexible and modular. It allows disparate applications and dynamic models to be integrated in a manner that minimizes (or eliminates) the need to rework or recreate the system as new models are added to the suite. In addition, an object-oriented design makes it easier to provide run-time feedback among models, thereby making it a more dynamic tool for exploring and providing insight into the interactions among ecosystem processes. Finally, an object-oriented design encourages the reuse of existing technology because OO-IDLAMS is able to integrate disparate models, databases, or applications executed in their native languages. Reuse is also accomplished through a structured approach to building a consistent and reusable object library. This reusability can substantially reduce the time and effort needed to develop future integrated ecosystem simulations.

Dolph, J. E.; Majerus, K. A.; Sydelko, P. J.; Taxon, T. N.

1999-04-09T23:59:59.000Z

429

Dissipative Particle Dynamics Simulation of Pore-Scale Multiphase Fluid Flow  

Science Conference Proceedings (OSTI)

Multiphase fluid flow through porous media involves complex fluid dynamics, and it is difficult to model such complex behavior, on the pore scale, using grid-based continuum models. In this paper, the application of dissipative particle dynamics (DPD), a relatively new mesoscale method, to the simulation of pore-scale multiphase fluid flows under a variety of flow conditions is described. We demonstrate that the conventional DPD method using purely repulsive conservative (nondissipative) particle-particle interactions is capable of modeling single-phase flow fields in saturated porous media. In order to simulate unsaturated multiphase flow through porous media, we applied a modified model for the conservative particle-particle interactions that combines short-range repulsive and long-range attractive interactions. This form for the conservative particle-particle interactions allows the behavior of multiphase systems consisting of gases, liquids, and solids to be simulated. We also demonstrated that the flow of both wetting and nonwetting fluids through porous media can be simulated by controlling the ratios between the fluid-fluid and fluid-solid (fluid-wall) interparticle interaction strengths.

Paul Meakin; Hai Huang; Moubin Liu

2007-04-01T23:59:59.000Z

430

Aqua ions-graphene interfacial and confinement behavior: Insights from isobaric-isothermal molecular dynamics  

SciTech Connect

We carry out a systematic microstructural characterization of the solid–fluid interface (SFI) of water and simple metal chloride aqueous solutions in contact with a free-standing plate or with two such plates separated by an interplate distance 0 ? h (Å) ? 30 at ambient conditions via isothermal–isobaric molecular dynamics. With this characterization, we target the interrogation of the system in search for answers to fundamental questions regarding the structure of the “external” and “internal” (confined) SFIs, the effect of the differential hydration behavior among species, and its link to species expulsion from confinement. For water at ambient conditions, we found that the structure of the “external” SFIs is independent of the interplate distance h in the range 0 ? h (Å) ? 30, that is, the absence of wall-mediated correlation effects between “external” and “internal” SFIs, and that for h < 9 Å the slit-pores dewet. Moreover, we observed a selective expulsion of ions caused by the differential hydration between the anion and the cations with a consequent charging of the slit-pore. All these observations were interpreted in terms of the axial profiles for precisely defined order parameters, including tetrahedral configuration, hydrogen bonding, and species coordination numbers.

Chialvo, A. A.; Cummings, Peter T.

2011-01-01T23:59:59.000Z

431

Role of Water States on Water Uptake and Proton Transport in Nafion using Molecular Simulations and Bimodal Network  

SciTech Connect

Using molecular simulations and a bimodal domain network, the role of water state on Nafion water uptake and water and proton transport is investigated. Although the smaller domains provide moderate transport pathways, their effectiveness remains low due to strong, resistive water molecules/domain surface interactions. The water occupancy of the larger domains yields bulk-like water, and causes the observed transition in the water uptake and significant increases in transport properties.

Michigan, U.; Hwang, Gi Suk; Kaviany, Massoud; Gostick, Jeffrey T.; Kientiz, Brian; Weber, Adam Z.; Kim, Moo Hwan

2010-11-19T23:59:59.000Z

432

Integrated dynamic and simulation model on coupled closed-loop workstation capacity controls in a multi-workstation production system  

Science Conference Proceedings (OSTI)

In this paper, a dynamic model coupled with a simulation model is introduced to control a multi-workstation production system such that a given performance measure is achieved. In particular, we consider closed loop capacity controls for regulating WIP ...

