National Library of Energy BETA

Sample records for molecular dynamics simulation

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

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

    studies of electrolytes and electrolyteelectrode interfaces Molecular dynamics simulation studies of electrolytes and electrolyteelectrode interfaces 2009 DOE Hydrogen Program...

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

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

    Molecular Dynamics Simulation Studies of Electrolytes and ElectrolyteElectrode Interfaces Molecular dynamics simulation studies of electrolytes and electrolyteelectrode...

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

    Office of Scientific and Technical Information (OSTI)

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

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

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

    Dynamics Simulation Studies of Electrolytes and ElectrolyteElectrode Interfaces Molecular Dynamics Simulation Studies of Electrolytes and ElectrolyteElectrode Interfaces 2010 DOE...

  5. Chapter 7 Molecular Dynamics Simulations of Fluoro Polymers

    E-Print Network [OSTI]

    Goddard III, William A.

    131 Chapter 7 Molecular Dynamics Simulations of Fluoro Polymers: Prediction of Glass Transition for molecular dynamics simulation of the uoro polymers: Polytetra uoroethylene PTFE, Polyvinylidene uoride PVDF using a Build-Anneal-Quench procedure. For PTFE, PVDF, and ETFE uoro polymers, these results predict

  6. Plasticity of metal wires in torsion: molecular dynamics and dislocation dynamics simulations

    E-Print Network [OSTI]

    Cai, Wei

    Plasticity of metal wires in torsion: molecular dynamics and dislocation dynamics simulations-4040 Abstract The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics metal wires controls the mechanisms of plastic deformation. For wires oriented along 110 , dislocations

  7. Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films 

    E-Print Network [OSTI]

    Kim, Bo Hung

    2010-07-14

    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...

  8. Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene

    E-Print Network [OSTI]

    Yi, Peng

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

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

    E-Print Network [OSTI]

    Cai, Wei

    Brittle and ductile fracture of semiconductor nanowires -- molecular dynamics simulations Keonwook November 9, 2006 Abstract Fracture of silicon and germanium nanowires in tension at room temperature potentials predict brittle fracture initiated by crack nucleation from the surface, most potentials predict

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

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

    Plimpton, Steve; Thompson, Aidan; Crozier, Paul

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

  11. Investigating Wear Mechanisms of Alkylsilane Monolayers through Molecular Dynamics Simulation

    E-Print Network [OSTI]

    represent the substrates used in laboratory studies of self-assembled monolayers, as a resultInvestigating Wear Mechanisms of Alkylsilane Monolayers through Molecular Dynamics Simulation detachment of chains based on bond distances · Investigate the influence of chain length on free

  12. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

    E-Print Network [OSTI]

    Rapaport, Dennis C.

    Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine D 2009; published 30 April 2009 A nanoscale-sized Stirling engine with an atomistic working fluid has s : 02.70.Ns, 05.70.Ln, 47.61. k The Stirling engine, an external combustion engine in- vented almost two

  13. Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation

    E-Print Network [OSTI]

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

  14. A Molecular Dynamics Simulation of Hydrogen Storage with SWNTs

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

  15. The stressstrain behavior of polymernanotube composites from molecular dynamics simulation

    E-Print Network [OSTI]

    Brenner, Donald W.

    -3538(03)00059-9 Composites Science and Technology 63 (2003) 1655­1661 www.elsevier.com/locate/compscitech * CorrespondingThe stress­strain behavior of polymer­nanotube composites from molecular dynamics simulation S, Hampton, VA 23681, USA c Department of Materials Science and Engineering, North Carolina State University

  16. Nonequilibrium molecular dynamics simulations of confined fluids...

    Office of Scientific and Technical Information (OSTI)

    simulations, density, velocity, and orientational profiles of the confined film were accumulated along the Z (perpendicular to the walls) and Y (parallel to the walls...

  17. Plasticity of metallic nanostructures : molecular dynamics simulations 

    E-Print Network [OSTI]

    Healy, Con

    2014-11-27

    During high speed cutting processes, metals are subject to high strains and strain rates. The dynamic nature of the deformation during high speed cutting makes it difficult to detect atomic scale deformation mechanisms ...

  18. Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations

    E-Print Network [OSTI]

    Cai, Wei

    Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations t The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics and dislocation wires controls the mechanisms of plastic deformation. For wires oriented along /1 1 0S, dislocations

  19. Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

    E-Print Network [OSTI]

    Fayer, Michael D.

    Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level

  20. Exploring the Reactivity of Carbene Cycloadditions with Electronic Structure Theory Calculations and Molecular Dynamics Simulations

    E-Print Network [OSTI]

    Sader, Charles Avery

    2015-01-01

    Electronic Structure Theory Calculations and Molecular DynamicsElectronic Structure Theory Calculations and Molecular Dynamicsdynamics simulation requires identification of an electronic structure calculation

  1. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

    E-Print Network [OSTI]

    Rapaport, D C

    2009-01-01

    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.

  2. Large-Scale Molecular Dynamics Simulations for Highly Parallel Infrastructures

    E-Print Network [OSTI]

    Pazúriková, Jana

    2014-01-01

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

  3. Kinetic distance and kinetic maps from molecular dynamics simulation

    E-Print Network [OSTI]

    Noe, Frank

    2015-01-01

    Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine...

  4. Molecular Dynamics Simulations of Solutions at Constant Chemical Potential

    E-Print Network [OSTI]

    Perego, Claudio; Parrinello, Michele

    2015-01-01

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

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

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

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

    E-Print Network [OSTI]

    Fu, Xuebing

    2008-10-10

    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 ...

  7. Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

    SciTech Connect (OSTI)

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

    2011-12-12

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

  8. Reaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties of chemically reacting mixtures

    E-Print Network [OSTI]

    Lisal, Martin

    diffusion) as well as reaction equilibria for chemically reacting mixtures. DOI: 10.1103/PhysRevE.70.) on chemical reaction equilibria is critical in many fields of science including mixture separationReaction ensemble molecular dynamics: Direct simulation of the dynamic equilibrium properties

  9. Recovering position-dependent diffusion from biased molecular dynamics simulations

    SciTech Connect (OSTI)

    Ljubeti?, Ajasja; Urban?i?, Iztok; Štrancar, Janez, E-mail: janez.strancar@ijs.si [Laboratory of Biophysics, Condensed Matter Physics Department, “Jožef Stefan” Institute, 1000 Ljubljana (Slovenia)] [Laboratory of Biophysics, Condensed Matter Physics Department, “Jožef Stefan” Institute, 1000 Ljubljana (Slovenia)

    2014-02-28

    All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

  10. Molecular Dynamics Simulations of Shock-Induced Thermite Reaction Vikas Tomar1,a

    E-Print Network [OSTI]

    Tomar, Vikas

    Molecular Dynamics Simulations of Shock-Induced Thermite Reaction Vikas Tomar1,a and Min Zhou1,b 1 Dynamics, Thermite Mixture Abstract. A computational framework for molecular dynamics (MD) simulations of shock-induced reactions in thermite mixtures is developed. The system under study is an Fe2O3+Al

  11. Enhanced molecular dynamics for simulating porous interphase layers in batteries.

    SciTech Connect (OSTI)

    Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan

    2009-10-01

    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.

  12. Molecular dynamics simulations of methane hydrate using polarizable force fields

    SciTech Connect (OSTI)

    Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

    2007-03-01

    Molecular dynamics simulations of methane hydrate have been carried out using the AMOEBA and COS/G2 polarizable force fields. Properties examined include the temperature dependence of the lattice constant, the OC and OO radial distribution functions and the vibrational spectra. Both the AMOEBA and COS/G2 models are found to successfully account for the available experimental data, with overall slightly better agreement with experiment being found for the AMOEBA model. Several properties calculated using the AMOEBA and COS/G2 models differ appreciable from the corresponding results obtained previously using the polarizable TIP4P-FQ model. This appears to be due to the inadequacy of the treatment of polarization, especially, the restriction of polarization to in-plane only, in the TIP4P-FQ model.

  13. Molecular dynamics simulations of a chemical reaction; conditions for local equilibrium in a temperature gradient

    E-Print Network [OSTI]

    Kjelstrup, Signe

    Molecular dynamics simulations of a chemical reaction; conditions for local equilibrium have examined a simple chemical reaction in a temperature gradient; 2F $ F2. A mechanical model molecular dynamics simulations showed that the chemical reaction is in local thermodynamic as well

  14. A Molecular Dynamics Simulation of Hydrogen Storage by SWNTs Tatsuto Kimuraa

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

  15. Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

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

    SciTech Connect (OSTI)

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

    2014-01-01

    Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.

  17. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    E-Print Network [OSTI]

    Radek Erban

    2015-08-12

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  18. Microelectronics Journal 39 (2008) 190201 Prototyping bio-nanorobots using molecular dynamics simulation and

    E-Print Network [OSTI]

    Mavroidis, Constantinos

    2008-01-01

    Abstract This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled-nano environments in VR, the operator can design and characterize through physical simulation and 3D visualization) in their native environment. Their use as elementary bio-nanorobotic components are also simulated and the results

  19. Molecular dynamics simulation of chains mobility in polyethylene crystal

    E-Print Network [OSTI]

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

    2014-01-17

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

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

    E-Print Network [OSTI]

    Gaddamanugu, Dhatri

    2010-07-14

    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...

  1. Graphitization of small diamond cluster --Molecular dynamics simulation A. Brdka a,, T.W. Zerda b

    E-Print Network [OSTI]

    Powles, Rebecca

    Elsevier B.V. All rights reserved. Keywords: Nanodiamond; Graphitization; Molecular dynamics simulation 1 of nanodiamond clus- ters (nD-c) [2] is the method that can provide carbon onions with uniform size in a large

  2. Plastic Deformation of Semicrystalline Polyethylene under Extension, Compression, and Shear Using Molecular Dynamics Simulation

    E-Print Network [OSTI]

    Kim, Jun Mo

    Plastic deformation of the stack of alternating crystal and amorphous layers typical of semicrystalline polyethylene is studied by molecular dynamics simulation. A previous investigation of the semicrystalline layered stack ...

  3. A continuum-atomistic method for incorporating Joule heating into classical molecular dynamics simulations

    E-Print Network [OSTI]

    Brenner, Donald W.

    binding electronic structure calculations, pertur- bation models, and quantum-classical Hamiltonians [6 depends on the degree of approximation used in solving the electronic structure problem, which can add-scale molecular dynamics (MD) simulation is not to model electron dynamics, but rather to numerically solve

  4. Coarse-grained Molecular Dynamics Simulation Approach for Polymer Nano-Composites Rubber

    E-Print Network [OSTI]

    Katsumoto, Shingo

    -composite materials are widely used in our daily life. Improvements by nano science and technology are required in orCoarse-grained Molecular Dynamics Simulation Approach for Polymer Nano-Composites Rubber Katsumi dynamics of entangled long- polymer melts and filled polymer rubber by us- ing coarse-grained model. We

  5. Molecular dynamics simulations of atomic-level brittle fracture mechanisms in amorphous silica

    E-Print Network [OSTI]

    Deymier, Pierre

    Molecular dynamics simulations of atomic-level brittle fracture mechanisms in amorphous silica Abstract We have examined the atomic dynamics of the brittle fracture process in amorphous silica using the change in local coordina- tion of atoms. Introduction The brittle fracture process has been a subject

  6. Large-Scale First-Principles Molecular Dynamics simulations on the BlueGene/L Platform

    E-Print Network [OSTI]

    Franchetti, Franz

    . Keywords Electronic structure. Molecular Dynamics. Ab initio simulations. First-principles simulations of the electronic properties of the system. The electronic structure calculation is the most time-consuming part the past three decades to the development of efficient implementations of the electronic structure

  7. Molecular dynamics simulation of formation process of single-walled carbon nanotubes by CCVD method

    E-Print Network [OSTI]

    Maruyama, Shigeo

    chemical vapor deposition (CCVD) method [4-7] has been contrived for a scalable, large-scale production of SWNTs, with various carbon-source molecules tested such as carbon monoxide [4, 7], methane [5 simulations [10, 11] with the Brenner potential [12] or tight-binding molecular dynamics (TBMD) simulation [13

  8. Simulating Perforation of Thin Plates Using Molecular Dynamics Approach Anton M. Krivtsov

    E-Print Network [OSTI]

    Krivtsov, Anton M.

    1 Simulating Perforation of Thin Plates Using Molecular Dynamics Approach Anton M. Krivtsov or molecules, but as elements of the mesoscale level, such as material grains [4,5]. Fig.1: Oblique perforation of plate by ogive-nose projectile. This approach is used in the current work to simulate perforation

  9. A Molecular Dynamics Simulation of the Turbulent Couette Minimal Flow Unit

    E-Print Network [OSTI]

    Smith, E R

    2015-01-01

    A molecular dynamics (MD) simulation of planar Couette flow is presented for the minimal channel in which turbulence structures can be sustained. Evolution over a single breakdown and regeneration cycle is compared to computational fluid dynamics (CFD) simulations. Qualitative similar structures are observed and turbulent statistics show excellent quantitative agreement. The molecular scale law of the wall is presented in which stick-slip molecular wall-fluid interactions replace the no-slip conditions. The impact of grid resolution is explored and the observed structures are seen to be dependant on averaging time and length scales. The kinetic energy spectra show a range of scales are present in the molecular system and that spectral content is dependent on the grid resolution employed. The subgrid velocity of the molecules is compared to spatial averaged velocity using joint probability density functions. Molecular trajectories, diffusions and Lagrangian statistics are presented. The importance of sub-grid ...

  10. Molecular dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels

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

    Tringe, J. W.; Ileri, N.; Levie, H. W.; Stroeve, P.; Ustach, V.; Faller, R.; Renaud, P.

    2015-08-01

    We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage.more »Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.« less

  11. Non-linear and Non-planar Free Thermal Vibration of SWNT in Molecular Dynamic Simulation

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Non-linear and Non-planar Free Thermal Vibration of SWNT in Molecular Dynamic Simulation Heeyuen Koh, James Cannon, Shohei Chiashi, Junichiro Shiomi and Shigeo Maruyama Department of Mechanical-mail: maruyama@photon.t.u-tokyo.ac.jp 1. Introduction Vibration of suspended and cantilevered nanotubes

  12. Molecular dynamics simulations of the elastic properties of polymer/carbon nanotube composites

    E-Print Network [OSTI]

    Elliott, James

    Molecular dynamics simulations of the elastic properties of polymer/carbon nanotube composites Yue of polymer/CNT composites was initially reported by Ajayan et al. [3]. In their research, multi-wall carbon 20 June 2006 Abstract Carbon nanotubes (CNTs) are promising additives to polymeric materials due

  13. Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide into a

    E-Print Network [OSTI]

    Molecular Dynamics Simulations of Folding and Insertion of the Ebola Virus Fusion Peptide- residue Ebola virus fusion peptide into a membrane bilayer. We applied a multi-resolution computational viruses, the filoviruses contain a highly compact genome, consisting of only seven encoded proteins

  14. Mechanical properties of connected carbon nanorings via molecular dynamics simulation Nan Chen and Mark T. Lusk*

    E-Print Network [OSTI]

    van Duin, Adri

    over carbon reinforced resins currently used in industry.5­7 Other approaches for mechanical design as elementary construction components, but other carbon nanostructures may offer additional choices in designingMechanical properties of connected carbon nanorings via molecular dynamics simulation Nan Chen

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

    E-Print Network [OSTI]

    Maruyama, Shigeo

    of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Non-stationary heat conduction in a single-picoseconds. The investigation was based on classical molecular dynamics simulations, where the heat pulse was generated. In a typical macroscopic description, a well-known model of heat wave propagation was formulated by Cattaneo

  16. Molecular dynamics simulation of atomic layer etching of silicon Satish D. Athavale and Demetre J. Economoua)

    E-Print Network [OSTI]

    Economou, Demetre J.

    one layer at a time. Much attention has been paid to deposition, but etching with atomic layerMolecular dynamics simulation of atomic layer etching of silicon Satish D. Athavale and Demetre J atomic layer etching ALET of Si. The total reaction yield Si atoms removed per ion was 0.172; 84

  17. Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes YASUSHI SHIBUTA, SHIGEO MARUYAMA Nucleation process of single-walled carbon nanotubes by the catalytic chemical with randomly distributed carbon-source molecules and a nickel cluster to investigate the metal-catalyzed growth

  18. Molecular Dynamics Simulation of Thin Films with Rough and Asymmetric Interfaces

    E-Print Network [OSTI]

    Walker, D. Greg

    Molecular Dynamics Simulation of Thin Films with Rough and Asymmetric Interfaces N.A. Roberts with the use of interfaces and shows that pristine, imperfect and asymmetric interfaces in thin films can interface whose features are of the order of the phonon wavelength. At a constant temperature difference

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

    E-Print Network [OSTI]

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

    2014-12-15

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

  20. The stressstrain behavior of polymernanotube composites from molecular dynamics simulation

    E-Print Network [OSTI]

    Brenner, Donald W.

    2002 Abstract Stress­strain curves of polymer­carbon nanotube composites generated from molecular years, single-walled carbon nanotube- polymer composites have generated considerable inter- est compared to conventional carbon-fiber-reinforced polymer composites. Even though some nanotube com- posite

  1. Hydrodynamical Simulations of Molecular Dynamics in Supersonic Turbulent Flow

    E-Print Network [OSTI]

    ) = R (T ; n; f) D (T ; n; f) ; (1d) where n is the hydrogen nuclei density, e is the internal energy analyse PDFs of density for the volume, mass, molec- ular mass and the energy distribution over the range density and f is the molecular hydrogen abundance (i.e. n(H 2 ) = fn). We consider the gas as a mixture

  2. Water harvesting using a conducting polymer: A study by molecular dynamics simulation

    SciTech Connect (OSTI)

    Ostwal, Mayur M.; Sahimi, Muhammad; Tsotsis, Theodore T. [Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211 (United States)

    2009-06-15

    The results of extensive molecular simulations of adsorption and diffusion of water vapor in polyaniline, made conducting by doping it with HCl or HBr over a broad range of temperatures, are reported. The atomistic model of the polymers was generated using energy minimization, equilibrium molecular dynamics simulations, and two different force fields. The computed sorption isotherms are in excellent agreement with the experimental data. The computed activation energies for the diffusion of water molecules in the polymers also compare well with what has been reported in the literature. The results demonstrate the potential of conducting polyaniline for water harvesting from air.

  3. Simulation and dynamics of entropy-driven, molecular self-assembly processes

    SciTech Connect (OSTI)

    Mayer, B.; Kohler, G.,; Rasmussen, S.,

    1997-04-01

    Molecular self-assembly is frequently found to generate higher-order functional structures in biochemical systems. One such example is the self-assembly of lipids in aqueous solution forming membranes, micelles, and vesicles; another is the dynamic formation and rearrangement of the cytoskeleton. These processes are often driven by local, short-range forces and therefore the dynamics is solely based on local interactions. In this paper, we introduce a cellular automata based simulation, the lattice molecular automaton, in which data structures, representing different molecular entities such as water and hydrophilic and hydrophobic monomers, share locally propagated force information on a hexagonal, two-dimensional lattice. The purpose of this level of description is the simulation of entropic and enthalpic flows in a microcanonical, molecular ensemble to gain insight about entropy-driven processes in molecular many-particle systems. Three applications are shown, i.e., modeling structural features of a polar solvent, cluster formation of hydrophobic monomers in a polar environment, and the self-assembly of polymers. Processes leading to phase separation on a molecular level are discussed. A thorough discussion of the computational details, advantages, and limitations of the lattice molecular automaton approach is given elsewhere [B. Mayer and S. Rasmussen (unpublished)]. {copyright} {ital 1997} {ital The American Physical Society}

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

    SciTech Connect (OSTI)

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael; Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl

    2011-09-01

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

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

    SciTech Connect (OSTI)

    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

    2012-01-01

    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.

  6. A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor

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

    Yang, L.H.; Brooks III, E.D.; Belak, J.

    1992-01-01

    A molecular dynamics algorithm for performing large-scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked-cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.

  7. Dispersion curves from short-time molecular dynamics simulation. 1. Diatomic chain results

    SciTech Connect (OSTI)

    Noid, D.W.; Broocks, B.T.; Gray, S.K.; Marple, S.L.

    1988-06-16

    The multiple signal classification method (MUSIC) for frequency estimation is used to compute the frequency dispersion curves of a diatomic chain from the time-dependent structure factor. In this paper, the authors demonstrate that MUSIC can accurately determine the frequencies from very short time trajectories. MUSIC is also used to show how the frequencies can vary in time, i.e., along a trajectory. The method is ideally suited for analyzing molecular dynamics simulations of large systems.