Tao Wu; Leyuan Shi; Benjamin Quirt; N. A. Duffie

2008-12-01T23:59:59.000Z

433

Detailed Simulations of Atmospheric Flow and Dispersion in Downtown Manhattan: An Application of Five Computational Fluid Dynamics Models  

Science Conference Proceedings (OSTI)

Computational fluid dynamics (CFD) model simulations of urban boundary layers have improved in speed and accuracy so that they are useful in assisting in planning emergency response activities related to releases of chemical or biological agents ...

Steven R. Hanna; Michael J. Brown; Fernando E. Camelli; Stevens T. Chan; William J. Coirier; Sura Kim; Olav R. Hansen; Alan H. Huber; R. Michael Reynolds

2006-12-01T23:59:59.000Z

434

Atomistic Time-Domain Simulations of Light-Harvesting and Charge-Transfer Dynamics in Novel Nanoscale Materials for Solar Hydrogen Production.  

DOE Green Energy (OSTI)

Funded by the DOE grant (i) we continued to study and analyze the atomistic detail of the electron transfer (ET) across the chromophore-TiO2 interface in Gratzel cell systems for solar hydrogen production. (ii) We extensively investigated the nature of photoexcited states and excited state dynamics in semiconductor quantum dots (QD) designed for photovoltaic applications. (iii) We continued a newly initiated research direction focusing on excited state properties and electron-phonon interactions in nanoscale carbon materials. Over the past year, the results of the DOE funded research were summarized in 3 review articles. 12 original manuscripts were written. The research results were reported in 28 invited talks at conferences and university seminars. 20 invitations were accepted for talks in the near future. 2 symposia at national and international meetings have being organized this year on topics closely related to the DOE funded project, and 2 more symposia have been planned for the near future. We summarized the insights into photoinduced dynamics of semiconductor QDs, obtained from our time-domain ab initio studies. QDs exhibit both molecular and bulk properties. Unlike either bulk or molecular materials, QD properties can be modified continuously by changing QD shape and size. However, the chemical and physical properties of molecular and bulk materials often contradict each other, which can lead to differing viewpoints about the behavior of QDs. For example, the molecular view suggests strong electron-hole and charge-phonon interactions, as well as slow energy relaxation due to mismatch between electronic energy gaps and phonon frequencies. In contrast, the bulk view advocates that the kinetic energy of quantum confinement is greater than electron-hole interactions, that charge-phonon coupling is weak, and that the relaxation through quasi-continuous bands is rapid. By synthesizing the bulk and molecular viewpoints, we clarified the controversies and provided a unified atomistic picture of the nature and dynamics of photoexcited states in semiconductor QDs. We also summarized our recent findings about the photoinduced electron dynamics at the chromophore-semiconductor interfaces from a time-domain ab initio perspective. The interface provides the foundation for a new, promising type of solar cell and presents a fundamentally important case study for several fields, including photo-, electro- and analytical chemistries, molecular electronics, and photography. Further, the interface offers a classic example of an interaction between an organic molecular species and an inorganic bulk material. Scientists employ different concepts and terminologies to describe molecular and solid states of matter, and these differences make it difficult to describe the interface with a single model. At the basic atomistic level of description, however, this challenge can be largely overcome. Recent advances in non-adiabatic molecular dynamics and time-domain density functional theory have created a unique opportunity for simulating the ultrafast, photoinduced processes on a computer very similar to the way that they occur in nature. These state-of-the-art theoretical tools offered a comprehensive picture of a variety of electron transfer processes that occur at the interface, including electron injection from the chromophore to the semiconductor, electron relaxation and delocalization inside the semiconductor, back-transfer of the electron to the chromophore and to the electrolyte, and regeneration of the neutral chromophore by the electrolyte. The ab initio time-domain modeling is particularly valuable for understanding these dynamic features of the ultrafast electron transfer processes, which cannot be represented by a simple rate description. We demonstrated using symmetry adapted cluster theory with configuration interaction (SAC-CI) that charging of small PbSe nanocrystals (NCs) greatly modifies their electronic states and optical excitations. Conduction and valence band transitions that are not available in neutral NCs dominate

Prezhdo, Oleg V.