  8. Ab initio molecular dynamics simulation of proton hopping in a model polymer membrane

    SciTech Connect (OSTI)

    Devanathan, Ramaswami; Idupulapati, Nagesh B.; Baer, Marcel D.; Mundy, Christopher J.; Dupuis, Michel

    2013-12-10

    We report the results of ab initio molecular dynamics simulations of a model NafionTM polymer membrane initially equilibrated using classical molecular dynamics simulations. We studied three hydration levels (?) of 3, 9, and 15 H2O/SO3- corresponding to dry, hydrated and saturated fuel cell membrane, respectively. The barrier for proton transfer from the SO3-–H3O+ contact ion pair to a solvent-separated ion pair decreased from 2.3 kcal/mol for ? = 3 to 0.8 kcal/mol for ? = 15. The barrier for proton transfer between two water molecules was in the range from 0.7 to 0.8 kcal/mol for the ? values studied. The number of proton shuttling events between a pair of water molecules is an order of magnitude more than the number of proton hops across three distinct water molecules. The proton diffusion coefficient at ? = 15 is about 0.9x10-5 cm2/s, which is in good agreement with experiment and our previous quantum hopping molecular dynamics simulations.

  9. Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

    E-Print Network [OSTI]

    Im, Wonpil; Roux, Benoî t

    2001-01-01

    A general method has been developed to include the electrostatic reaction field in Brownian dynamics (BD) simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent ...

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

    E-Print Network [OSTI]

    Han, Kunwoo

    2009-06-02

    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. ...

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

    E-Print Network [OSTI]

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

    2015-04-21

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

  12. High Performance Molecular Dynamic Simulation on Single and Multi-GPU Systems

    SciTech Connect (OSTI)

    Villa, Oreste; Chen, Long; Krishnamoorthy, Sriram

    2010-05-30

    The programming techniques supported and employed on these GPUs and Multi-GPUs systems are not sufficient to address problems exhibiting irregular, and unbalanced workload such as Molecular Dynamic (MD) simulations of systems with non-uniform densities. In this paper, we propose a task-based dynamic load-balancing solution to employ on MD simulations for single- and multi-GPU systems. The solution allows load balancing at a finer granularity than what is supported in existing APIs such as NVIDIA’s CUDA. Experimental results with a single-GPU configuration show that our fine-grained task solution can utilize the hardware more efficiently than the CUDA scheduler. On multi-GPU systems, our solution achieves near-linear speedup, load balance, and significant performance improvement over techniques based on standard CUDA APIs.

  13. A model of lipid-free Apolipoprotein A-I revealed by iterative molecular dynamics simulation

    SciTech Connect (OSTI)

    Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli

    2015-03-20

    Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipidfree apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.

  14. A model of lipid-free Apolipoprotein A-I revealed by iterative molecular dynamics simulation

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

    Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli

    2015-03-20

    Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore,more »by integrating various experimental results, we proposed a new structural model for lipidfree apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.« less

  15. Adhesion between elastic solids with randomly rough surfaces: comparison of analytical theory with molecular dynamics simulations

    E-Print Network [OSTI]

    N. Mulakaluri; B. N. J. Persson

    2011-12-22

    The adhesive contact between elastic solids with randomly rough, self affine fractal surfaces is studied by molecular dynamics (MD) simulations. The interfacial binding energy obtained from the simulations of nominally flat and curved surfaces is compared with the predictions of the contact mechanics theory by Persson. Theoretical and simulation results agree rather well, and most of the differences observed can be attributed to finite size effects and to the long-range nature of the interaction between the atoms in the block and the substrate in the MD model, as compared to the analytical theory which is for an infinite system with interfacial contact interaction. For curved surfaces (JKR-type of problem) the effective interfacial energy exhibit a weak hysteresis which may be due to the influence of local irreversible detachment processes in the vicinity of the opening crack tip during pull-off.

  16. Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer: an application to polymer lubrication

    E-Print Network [OSTI]

    Shugo Yasuda; Ryoichi Yamamoto

    2014-07-16

    The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid elements to calculate the local stresses and temperatures and are synchronized at certain time intervals to satisfy the macroscopic heat- and momentum- transport equations. This method is applied to the lubrication of a polymeric liquid composed of short chains with ten beads between parallel plates. The rheological properties and conformation of polymer chains coupled with the local viscous heating are investigated with a non-dimensional parameter, i.e., the Nahme-Griffith number, which is defined by the ratio of the viscous heating to the thermal conduction at the characteristic temperature required to sufficiently change the viscosity. The present simulation demonstrates that strong shear thinning and transitional behavior of the conformation of the polymer chains occur with a rapid temperature rise when the Nahme-Griffith number exceeds unity. The results also clarify that the reentrant transition of the linear stress-optical relation occurs for large shear stresses due to the coupling of the conformation of polymer chains and heat generation under shear flows.

  17. Entropic measure to prevent energy over-minimization in molecular dynamics simulations

    E-Print Network [OSTI]

    Rydzewski, Jakub; Nowak, Wieslaw

    2015-01-01

    Geometry optimization via energy minimization is one of the most common steps in computer modelling of biological structures. Nowadays computer power encourage numerous researches to use conjugated gradient minimizations exceeding 1000 steps. However, our research reveals that such over-minimization may lead to thermodynamically unstable conformations. We show that these conformations are not optimum starting points for equilibrium molecular dynamics simulations. We propose a measure based on the Pareto front of total entropy for quality assessment of minimized protein which warrants a proper selection of minimization steps.

  18. Molecular dynamics simulations of organic SIMS with Cu{sub n} (n=1-3) clusters

    SciTech Connect (OSTI)

    Townes, J. A.; White, A. K.; Krantzman, K. D.; Garrison, B. J.

    1999-06-10

    Molecular dynamics simulations have been performed to study the effect of cluster size on the emission yield and damage cross section in organic SIMS. A model system composed of a monolayer of biphenyl molecules on a Cu(001) substrate was bombarded with Cu{sub n} (n=1-3) projectiles at kinetic energies of 0.100 keV per atom. The yield increases with cluster size, but a nonlinear enhancement in yield is not observed. The yield-to-damage ratio, on the other hand, increases with the use of clusters, indicating that clusters have the potential to improve the sensitivity of SIMS.

  19. Molecular Dynamics Simulations of Displacement Cascades in Single and Polycrystalline Zirconia

    SciTech Connect (OSTI)

    Du Jincheng

    2009-03-10

    Displacement cascades in zirconia have been studied using classical molecular dynamics simulations. Polycrystalline zirconia with nano-meter grains were created using Voronoi polyhedra construction and studied in comparison with single crystalline zirconia. The results show that displacement cascades with similar kinetic energy generated larger number of displaced atoms in polycrystalline than in the single crystal structure. The fraction of atoms with coordination number change was also higher in polycrystalline zirconia that was explained to be due to the diffusion of oxygen and relaxation at grain boundaries.

  20. ENS'05 Paris, France, 14-16 December 2005 PROTOTYPING BIO-NANOROBOTS USING MOLECULAR DYNAMIC SIMULATION

    E-Print Network [OSTI]

    Mavroidis, Constantinos

    @coe.neu.edu ABSTRACT This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled the operator can design, characterize and prototype the behavior of bio-nanorobotic components and structures) in their native environment. Their use as elementary bio-nanorobotic components are also simulated and the results

  1. Lubricant characterization by molecular simulation

    SciTech Connect (OSTI)

    Moore, J.D.; Cui, S.T.; Cummings, P.T.; Cochran, H.D.

    1997-12-01

    The authors have reported the calculation of the kinematic viscosity index of squalane from nonequilibrium molecular dynamics simulations. This represents the first accurate quantitative prediction of this measure of lubricant performance by molecular simulation. Using the same general alkane potential model, this computational approach offers the possibility of predicting the performance of potential lubricants prior to synthesis. Consequently, molecular simulation is poised to become an important tool for future lubricant development.

  2. Study on the thermal resistance in secondary particles chain of silica aerogel by molecular dynamics simulation

    SciTech Connect (OSTI)

    Liu, M. [Institute of Engineering Thermophysics, Chinese Academy of Sciences, Beijing100190 (China); Department of Physics, University of Chinese Academy of Sciences, Beijing 100049 (China); Qiu, L., E-mail: qiulin111@sina.com, E-mail: jzzhengxinghua@163.com; Zheng, X. H., E-mail: qiulin111@sina.com, E-mail: jzzhengxinghua@163.com; Zhu, J.; Tang, D. W. [Institute of Engineering Thermophysics, Chinese Academy of Sciences, Beijing100190 (China)

    2014-09-07

    In this article, molecular dynamics simulation was performed to study the heat transport in secondary particles chain of silica aerogel. The two adjacent particles as the basic heat transport unit were modelled to characterize the heat transfer through the calculation of thermal resistance and vibrational density of states (VDOS). The total thermal resistance of two contact particles was predicted by non-equilibrium molecular dynamics simulations (NEMD). The defects were formed by deleting atoms in the system randomly first and performing heating and quenching process afterwards to achieve the DLCA (diffusive limited cluster-cluster aggregation) process. This kind of treatment showed a very reasonable prediction of thermal conductivity for the silica aerogels compared with the experimental values. The heat transport was great suppressed as the contact length increased or defect concentration increased. The constrain effect of heat transport was much significant when contact length fraction was in the small range (<0.5) or the defect concentration is in the high range (>0.5). Also, as the contact length increased, the role of joint thermal resistance played in the constraint of heat transport was increasing. However, the defect concentration did not affect the share of joint thermal resistance as the contact length did. VDOS of the system was calculated by numerical method to characterize the heat transport from atomic vibration view. The smaller contact length and greater defect concentration primarily affected the longitudinal acoustic modes, which ultimately influenced the heat transport between the adjacent particles.

  3. Diffusion of a Janus nanoparticle in an explicit solvent: A molecular dynamics simulation study

    E-Print Network [OSTI]

    Ali Kharazmi; Nikolai V. Priezjev

    2015-05-14

    Molecular dynamics simulations are carried out to study the translational and rotational diffusion of a single Janus particle immersed in a dense Lennard-Jones fluid. We consider a spherical particle with two hemispheres of different wettability. The analysis of the particle dynamics is based on the time-dependent orientation tensor, particle displacement, as well as the translational and angular velocity autocorrelation functions. It was found that both translational and rotational diffusion coefficients increase with decreasing surface energy at the nonwetting hemisphere, provided that the wettability of the other hemisphere remains unchanged. We also observed that in contrast to homogeneous particles, the nonwetting hemisphere of the Janus particle tends to rotate in the direction of the displacement vector during the rotational relaxation time.

  4. Interfacial water on crystalline silica: A comparative molecular dynamics simulation study

    SciTech Connect (OSTI)

    Ho, Tuan A. [University of Oklahoma, Norman; Argyris, D. [University of Oklahoma, Norman; Cole, David [Ohio State University; Striolo, Alberto [Oklahoma University

    2011-01-01

    All-atom molecular dynamics simulations were conducted to study the dynamics of aqueous electrolyte solutions confined in slit-shaped silica nanopores of various degrees of protonation. Five degrees of protonation were prepared by randomly removing surface hydrogen atoms from fully protonated crystalline silica surfaces. Aqueous electrolyte solutions containing NaCl or CsCl salt were simulated at ambient conditions. In all cases, the ionic concentration was 1 M. The results were quantified in terms of atomic density distributions within the pores, and the self-diffusion coefficient along the direction parallel to the pore surface. We found evidence for ion-specific properties that depend on ion surface, water ion, and only in some cases ion ion correlations. The degree of protonation strongly affects the structure, distribution, and the dynamic behavior of confined water and electrolytes. Cl ions adsorb on the surface at large degrees of protonation, and their behavior does not depend significantly on the cation type (either Na+ or Cs+ ions are present in the systems considered). The cations show significant ion-specific behavior. Na+ ions occupy different positions within the pore as the degree of protonation changes, while Cs+ ions mainly remain near the pore center at all conditions considered. For a given degree of protonation, the planar self-diffusion coefficient of Cs+ is always greater than that of Na+ ions. The results are useful for better understanding transport under confinement, including brine behavior in the subsurface, with important applications such as environmental remediation.

  5. A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

    SciTech Connect (OSTI)

    Shimojo, Fuyuki; Hattori, Shinnosuke [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States) [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States)] [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Kunaseth, Manaschai [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States) [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); National Nanotechnology Center, Pathumthani 12120 (Thailand); Ohmura, Satoshi [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States) [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Department of Physics, Kyoto University, Kyoto 606-8502 (Japan); Shimamura, Kohei [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States) [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan); Department of Applied Quantum Physics and Nuclear Engineering, Kyushu University, Fukuoka 819-0395 (Japan)

    2014-05-14

    We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786?432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16?661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.

  6. Quantify Water Extraction by TBP/Dodecane via Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Khomami, Bamin; Cui, Shengting; de Almeida, Valmor F.; Felker, Kevin

    2013-05-16

    The purpose of this project is to quantify the interfacial transport of water into the most prevalent nuclear reprocessing solvent extractant mixture, namely tri-butyl- phosphate (TBP) and dodecane, via massively parallel molecular dynamics simulations on the most powerful machines available for open research. Specifically, we will accomplish this objective by evolving the water/TBP/dodecane system up to 1 ms elapsed time, and validate the simulation results by direct comparison with experimentally measured water solubility in the organic phase. The significance of this effort is to demonstrate for the first time that the combination of emerging simulation tools and state-of-the-art supercomputers can provide quantitative information on par to experimental measurements for solvent extraction systems of relevance to the nuclear fuel cycle. Results: Initially, the isolated single component, and single phase systems were studied followed by the two-phase, multicomponent counterpart. Specifically, the systems we studied were: pure TBP; pure n-dodecane; TBP/n-dodecane mixture; and the complete extraction system: water-TBP/n-dodecane two phase system to gain deep insight into the water extraction process. We have completely achieved our goal of simulating the molecular extraction of water molecules into the TBP/n-dodecane mixture up to the saturation point, and obtained favorable comparison with experimental data. Many insights into fundamental molecular level processes and physics were obtained from the process. Most importantly, we found that the dipole moment of the extracting agent is crucially important in affecting the interface roughness and the extraction rate of water molecules into the organic phase. In addition, we have identified shortcomings in the existing OPLS-AA force field potential for long-chain alkanes. The significance of this force field is that it is supposed to be optimized for molecular liquid simulations. We found that it failed for dodecane and/or longer chains for this particular solvent extraction application. We have proposed a simple way to circumvent the artificial crystallization of the chains at ambient temperature.

  7. Molecular dynamics simulations of grain boundary thermal resistance in UO2

    SciTech Connect (OSTI)

    Tianyi Chen; Di Chen; Bulent H. Sencer; Lin Shao

    2014-09-01

    By means of molecular dynamics (MD) simulations, we have calculated Kaptiza resistance of UO2 with or without radiation damage. For coincident site lattice boundaries of different configurations, the boundary thermal resistance of unirradiated UO2 can be well described by a parameter-reduced formula by using boundary energies as variables. We extended the study to defect-loaded UO2 by introducing damage cascades in close vicinity to the boundaries. Following cascade annealing and defect migrations towards grain boundaries, the boundary energy increases and so does Kaptiza resistance. The correlations between these two still follow the same formula extracted from the unirradiated UO2. The finding will benefit multi-scale modeling of UO2 thermal properties under extreme radiation conditions by combining effects from boundary configurations and damage levels.

  8. Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates

    E-Print Network [OSTI]

    Yasuda, Shugo

    2015-01-01

    The Synchronized Molecular-Dynamics simulation which was recently proposed by authors [Phys. Rev. X {\\bf 4}, 041011 (2014)] is applied to the analysis of polymer lubrication between parallel plates. The rheological properties, conformational change of polymer chains, and temperature rise due to the viscous heating are investigated with changing the values of thermal conductivity of the polymeric liquid. It is found that at a small applied shear stress on the plate, the temperature of polymeric liquid only slightly increases in inverse proportion to the thermal conductivity and the apparent viscosity of polymeric liquid is not much affected by changing the thermal conductivity. However, at a large shear stress, the transitional behaviors of the polymeric liquid occur due to the interplay of the shear deformation and viscous heating by changing the thermal conductivity. This transition is characterized by the Nahme-Griffith number $Na$ which is defined as the ratio of the viscous heating to the thermal conducti...

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

    SciTech Connect (OSTI)

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

    2008-08-01

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

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

    SciTech Connect (OSTI)

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

    2008-06-01

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

  11. HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation

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

    Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; et al

    2015-03-04

    Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density lipoproteins (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing the risk of cardiovascular diseases (CVD). Although the crystal structure of CETP is known, little is known regarding how CETP binds to HDL. Here, we investigated how various HDL-like particles interact with CETP by electron microscopy and molecular dynamics simulations. Results showed that CETP binds to HDL via hydrophobic interactions rather than protein-protein interactions. The HDL surface lipid curvature generates a hydrophobicmore »environment, leading to CETP hydrophobic distal end interaction. This interaction is independent of other HDL components, such as apolipoproteins, cholesteryl esters and triglycerides. Thus, disrupting these hydrophobic interactions could be a new therapeutic strategy for attenuating the interaction of CETP with HDL.« less

  12. Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers

    SciTech Connect (OSTI)

    Guallar, V.; Batista, V.S.; Miller, W.H. [Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)] [Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    1999-05-01

    An {ital ab initio} excited state potential energy surface is constructed for describing excited state double proton transfer in the tautomerization reaction of photo-excited 7-azaindole dimers, and the ultrafast dynamics is simulated using the semiclassical (SC) initial value representation (IVR). The potential energy surface, determined in a reduced dimensionality, is obtained at the CIS level of quantum chemistry, and an approximate version of the SC-IVR approach is introduced which scales {ital linearly} with the number of degrees of freedom of the molecular system. The accuracy of this approximate SC-IVR approach is verified by comparing our semiclassical results with full quantum mechanical calculations. We find that proton transfer usually occurs during the first intermonomer symmetric-stretch vibration, about 100 fs after photoexcitation of the system, and produces an initial 15 percent population decay of the reactant base-pair, which is significantly reduced by isotopic substitution. {copyright} {ital 1999 American Institute of Physics.} thinsp

  13. Molecular dynamics simulations of 30 and 2 keV Ga in Si

    SciTech Connect (OSTI)

    Giannuzzi, Lucille A.; Garrison, Barbara J.

    2007-09-15

    Focused Ga{sup +} ion beams are routinely used at high incident angles for specimen preparation. Molecular dynamics simulations of 2 and 30 keV Ga bombardment of Si(011) at a grazing angle of 88 deg. were conducted to assess sputtering characteristics and damage depth. The bombardment of atomically flat surfaces and surfaces with vacancies shows little energy transfer yielding ion reflection. The bombardment of surfaces with adatoms allows for the coupling of the energy of motion parallel to the surface into the substrate resulting in sputtering. The adatom and one other Si atom eject, and motion in the substrate occurs down to a depth of 13 A. Experimental evidence shows that sputtering is a reality, suggesting that an atomically flat surface is never achieved.

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

    E-Print Network [OSTI]

    Lisal, Martin

    considering the solubility of solid electrolytes in solvents, one can view the dissolution process into individual ionic species in the solvent. At saturation, the solid electrolyte may be regarded as a reservoirMolecular Simulations of Aqueous Electrolyte Solubility: 1. The Expanded-Ensemble Osmotic Molecular

  15. A new algorithm for contact angle estimation in molecular dynamics simulations

    E-Print Network [OSTI]

    Sumith YD; Shalabh C. Maroo

    2015-05-22

    It is important to study contact angle of a liquid on a solid surface to understand its wetting properties, capillarity and surface interaction energy. While performing transient molecular dynamics (MD) simulations it requires calculating the time evolution of contact angle. This is a tedious effort to do manually or with image processing algorithms. In this work we propose a new algorithm to estimate contact angle from MD simulations directly and in a computationally efficient way. This algorithm segregates the droplet molecules from the vapor molecules using Mahalanobis distance (MND) technique. Then the density is smeared onto a 2D grid using 4th order B-spline interpolation function. The vapor liquid interface data is estimated from the grid using density filtering. With the interface data a circle is fitted using Landau method. The equation of this circle is solved for obtaining the contact angle. This procedure is repeated by rotating the droplet about the vertical axis. We have applied this algorithm to a number of studies (different potentials and thermostat methods) which involves the MD simulation of water.

  16. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

    SciTech Connect (OSTI)

    Wall, Michael E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Van Benschoten, Andrew H. [Univ. of California, San Francisco, CA (United States); Sauter, Nicholas K. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Adams, Paul D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Fraser, James S. [Univ. of California, San Francisco, CA (United States); Terwilliger, Thomas C. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-12-01

    X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-?s MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

  17. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

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

    Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

    2014-12-01

    X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-?s MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore »of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

  18. Transport properties of CO2-expanded acetonitrile from molecular dynamics simulations

    E-Print Network [OSTI]

    Houndonougbo, Yao; Laird, Brian Bostian; Kuczera, Krzysztof

    2007-02-21

    Carbon-dioxide-expanded liquids, which are mixtures of organic liquids and compressed CO2, are novel media used in chemical processing. The authors present a molecular simulation study of the transport properties of liquid mixtures formed...

  19. Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

    E-Print Network [OSTI]

    Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations The heat capacity has played a major role in relating microscopic and macroscopic properties of proteins, and configurational averaging. To better understand these factors on calculating a protein heat capacity, we provide

  20. THE JOURNAL OF CHEMICAL PHYSICS 138, 244310 (2013) Molecular dynamics simulations for CO2 spectra. IV. Collisional line-mixing

    E-Print Network [OSTI]

    Boyer, Edmond

    2013-01-01

    atmosphere of Venus (about 96.5% of CO2) where the pressure is high (up to 90 bar). Similarly, narrow involving CO2 with a few for the pure gas in the infrared at high pressure12­17 and Raman Q branches.4THE JOURNAL OF CHEMICAL PHYSICS 138, 244310 (2013) Molecular dynamics simulations for CO2 spectra

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

    E-Print Network [OSTI]

    de Gispert, Adrià

    A molecular dynamics simulation of the melting points and glass transition temperatures of myo transition temperature are calculated for myo- and neo-inositol, using the condensed-phase optimized temperatures for myo- and neo-inositol also compare very well to the experimentally obtained data. The glass

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

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

  3. Development of EEM based silicon–water and silica–water wall potentials for non-reactive molecular dynamics simulations

    SciTech Connect (OSTI)

    Kim, Junghan; Iype, Eldhose; Frijns, Arjan J.H.; Nedea, Silvia V.; Steenhoven, Anton A. van

    2014-07-01

    Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.

  4. Ab initio molecular dynamics simulation of pressure-induced phase transformation of BeO

    SciTech Connect (OSTI)

    Xiao, H. Y.; Duan, G.; Zu, X. T.; Weber, W. J.

    2011-05-05

    Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ ? RS and ZB ? RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ ? RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchange–correlation functional employed and the way of applying pressure.

  5. Molecular dynamics simulations of shock waves in hydroxyl-terminated polybutadiene melts: Mechanical and structural responses

    SciTech Connect (OSTI)

    Fröhlich, Markus G. E-mail: ThompsonDon@missouri.edu; Sewell, Thomas D. Thompson, Donald L. E-mail: ThompsonDon@missouri.edu

    2014-01-14

    The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup ?1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ?0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.

  6. Binding kinetics of membrane-anchored receptors and ligands: molecular dynamics simulations and theory

    E-Print Network [OSTI]

    Jinglei Hu; Guang-Kui Xu; Reinhard Lipowsky; Thomas R. Weikl

    2015-11-24

    The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring of the proteins. In this article, we (i) present detailed data for the binding of membrane-anchored proteins from coarse-grained molecular dynamics simulations, and (ii) provide a theory that describes how the binding kinetics depends on the average separation and thermal roughness of the adhering membranes, and on the anchoring, lengths, and length variations of the proteins. An important element of our theory is the tilt of bound receptor-ligand complexes and transition-state complexes relative to the membrane normals. This tilt results from an interplay of the anchoring energy and rotational entropy of the complexes and facilitates the formation of receptor-ligand bonds at membrane separations smaller than the preferred separation for binding. In our simulations, we have considered both lipid-anchored and transmembrane receptor and ligand proteins. We find that the binding equilibrium constant and binding on-rate constant of lipid-anchored proteins are considerably smaller than the binding constant and on-rate constant of rigid transmembrane proteins with identical binding domains.

  7. Homogeneous SPC/E water nucleation in large molecular dynamics simulations

    E-Print Network [OSTI]

    Angelil, R; Tanaka, K; Tanaka, H

    2015-01-01

    We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to $\\sim 4\\cdot 10^6$ molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to $\\sim 10^{19}\\,\\textrm{cm}^{-3}\\textrm{s}^{-1}$, helping close the gap between experimentally measured rates $\\sim 10^{17}\\,\\textrm{cm}^{-3}\\textrm{s}^{-1}$. We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst, a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run avera...

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

    E-Print Network [OSTI]

    Guido Tiana; Carlo Camilloni

    2012-07-05

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

  9. Self-siphon simulation using molecular dynamics method: a preliminary study

    E-Print Network [OSTI]

    Viridi, Sparisoma; Khotimah, Siti Nurul; Novitrian,; Masterika, Fannia

    2011-01-01

    A self activated siphon, which is also known as self-siphon or self-priming siphon, is simulated using molecular dynamics (MD) method in order to study its behavior, especially why it has a critical height that prevents fluid from flowing through it. The trajectory of the fluid interface with air in front of the flow or the head is also fitted the trajectory modeled by parametric equations s, which is derived from geometry construction of the self-siphon. Numerical equations solved using MD method is derived from equations of motion of the head which is obtained by introducing all considered forces influencing the movement of it. Time duration needed for fluid to pass the entire tube of the self-siphon, {\\tau}, obtained from the simulation is compared quantitatively to the observation data from the previous work and it shows inverse behavior. Length of the three vertical segments are varied independently using a parameter for each segment, which are N5, N3, and N1. Room parameters of N5, N3, and N1 are constr...

  10. 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]

    Rich, Sarah Celeste

    2008-01-01

    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 ...

  11. Instabilities in Molecular Dynamics Integrators used in Hybrid Monte Carlo Simulations

    E-Print Network [OSTI]

    B. Joo; UKQCD Collaboration

    2001-10-11

    We discuss an instability in the leapfrog integration algorithm, widely used in current Hybrid Monte Carlo (HMC) simulations of lattice QCD. We demonstrate the instability in the simple harmonic oscillator (SHO) system where it is manifest. We demonstrate the instability in HMC simulations of lattic QCD with dynamical Wilson-Clover fermions and discuss implications for future simulations of lattice QCD.

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

    SciTech Connect (OSTI)

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

    1994-12-01

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

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

    E-Print Network [OSTI]

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

    2006-01-01

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

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

    SciTech Connect (OSTI)

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

    2014-03-21

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

  15. Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates

    E-Print Network [OSTI]

    Shugo Yasuda; Ryoichi Yamamoto

    2015-03-25

    The Synchronized Molecular-Dynamics simulation which was recently proposed by authors [Phys. Rev. X {\\bf 4}, 041011 (2014)] is applied to the analysis of polymer lubrication between parallel plates. The rheological properties, conformational change of polymer chains, and temperature rise due to the viscous heating are investigated with changing the values of thermal conductivity of the polymeric liquid. It is found that at a small applied shear stress on the plate, the temperature of polymeric liquid only slightly increases in inverse proportion to the thermal conductivity and the apparent viscosity of polymeric liquid is not much affected by changing the thermal conductivity. However, at a large shear stress, the transitional behaviors of the polymeric liquid occur due to the interplay of the shear deformation and viscous heating by changing the thermal conductivity. This transition is characterized by the Nahme-Griffith number $Na$ which is defined as the ratio of the viscous heating to the thermal conduction at a characteristic temperature. When the Nahme-Griffith number exceeds the unity, the temperature of polymeric liquid increases rapidly and the apparent viscosity also exponentially decreases as the thermal conductivity decreases. The conformation of polymer chains is stretched and aligned by the shear flow for $Na1$.

  16. Molecular dynamics simulation for arrangement of nickel atoms filled in carbon nanotubes

    SciTech Connect (OSTI)

    Bai, Liu Zhenyu, Zhao; Lirui, Liu

    2014-08-28

    Carbon Nanotubes (CNTs) filled with metals can be used in capacitors, sensors, rechargeable batteries, and so on. Atomic arrangement of the metals has an important role in the function of the composites. The tips of CNTs were opened, and then nickel was filled by means of hydrothermal oxidation/ultrasonic vibration method. The tests of TEM, HREM, and EDX (energy-dispersive X-ray spectroscopy) analysis showed that Ni was filled in CNTs successfully. The atomic arrangement of nickel filled into single wall carbon nanotubes was investigated by molecular dynamics simulation. The radial distribution function and bond orientation order were established to analyze the atomic arrangement of nickel filled in carbon nanotubes during the cooling process. The results show that nickel atoms became in order gradually and preferably crystallized on the inner wall of carbon nanotubes when the temperature decreased from 1600?K. After it cooled to 100?K, the arrangement of nickel atoms in outermost circle was regular and dense, but there were many defects far from the wall of CNTs. According to the calculation of bond orientation order parameters Q{sub 6} and its visualization, the structure of nickel is Face-centered cube (f.c.c). (1,1,1){sub Ni} was close on the inner surface of carbon nanotubes. Radial direction of CNTs was [1,1,1] crystal orientation. Axial direction of CNTs, namely, filling direction, was [1{sup ¯}, 1{sup ¯},2] crystal orientation.

  17. Segregated structure of ring polymer melts near the surface: Molecular dynamics simulation study

    E-Print Network [OSTI]

    Eunsang Lee; YounJoon Jung

    2015-10-20

    We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are similar to each other because the length scale of surface-monomer excluded volume interaction is smaller than the size of an ideal blob of the ring. In a long length scale, while the Silberberg hypothesis can be used to provide a physical origin of confined linear polymer results, it no longer holds for a ring polymer case. We also present different structural properties of ring and linear polymers in a melt, including the size of polymers, an adsorbed amount, and the coordination number of a polymer. Our observation reveals that a confined ring in a melt adopts highly segregated conformation due to a topological excluded volume repulsion, which may provide a new perspective to understand the nature of biological processes, such as territorial segregation of chromosomes in eukaryotic nuclei.

  18. Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone

    SciTech Connect (OSTI)

    Batista, V.S.; Miller, W.H. [Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)] [Department of Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    1998-01-01

    In this paper we investigate the nonadiabatic ultrafast dynamics of interconversion between the two lower lying excited states of {sup 1}A{sup {double_prime}} symmetry (1 {sup 1}A{sup {double_prime}} and 2 {sup 1}A{sup {double_prime}}) of ozone following photoexcitation of the molecule in the gas phase with visible light. Our algorithm involves a semiclassical initial value representation method which is able to describe electronically nonadiabatic processes within the time dependent picture through the quantization of the classical electron{endash}nuclear model Hamiltonian of Meyer and Miller [J. Chem. Phys. {bold 70}, 7 (1979)]. We explore the capabilities of these techniques as applied to studying the dynamics of a realistic reaction of photodissociation on full {ital ab initio} electronic potential energy surfaces. Our semiclassical results provide an intuitive understanding of the most fundamental dynamical features involved in the process of predissociation, such as decay and recurrence events, as well as an interpretation of experimental studies of the Chappuis band of ozone in the frequency domain. {copyright} {ital 1998 American Institute of Physics.}

  19. Mapping molecular dynamics computations to hypercubes 

    E-Print Network [OSTI]

    Lakamsani, Vamsee Krishna

    1993-01-01

    This thesis proposes an approach for systematic modeling, mapping and performance analysis of a Grand Challenge application problem in computational biology called Molecular Dynamics Simulation of Proteins. Molecular Dynamics (MD) is an important...

  20. Assessment of Molecular Modeling & Simulation

    SciTech Connect (OSTI)

    2002-01-03

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

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

    SciTech Connect (OSTI)

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

    2014-05-07

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

  2. A Study of UO2 Grain Boundary Structure and Thermal Resistance Change under Irradiation using Molecular Dynamics Simulations 

    E-Print Network [OSTI]

    Chen, Tianyi

    2013-08-02

    OF UO2 GRAIN BOUNDARY STUCTURE AND THERMAL RESISTANCE CHANGE UNDER IRRADIATION USING MOLECULAR DYNAMICS SIMULATIONS A Thesis by TIANYI CHEN Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment...] As the fuel expands to reach the cladding, the fuel cladding interaction begins to draw attention. The first thing is the fuel/cladding mechanical interaction. This phenomenon is very serious in early designed reactors since they do not have enough spaces...

  3. Inter-cage dynamics in structure I, II, and H fluoromethane hydrates as studied by NMR and molecular dynamics simulations

    SciTech Connect (OSTI)

    Trueba, Alondra Torres; Kroon, Maaike C.; Peters, Cor J.; Moudrakovski, Igor L.; Ratcliffe, Christopher I.; Ripmeester, John A.; Alavi, Saman

    2014-06-07

    Prospective industrial applications of clathrate hydrates as materials for gas separation require further knowledge of cavity distortion, cavity selectivity, and defects induction by guest-host interactions. The results presented in this contribution show that under certain temperature conditions the guest combination of CH{sub 3}F and a large polar molecule induces defects on the clathrate hydrate framework that allow intercage guest dynamics. {sup 13}C NMR chemical shifts of a CH{sub 3}F/CH{sub 4}/TBME sH hydrate and a temperature analysis of the {sup 2}H NMR powder lineshapes of a CD{sub 3}F/THF sII and CD{sub 3}F/TBME sH hydrate, displayed evidence that the populations of CH{sub 4} and CH{sub 3}F in the D and D{sup ?} cages were in a state of rapid exchange. A hydrogen bonding analysis using molecular dynamics simulations on the TBME/CH{sub 3}F and TBME/CH{sub 4} sH hydrates showed that the presence of CH{sub 3}F enhances the hydrogen bonding probability of the TBME molecule with the water molecules of the cavity. Similar results were obtained for THF/CH{sub 3}F and THF/CH{sub 4} sII hydrates. The enhanced hydrogen bond formation leads to the formation of defects in the water hydrogen bonding lattice and this can enhance the migration of CH{sub 3}F molecules between adjacent small cages.

  4. Is the Calcite-Water Interface Understood? Direct Comparisons of Molecular Dynamics Simulations with Specular X-ray Reflectivity Data

    SciTech Connect (OSTI)

    Fenter, Paul; Kerisit, Sebastien N.; Raiteri, Paolo; Gale, Julian D.

    2013-04-01

    New insights into the structure of the calcite-water interface are obtained through direct model-independent comparison of multiple classical molecular dynamics (MD) simulations with high-resolution specular X-ray reflectivity (XR) data. This set of comparisons, with four different state-of-the-art force fields (including two non-polarizable, one polarizable, and one reactive force field), reveal new insights into the absolute accuracy of the simulated structures and the uniqueness of the XR-derived structural results. These four simulations, while qualitatively similar, have visibly distinct interfacial structure, and are distinguished through a quantitative comparison of the XR signals calculated from these simulations with experimental XR data. The results demonstrate that the simulated calcite-water interface structures, as a whole, are not consistent with the XR data (i.e., within their precision and accuracy). This disagreement is largely due to the simulation of the calcite lattice. The simulated interfacial water profiles show substantially different levels of agreement with the XR data. Of these, the rigid-ion model (RIM) simulations show the best consistency with the experimental XR data. Further model-dependent comparisons of the structural parameters that describe the interfacial structure (derived from both the MD simulations and the XR data) provide further insight into the sources of differences between these two approaches. Using the new insights from the RIM simulations, new structures of the calcite-water interface consistent with both the experimental data and the simulation are identified and compared to recent results.

  5. Molecular Simulations of Electrolytes and Electrolyte/Electrode...

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

    electrode interfaces Molecular dynamics simulation studies of electrolytes and electrolyteelectrode interfaces Linking Ion Solvation and Lithium Battery Electrolyte Properties...

  6. Hybrid Quantum Mechanics/Molecular Mechanics-Based Molecular Dynamics Simulation of Acid-Catalyzed Dehydration of Polyols in Liquid Water

    SciTech Connect (OSTI)

    Caratzoulas, Stavros; Courtney, Timothy; Vlachos, Dionisios G.

    2011-01-01

    We use the conversion of protonated glycerol to acrolein for a case study of the mechanism of acid-catalyzed dehydration of polyols in aqueous environments. We employ hybrid Quamtum Mechanics/Molecular Mechanics Molecular Dynamics (QM/MM MD) simulations with biased sampling and perform free energy calculations for the elementary steps of the reaction. We investigate the effects of solvent dynamics and in particular the role of quantum mechanical water in the dehydration mechanism. We present results supporting a mechanism that proceeds via water-mediated proton transfers and thus through an enol intermediate. We find that the first dehydration may take place by two, low-energy pathways requiring, respectively, 20.9 and 18.8 kcal/mol of activation free energy. The second dehydration requires 19.9 kcal/mol of activation free energy while for the overall reaction we compute a free energy change of -8 kcal/mol.

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

    SciTech Connect (OSTI)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2013-12-21

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

  8. Superstatistical velocity distributions of cold trapped ions in molecular dynamics simulations

    E-Print Network [OSTI]

    Rouse, I

    2015-01-01

    We present a realistic molecular-dynamics treatment of laser-cooled ions in radiofrequency ion traps which avoids previously made simplifications such as modeling laser cooling as a friction force and combining individual heating mechanisms into a single effective heating force. Based on this implementation, we show that infrequent energetic collisions of single ions with background gas molecules lead to pronounced heating of the entire ion ensemble and a time-varying secular ensemble temperature which manifests itself in a superstatistical time-averaged velocity distribution of the ions. The effect of this finding on the experimental determination of ion temperatures and rate constants for cold chemical reactions is discussed.

  9. Study of iron structure stability in high temperature molten lead-bismuth eutectic with oxygen injection using molecular dynamics simulation

    SciTech Connect (OSTI)

    Arkundato, Artoto [Physics Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Su'ud, Zaki [Physics Department, Faculty of Mathematical and Natural Sciences, Bandung Institute of Technology, Jl. Ganesha 10, Bandung (Indonesia); Sudarko [Chemistry Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Shafii, Mohammad Ali [Physics Department, Faculty of Mathematical and Natural Sciences, Andalas University, Padang (Indonesia); Celino, Massimo [ENEA, CR Casaccia, Via Anguillarese 301, Rome (Italy)

    2014-09-30

    Corrosion of structural materials in high temperature molten lead-bismuth eutectic is a major problem for design of PbBi cooled reactor. One technique to inhibit corrosion process is to inject oxygen into coolant. In this paper we study and focus on a way of inhibiting the corrosion of iron using molecular dynamics method. For the simulation results we concluded that effective corrosion inhibition of iron may be achieved by injection 0.0532 wt% to 0.1156 wt% oxygen into liquid lead-bismuth. At this oxygen concentration the structure of iron material will be maintained at about 70% in bcc crystal structure during interaction with liquid metal.

  10. Radiation damage in cubic-ZrO2 and yttria-stabilized zirconia from molecular dynamics simulations

    SciTech Connect (OSTI)

    Aidhy, Dilpuneet S; Zhang, Yanwen; Weber, William J

    2015-01-01

    We perform molecular dynamics simulation on cubic ZrO2 and yttria-stabilized zirconia (YSZ) to elucidate defect cluster formation resulting from radiation damage, and evaluate the impact of Y-dopants. Interstitial clusters composed of split-interstitial building blocks, i.e., Zr-Zr or Y-Zr are formed. Oxygen vacancies control cation defect migration; in their presence, Zr interstitials aggregate to form split-interstitials whereas in their absence Zr interstitials remain immobile, as isolated single-interstitials. Y-doping prevents interstitial cluster formation due to sequestration of oxygen vacancies.

  11. Ab-Initio Molecular Dynamics

    E-Print Network [OSTI]

    Thomas D. Kühne

    2013-03-26

    Computer simulation methods, such as Monte Carlo or Molecular Dynamics, are very powerful computational techniques that provide detailed and essentially exact information on classical many-body problems. With the advent of 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 and the recently devised efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics, which unifies best of both schemes are discussed. The predictive power of this novel second-generation Car-Parrinello approach is demonstrated by a series of applications ranging from liquid metals, to semiconductors and water. This development allows for ab-initio molecular dynamics simulations on much larger length and time scales than previously thought feasible.

  12. Ab-Initio Molecular Dynamics

    E-Print Network [OSTI]

    Kühne, Thomas D

    2012-01-01

    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.

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

    E-Print Network [OSTI]

    D. C. Rapaport

    2014-11-13

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

  14. Slip behavior in liquid films on surfaces of patterned wettability: Comparison between continuum and molecular dynamics simulations

    E-Print Network [OSTI]

    Nikolai V. Priezjev; Anton A. Darhuber; Sandra M. Troian

    2005-05-10

    We investigate the behavior of the slip length in Newtonian liquids subject to planar shear bounded by substrates with mixed boundary conditions. The upper wall, consisting of a homogenous surface of finite or vanishing slip, moves at a constant speed parallel to a lower stationary wall, whose surface is patterned with an array of stripes representing alternating regions of no-shear and finite or no-slip. Velocity fields and effective slip lengths are computed both from molecular dynamics (MD) simulations and solution of the Stokes equation for flow configurations either parallel or perpendicular to the stripes. Excellent agreement between the hydrodynamic and MD results is obtained when the normalized width of the slip regions, $a/\\sigma \\gtrsim {\\cal O}(10)$, where $\\sigma$ is the (fluid) molecular diameter characterizing the Lennard-Jones interaction. In this regime, the effective slip length increases monotonically with $a/\\sigma$ to a saturation value. For $a/\\sigma \\lesssim {\\cal O}(10)$ and transverse flow configurations, the non-uniform interaction potential at the lower wall constitutes a rough surface whose molecular scale corrugations strongly reduce the effective slip length below the hydrodynamic results. The translational symmetry for longitudinal flow eliminates the influence of molecular scale roughness; however, the reduced molecular ordering above the wetting regions of finite slip for small values of $a/\\sigma$ increases the value of the effective slip length far above the hydrodynamic predictions. The strong inverse correlation between the effective slip length and the liquid structure factor representative of the first fluid layer near the patterned wall illustrates the influence of molecular ordering effects on slip in non-inertial flows.