2012-03-22T23:59:59.000Z

435

Atomistic Time-Domain Simulations of Light-Harvesting and Charge-Transfer Dynamics in Novel Nanoscale Materials for Solar Hydrogen Production.  

Science Conference Proceedings (OSTI)

Funded by the DOE grant (i) we continued to study and analyze the atomistic detail of the electron transfer (ET) across the chromophore-TiO2 interface in Gratzel cell systems for solar hydrogen production. (ii) We extensively investigated the nature of photoexcited states and excited state dynamics in semiconductor quantum dots (QD) designed for photovoltaic applications. (iii) We continued a newly initiated research direction focusing on excited state properties and electron-phonon interactions in nanoscale carbon materials. Over the past year, the results of the DOE funded research were summarized in 3 review articles. 12 original manuscripts were written. The research results were reported in 28 invited talks at conferences and university seminars. 20 invitations were accepted for talks in the near future. 2 symposia at national and international meetings have being organized this year on topics closely related to the DOE funded project, and 2 more symposia have been planned for the near future. We summarized the insights into photoinduced dynamics of semiconductor QDs, obtained from our time-domain ab initio studies. QDs exhibit both molecular and bulk properties. Unlike either bulk or molecular materials, QD properties can be modified continuously by changing QD shape and size. However, the chemical and physical properties of molecular and bulk materials often contradict each other, which can lead to differing viewpoints about the behavior of QDs. For example, the molecular view suggests strong electron-hole and charge-phonon interactions, as well as slow energy relaxation due to mismatch between electronic energy gaps and phonon frequencies. In contrast, the bulk view advocates that the kinetic energy of quantum confinement is greater than electron-hole interactions, that charge-phonon coupling is weak, and that the relaxation through quasi-continuous bands is rapid. By synthesizing the bulk and molecular viewpoints, we clarified the controversies and provided a unified atomistic picture of the nature and dynamics of photoexcited states in semiconductor QDs. We also summarized our recent findings about the photoinduced electron dynamics at the chromophore-semiconductor interfaces from a time-domain ab initio perspective. The interface provides the foundation for a new, promising type of solar cell and presents a fundamentally important case study for several fields, including photo-, electro- and analytical chemistries, molecular electronics, and photography. Further, the interface offers a classic example of an interaction between an organic molecular species and an inorganic bulk material. Scientists employ different concepts and terminologies to describe molecular and solid states of matter, and these differences make it difficult to describe the interface with a single model. At the basic atomistic level of description, however, this challenge can be largely overcome. Recent advances in non-adiabatic molecular dynamics and time-domain density functional theory have created a unique opportunity for simulating the ultrafast, photoinduced processes on a computer very similar to the way that they occur in nature. These state-of-the-art theoretical tools offered a comprehensive picture of a variety of electron transfer processes that occur at the interface, including electron injection from the chromophore to the semiconductor, electron relaxation and delocalization inside the semiconductor, back-transfer of the electron to the chromophore and to the electrolyte, and regeneration of the neutral chromophore by the electrolyte. The ab initio time-domain modeling is particularly valuable for understanding these dynamic features of the ultrafast electron transfer processes, which cannot be represented by a simple rate description. We demonstrated using symmetry adapted cluster theory with configuration interaction (SAC-CI) that charging of small PbSe nanocrystals (NCs) greatly modifies their electronic states and optical excitations. Conduction and valence band transitions that are not available in neutral NCs dominate

Prezhdo, Oleg V.

2012-03-22T23:59:59.000Z

436

Applying Computational Science to Education: The Molecular Workbench Paradigm  

Science Conference Proceedings (OSTI)

The Molecular Workbench offers highly interactivemolecular dynamics simulations to help students learn difficult scientific concepts. The software demonstrates how scientists can transform research tools into educational tools. Research studies show that students learn better using computational models.