  15. 369 TFlop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer

    SciTech Connect (OSTI)

    Swaminarayan, Sriram; Germann, Timothy C; Kadau, Kai; Fossum, Gordon C

    2008-01-01

    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.

  16. A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-01

    Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N3) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix, based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.

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

    SciTech Connect (OSTI)

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

    2014-01-01

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

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

    SciTech Connect (OSTI)

    Stuart, Steven J.

    2014-02-25

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

  19. Structural, vibrational, and elastic properties of a calcium aluminosilicate glass from molecular dynamics simulations: The role of the potential

    SciTech Connect (OSTI)

    Bauchy, M., E-mail: bauchy@mit.edu [Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA and Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095 (United States)

    2014-07-14

    We study a calcium aluminosilicate glass of composition (SiO{sub 2}){sub 0.60}(Al{sub 2}O{sub 3}){sub 0.10}(CaO){sub 0.30} by means of molecular dynamics. To this end, we conduct parallel simulations, following a consistent methodology, but using three different potentials. Structural and elastic properties are analyzed and compared to available experimental data. This allows assessing the respective abilities of the potentials to produce a realistic glass. We report that, although all these potentials offer a reasonable glass structure, featuring tricluster oxygen atoms, their respective vibrational and elastic predictions differ. This allows us to draw some general conclusions about the crucial role, or otherwise, of the interaction potential in silicate systems.

  20. Multicomponent ballistic transport in narrow single wall carbon nanotubes: Analytic model and molecular dynamics simulations

    E-Print Network [OSTI]

    Adler, Joan

    online 27 January 2011) The transport of gas mixtures through molecular-sieve membranes such as narrow The transport of gas mixtures through molecular-sieve membranes and catalysts has been a subject of intensive inMulticomponent ballistic transport in narrow single wall carbon nanotubes: Analytic model

  1. Transmembrane Signaling of Chemotaxis Receptor Tar: Insights from Molecular Dynamics Simulation Studies

    E-Print Network [OSTI]

    Park, Hahnbeom; Im, Wonpil; Seok, Chaok

    2011-06-22

    Transmembrane signaling of chemotaxis receptors has long been studied, but how the conformational change induced by ligand binding is transmitted across the bilayer membrane is still elusive at the molecular level. To ...

  2. Molecular Dynamic Simulation of Thermo-Mechanical Properties of Ultra-Thin Poly(methyl methacrylate) Films 

    E-Print Network [OSTI]

    Silva Hernandez, Carlos Ardenis A.

    2011-08-08

    The thermal conductivity of PMMA films with thicknesses from 5 to 50 nanometers and layered over a treated silicon substrate is explored numerically by the application of the reverse non-equilibrium molecular dynamics (NEMD) technique...

  3. Molecular dynamics simulations of low-energy ,,25200 eV... argon ion interactions with silicon surfaces: Sputter yields and product

    E-Print Network [OSTI]

    Economou, Demetre J.

    Molecular dynamics simulations of low-energy ,,25­200 eV... argon ion interactions with silicon surfaces: Sputter yields and product formation pathways Nawoyuki A. Kubota and Demetre J. Economoua) Plasma energy ( 200 eV ion interactions with surfaces. In particular, atomic layer etching requires etching

  4. Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

    E-Print Network [OSTI]

    Walter, Nils G.

    Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H+ Forms. Biochemical and structural data have implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants of the protonation states of G8 and A38, and the inactivating A-1(2-methoxy) substitution employed in crystallography

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

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

  6. Dynamics in a supercooled molecular liquid: Theory and simulations Adele Rinaldi, Francesco Sciortino, and Piero Tartaglia

    E-Print Network [OSTI]

    Sciortino, Francesco

    , computer simulations are starting to provide a detailed pic- ture of the structure of the potential energy; published 22 May 2001 We report extensive simulations of liquid supercooled states for a simple three precisely in a large q-vector range self-correlation and collective correlation functions, providing a clean

  7. A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

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

    Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean -Luc; Emigh, Aiyana; Lightstone, Felice C.; Salsbury , Jr, Freddie

    2015-04-13

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone andmore »sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.« less

  8. Molecular dynamics simulation of diffusion coefficients and structural properties of some alkylbenzenes in supercritical carbon dioxide at infinite dilution

    SciTech Connect (OSTI)

    Wang, Jinyang; Zhong, Haimin; Qiu, Wenda; Chen, Liuping; Feng, Huajie

    2014-03-14

    The binary infinite dilute diffusion coefficients, D{sub 12}{sup ?}, of some alkylbenzenes (Ph-C{sub n}, from Ph-H to Ph-C{sub 12}) from 313 K to 333 K at 15 MPa in supercritical carbon dioxide (scCO{sub 2}) have been studied by molecular dynamics (MD) simulation. The MD values agree well with the experimental ones, which indicate MD simulation technique is a powerful way to predict and obtain diffusion coefficients of solutes in supercritical fluids. Besides, the local structures of Ph-C{sub n}/CO{sub 2} fluids are further investigated by calculating radial distribution functions and coordination numbers. It qualitatively convinces that the first solvation shell of Ph-C{sub n} in scCO{sub 2} is significantly influenced by the structure of Ph-C{sub n} solute. Meanwhile, the mean end-to-end distance, the mean radius of gyration and dihedral angle distribution are calculated to gain an insight into the structural properties of Ph-C{sub n} in scCO{sub 2}. The abnormal trends of radial distribution functions and coordination numbers can be reasonably explained in term of molecular flexibility. Moreover, the computed results of dihedral angle clarify that flexibility of long-chain Ph-C{sub n} is the result of internal rotation of C-C single bond (?{sub c-c}) in alkyl chain. It is interesting that compared with n-alkane, because of the existence of benzene ring, the flexibility of alkyl chain in Ph-C{sub n} with same carbon atom number is significantly reduced, as a result, the carbon chain dependence of diffusion behaviors for long-chain n-alkane (n ? 5) and long-chain Ph-C{sub n} (n ? 4) in scCO{sub 2} are different.

  9. Molecular dynamics simulations of water confined between matched pairs of hydrophobic and hydrophilic self-assembled monolayers.

    SciTech Connect (OSTI)

    Chandross, Michael Evan; Grest, Gary Stephen; Lane, J. Matthew D.; Lorenz, Christian Douglas (King's College London, London, UK); Stevens, Mark Jackson

    2008-12-01

    We have conducted a molecular dynamics (MD) simulation study of water confined between methyl-terminated and carboxyl-terminated alkylsilane self-assembled monolayers (SAMs) on amorphous silica substrates. In doing so, we have investigated the dynamic and structural behavior of the water molecules when compressed to loads ranging from 20 to 950 MPa for two different amounts of water (27 and 58 water molecules/nm{sup 2}). Within the studied range of loads, we observe that no water molecules penetrate the hydrophobic region of the carboxyl-terminated SAMs. However, we observe that at loads larger than 150 MPa water molecules penetrate the methyl-terminated SAMs and form hydrogen-bonded chains that connect to the bulk water. The diffusion coefficient of the water molecules decreases as the water film becomes thinner and pressure increases. When compared to bulk diffusion coefficients of water molecules at the various loads, we found that the diffusion coefficients for the systems with 27 water molecules/nm{sup 2} are reduced by a factor of 20 at low loads and by a factor of 40 at high loads, while the diffusion coefficients for the systems with 58 water molecules/nm{sup 2} are reduced by a factor of 25 at all loads.

  10. Effect of bound state of water on hydronium ion mobility in hydrated Nafion using molecular dynamics simulations

    SciTech Connect (OSTI)

    Mabuchi, Takuya, E-mail: mabuchi@nanoint.ifs.tohoku.ac.jp [Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8577 (Japan); Tokumasu, Takashi [Institute of Fluid Science, Tohoku University, Sendai, Miyagi 980-8577 (Japan)

    2014-09-14

    We have performed a detailed analysis of the structural properties of the sulfonate groups in terms of isolated and overlapped solvation shells in the nanostructure of hydrated Nafion membrane using classical molecular dynamics simulations. Our simulations have demonstrated the correlation between the two different areas in bound water region, i.e., the first solvation shell, and the vehicular transport of hydronium ions at different water contents. We have employed a model of the Nafion membrane using the improved force field, which is newly modified and validated by comparing the density and water diffusivity with those obtained experimentally. The first solvation shells were classified into the two types, the isolated area and the overlapped area. The mean residence times of solvent molecules explicitly showed the different behaviors in each of those areas in terms of the vehicular transport of protons: the diffusivity of classical hydronium ions in the overlapped area dominates their total diffusion at lower water contents while that in the isolated area dominates for their diffusion at higher water contents. The results provided insights into the importance role of those areas in the solvation shells for the diffusivity of vehicular transport of hydronium ions in hydrated Nafion membrane.

  11. A phenomenological electronic stopping power model for molecular dynamics and Monte Carlo simulation of ion implantation into silicon

    E-Print Network [OSTI]

    Cai, D; Snell, C M; Beardmore, K M; Cai, David; Gronbech-Jensen, Niels; Snell, Charles M.; Beardmore, Keith M.

    1996-01-01

    It is crucial to have a good phenomenological model of electronic stopping power for modeling the physics of ion implantation into crystalline silicon. In the spirit of the Brandt-Kitagawa effective charge theory, we develop a model for electronic stopping power for an ion, which can be factorized into (i) a globally averaged effective charge taking into account effects of close and distant collisions by target electrons with the ion, and (ii) a local charge density dependent electronic stopping power for a proton. This phenomenological model is implemented into both molecular dynamics and Monte Carlo simulations. There is only one free parameter in the model, namely, the one electron radius rs0 for unbound electrons. By fine tuning this parameter, it is shown that the model can work successfully for both boron and arsenic implants. We report that the results of the dopant profile simulation for both species are in excellent agreement with the experimental profiles measured by secondary-ion mass spectrometry(...

  12. Molecular Dynamics Simulations of a Set of Isoniazid Derivatives Bound to

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

    13084-971, POB 6154, Brazil 2 Laboratory of Molecular Modeling and Design (M/C-781), College of Pharmacy was used to calculate the solvation energy of the lowest-energy conformation obtained from each MDS. Structural parameters as well as binding energy contributions were considered in this analysis

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

    E-Print Network [OSTI]

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

  14. Effects of macroH2A and H2A.Z on nucleosome structure and dynamics as elucidated by molecular dynamics simulations

    E-Print Network [OSTI]

    Bowerman, Samuel

    2015-01-01

    Eukaryotes tune the transcriptional activity of their genome by altering the nucleosome core particle through multiple chemical processes. In particular, replacement of the canonical H2A histone with the variants macroH2A and H2A.Z has been shown to affect DNA accessibility and nucleosome stability; however, the processes by which this occurs remain poorly understood. Here, we elucidate the molecular mechanisms of these variants with an extensive molecular dynamics study of the canonical nucleosome along with three variant-containing structures: H2A.Z, macroH2A, and an H2A mutant with macroH2A-like L1 loops. Simulation results show that variant L1 loops play a pivotal role in stabilizing DNA binding to the octamer through direct interactions, core structural rearrangements, and altered allosteric networks in the nucleosome. All variants influence dynamics; however, macroH2A-like systems have the largest effect on energetics. In addition, we provide a comprehensive analysis of allosteric networks in the nucleo...

  15. Molecular dynamics simulations of the effects of salts on the aggregation properties of benzene in water.

    SciTech Connect (OSTI)

    Smith, P. E.

    2003-07-16

    The specific aims of the project were: to provide an atomic level description of the interactions between benzene, water and ions in solutions. To determine the degree of association between two benzene molecules in aqueous and salt solutions. To investigate the structure and dynamics of the interface between benzene and water or salt solution.

  16. Molecular Dynamics Simulations of Supported Pt Nanoclusters with Sutton-Chen Potentials

    E-Print Network [OSTI]

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

    -time ab-initio calculations may provide fundamental insight into the dynamical electronic and physical structure of catalytic nanoparticles, yet these calculations can prove to be extremely computationally structural disorder, negative thermal expan- sion, and thermally induced changes in electronic struc- ture.3

  17. Force and heat current formulas for many-body potentials in molecular dynamics simulation with applications to thermal conductivity calculations

    E-Print Network [OSTI]

    Fan, Zheyong; Wang, Hui-Qiong; Zheng, Jin-Cheng; Donadio, Davide; Harju, Ari

    2015-01-01

    We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems descried by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimen...

  18. Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces

    E-Print Network [OSTI]

    Changsun Eun; Max L. Berkowitz

    2011-06-01

    We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes; it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in case of charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo, as the two plates are brought together.

  19. Quantum path integral molecular dynamics simulations on transport properties of dense liquid helium

    E-Print Network [OSTI]

    Kang, Dongdong; Sun, Huayang; Yuan, Jianmin

    2015-01-01

    Transport properties of dense liquid helium under the conditions of planet's core and cool atmosphere of white dwarfs have been investigated by using the improved centroid path-integral simulations combined with density functional theory. The self-diffusion is largely higher and the shear viscosity is notably lower predicted with the quantum mechanical description of the nuclear motion compared with the description by Newton equation. The results show that nuclear quantum effects (NQEs), which depends on the temperature and density of the matter via the thermal de Broglie wavelength and the ionization of electrons, are essential for the transport properties of dense liquid helium at certain astrophysical conditions. The Stokes-Einstein relation between diffusion and viscosity in strongly coupled regime is also examined to display the influences of NQEs.

  20. A Molecular Dynamics Simulation of Hydrogen Storage in Single Walled Carbon Nanotubes Shigeo MARUYAMA, Eng. Res. Inst., The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8656

    E-Print Network [OSTI]

    Maruyama, Shigeo

    A Molecular Dynamics Simulation of Hydrogen Storage in Single Walled Carbon Nanotubes Shigeo : Molecular Dynamics Method, Hydrogen Storage, Single Walled Carbon Nanotubes, Lennard-Jones (1-4) (5) Dillon,10) A = 2.361×10-21 J/Å SWNT 5376 or 9000 Hydrogen Molecules 30 nm 10 nm 3.388 nm 7 Full SWNT (560 C atoms

  1. Protein-Folding Dynamics: Overview of Molecular

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Protein-Folding Dynamics: Overview of Molecular Simulation Techniques Harold A. Scheraga, Mey folding in silico. Although just a few years ago the dynamic be- havior of a protein molecule could models of proteins now make it possible to study protein- folding pathways from completely unfolded

  2. Introduction to Accelerated Molecular Dynamics

    SciTech Connect (OSTI)

    Perez, Danny [Los Alamos National Laboratory

    2012-07-10

    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.

  3. Adapting SAFT-? perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

    SciTech Connect (OSTI)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard

    2014-07-14

    In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-? WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-? refers to the particular form of “statistical associating fluid theory” that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH{sub 2} and CH{sub 3} and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ?2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ?1% from simulation data while the theory reproduces the excess accumulation of ethane at the interface.

  4. Scattering Density Profile Model of POPG Bilayers as Determined by Molecular Dynamics Simulations and Small-Angle Neutron and X-ray Scattering Experiments

    SciTech Connect (OSTI)

    Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Holland, B [University of Guelph; Gray, C.G [University of Guelph; Tomberli, B [Brandon University; Katsaras, John [ORNL

    2012-01-01

    We combine molecular dynamics (MD) simulations and experiment, both small-angle neutron (SANS) and small-angle X-ray scattering (SAXS), to determine the precise structure of bilayers composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG), a lipid commonly encountered in bacterial membranes. Experiment and simulation are used to develop a one-dimensional scattering density profile (SDP) model suitable for the analysis of experimental data. The joint refinement of such data (i.e., SANS and SAXS) results in the area per lipid that is then used in the fixed-area simulations. In the final step, the direct comparison of simulated-to-experimental data gives rise to the detailed structure of POPG bilayers. From these studies we conclude that POPG s molecular area is 66.0 +/- 1.3 ^2, its overall bilayer thickness is 36.7 +/- 0.7 , and its hydrocarbon region thickness is 27.9 ( 0.6 , assuming a simulated value of 1203 ^3 for the total lipid volume.

  5. Simulations of the quart (101-bar1)/water interface: A comparison of classical force fields, ab initi molecular dynamics, and x-ray reflectivity experiments.

    SciTech Connect (OSTI)

    Skelton, Adam; Fenter, Paul; Kubicki, James D.; Wesolowski, David J; Cummings, Peter T

    2011-01-01

    Classical molecular dynamics (CMD) simulations of the (1011) surface of quartz interacting with bulk liquid water are performed using three different classical force fields, Lopes et al., ClayFF, and CHARMM water contact angle (CWCA), and compared to ab initio molecular dynamics (AIMD) and X-ray reflectivity (XR) results. The axial densities of the water and surface atoms normal to the surface are calculated and compared to previous XR experiments. Favorable agreement is shown for all the force fields with respect to the position of the water atoms. Analyses such as the radial distribution functions between water and hydroxyl atoms and the average cosine of the angle between the water dipole vector and the normal of the surface are also calculated for each force field. Significant differences are found between the different force fields from such analyses, indicating differing descriptions of the structured water in the near vicinity of the surface. AIMD simulations are also performed to obtain the water and hydroxyl structure for comparison among the predictions of the three classical force fields to better understand which force field is most accurate. It is shown that ClayFF exhibits the best agreement with the AIMD simulations for water hydroxyl radial distribution functions, suggesting that ClayFF treats the hydrogen bonding more accurately.

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

    E-Print Network [OSTI]

    Leung, Kevin; 10.1039/B925853A

    2010-01-01

    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.

  7. Femtosecond photoelectron spectroscopy of the I{sub 2}{sup {minus}} anion: A semiclassical molecular dynamics simulation method

    SciTech Connect (OSTI)

    Batista, V.S.; Zanni, M.T.; Greenblatt, B.J.; Neumark, D.M.; Miller, W.H. [Department of Chemistry, University of California, Berkeley, California 94720 (United States)] [Department of Chemistry, University of California, Berkeley, California 94720 (United States); [Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    1999-02-01

    In this paper we describe a new semiclassical method for simulating femtosecond pump{endash}probe photoelectron spectroscopy, and its implementation to study the excited state photodissociation dynamics of the I{sub 2}{sup {minus}} anion. Our algorithm involves a forward{endash}backward (FB) semiclassical (SC) initial value representation (IVR) method for calculating the time dependent photodetachment spectrum P({epsilon},{Delta}t) as a function of the kinetic energy {epsilon} of the photodetached electron and the delay time {Delta}t between the pump and probe pulses. We describe the radiation-chromophore interaction perturbatively to first order in both pulse fields, assuming the Condon approximation for the electronic transition dipole moments. Our computed spectra are in excellent agreement with full quantum mechanical simulations. {copyright} {ital 1999 American Institute of Physics.}

  8. Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

    E-Print Network [OSTI]

    Pal, Anirban; Raha, Soumyendu; Bhattacharya, Baidurya

    2015-01-01

    We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nanoindentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr Cr interaction and the Morse potential for Cr C interactions. We study the performance of our algorithm for a range of MPIthread combinations and find the performance to depend strongly on the computational task and load sharing in the multicore processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favourably with that achieved by stan...

  9. Functional Domain Motions in Proteins on the 1 100 ns Timescale: Comparison of Neutron Spin-Echo Spectroscopy of Phosphoglycerate Kinase with Molecular-Dynamics Simulation

    SciTech Connect (OSTI)

    Smolin, Nikolai [ORNL; Biehl, R [Southern Methodist University, Dallas; Kneller, Gerald [University of Orleans; Richter, Dieter O [ORNL; Smith, Jeremy C [ORNL

    2011-01-01

    Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the 1 100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.

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

    E-Print Network [OSTI]

    Diddo Diddens; Andreas Heuer

    2013-02-20

    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.

  11. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

    SciTech Connect (OSTI)

    Nawrocki, Grzegorz; Cieplak, Marek

    2014-03-07

    The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper—the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO—it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

  12. Ejection of matrix-polymer clusters in matrix-assisted laser evaporation: Coarse-grained molecular dynamics simulations

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Ejection of matrix-polymer clusters in matrix-assisted laser evaporation: Coarse-grained molecular, as related to the matrix-assisted laser evaporation (MAPLE) technique for polymer film deposition. Coarse- grained description of molecular matrix and polymer molecules is used in the model, allowing for large

  13. SImulating the LifeCycle of molecular Clouds (SILCC): II. Dynamical evolution of the supernova-driven ISM and the launching of outflows

    E-Print Network [OSTI]

    Girichidis, Philipp; Naab, Thorsten; Gatto, Andrea; Wünsch, Richard; Glover, Simon C O; Klessen, Ralf S; Clark, Paul C; Peters, Thomas; Derigs, Dominik; Baczynski, Christian

    2015-01-01

    The SILCC project (SImulating the Life-Cycle of molecular Clouds) aims at a more self-consistent understanding of the interstellar medium (ISM) on small scales and its link to galaxy evolution. We present three-dimensional (magneto)hydrodynamic simulations of the ISM in a vertically stratified box including self-gravity, an external potential due to the stellar component of the galactic disc, and stellar feedback in the form of an interstellar radiation field and supernovae (SNe). The cooling of the gas is based on a chemical network that follows the abundances of H+, H, H2, C+, and CO and takes shielding into account consistently. We vary the SN feedback by comparing different SN rates, clustering and different positioning, in particular SNe in density peaks and at random positions, which has a major impact on the dynamics. Only for random SN positions the energy is injected in sufficiently low-density environments to reduce energy losses and enhance the effective kinetic coupling of the SNe with the gas. Th...

  14. Molecular dynamics simulations of single-layer molybdenum disulphide (MoS2): Stillinger-Weber parametrization, mechanical properties, and

    E-Print Network [OSTI]

    Park, Harold S.

    , Bauhaus-University Weimar, Marienstr. 15, D-99423 Weimar, Germany 2 Department of Mechanical Engineering for the energy gap and the crossover in the phonon spectrum. Using this potential, we perform classical molecular the usage of a hafnium oxide gate dielectric. Considering its large intrinsic direct bandgap of 1.8 eV,9

  15. Does fluoride disrupt hydrogen bond network in cationic lipid bilayer? Time-dependent fluorescence shift of Laurdan and molecular dynamics simulations

    SciTech Connect (OSTI)

    Pokorna, Sarka; Jurkiewicz, Piotr; Hof, Martin; Vazdar, Mario; Cwiklik, Lukasz; Jungwirth, Pavel

    2014-12-14

    Time-dependent fluorescence shift (TDFS) of Laurdan embedded in phospholipid bilayers reports on hydration and mobility of the phospholipid acylgroups. Exchange of H{sub 2}O with D{sub 2}O prolongs the lifetime of lipid-water and lipid-water-lipid interactions, which is reflected in a significantly slower TDFS kinetics. Combining TDFS measurements in H{sub 2}O and D{sub 2}O hydrated bilayers with atomistic molecular dynamics (MD) simulations provides a unique tool for characterization of the hydrogen bonding at the acylgroup level of lipid bilayers. In this work, we use this approach to study the influence of fluoride anions on the properties of cationic bilayers composed of trimethylammonium-propane (DOTAP). The results obtained for DOTAP are confronted with those for neutral phosphatidylcholine (DOPC) bilayers. Both in DOTAP and DOPC H{sub 2}O/D{sub 2}O exchange prolongs hydrogen-bonding lifetime and does not disturb bilayer structure. These results are confirmed by MD simulations. TDFS experiments show, however, that for DOTAP this effect is cancelled in the presence of fluoride ions. We interpret these results as evidence that strongly hydrated fluoride is able to steal water molecules that bridge lipid carbonyls. Consequently, when attracted to DOTAP bilayer, fluoride disrupts the local hydrogen-bonding network, and the differences in TDFS kinetics between H{sub 2}O and D{sub 2}O hydrated bilayers are no longer observed. A distinct behavior of fluoride is also evidenced by MD simulations, which show different lipid-ion binding for Cl{sup ?} and F{sup ?}.

  16. Dynamic Positioning Simulator Dynamic Positioning Simulator

    E-Print Network [OSTI]

    Vuik, Kees

    to the ocean floor, without using anchors accomplished by two or more propulsive devices controlled by inputs Dynamic Positioning: No tugboats needed; Offshore set-up is quick; Power saving; Precision situations more on Ship: Wind Force Fw = 1 2 air V 2 rw CXw (rw )AT 1 2 air V 2 rw CYw (rw )AL Mw = 1 2 air V 2 rw CMw (rw

  17. 1416 IEEE TRANSACTIONS ON PLASMA SCIENCE, VOL. 27, NO. 5, OCTOBER 1999 A Molecular Dynamics Simulation of Ultrathin

    E-Print Network [OSTI]

    Economou, Demetre J.

    of oxides and other con- taminants. In the Si etching case, surface micromasking by residual oxide can lead Simulation of Ultrathin Oxide Films on Silicon: Growth by Thermal O Atoms and Sputtering by 100 eV Ar Ions and sputtering of ultrathin oxide films on (100) Si surfaces. A multibody potential which stabilized the Si/SiO2

  18. Effects of water on chemomechanical instabilities in amorphous silica : nanoscale experiments and molecular simulation

    E-Print Network [OSTI]

    Silva, Emílio César Cavalcante Melo da

    2007-01-01

    We elucidate the tensile failure mechanism of amorphous silica and the effects of water on the process, combining: (a) atomic force microscope (AFM) bending tests, (b) molecular dynamics (MD) simulation and (c) molecular ...

  19. Quantitative in-situ scanning electron microscope pull-out experiments and molecular dynamics simulations of carbon nanotubes embedded in palladium

    SciTech Connect (OSTI)

    Hartmann, S., E-mail: steffen.hartmann@etit.tu-chemnitz.de; Blaudeck, T.; Hermann, S.; Wunderle, B. [Technische Universität Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Hölck, O. [Technische Universität Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Fraunhofer IZM Berlin, Gustav-Meyer-Allee 25, 13355 Berlin (Germany); Schulz, S. E.; Gessner, T. [Technische Universität Chemnitz, Reichenhainer Str. 70, 09126 Chemnitz (Germany); Fraunhofer ENAS Chemnitz, Technologie-Campus 3, 09126 Chemnitz (Germany)

    2014-04-14

    In this paper, we present our results of experimental and numerical pull-out tests on carbon nanotubes (CNTs) embedded in palladium. We prepared simple specimens by employing standard silicon wafers, physical vapor deposition of palladium and deposition of CNTs with a simple drop coating technique. An AFM cantilever with known stiffness connected to a nanomanipulation system was utilized inside a scanning electron microscope (SEM) as a force sensor to determine forces acting on a CNT during the pull-out process. SEM-images of the cantilever attached to a CNT have been evaluated for subsequent displacement steps with greyscale correlation to determine the cantilever deflection. We compare the experimentally obtained pull-out forces with values of numerical investigations by means of molecular dynamics and give interpretations for deviations according to material impurities or defects and their influence on the pull-out data. We find a very good agreement of force data from simulation and experiment, which is 17 nN and in the range of 10–61 nN, respectively. Our findings contribute to the ongoing research of the mechanical characterization of CNT-metal interfaces. This is of significant interest for the design of future mechanical sensors utilizing the intrinsic piezoresistive effect of CNTs or other future devices incorporating CNT-metal interfaces.

  20. Microscale swimming: The molecular dynamics approach

    E-Print Network [OSTI]

    D. C. Rapaport

    2007-12-06

    The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in specifying the swimmer design and its coupling with the surrounding fluid. A series of two-dimensional swimming bodies employing a variety of propulsion mechanisms -- motivated by biological and microrobotic designs -- is investigated, including the use of moving limbs, changing body shapes and fluid jets. The swimming efficiency and the nature of the induced, time-dependent flow fields are found to differ widely among body designs and propulsion mechanisms.

  1. Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

    E-Print Network [OSTI]

    Ghosh, Soumadwip; Chakrabarti, Rajarshi

    2015-01-01

    The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations we investigate the preferential binding of metal ion such as Na+ and molecular ions such as tetramethyl ammonium (TMA+) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO+) to double stranded DNA. The thermodynamic driving force for a particular molecular ion- DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO+. The ion binding processes are found to be entropically favourable. In addition, the contribution of hy...

  2. Generation of Realistic Amorphous Al2O3 And ZrO2 Samples By Hybrid Classical and First-Principle Molecular Dynamics Simulations

    E-Print Network [OSTI]

    Kummel, Andrew C.

    Generation of Realistic Amorphous Al2O3 And ZrO2 Samples By Hybrid Classical and First-ZrO2 were generated by a hybrid classical and density functional theory (DFT) "melt and quench" molecular dynamics approach. The generated samples demonstrated good correlation with reference experimental

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

    Office of Scientific and Technical Information (OSTI)

    Molecular Simulation of Carbon Dioxide Nanodroplets on Clay in Deep Saline Aquifers. Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide Nanodroplets...

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

    Office of Scientific and Technical Information (OSTI)

    Molecular Simulation of Carbon Dioxide Brine and Clay Mineral Interactions and Determination of Contact Angles. Citation Details In-Document Search Title: Molecular Simulation of...

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

    Office of Scientific and Technical Information (OSTI)

    Molecular Simulation of Carbon Dioxide Nanodroplets on Clay Surfaces in Deep Saline Aquifers. Citation Details In-Document Search Title: Molecular Simulation of Carbon Dioxide...

  6. Supplementary Material A Molecular Dynamics Approach to the Structural

    E-Print Network [OSTI]

    Caflisch, Amedeo

    , the self-assembly process of hexamers was considered. Eighteen MD simulations of six peptides wereSupplementary Material A Molecular Dynamics Approach to the Structural Characterization of Amyloid trajectory, underwent a cluster analysis based on structural similarity1 . Single-peptide conformations were

  7. Microscale Swimming: The Molecular Dynamics Approach D. C. Rapaport*

    E-Print Network [OSTI]

    Rapaport, Dennis C.

    -dimensional swimming bodies employing a variety of propulsion mechanisms--motivated by biological and microrobotic among body designs and propulsion mechanisms. DOI: 10.1103/PhysRevLett.99.238101 PACS numbers: 47.63.Gd-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation

  8. Simulations with dynamical HISQ quarks

    E-Print Network [OSTI]

    A. Bazavov; C. Bernard; C. DeTar; W. Freeman; Steven Gottlieb; U. M. Heller; J. E. Hetrick; J. Laiho; L. Levkova; M. Oktay; J. Osborn; R. L. Sugar; D. Toussaint; R. S. Van de Water

    2010-12-06

    We report on the status of a program of generating and using configurations with four flavors of dynamical quarks, using the HISQ action. We study the lattice spacing dependence of physical quantities in these simulations, using runs at several lattice spacings, but with the light quark mass held fixed at two tenths of the strange quark mass. We find that the lattice artifacts in the HISQ simulations are much smaller than those in the asqtad simulations at the same lattice spacings and quark masses. We also discuss methods for setting the scale, or assigning a lattice spacing to ensembles run at unphysical parameters.

  9. THERMODYNAMICS Molecular Simulation of Multicomponent Reaction

    E-Print Network [OSTI]

    Lisal, Martin

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

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

    Office of Scientific and Technical Information (OSTI)

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

  11. First principles molecular dynamics without self-consistent field optimization

    SciTech Connect (OSTI)

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-28

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

  12. Molecular Dynamics in Formation Process of Single-Walled Carbon Nanotubes Yasushi SHIBUTA and Shigeo MARUYAMA

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Molecular Dynamics in Formation Process of Single-Walled Carbon Nanotubes Yasushi SHIBUTA The mechanism in the nucleation and formation of single-walled carbon nanotubes (SWNTs) was investigated using molecular dynamics simulations. When initial state was chosen so that carbon and nickel atoms were randomly

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

    E-Print Network [OSTI]

    de Groot, Bert

    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

  14. Calculation of heat capacities of light and heavy water by path-integral molecular dynamics

    E-Print Network [OSTI]

    Nielsen, Steven O.

    Calculation of heat capacities of light and heavy water by path-integral molecular dynamics 30 September 2005 As an application of atomistic simulation methods to heat capacities, path-integral has estimated the heat capacities too high, the quantum simulation based on path-integral molecular

  15. Multielectron effects in high harmonic generation in N_2 and benzene: simulation using a non-adiabatic quantum molecular dynamics approach for laser-molecule interactions

    E-Print Network [OSTI]

    Dundas, Daniel

    2012-01-01

    A mixed quantum-classical approach is introduced which allows the dynamically response of molecules driven far from equilibrium to be modeled. This method is applied here to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations can be performed. The approach is applied to the study of high harmonic generation in N_2 and benzene using linearly-polarized laser pulses and to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N_2 an enhancement ...

  16. Molecular dynamics simulations of the electrical double layer on smectite surfaces contacting concentrated mixed electrolyte (NaCl-CaCl?) solutions

    SciTech Connect (OSTI)

    Bourg, Ian C.; Sposito, Garrison

    2011-01-01

    We report new molecular dynamics results elucidating the structure of the electrical double layer (EDL) on smectite surfaces contacting mixed NaCl–CaCl2 electrolyte solutions in the range of concentrations relevant to pore waters in geologic repositories for CO2 or high-level radioactive waste (0.34–1.83 molc dm-3). Our results confirm the existence of three distinct ion adsorption planes (0-, ?-, and d-planes), often assumed in EDL models, but with two important qualifications: (1) the location of the ?- 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+ ion pairs. Therefore, at concentrations {>=0.34 molc dm-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.

  17. A molecular dynamics study of polymer/graphene interfacial systems

    SciTech Connect (OSTI)

    Rissanou, Anastassia N.; Harmandaris, Vagelis

    2014-05-15

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

  18. Simulated Quantum Computation of Molecular Energies

    E-Print Network [OSTI]

    Alán Aspuru-Guzik; Anthony D. Dutoi; Peter J. Love; Martin Head-Gordon

    2006-04-26

    The calculation time for the energy of atoms and molecules scales exponentially with system size on a classical computer but polynomially using quantum algorithms. We demonstrate that such algorithms can be applied to problems of chemical interest using modest numbers of quantum bits. Calculations of the water and lithium hydride molecular ground-state energies have been carried out on a quantum computer simulator using a recursive phase-estimation algorithm. The recursive algorithm reduces the number of quantum bits required for the readout register from about 20 to 4. Mappings of the molecular wave function to the quantum bits are described. An adiabatic method for the preparation of a good approximate ground-state wave function is described and demonstrated for a stretched hydrogen molecule. The number of quantum bits required scales linearly with the number of basis functions, and the number of gates required grows polynomially with the number of quantum bits.

  19. Structure, solvation, and dynamics of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} complexes with 3-hydroxyflavone and perchlorate anion in acetonitrile medium: A molecular dynamics simulation study

    SciTech Connect (OSTI)

    Agieienko, Vira N.; Kolesnik, Yaroslav V.; Kalugin, Oleg N.

    2014-05-21

    Molecular dynamics simulations of complexes of Mg{sup 2+}, Ca{sup 2+}, Sr{sup 2+}, and Ba{sup 2+} with 3-hydroxyflavone (flavonol, 3HF) and ClO {sub 4}{sup ?} in acetonitrile were performed. The united atoms force field model was proposed for the 3HF molecule using the results of DFT quantum chemical calculations. 3HF was interpreted as a rigid molecule with two internal degrees of freedom, i.e., rotation of the phenyl ring and of the OH group with respect to the chromone moiety. The interatomic radial distribution functions showed that interaction of the cations with flavonol occurs via the carbonyl group of 3HF and it is accompanied with substitution of one of the acetonitrile molecules in the cations’ first solvation shells. Formation of the cation–3HF complexes does not have significant impact on the rotation of the phenyl ring with respect to the chromone moiety. However, the orientation of the flavonol's OH-group is more sensitive to the interaction with doubly charged cations. When complex with Mg{sup 2+} is formed, the OH-group turns out of the plane of the chromone moiety that leads to rupture of intramolecular H-bond in the ligand molecule. Complexation of Ca{sup 2+}, Sr{sup 2+}, and BaClO {sub 4}{sup +} with 3HF produces two structures with different OH-positions, as in the free flavonol with the intramolecular H-bond and as in the complex with Mg{sup 2+} with disrupted H-bonding. It was shown that additional stabilization of the [MgClO{sub 4}(3HF)]{sup +} and [BaClO{sub 4}(3HF)]{sup +} complexes is determined by strong affinity of perchlorate anion to interact with flavonol via intracomplex hydrogen bond between an oxygen atom of the anion and the hydrogen atom of the 3-hydroxyl group. Noticeable difference in the values of the self-diffusion coefficients for Kt{sup 2+} from one side and ClO {sub 4}{sup ?}, 3HF, and AN in the cations’ coordination shell from another side implies quite weak interaction between cation, anion, and ligands in the investigated complexes.

  20. Reaction dynamics in polyatomic molecular systems

    SciTech Connect (OSTI)

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

    1993-12-01

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

  1. PARALLEL MOLECULAR DYNAMICS WITH THE EMBEDDED ATOM METHOD STEVEN J. PLIMPTON and BRUCE A. HENDRICKSON

    E-Print Network [OSTI]

    Plimpton, Steve

    ,2] is a popular choice for the energy functional in MD simulations. It overcomes the volume­ dependent limitation capabilities for using molecular dynamics (MD) to simulate larger numbers of atoms and longer time scales community for modeling solids and liquids at the atomic level. Each atom in the simulation is treated

  2. Simulation and sequential dynamical systems

    SciTech Connect (OSTI)

    Mortveit, H.S.; Reidys, C.M.

    1999-06-01

    Computer simulations have a generic structure. Motivated by this the authors present a new class of discrete dynamical systems that captures this structure in a mathematically precise way. This class of systems consists of (1) a loopfree graph {Upsilon} with vertex set {l_brace}1,2,{hor_ellipsis},n{r_brace} where each vertex has a binary state, (2) a vertex labeled set of functions (F{sub i,{Upsilon}}:F{sub 2}{sup n} {yields} F{sub 2}{sup n}){sub i} and (3) a permutation {pi} {element_of} S{sub n}. The function F{sub i,{Upsilon}} updates the state of vertex i as a function of the states of vertex i and its {Upsilon}-neighbors and leaves the states of all other vertices fixed. The permutation {pi} represents the update ordering, i.e., the order in which the functions F{sub i,{Upsilon}} are applied. By composing the functions F{sub i,{Upsilon}} in the order given by {pi} one obtains the dynamical system (equation given in paper), which the authors refer to as a sequential dynamical system, or SDS for short. The authors will present bounds for the number of functionally different systems and for the number of nonisomorphic digraphs {Gamma}[F{sub {Upsilon}},{pi}] that can be obtained by varying the update order and applications of these to specific graphs and graph classes.

  3. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    E-Print Network [OSTI]

    Leone, Stephen R.

    2010-01-01

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

  4. Molecular Simulations of Electrolytes and Electrolyte/Electrode...

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

    Molecular Simulations of Electrolytes and ElectrolyteElectrode Interfaces Grant D. Smith and Oleg Borodin Department of Materials Science & Engineering University of Utah 0218...

  5. Mo l e c u l a r Ph y s i c s , 1996, Vo l . 87, No . 1, 167 187 Molecular dynamics simulations of uorinated ethanes

    E-Print Network [OSTI]

    Lisal, Martin

    of ¯ uorinated ethanes By MARTIN LI! SAL simulations for three isomeric pairs of ¯ uorinated ethanes : CHF # CHF # (HFC-134) and CF $ CH # F (HFC-134a) simulations with an isotropic atom± atom potential for three isomeric pairs of ¯ uorinated ethanes : CHF # CHF

  6. Control-volume representation of molecular dynamics

    E-Print Network [OSTI]

    E. R. Smith; D. M. Heyes; D. Dini; T. A. Zaki

    2012-05-24

    A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' Transport Theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-Control-Volume (\\CV) conversion function $\\vartheta_{i}$, for each molecule $i$. The \\CV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the Volume Average (VA, Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, Todd et al, Phys. Rev. E 52, 1627 (1995)) emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and non-equilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative, and is therefore ideally suited to obtain macroscopic properties from a discrete system.

  7. Parallel Implementation of Power System Dynamic Simulation

    SciTech Connect (OSTI)

    Jin, Shuangshuang; Huang, Zhenyu; Diao, Ruisheng; Wu, Di; Chen, Yousu

    2013-07-21

    Dynamic simulation of power system transient stability is important for planning, monitoring, operation, and control of electrical power systems. However, modeling the system dynamics and network involves the computationally intensive time-domain solution of numerous differential and algebraic equations (DAE). This results in a transient stability implementation that may not maintain the real-time constraints of an online security assessment. This paper presents a parallel implementation of the dynamic simulation on a high-performance computing (HPC) platform using parallel simulation algorithms and computation architectures. It enables the simulation to run even faster than real time, enabling the “look-ahead” capability of upcoming stability problems in the power grid.