Robert F. Tinker; Qian Xie

2008-01-01T23:59:59.000Z

437

Hybrid atomistic-continuum method for the simulation of dense fluid flows  

Science Conference Proceedings (OSTI)

We present a hybrid atomistic-continuum method for multiscale simulations of dense fluids. In this method, the atomistic part is described using a molecular dynamics description, while the continuum flow is described by a finite volume discretization ... Keywords: Hybrid algorithms, Molecular dynamics, Multiscale simulation, Nanofluidics

Thomas Werder; Jens H. Walther; Petros Koumoutsakos

2005-05-01T23:59:59.000Z

438

Application of a kinetic energy partitioning scheme for ab initio molecular dynamics to reactions associated with ionization in water tetramers  

SciTech Connect

We give the details of a partitioning scheme of the kinetic energy in molecular dynamics based on instantaneous internal coordinates and atomic velocities. The scheme applied to the analysis of the short-time dynamics after ionization in ‘cyclic’ and ‘branched’ water tetramers illustrates that the tetrameric systems can be usefully partitioned into two subsystems, a ‘reactive trimer’ and a ‘solvent’ molecule. The partitioned kinetic energy exhibits a broad peak that can be assigned to the interaction between the two sub-systems, and a sharper peak arising from the proton transfer that occurs upon ionization. Comparison of the dynamics in tetramer clusters suggests that the stability of the hydroxyl radical formed upon ionization depends on the instantaneous configuration of the water molecules around the ionized water. These findings are consistent with those reported earlier for the (H2O)17 cluster. This work was supported in part by the Division of Chemical Sciences, Office of Basic Energy Sciences, of the U.S. Department of Energy (DOE). This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). The EMSL is funded by DOE’s Office of Biological and Environmental Research. PNNL is operated by Battelle for DOE.

Furuhama, Ayako; Dupuis, Michel; Hirao, Kimihiko

2008-05-29T23:59:59.000Z

439

Molecular dynamics study of photodissociation of water in crystalline and amorphous ice  

E-Print Network (OSTI)

We present results of classical dynamics calculations, performed to study the photodissociation of water in crystalline and amorphous ice surfaces at a surface temperature of 10 K. Dissociation in the top six monolayers is considered. Desorption of H2O has a low probability (less than 0.5% yield per absorbed photon) for both types of ice. The final outcome strongly depends on the original position of the photodissociated molecule. For molecules in the first bilayer of crystalline ice and the corresponding layers in amorphous ice, desorption of H atoms dominates. In the second bilayer H atom desorption, trapping of the H and OH fragments in the ice, and recombination of H and OH are of roughly equal importance. Deeper into the ice H atom desorption becomes less important and trapping and recombination dominate. The distribution of distances traveled by H atoms in the ice peaks at 6 - 7 Angstroms with a tail going to about 60 Angstroms for both types of ice. The mobility of OH radicals is low within the ice with most probable distances traveled of 2 and 1 Angstroms for crystalline and amorphous ice, respectively. OH is however quite mobile on top of the surface, where it has been found to travel more than 80 Angstroms. Simulated absorption spectra of crystalline ice, amorphous ice, and liquid water are found to be in very good agreement with experiments.

Stefan Andersson; Ayman Al-Halabi; Geert-Jan Kroes; Ewine F. van Dishoeck

2005-12-23T23:59:59.000Z

440

Development of dynamic models of reactive distillation columns for simulation and determination of control  

E-Print Network (OSTI)

Dynamic models of a reactive distillation column have been developed and implemented in this work. A model describing the steady state behavior of the system has been built in a first step. The results from this steady state model have been compared to data provided from an industrial collaborator and the reconciled model formed the basis for the development of a dynamic model. Four controlled and four manipulated variables have been determined in a subsequent step and step tests for the manipulated variables were simulated. The data generated by the step responses was used for fitting transfer functions between the manipulated and the controlled variables. RGA analysis was performed to find the optimal pairing for controller design. Feedback controllers of PID type were designed between the paired variables found from RGA and the controllers were implemented on the column model. Both servo and regulatory problems have been considered and tested.

Chakrabarty, Arnab

2004-12-01T23:59:59.000Z

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