  8. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect (OSTI)

    Nesbitt, David J.

    2011-07-11

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

  9. Molecular dynamics studies of interfacial water at the alumina surface.

    SciTech Connect (OSTI)

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

    2011-01-01

    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.

  10. Molecular dynamics modeling of orientation-induced nucleation in short alkanes : toward molecular modeling of flow-induced crystallization in polymers

    E-Print Network [OSTI]

    ?jurdjevi?, Predrag (Predrag Dragutin)

    2013-01-01

    The enhancement of the primary flow-induced nucleation rate in short chain alkanes (C20 and C150) has been examined for different levels of orientation by atomistic molecular dynamics simulations. The nucleation rate has ...

  11. Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo

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

    White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; Mozyrsky, Dmitry

    2015-07-07

    Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficientmore »as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.« less

  12. Dynamic Properties of Molecular Motors in Burnt-Bridge Models

    E-Print Network [OSTI]

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

    2007-05-04

    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.

  13. Molecular Structure and Transport Dynamics in Perfluoro Sulfonyl Imide Membranes

    SciTech Connect (OSTI)

    Idupulapati, Nagesh B.; Devanathan, Ramaswami; Dupuis, Michel

    2011-05-25

    We report a detailed and comprehensive analysis of the nanostructure, transport dynamics of water and hydronium and water percolation in hydrated perfluoro sulfonyl imides (PFSI), a polymer considered for proton transport in PEM fuel cells, using classical molecular dynamics simulations. The dynamical changes are related to the changes in the membrane nanostructure. Water network percolation threshold, the level at which a consistent spanning water network starts to develop in the membrane, lies between hydration level (?) 6 and 7. The higher acidity of the sulfonyl imide acid group of PFSI compared to Nafion reported in our earlier ab initio study, translates into more free hydronium ions at low hydration levels. Nevertheless, the calculated diffusion coefficients of the H3O+ ions and H2O molecules as a function the hydration level were observed to be almost the same as that of Nafion, indicating similar conductivity and consistent with the experimental observations. This research was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, a U.S. Department of Energy (DOE) national scientific user facility located at the Pacific Northwest National Laboratory (PNNL). 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.

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

    E-Print Network [OSTI]

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

    2006-12-20

    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.

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

    E-Print Network [OSTI]

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

    2009-01-22

    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.

  16. Rotational Relaxation of Ionic Molecules in Electrolyte Solutions. Anisotropy Relaxation and Molecular Dynamics Study

    E-Print Network [OSTI]

    Kurnikova, Maria

    and the metal cation. Conductivity measure- ments and ab initio electronic structure calculations are used structure and the solute dynamics occur for ionic solute molecules. Both experimental4-10 and theoretical11 of experimental studies, ab initio electronic struc- ture, and molecular dynamics (MD) simulation is used

  17. Controlling protein molecular dynamics: How to accelerate folding while preserving the native state

    E-Print Network [OSTI]

    Nerukh, Dmitry

    Controlling protein molecular dynamics: How to accelerate folding while preserving the native state state of the protein and at the same time, reduce the folding time in the simulation. We investigate 2008; accepted 14 October 2008; published online 11 December 2008 The dynamics of peptides and proteins

  18. ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Kimberly Chenoweth, Adri C. T. van Duin, and William A. Goddard, III*

    E-Print Network [OSTI]

    Goddard III, William A.

    MoOx heterogeneous cata- lysts,22 fuel cells,23 crack propagation in silicon crystals,24 dissociation of H2 on Pt additional transition states and chemical reactivity of systems relevant to these reactions and optimizedFF potential obtained after parameter optimization, we performed a range of NVT-MD simulations on various

  19. "#Molecular Dynamics Simulation of Mechanical Properties for Polycrystal Materials Corresponding author: A.M. Krivtsov, e-mail: krivtsov@AK5744.spb.edu

    E-Print Network [OSTI]

    Krivtsov, Anton M.

    for the continuum mechanics approach, hindering the effective use of the well-established methods such as the finite element method and the boundary element methods. In the presented paper a discrete technique based technique for simulation of percussive drilling in hard rock formations is discussed. 1. INTRODUCTION

  20. Accelerated molecular dynamics methods: introduction and recent developments

    SciTech Connect (OSTI)

    Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO

    2009-01-01

    A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what reaction pathways may be important, we return instead to a molecular dynamics treatment, in which the trajectory itself finds an appropriate way to escape from each state of the system. Since a direct integration of the trajectory would be limited to nanoseconds, while we are seeking to follow the system for much longer times, we modify the dynamics in some way to cause the first escape to happen much more quickly, thereby accelerating the dynamics. The key is to design the modified dynamics in a way that does as little damage as possible to the probability for escaping along a given pathway - i.e., we try to preserve the relative rate constants for the different possible escape paths out of the state. We can then use this modified dynamics to follow the system from state to state, reaching much longer times than we could reach with direct MD. The dynamics within any one state may no longer be meaningful, but the state-to-state dynamics, in the best case, as we discuss in the paper, can be exact. We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics. Each of these methods has its own advantages, and we and others have applied these methods to a wide range of problems. The purpose of this article is to give the reader a brief introduction to how these methods work, and discuss some of the recent developments that have been made to improve their power and applicability. Note that this brief review does not claim to be exhaustive: various other methods aiming at similar goals have been proposed in the literature. For the sake of brevity, our focus will exclusively be on the methods developed by the group.

  1. Fluid transport properties by equilibrium molecular dynamics. II. Multicomponent systems

    E-Print Network [OSTI]

    Dysthe, Dag Kristian

    Fluid transport properties by equilibrium molecular dynamics. II. Multicomponent systems D. K than 25 years molecular dynamics has been used to study fluid transport properties. Such MD studies and multicenter molecular models.8­16 d The study of transport properties of certain fluids and classes of fluids

  2. Investigation of Interfacial and Bulk Dissociation of HBr, HCl, and HNO3 Using Density Functional Theory-Based Molecular Dynamics Simulations

    SciTech Connect (OSTI)

    Baer, Marcel; Tobias, Douglas J.; Mundy, Christopher J.

    2014-12-18

    In this study we investigate the free energy barrier associated with the dissociation of strong acids, XH (HBr, HCl and HNO3) deprotonation, and subsequent formation of ionpairs, X–___H3O+ in the vicinity of the air-water interface. We will show that the free energy for acid dissociation for HCl and HNO3 show significant differences at the air-water than under bulk solvation conditions producing a picture where at the interface associated molecular species can be stable. For the strongest acid we consider, HBr the more traditional picture of acids is preserved in the vicinity of the air-water interface. Our results have implications for our understanding of acids, and their surface tensions at the air-water interface.

  3. Molecular simulations of MEMS and membrane coatings (PECASE).

    SciTech Connect (OSTI)

    Javaid, Asad (Texas A& M University, College Station, TX); Aydogmus, Turkan (Texas A& M University, College Station, TX); Ford, David M. (Texas A& M University, College Station, TX)

    2004-03-01

    The goal of this Laboratory Directed Research & Development (LDRD) effort was to design, synthesize, and evaluate organic-inorganic nanocomposite membranes for solubility-based separations, such as the removal of higher hydrocarbons from air streams, using experiment and theory. We synthesized membranes by depositing alkylchlorosilanes on the nanoporous surfaces of alumina substrates, using techniques from the self-assembled monolayer literature to control the microstructure. We measured the permeability of these membranes to different gas species, in order to evaluate their performance in solubility-based separations. Membrane design goals were met by manipulating the pore size, alkyl group size, and alkyl surface density. We employed molecular dynamics simulation to gain further understanding of the relationship between membrane microstructure and separation performance.

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

    SciTech Connect (OSTI)

    Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M.

    2014-10-15

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

  5. Annual Report 1999 Environmental Dynamics and Simulation

    SciTech Connect (OSTI)

    NS Foster-Mills

    2000-06-28

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

  6. Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

    Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

    2015-06-26

    A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore »science, chemistry, and biology.« less

  7. Mechanical unfolding of a beta-hairpin using molecular dynamics

    SciTech Connect (OSTI)

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

    1999-10-16

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

  8. Stochastic simulations of cargo transport by processive molecular motors Christian B. Korn,1

    E-Print Network [OSTI]

    Schwarz, Ulrich

    Stochastic simulations of cargo transport by processive molecular motors Christian B. Korn,1 Stefan kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic

  9. Driven cavity flow: from molecular dynamics to continuum hydrodynamics

    E-Print Network [OSTI]

    Tiezheng Qian; Xiao-Ping Wang

    2004-03-06

    Molecular dynamics (MD) simulations have been carried out to investigate the slip of fluid in the lid driven cavity flow where the no-slip boundary condition causes unphysical stress divergence. The MD results not only show the existence of fluid slip but also verify the validity of the Navier slip boundary condition. To better understand the fluid slip in this problem, a continuum hydrodynamic model has been formulated based upon the MD verification of the Navier boundary condition and the Newtonian stress. Our model has no adjustable parameter because all the material parameters (density, viscosity, and slip length) are directly determined from MD simulations. Steady-state velocity fields from continuum calculations are in quantitative agreement with those from MD simulations, from the molecular-scale structure to the global flow. The main discovery is as follows. In the immediate vicinity of the corners where moving and fixed solid surfaces intersect, there is a core partial-slip region where the slippage is large at the moving solid surface and decays away from the intersection quickly. In particular, the structure of this core region is nearly independent of the system size. On the other hand, for sufficiently large system, an additional partial-slip region appears where the slippage varies as $1/r$ with $r$ denoting the distance from the corner along the moving solid surface. The existence of this wide power-law region is in accordance with the asymptotic $1/r$ variation of stress and the Navier boundary condition.

  10. Efficient dynamic synchronous machine simulation with harmonics

    SciTech Connect (OSTI)

    Haskew, T.A.; Stern, H.P.; Chen, Z. [Univ. of Alabama, Tuscaloosa, AL (United States). Dept. of Electrical Engineering] [Univ. of Alabama, Tuscaloosa, AL (United States). Dept. of Electrical Engineering

    1996-06-01

    Within this paper, an efficient procedure for the dynamic simulation of faulted synchronous machines operating in the presence of harmonics is presented. The algorithm employs steady-state frequency domain techniques for simulation of the transmission system sequence networks and time domain methods for the synchronous machines represented in the odq frame of reference. The procedure affords greater accuracy than conventional fault analysis techniques based strictly on steady-state methods, yet requires far less computational time than full system dynamic simulations such as those using the EMTP.

  11. Molecular Simulation of Novel Carbonaceous Materials for Hydrogen

    E-Print Network [OSTI]

    Wu, Jianzhong

    Molecular Simulation of Novel Carbonaceous Materials for Hydrogen Storage Dapeng Cao, Pingyun Feng graphitic carbon inverse opal (GCIO) provides an excellent absorbent for hydrogen storage at room a good candidate for inexpensive storage of hydrogen in future automobile vehicles. Hydrogen

  12. Wave Packet Simulations of Antiproton Scattering on Molecular Hydrogen

    E-Print Network [OSTI]

    Stegeby, Henrik; Piszczatowski, Konrad; Karlsson, Hans O

    2015-01-01

    The problem of antiproton scattering on the molecular Hydrogen is investigated by means of wave packet dynamics. The electronically potential energy surfaces of the antiproton H2 system are presented within this work. Excitation and dissociation probabilities of the molecular Hydrogen for collision energies in the ultra low energy regime below 10 eV are computed.

  13. Wave Packet Simulations of Antiproton Scattering on Molecular Hydrogen

    E-Print Network [OSTI]

    Henrik Stegeby; Markus Kowalewski; Konrad Piszczatowski; Hans O. Karlsson

    2015-07-30

    The problem of antiproton scattering on the molecular Hydrogen is investigated by means of wave packet dynamics. The electronically potential energy surfaces of the antiproton H2 system are presented within this work. Excitation and dissociation probabilities of the molecular Hydrogen for collision energies in the ultra low energy regime below 10 eV are computed.

  14. Stochastic simulations of cargo transport by processive molecular motors

    E-Print Network [OSTI]

    Christian B. Korn; Stefan Klumpp; Reinhard Lipowsky; Ulrich S. Schwarz

    2009-12-11

    We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines the numerical integration of a Langevin equation for the motion of a sphere with kinetic rules for the molecular motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic interactions between sphere and wall. The kinetic rules for the motors include binding to and unbinding from the filament as well as active motor steps. We find that the simulated mean transport length increases exponentially with the number of bound motors, in good agreement with earlier results. The number of motors in binding range to the motor track fluctuates in time with a Poissonian distribution, both for springs and cables being used as models for the linker mechanics. Cooperativity in the sense of equal load sharing only occurs for high values for viscosity and attachment time.

  15. Molecular dynamics study of fracture accompanied by chemical reaction

    E-Print Network [OSTI]

    Krivtsov, Anton M.

    Molecular dynamics study of fracture accompanied by chemical reaction Anton M. Krivtsov akrivtsov@bk.ru Abstract A molecular dynamics model for fracture accompanied by chemical reac- tion is suggested. Crack of the initial and new specimen surfaces during the fracture process is taken into account. It is pos- tulated

  16. Molecular beam studies of reaction dynamics

    SciTech Connect (OSTI)

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

    1993-12-01

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

  17. The use of molecular dynamics for the thermodynamic properties of simple and transition metals

    SciTech Connect (OSTI)

    Straub, G.K.

    1987-04-01

    The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated.

  18. Osmosis : a molecular dynamics computer simulation study 

    E-Print Network [OSTI]

    Lion, Thomas

    2013-11-28

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and ...

  19. Molecular Dynamics Simulations of RNA Systems

    E-Print Network [OSTI]

    Westhof, Eric

    -1158 Hartmann PMU: WSL(W) 07/09/2004 ScalaLF&SansLF (0).3.04.05 (170Â240mm) pp. 560­576 III-34_P (p A/neomycin B 21 10.0 Naþ 124 34.2 MD Methods 561 (V7(M) 9/9/04 15:13) VCH/G J-1158 Hartmann PMU: WSL

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

    Office of Scientific and Technical Information (OSTI)

    ; Martinez, D A ; Pound, M W ; Heeter, R F ; Casner, A ; Mancini, R C Publication Date: 2015-01-16 OSTI Identifier: 1179389 Report Number(s): LLNL-CONF-666498 DOE Contract Number:...

  1. Molecular Dynamics Simulation Studies of Electrolytes and

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankADVANCED MANUFACTURING OFFICESpecialAPPENDIX F Wetlandsof Energy ModelSEI LayerManufactured Housing

  2. Molecular dynamics simulation studies of electrolytes and

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankADVANCED MANUFACTURING OFFICESpecialAPPENDIX F Wetlandsof Energy ModelSEIelectrolyte/electrode

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

    E-Print Network [OSTI]

    Heinz, Stefan

    to derive a hierarchy of algebraic expressions for the molecular stress tensor and heat flux. A scaling of ordinary irreversible thermodynamics [3]) transport equations for the molecular stress tensor and heat flux equations. The stochastic model is used to derive fluid dynamic equations where the molecular stress tensor

  4. Reweighted ensemble dynamics simulations: theory, improvement, and application

    E-Print Network [OSTI]

    Linchen Gong; Xin Zhou; Zhong-Can Ou-Yang

    2015-02-22

    Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provides schemes on selection of basis functions, determination of free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enable to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.

  5. Correlation between surface topography and slippage: a Molecular Dynamics study

    E-Print Network [OSTI]

    Nikita Tretyakov; Marcus Müller

    2013-02-21

    Using Molecular Dynamics simulations of a polymer liquid flowing past flat and patterned surfaces, we investigate the influence of corrugation, wettability and pressure on slippage and friction at the solid-liquid interface. For one-dimensional, rectangular grooves, we observe a gradual crossover between the Wenzel state, where the liquid fills the grooves, and the Cassie state, where the corrugation supports the liquid and the grooves are filled with vapor. Using two independent flow set-ups, we characterize the near-surface flow by the slip length, $\\delta$, and the position, $z_\\textrm{h}$, at which viscous and frictional stresses are balanced according to Navier's partial slip boundary condition. This hydrodynamic boundary position depends on the pressure inside the channel and may be located above the corrugated surface. In the Cassie state, we observe that the edges of the corrugation contribute to the friction.

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

    E-Print Network [OSTI]

    Bryant, Zev

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

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

    E-Print Network [OSTI]

    Tománek, David

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

  8. Discrete molecular dynamics studies of the folding of a protein-like model

    E-Print Network [OSTI]

    Buldyrev, Sergey

    Discrete molecular dynamics studies of the folding of a protein-like model Nikolay V Dokholyan1 to resolve in time the folding of model proteins in computer simulations. Different computational approaches). Results: We used the recently proposed approach of Zhou and Karplus to study the folding of a protein

  9. Classical trajectory studies of the molecular dissociation dynamics of formaldehyde: H, CO + H, + CO

    E-Print Network [OSTI]

    Miller, William H.

    Classical trajectory studies of the molecular dissociation dynamics of formaldehyde: H, CO + H to simulate the unimolecular decomposition of formaldehyde in the ground electronic state (Se). Global for the current potential surfaces are suggested. I. INTRODUCTION Formaldehyde has been studied extensively during

  10. Principles of Modern Molecular Simulation Methods

    E-Print Network [OSTI]

    Shell, M. Scott

    bottom-up top-down Simulations at different scales #12;Topics covered Ab initio and electronic structurePy + SciPy NumPy ­ very fast linear algebra and array routines, random number generation Sci, interpolation, Fourier transforms & signal processing, linear algebra, statistics Python + NumPy + SciPy rivals

  11. Ultrafast reaction dynamics in cluster ions: Simulation of the transient photoelectron spectrum of I2 Arn photodissociation

    E-Print Network [OSTI]

    Faeder, Jim

    Hamiltonian model of electronic structure with nonadiabatic molecular dynamics simulations, we calculate of the electronic structure of a manifold of states strongly coupled to the many solvent degrees of freedomUltrafast reaction dynamics in cluster ions: Simulation of the transient photoelectron spectrum

  12. Molecular Dynamics Study of Stiffness in Polystyrene and Polyethylene

    E-Print Network [OSTI]

    Hamed Nazarpourfard; Mahdi Ahmadi Borji

    2015-04-26

    In this paper, we have studied polystyrene (PS) and polyethylene (PE) stiffness by 3-dimensional Langevin Molecular Dynamics simulation. Hard polymers have a very small bending, and thus, their end-to-end distance is more than soft polymers. Quantum dot lasers can be established as colloidal particles dipped in a liquid and grafted by polymer brushes to maintain the solution. Here by a study on molecular structures of PS and PE, we show that the principle reason lies on large phenyl groups around the backbone carbons of PS, rather than a PE with Hydrogen atoms. Our results show that the mean radius of PS random coil is more than PE which directly affects the quantum dot maintenance. In addition, effect of temperature increase on the mean radius is investigated. Our results show that by increasing temperature, both polymers tend to lengthen, and at all temperatures a more radius is predicted for PS rather than PE, but interestingly, with a difference in short and long chains. We show that stiffness enhancement is not the same at short and long polymers and the behavior is very different. Our results show a good consonance with both experimental and theoretical studies.

  13. Molecular Dynamics Study of Stiffness in Polystyrene and Polyethylene

    E-Print Network [OSTI]

    Mahdi Ahmadi Borji

    2015-10-10

    In this paper, we have studied polystyrene (PS) and polyethylene (PE) stiffness by 3-dimensional Langevin Molecular Dynamics simulation. Hard polymers have a very small bending, and thus, their end-to-end distance is more than soft polymers. Quantum dot lasers can be established as colloidal particles dipped in a liquid and grafted by polymer brushes to maintain the solution. Here by a study on molecular structures of PS and PE, we show that the principle reason lies on large phenyl groups around the backbone carbons of PS, rather than a PE with Hydrogen atoms. Our results show that the mean radius of PS random coil is more than PE which directly affects the quantum dot maintenance. In addition, effect of temperature increase on the mean radius is investigated. Our results show that by increasing temperature, both polymers tend to lengthen, and at all temperatures a more radius is predicted for PS rather than PE, but interestingly, with a difference in short and long chains. We show that stiffness enhancement is not the same at short and long polymers and the behavior is very different. Our results show a good consonance with both experimental and theoretical studies.

  14. Molecular Dynamics Study of Stiffness in Polystyrene and Polyethylene

    E-Print Network [OSTI]

    Nazarpourfard, Hamed

    2015-01-01

    In this paper, we have studied polystyrene (PS) and polyethylene (PE) stiffness by 3-dimensional Langevin Molecular Dynamics simulation. Hard polymers have a very small bending, and thus, their end-to-end distance is more than soft polymers. Quantum dot lasers can be established as colloidal particles dipped in a liquid and grafted by polymer brushes to maintain the solution. Here by a study on molecular structures of PS and PE, we show that the principle reason lies on large phenyl groups around the backbone carbons of PS, rather than a PE with Hydrogen atoms. Our results show that the mean radius of PS random coil is more than PE which directly affects the quantum dot maintenance. In addition, effect of temperature increase on the mean radius is investigated. Our results show that by increasing temperature, both polymers tend to lengthen, and at all temperatures a more radius is predicted for PS rather than PE, but interestingly, with a difference in short and long chains. We show that stiffness enhancement...

  15. Multiscale molecular dynamics using the matched interface and boundary method

    SciTech Connect (OSTI)

    Geng Weihua [Department of Mathematics, Michigan State University, East Lansing, MI 48824 (United States); Wei, G.W., E-mail: wei@math.msu.ed [Department of Mathematics, Michigan State University, East Lansing, MI 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824 (United States)

    2011-01-20

    The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.

  16. Physics results from dynamical overlap fermion simulations

    E-Print Network [OSTI]

    Shoji Hashimoto

    2008-11-08

    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.

  17. Laboratory Simulations of Molecular Hydrogen Formation in the Early Universe

    E-Print Network [OSTI]

    Savin, Daniel Wolf

    Laboratory Simulations of Molecular Hydrogen Formation in the Early Universe: A Progress Report D Heidelberg, Germany Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, Il-la-Neuve B-1348, Belgium Abstract. During the epoch of protogalaxy and first star formation, H2 is the main

  18. Molecular simulations of supercritical fluid permeation through disordered microporous

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    and wastewater treatment,? gas separation,? energy storage,? carbon dioxide sequestration or gas production fromMolecular simulations of supercritical fluid permeation through disordered microporous carbons, FRANCE E-mail: botan@mit.edu Abstract Fluid transport through microporous carbon-based materials

  19. Molecular Simulation of Hydrogen Storage in SWNT ? Shigeo MARUYAMAa

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

  20. Filaments in simulations of molecular cloud formation

    SciTech Connect (OSTI)

    Gómez, Gilberto C.; Vázquez-Semadeni, Enrique

    2014-08-20

    We report on the filaments that develop self-consistently in a new numerical simulation of cloud formation by colliding flows. As in previous studies, the forming cloud begins to undergo gravitational collapse because it rapidly acquires a mass much larger than the average Jeans mass. Thus, the collapse soon becomes nearly pressureless, proceeding along its shortest dimension first. This naturally produces filaments in the cloud and clumps within the filaments. The filaments are not in equilibrium at any time, but instead are long-lived flow features through which the gas flows from the cloud to the clumps. The filaments are long-lived because they accrete from their environment while simultaneously accreting onto the clumps within them; they are essentially the locus where the flow changes from accreting in two dimensions to accreting in one dimension. Moreover, the clumps also exhibit a hierarchical nature: the gas in a filament flows onto a main, central clump but other, smaller-scale clumps form along the infalling gas. Correspondingly, the velocity along the filament exhibits a hierarchy of jumps at the locations of the clumps. Two prominent filaments in the simulation have lengths ?15 pc and masses ?600 M {sub ?} above density n ? 10{sup 3} cm{sup –3} (?2 × 10{sup 3} M {sub ?} at n > 50 cm{sup –3}). The density profile exhibits a central flattened core of size ?0.3 pc and an envelope that decays as r {sup –2.5} in reasonable agreement with observations. Accretion onto the filament reaches a maximum linear density rate of ?30 M {sub ?} Myr{sup –1} pc{sup –1}.

  1. Control of molecular dynamics with zero-area fields: Application to molecular orientation and photofragmentation

    E-Print Network [OSTI]

    D. Sugny; Stéphane Vranckx; Mamadou Ndong; Nathalie Vaeck; Osman Atabek; Michèle Desouter-Lecomte

    2014-12-15

    The constraint of time-integrated zero-area on the laser field is a fundamental, both theoretical and experimental requirement in the control of molecular dynamics. By using techniques of local and optimal control theory, we show how to enforce this constraint on two benchmark control problems, namely molecular orientation and photofragmentation. The origin and the physical implications on the dynamics of this zero-area control field are discussed.

  2. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    SciTech Connect (OSTI)

    Steven R Prescott; Curtis Smith

    2011-07-01

    Through continued advancement in computational resources, development that was previously done by trial and error production is now performed through computer simulation. These virtual physical representations have the potential to provide accurate and valid modeling results and are being used in many different technical fields. Risk assessment now has the opportunity to use 3D simulation to improve analysis results and insights, especially for external event analysis. By using simulations, the modeler only has to determine the likelihood of an event without having to also predict the results of that event. The 3D simulation automatically determines not only the outcome of the event, but when those failures occur. How can we effectively incorporate 3D simulation into traditional PRA? Most PRA plant modeling is made up of components with different failure modes, probabilities, and rates. Typically, these components are grouped into various systems and then are modeled together (in different combinations) as a “system” with logic structures to form fault trees. Applicable fault trees are combined through scenarios, typically represented by event tree models. Though this method gives us failure results for a given model, it has limitations when it comes to time-based dependencies or dependencies that are coupled to physical processes which may themselves be space- or time-dependent. Since, failures from a 3D simulation are naturally time related, they should be used in that manner. In our simulation approach, traditional static models are converted into an equivalent state diagram representation with start states, probabilistic driven movements between states and terminal states. As the state model is run repeatedly, it converges to the same results as the PRA model in cases where time-related factors are not important. In cases where timing considerations are important (e.g., when events are dependent upon each other), then the simulation approach will typically provide superior results and insights. We also couple the state model with the dynamic 3D simulation analysis representing events (such as flooding) to determine which (if any) components fail. Not only does the simulation take into account any failed items from the state model, but any failures caused by the simulation are incorporated back into the state model and factored into the overall results. Using this method we incorporate accurate 3D simulation results, eliminate static-based PRA issues, and have time ordered failure information.

  3. Dynamical analysis of highly excited molecular spectra

    SciTech Connect (OSTI)

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

    1993-12-01

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

  4. Ab initio molecular-dynamics method based on the restricted path integral: Application to the electron plasma and liquid alkali metal

    E-Print Network [OSTI]

    Deymier, Pierre

    Ab initio molecular-dynamics method based on the restricted path integral: Application on the discretized path-integral representation of quantum particles. Fermi statistics is automatically generated by an effective exchange potential. This path-integral molecular-dynamics method is able to simulate electron

  5. Stochastic Roadmap Simulation: An efficient Representation and Algorithm for Analyzing Molecular Motion

    E-Print Network [OSTI]

    Brutlag, Doug

    Stochastic Roadmap Simulation: An efficient Representation and Algorithm for Analyzing Molecular. This paper introduces Stochastic Roadmap Simulation (SRS) as a new computational approach for explor- ing

  6. Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

    SciTech Connect (OSTI)

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

    2010-12-01

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

  7. Hidden scale invariance in molecular van der Waals liquids: A simulation study

    E-Print Network [OSTI]

    Thomas B. Schrøder; Ulf R. Pedersen; Nicholas Bailey; Søren Toxværd; Jeppe C. Dyre

    2009-09-18

    Results from molecular dynamics simulations of two viscous molecular model liquids -- the Lewis-Wahnstrom model of ortho-terphenyl and an asymmetric dumbbell model -- are reported. We demonstrate that the liquids have a ``hidden'' approximate scale invariance: Equilibrium potential energy fluctuations are accurately described by inverse power law (IPL) potentials, the radial distribution functions are accurately reproduced by the IPL's, and the radial distribution functions obey the IPL predicted scaling properties to a good approximation. IPL scaling of the dynamics also applies -- with the scaling exponent predicted by the equilibrium fluctuations. In contrast, the equation of state does not obey the IPL scaling. We argue that our results are general for van der Waals liquids, but do not apply, e.g., for hydrogen-bonded liquids.

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

    SciTech Connect (OSTI)

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

    2008-05-01

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

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

    SciTech Connect (OSTI)

    Richters, Dorothee; Kühne, Thomas D.

    2014-04-07

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

  10. A field-theoretic approach to linear scaling \\textit{ab-initio} molecular dynamics

    E-Print Network [OSTI]

    Richters, Dorothee; Kühne, Thomas D

    2012-01-01

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

  11. Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

    E-Print Network [OSTI]

    Sushko, Gennady B; Verkhovtsev, Alexey V; Volkov, Sergey N; Solov'yov, Andrey V

    2015-01-01

    The concept of molecular mechanics force field has nowadays been widely accepted for studying various processes in biomolecular systems. In this paper we suggest a modification for the standard CHARMM force field, that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, in this paper we provide several case studies where dynamical topology is necessary. In particular, it is shown, that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation or collision induced damage, transformation and fragmentation processes involving biomolecular systems.

  12. State-to-state dynamics of molecular energy transfer

    SciTech Connect (OSTI)

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

    1993-12-01

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

  13. VUV studies of molecular photofragmentation dynamics

    SciTech Connect (OSTI)

    White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

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

  14. On sequential dynamical systems and simulation

    SciTech Connect (OSTI)

    Barrett, C.L.; Mortveit, H.S.; Reidys, C.M.

    1999-06-01

    The generic structure of computer simulations motivates a new class of discrete dynamical systems that captures this structure in a mathematically precise way. This class of systems consists of (1) a loopfree graph {Upsilon} with vertex set {l_brace}1,2,{hor_ellipsis},n{r_brace} where each vertex has a binary state, (2) a vertex labeled set of functions (F{sub i,{Upsilon}}:F{sub 2}{sup n} {r_arrow} F{sub 2}{sup n}){sub i} and (3) a permutation {pi} {element_of} S{sub n}. The function F{sub i,{Upsilon}} updates the state of vertex i as a function of the states of vertex i and its {Upsilon}-neighbors and leaves the states of all other vertices fixed. The permutation {pi} represents the update ordering, i.e., the order in which the functions F{sub i,{Upsilon}} are applied. By composing the functions F{sub i,{Upsilon}} in the order given by {pi} one obtains the dynamical system (equation given in paper) which the authors refer to as a sequential dynamical system, or SDS for short. The authors will present bounds for the number of functionally different systems and for the number of nonisomorphic digraphs {Gamma}[F{sub {Upsilon}},{pi}] that can be obtained by varying the update order and applications of these to specific graphs and graph classes. This will be done using both combinatorial/algebraic techniques and probabilistic techniques. Finally the authors give results on dynamical system properties for some special systems.

  15. Accelerated Molecular Dynamics Methods | Department of Energy

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious Rank EERE:Financing ToolInternationalReportOffice |4-01r2.pdfATVM GuidanceDepartmentUsof EnergyMolecular

  16. A Quasi-Dynamic HVAC and Building Simulation Methodology 

    E-Print Network [OSTI]

    Davis, Clinton Paul

    2012-07-16

    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...

  17. Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory

    E-Print Network [OSTI]

    Marsalek, Ondrej

    2015-01-01

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive pro...

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

    SciTech Connect (OSTI)

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

    2013-12-16

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

  19. Dynamics of Molecular Motors in Reversible Burnt-Bridge Models

    E-Print Network [OSTI]

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

    2009-11-22

    Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random walkers that can destroy or rebuild periodically distributed weak connections ("bridges") when crossing them, with probabilities $p_1$ and $p_2$ correspondingly. Dynamic properties, such as velocities and dispersions, are obtained in exact and explicit form for arbitrary values of parameters $p_1$ and $p_2$. For the unbiased random walker, reversible burning of the bridges results in a biased directed motion with a dynamic transition observed at very small concentrations of bridges. In the case of backward biased molecular motor its backward velocity is reduced and a reversal of the direction of motion is observed for some range of parameters. It is also found that the dispersion demonstrates a complex, non-monotonic behavior with large fluctuations for some set of parameters. Complex dynamics of the system is discussed by analyzing the behavior of the molecular motors near burned bridges.

  20. Molecular Dynamics of Methanol Monocation (CH3OH+ ) in Strong

    E-Print Network [OSTI]

    Schlegel, H. Bernhard

    Molecular Dynamics of Methanol Monocation (CH3OH+ ) in Strong Laser Fields Bishnu Thapa and H surfaces of methanol neutral, monocation, and singlet and triplet dication were explored using the CBS in the presence of a 2.9 × 1014 W/cm2 800 nm laser field for methanol monocation on the ground state potential

  1. Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble

    E-Print Network [OSTI]

    Stanley, H. Eugene

    Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble Feng Ding for the interpretation of experimental results and understanding of protein folding mechanics, which has at- tracted, 1999; Guerois and Serrano, 2000) have been proposed to predict the transition states in protein folding

  2. Implementation of Green's function molecular dynamics: an extension to LAMMPS

    E-Print Network [OSTI]

    Mueser, Martin

    -Materials Technology Laboratory, Natural Resources Canada, Ottawa, Ontario, K1A 0G1, Canada 2 Corresponding authors, e, FFTW 2.1.5 Subprograms used: LAMMPS version 22 Jan 2008 Nature of problem and solution method: Using to reproduce the effects of long-range elastic deformations. Green's function molecular dynamics (GFMD) in

  3. Molecular dynamics of liquid benzene via femtosecond pulses laser excitation

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1749 Molecular dynamics of liquid benzene via femtosecond pulses laser excitation J. Etchepare, G moléculaires. Abstract. 2014 We analyse the complex response of liquid benzene to the applied 45 fs FHWM new results obtained by the transient grating temporal behaviour analysis of benzene, a molecule

  4. Ion assisted structural collapse of a single stranded DNA: a molecular dynamics approach

    E-Print Network [OSTI]

    Ghosh, Soumadwip; Chakrabarti, Rajarshi

    2015-01-01

    The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of additional salt, a source of excess oppositely charged ions. Under such conditions single stranded DNA adopts a collapsed coil like conformation, typically characterized by stacking base pairs. Using atomistic molecular dynamics simulation, we demonstrate that in the presence of additional divalent salt (MgCl2) single stranded DNA (Dickerson Drew dodecamer) initially collapses and then expands with increasing salt concentration. This is due to the overcharging induced DNA chain swelling, a dominant factor at a higher divalent salt concentration. In a nutshell, our simulations show how in the presence of divalent salt, non-sequential base stacking and overcharging competes and affect single stranded DNA dynamics unlike a monovalent salt.

  5. Simulations of vibrational relaxation in dense molecular fluids

    SciTech Connect (OSTI)

    Holian, B.L.

    1985-07-01

    In the understanding of high-temperatre and -pressure chemistry in explosives, first step is the study of the transfer of energy from translational degrees of freedom into internal vibrations of the molecules. We present new methods using nonequilibrium molecular dynamics (NEMD) for measuring vibrational relaxation in a diatomic fluid, where we expect a classical treatment of many-body collisions to be relevant because of the high densities (2 to 3 times compressed compared to the normal fluid) and high temperatures (2000 to 4000 K) involved behind detonation waves. NEMD techniques are discussed, including their limitations, and qualitative results presented.

  6. Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

    E-Print Network [OSTI]

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

    2009-10-02

    Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations arising either from the solvent fluctuations or from base-pair vibrational modes can be taken into account in a straightforward way through time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the onsite energies along the DNA wire.

  7. Water network dynamics at the critical moment of a peptide's -turn formation: A molecular dynamics study

    E-Print Network [OSTI]

    Nerukh, Dmitry

    Water network dynamics at the critical moment of a peptide's -turn formation: A molecular dynamics-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of -turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding

  8. xMDFF: molecular dynamics flexible fitting of low-resolution...

    Office of Scientific and Technical Information (OSTI)

    xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures Citation Details In-Document Search Title: xMDFF: molecular dynamics flexible fitting of...

  9. Discrete Mathematics and Theoretical Computer Science AB(DMCS), 2003, 3142 Cellular Automata for Simulating Molecular

    E-Print Network [OSTI]

    Rasmussen, Steen

    for Simulating Molecular Self-Assembly Martin Nilsson and Steen Rasmussen Los Alamos National Laboratory, Los Alamos, NM 87545, USA. We present a lattice gas technique for simulating molecular self-assembly micelles is formed. Keywords: Cellular Automata, Lattice Gas, Molecular Self-Assembly, Statistical

  10. A parallel algorithm for step- and chain-growth polymerization in Molecular Dynamics

    E-Print Network [OSTI]

    Pierre de Buyl; Erik Nies

    2015-03-03

    Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

  11. Dynamic wind turbine models in power system simulation tool

    E-Print Network [OSTI]

    Dynamic wind turbine models in power system simulation tool DIgSILENT Anca D. Hansen, Florin Iov Iov, Poul Sørensen, Nicolaos Cutululis, Clemens Jauch, Frede Blaabjerg Title: Dynamic wind turbine system simulation tool PowerFactory DIgSILENT for different wind turbine concepts. It is the second

  12. Dynamic Simulation of Electric Machines on FPGA Boards

    E-Print Network [OSTI]

    Zambreno, Joseph A.

    Dynamic Simulation of Electric Machines on FPGA Boards Hao Chen, Song Sun, Dionysios C. Aliprantis, and Joseph Zambreno Department of Electrical and Computer Engineering Iowa State University, Ames, IA 50011 USA Abstract--This paper presents the implementation of an induc- tion machine dynamic simulation

  13. Integrated Dynamic Simulation for Process Optimization and Control

    E-Print Network [OSTI]

    Rubloff, Gary W.

    Integrated Dynamic Simulation for Process Optimization and Control G. Brian Lu, Laura L. Tedder ­ Film Deposition · Applications in Process Optimization for Manufacturing and the Environment ­ Process efficient processes, equipment, sensor, and control systems #12;Dynamic Simulators for Sensor-Based Process

  14. Dynamic Simulation Model of a Consumer Foods Production Process !

    E-Print Network [OSTI]

    Sun, Yu

    schedule based on product list The SIMUL8 Component 1. Over 200 lines of simula0on code 2. ReadsDynamic Simulation Model of a Consumer Foods Production Process ! Goals · Create a dynamic simula0 Created par0ally automated Excel files to go handin hand with simula0on o Contains all SKUs and meat

  15. Enhanced reactivity of nanoenergetic materials: A first-principles molecular dynamics study based on divide-and-conquer density

    E-Print Network [OSTI]

    Southern California, University of

    a stage for first-principles molecular dynamics simulation of thermite reaction at an Al/Fe2O3 interface experimental observation in thermite nanowire arrays. © 2009 American Institute of Physics. DOI: 10 to drive nanofluidics.1,2 Most widely used energetic materials for device integration are thermites, which

  16. Correlations and Symmetry of Interactions Influence Collective Dynamics of Molecular Motors

    E-Print Network [OSTI]

    Daniel Celis-Garza; Hamid Teimouri; Anatoly B. Kolomeisky

    2015-03-02

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations.

  17. Simulations of Evolving or Outbursting Molecular Protostellar Jets

    E-Print Network [OSTI]

    Alexander Rosen; Michael D. Smith

    2003-04-25

    The kinematic and radiative power of molecular jets is expected to change as a protostar undergoes permanent or episodal changes in the rate at which it accretes. We study here the consequences of evolving jet power on the spatial and velocity structure, as well as the fluxes, of molecular emission from the bipolar outflow. We consider a jet of rapidly increasing density and a jet in which the mass input is abruptly cut off. We perform three dimensional hydrodynamic simulations with atomic and molecular cooling and chemistry. In this work, highly collimated and sheared jets are assumed. We find that position-velocity diagrams, velocity-channel maps and the relative H$_2$ and CO fluxes are potentially the best indicators of the evolutionary stage. In particular, the velocity width of the CO lines may prove most reliable although the often-quoted mass-velocity power-law index is probably not. We demonstrate how the relative H$_2$ 1--0 S(1) and CO J=1--0 fluxes evolve and apply this to interpret the phase of several outflows.

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

    SciTech Connect (OSTI)

    Krishna, Rajamani; van Baten, Jasper M

    2011-01-01

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

  19. Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

    SciTech Connect (OSTI)

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

    2010-03-14

    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.

  20. Fast Thermal Simulation for Architecture Level Dynamic Thermal Management

    E-Print Network [OSTI]

    Tan, Sheldon X.-D.

    Fast Thermal Simulation for Architecture Level Dynamic Thermal Management Pu Liu, Zhenyu Qi, Hang temperature by dynamic thermal managements becomes necessary. This paper proposes a novel approach to the thermal analysis at chip architecture level for efficient dynamic thermal management. Our new approach

  1. Simulation of chemical reaction dynamics on an NMR quantum computer

    E-Print Network [OSTI]

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

    2011-05-21

    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.

  2. Kinetic simulations of plasmoid chain dynamics

    SciTech Connect (OSTI)

    Markidis, S. [High Performance Computing and Visualization (HPCViz) Department, KTH Royal Institute of Technology, Stockholm (Sweden)] [High Performance Computing and Visualization (HPCViz) Department, KTH Royal Institute of Technology, Stockholm (Sweden); Henri, P. [Université de Nice Sophia Antipolis, CNRS, Observatoire de la Côte d'Azur, Nice (France)] [Université de Nice Sophia Antipolis, CNRS, Observatoire de la Côte d'Azur, Nice (France); Lapenta, G. [Centrum voor Plasma-Astrofysica, Department Wiskunde, Katholieke Universiteit Leuven, Leuven (Belgium)] [Centrum voor Plasma-Astrofysica, Department Wiskunde, Katholieke Universiteit Leuven, Leuven (Belgium); Divin, A. [Swedish Institute of Space Physics, Uppsala (Sweden)] [Swedish Institute of Space Physics, Uppsala (Sweden); Goldman, M.; Newman, D. [Department of Physics and CIPS, University of Colorado, Boulder 80309-0390 (United States)] [Department of Physics and CIPS, University of Colorado, Boulder 80309-0390 (United States); Laure, E. [PDC and High Performance Computing and Visualization (HPCViz) Department, KTH Royal Institute of Technology, Stockholm (Sweden)] [PDC and High Performance Computing and Visualization (HPCViz) Department, KTH Royal Institute of Technology, Stockholm (Sweden)

    2013-08-15

    The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids.

  3. Learning Curve: A Simulation-based Approach to Dynamic Pricing

    E-Print Network [OSTI]

    Greenwald, Amy

    , a market simulator designed for analyzing agent pricing strategies in markets under finite time horizons algorithms using a market simulator that is capable of simulating many different market scenarios, the market environment, and the seller's supply at the moment of the transaction. As dynamic pricing becomes

  4. Collective dynamics of molecular motors pulling on fluid membranes

    E-Print Network [OSTI]

    O. Campas; Y. Kafri; K. B. Zeldovich; J. Casademunt; J. -F. Joanny

    2005-12-08

    The collective dynamics of $N$ weakly coupled processive molecular motors are considered theoretically. We show, using a discrete lattice model, that the velocity-force curves strongly depend on the effective dynamic interactions between motors and differ significantly from a simple mean field prediction. They become essentially independent of $N$ if it is large enough. For strongly biased motors such as kinesin this occurs if $N\\gtrsim 5$. The study of a two-state model shows that the existence of internal states can induce effective interactions.

  5. Tensor-optimized antisymmetrized molecular dynamics in nuclear physics

    E-Print Network [OSTI]

    Myo, Takayuki; Ikeda, Kiyomi; Horiuchi, Hisashi; Suhara, Tadahiro

    2015-01-01

    We develop a new formalism to treat nuclear many-body systems using bare nucleon-nucleon interaction. It has become evident that the tensor interaction plays important role in nuclear many-body systems due to the role of the pion in strongly interacting system. We take the antisymmetrized molecular dynamics (AMD) as a basic framework and add a tensor correlation operator acting on the AMD wave function using the concept of the tensor-optimized shell model (TOSM). We demonstrate a systematical and straightforward formulation utilizing the Gaussian integration and differentiation method and the antisymmetrization technique to calculate all the matrix elements of the many-body Hamiltonian. We can include the three-body interaction naturally and calculate the matrix elements systematically in the progressive order of the tensor correlation operator. We call the new formalism "tensor-optimized antisymmetrized molecular dynamics".

  6. Criteria for the accuracy of small polaron quantum master equation in simulating excitation energy transfer dynamics

    SciTech Connect (OSTI)

    Chang, Hung-Tzu; Cheng, Yuan-Chung [Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan (China)] [Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan (China); Zhang, Pan-Pan [Department of Physics and Institute of Modern Physics, Ningbo University, Ningbo 315211 (China)] [Department of Physics and Institute of Modern Physics, Ningbo University, Ningbo 315211 (China)

    2013-12-14

    The small polaron quantum master equation (SPQME) proposed by Jang et al. [J. Chem. Phys. 129, 101104 (2008)] is a promising approach to describe coherent excitation energy transfer dynamics in complex molecular systems. To determine the applicable regime of the SPQME approach, we perform a comprehensive investigation of its accuracy by comparing its simulated population dynamics with numerically exact quasi-adiabatic path integral calculations. We demonstrate that the SPQME method yields accurate dynamics in a wide parameter range. Furthermore, our results show that the accuracy of polaron theory depends strongly upon the degree of exciton delocalization and timescale of polaron formation. Finally, we propose a simple criterion to assess the applicability of the SPQME theory that ensures the reliability of practical simulations of energy transfer dynamics with SPQME in light-harvesting systems.

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

    SciTech Connect (OSTI)

    Hall G. E.; Goncharov, V.

    2012-05-29

    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.

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

    SciTech Connect (OSTI)

    Hall, G.E.

    2011-05-31

    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.

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

    E-Print Network [OSTI]

    Lin, Shangchao

    2012-01-01

    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 ...

  10. Poiseuille flow past a nanoscale cylinder in a slit channel: Lubrication theory versus molecular dynamics analysis

    E-Print Network [OSTI]

    Amir M. Rahmani; Yang Shao; Mehlam Jupiterwala; Carlos E. Colosqui

    2015-04-13

    Plane Poiseuille flow past a nanoscale cylinder that is arbitrarily confined (i.e., symmetrically or asymmetrically confined) in a slit channel is studied via hydrodynamic lubrication theory and molecular dynamics simulations, considering cases where the cylinder remains static or undergoes thermal motion. Lubrication theory predictions for the drag force and volumetric flow rate are in close agreement with molecular dynamics simulations of flows having molecularly thin lubrication gaps, despite the presence of significant structural forces induced by the crystalline structure of the modeled solid. While the maximum drag force is observed in symmetric confinement, i.e., when the cylinder is equidistant from both channel walls, the drag decays significantly as the cylinder moves away from the channel centerline and approaches a wall. Hence, significant reductions in the mean drag force on the cylinder and hydraulic resistance of the channel can be observed when thermal motion induces random off-center displacements. Analytical expressions and numerical results in this work provide useful insights into the hydrodynamics of colloidal solids and macromolecules in confinement.

  11. MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS

    SciTech Connect (OSTI)

    Athanassios Z. Panagiotopoulos

    2009-09-09

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

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

    SciTech Connect (OSTI)

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

    2009-04-03

    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.

  13. Magnetic Materials at finite Temperatures: thermodynamics and combined spin and molecular dynamics derived from first principles calculations

    SciTech Connect (OSTI)

    Eisenbach, Markus; Perera, Meewanage Dilina N; Landau, David P; Nicholson, Don M; Yin, Junqi; Brown, Greg

    2015-01-01

    We present a unified approach to describe the combined behavior of the atomic and magnetic degrees of freedom in magnetic materials. Using Monte Carlo simulations directly combined with first principles the Curie temperature can be obtained ab initio in good agreement with experimental values. The large scale constrained first principles calculations have been used to construct effective potentials for both the atomic and magnetic degrees of freedom that allow the unified study of influence of phonon-magnon coupling on the thermodynamics and dynamics of magnetic systems. The MC calculations predict the specific heat of iron in near perfect agreement with experimental results from 300K to above Tc and allow the identification of the importance of the magnon-phonon interaction at the phase-transition. Further Molecular Dynamics and Spin Dynamics calculations elucidate the dynamics of this coupling and open the potential for quantitative and predictive descriptions of dynamic structure factors in magnetic materials using first principles derived simulations.

  14. Simulation Algorithms in Vehicle System Dynamics MARTIN ARNOLD

    E-Print Network [OSTI]

    be considered as integration platform for simulation in vehicle system dynamics. In the present report we report the analysis of distributed physical phenomena like the elastic deformation of car components

  15. Physics issues in simulations with dynamical overlap fermions

    E-Print Network [OSTI]

    Thomas DeGrand; Stefan Schaefer

    2004-12-01

    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.

  16. Large-Scale Hybrid Dynamic Simulation Employing Field Measurements

    SciTech Connect (OSTI)

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

    2004-06-30

    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.

  17. Modelling and Dynamic Simulation for Process Control

    E-Print Network [OSTI]

    Skogestad, Sigurd

    principles for model development are outlined, and these principles are applied to a simple ash tank (which. In this paper we consider dynamic process models obtained using fundamental principles (eg. based reactor, a simple trend analysis using temperature measurements may be suÆcient. Dynamic models

  18. Reweighting QCD simulations with dynamical overlap fermions

    E-Print Network [OSTI]

    Thomas DeGrand

    2008-10-03

    I apply a recently developed algorithm for reweighting simulations of lattice QCD from one quark mass to another to simulations performed with overlap fermions in the epsilon regime. I test it by computing the condensate from distributions of the low lying eigenvalues of the Dirac operator. Results seem favorable.

  19. Dynamic Spherical Volumetric Simplex Splines with Applications in Biomedical Simulation

    E-Print Network [OSTI]

    Hua, Jing

    Dynamic Spherical Volumetric Simplex Splines with Applications in Biomedical Simulation Yunhao Tan computational framework based on dy- namic spherical volumetric simplex splines for simulation of genus- zero to reconstruct the high-fidelity digi- tal model of a real-world object with spherical volumetric simplex splines

  20. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    SciTech Connect (OSTI)

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

    2014-03-15

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

  1. A multiscale Molecular Dynamics approach to Contact Mechanics

    E-Print Network [OSTI]

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

    2006-01-05

    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.

  2. Generalized extended Lagrangian Born-Oppenheimer molecular dynamics

    SciTech Connect (OSTI)

    Niklasson, Anders M. N. Cawkwell, Marc J.

    2014-10-28

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

  3. Molecular dynamics of wetting layer formation and forced water invasion in angular nanopores with mixed wettability

    SciTech Connect (OSTI)

    Sedghi, Mohammad Piri, Mohammad; Goual, Lamia

    2014-11-21

    The depletion of conventional hydrocarbon reservoirs has prompted the oil and gas industry to search for unconventional resources such as shale gas/oil reservoirs. In shale rocks, considerable amounts of hydrocarbon reside in nanoscale pore spaces. As a result, understanding the multiphase flow of wetting and non-wetting phases in nanopores is important to improve oil and gas recovery from these formations. This study was designed to investigate the threshold capillary pressure of oil and water displacements in a capillary dominated regime inside nanoscale pores using nonequilibrium molecular dynamics (NEMD) simulations. The pores have the same cross-sectional area and volume but different cross-sectional shapes. Oil and water particles were represented with a coarse grained model and the NEMD simulations were conducted by assigning external pressure on an impermeable piston. Threshold capillary pressures were determined for the drainage process (water replaced by oil) in different pores. The molecular dynamics results are in close agreements with calculations using the Mayer-Stowe-Princen (MS-P) method which has been developed on the premise of energy balance in thermodynamic equilibrium. After the drainage simulations, a change in wall particles’ wettability from water-wet to oil-wet was implemented based on the final configuration of oil and water inside the pore. Waterflooding simulations were then carried out at the threshold capillary pressure. The results show that the oil layer formed between water in the corner and in the center of the pore is not stable and collapses as the simulation continues. This is in line with the predictions from the MS-P method.

  4. Simulation Methodologies for Satellite Solar Array Dynamics 

    E-Print Network [OSTI]

    Mohsenizadeh, Navid

    2010-07-16

    The purpose of the present thesis is to furnish diverse studies on the dynamic response of satellite solar arrays. The term flexible structure or, briefly, structure has different interpretations and definitions, depending ...

  5. Molecular Simulation of Water Extraction into a Tri-n-Butyl-Phosphate/n-Dodecane Solution

    SciTech Connect (OSTI)

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

    2013-01-01

    Abstract: Molecular dynamics simulations were performed to investigate water extraction into a solution of 30 vol% tri-n-butyl-phosphate (TBP) in n-dodecane. This solvent extraction mixture is commonly used in hydrometallurgical and nuclear fuel recycling operations for recovering metals from aqueous streams. It is known that water is coextracted in the organic phase and that it competes with metal ions for the available extractant agent (TBP). Therefore investigating pure water extraction provides a realistic prototype to test molecular simulation methods for the first time in this area. Our computational results indicate that the TBP electric dipole moment has a significant effect on the predicted water solubility. A larger TBP dipole moment decreases the aqueous-organic interfacial tension, leading to increased roughness of the aqueous-organic interface. Interfacial roughness has a significant effect on disrupting the interfacial water hydrogen bonding structure, resulting in a greater number of dangling water molecules at the interface. This enhances the probability of water molecules to break away from the aqueous phase and to migrate into the bulk of the organic phase. Therefore, the magnitude of the TBP dipole moment is a crucial factor in controlling water hydrogen bond breaking at the aqueous-organic interface. By slightly lowering the atomic partial charges of the TBP atoms, to produce a dipole moment that better agrees with experimental data, we were able to predict water solubility in close agreement with experimental measurements. Hence we demonstrate that a molecular modeling and simulation approach may provide quantitative support to experimental programs in this area. In addition, our simulation results shed light into the molecular mechanism of water extraction, the critical role of TBP, and the structural forms of water molecules both at the interface and in the bulk of the organic phase. Specifically, it is found that water molecules are extracted either as single molecules or as clusters. Furthermore, within the organic phase, the extracted water forms clusters with up to 20 water molecules, however, more than 70% of these water clusters contain less than 5 water molecules when the water extraction process reaches saturation.

  6. Molecular dynamics and neutron scattering study of the dependence of polyelectrolyte dendrimer conformation on counterion behavior

    SciTech Connect (OSTI)

    Chen, Wei-Ren [ORNL; Do, Changwoo [ORNL; Egami, T [University of Tennessee, Knoxville (UTK); Hong, Kunlun [ORNL; Li, Xin [ORNL; Liu, Emily [Rensselaer Polytechnic Institute (RPI); Liu, Yun [National Institute of Standards and Technology (NIST); Porcar, L. [National Institute of Standards and Technology (NIST); Smith, Gregory Scott [ORNL; Smith, Sean C [ORNL; Wu, Bin [ORNL

    2012-01-01

    Atomistic molecular dynamics (MD) simulations and contrast variation small angle neutron scattering (SANS) technique have been used to investigate the generation-5 (G5) polyelectrolyte polyamidoamine (PAMAM) starburst dendrimer with respect to its conformational dependence on counterion behavior at different levels of molecular charge. Satisfactory agreement is seen between the simulated results, such as the excess intra-dendrimer scattering length density (SLD) distribution and hydration level, and their experimental counterparts. The conformational evolution of charged dendrimer appears to be highly dependent on the association behavior of counterion. We explore the nature of the distribution of counterions around charged amines and qualitatively account for its sensitivity to the counterion valency on the difference of excess free energy. Moreover, via extending the concept of electrical double layer for compact charged colloids, we define an effective radius of charged dendrimer based on the spatial distribution of counterions in its vicinity. Within the same framework, the correlation between the strength of intra-dendrimer electrostatic repulsion and counterion valency and dynamics is also addressed.

  7. A Molecular Dynamics Study of Chemical Reactions of Solid Pentaerythritol Tetranitrate at Extreme Conditions

    SciTech Connect (OSTI)

    Wu, C J; Manaa, M R; Fried, L E

    2006-05-30

    We have carried out density functional based tight binding (DFTB) molecular dynamics (MD) simulation to study energetic reactions of solid Pentaerythritol Tetranitrate (PETN) at conditions approximating the Chapman-Jouguet (CJ) detonation state. We found that the initial decomposition of PETN molecular solid is characterized by uni-molecular dissociation of the NO{sub 2}groups. Interestingly, energy release from this powerful high explosive was found to proceed in several stages. The large portion of early stage energy release was found to be associated with the formation of H{sub 2}O molecules within a few picoseconds of reaction. It took nearly four times as long for majority of CO{sub 2} products to form, accompanied by a slow oscillatory conversion between CO and CO{sub 2}. The production of N{sub 2} starts after NO{sub 2} loses its oxygen atoms to hydrogen or carbon atoms to form H{sub 2}O or CO. We identified many intermediate species that emerge and contribute to reaction kinetics, and compared our simulation with a thermo-chemical equilibrium calculation. In addition, a detailed chemical kinetics of formation of H{sub 2}O, CO, and CO{sub 2} were developed. Rate constants of formations of H{sub 2}O, CO{sub 2} and N{sub 2} were reported.

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

    E-Print Network [OSTI]

    Stephen J. Cox; Shawn M. Kathmann; Ben Slater; Angelos Michaelides

    2015-05-29

    Ice formation is one of the most common and important processes on earth and almost always occurs at the surface of a material. A basic understanding of how the physicochemical properties of a material's surface affect its ability to form ice has remained elusive. Here, we use molecular dynamics simulations to directly probe heterogeneous ice nucleation at a hexagonal surface of a nanoparticle of varying hydrophilicity. Surprisingly, we find that structurally identical surfaces can both inhibit and promote ice formation and analogous to a chemical catalyst, it is found that an optimal interaction between the surface and the water exists for promoting ice nucleation. We use our microscopic understanding of the mechanism to design a modified surface in silico with enhanced ice nucleating ability.

  9. Atomistic Simulation of Nafion Membrane: 2. Dynamics of Water Molecules and Hydronium Ions

    SciTech Connect (OSTI)

    Devanathan, Ram; Venkatnathan, Arun; Dupuis, Michel

    2007-10-20

    We have performed a detailed and comprehensive analysis of the dynamics of water molecules and hydronium ions in hydrated Nafion using classical molecular dynamics simulations with the DREIDING force field. In addition to calculating diffusion coefficients as a function of hydration level, we have also determined mean residence time of H2O molecules and H3O+ ions in the first solvation shell of SO3- groups. The diffusion coefficient of H2O molecules increases with increasing hydration level and is in good agreement with experiment. The mean residence time of H2O molecules decreases with increasing membrane hydration from 1 ns at a low hydration level to 75 ps at the highest hydration level studied. These dynamical changes are related to the changes in membrane nanostructure reported in the first part of this work. Our results provide insights into slow proton dynamics observed in neutron scattering experiments and are consistent with the Gebel model of Nafion structure.

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

    E-Print Network [OSTI]

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

    2007-03-22

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

  11. A Simulation Environment for the Dynamic Evaluation of Disaster Preparedness Policies

    E-Print Network [OSTI]

    Swarup, Samarth

    capturing dynamics. We have developed a data-centric simulation environment for applying a systems approach

  12. A Scalable Parallel Monte Carlo Method for Free Energy Simulations of Molecular Systems

    E-Print Network [OSTI]

    Chan, Derek Y C

    A Scalable Parallel Monte Carlo Method for Free Energy Simulations of Molecular Systems MALEK O for problems where the energy dominates the entropy. An example is parallel tempering, in which simulations the free energy of the system as a direct output of the simulation. Traditional Metropolis MC samples phase

  13. SimSect Hybrid Dynamical Simulation Environment

    E-Print Network [OSTI]

    Saranlý, Uluç

    ) runner and a compliant hexapod. The former example illustrates the basic elements of programming models. It was mainly built to simulate a hexapod robot with compliant legs. It can. however, be used to define with the Spring­Loaded Inverted Pendulum(SLIP) and the Compliant Hexapod Model definitions. 1.3 Overview Sim

  14. SimSect Hybrid Dynamical Simulation Environment

    E-Print Network [OSTI]

    Saranlý, Uluç

    ) runner and a compliant hexapod. The former example illustrates the basic elements of programming models. It was mainly built to simulate a hexapod robot with compliant legs. It can. however, be used to define with the Spring-Loaded Inverted Pendulum(SLIP) and the Compliant Hexapod Model definitions. 1.3 Overview Sim

  15. Use dynamic simulation to model HPU reactor depressuring

    SciTech Connect (OSTI)

    Ernest, J.B.; Depew, C.A. (Fluor Daniel, Inc., Irvine, CA (United States))

    1995-01-01

    Dynamic simulation is the best available method for the analysis of hydroprocessing unit (HPU) depressuring. Depressuring is crucial for the safe operation of hydrocracking and other HPUs with catalysts that have hydrocracking activity. Effective design for depressuring is valuable for all types of HPUs, both grass-roots and revamps. Reactor loop depressuring can set design temperatures and pressures for the reactor effluent cooling train and other equipment and piping in an HPU. Unfortunately, usual methods for determining equipment and piping design conditions during depressuring leave much room for improvement because they poorly account for time-dependent temperature and pressure changes. Dynamic simulation makes it practical to more accurately estimate these transient conditions. The paper discusses depressuring design, including the nature of depressuring, the impact of depressuring on design, and depressuring calculation methods. The author then describes modeling of hydroprocessing unit depressuring by discussing the general and particular correspondence of simulation modules to physical equipment using the base case of total electrical power failure. The special data that is required for dynamic simulation is described and typical simulation results are given. Lastly, the advantages of dynamic simulation are summarized.

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

    SciTech Connect (OSTI)

    Jang, Seogjoo; Sinitskiy, Anton V.; Voth, Gregory A.

    2014-04-21

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

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

    SciTech Connect (OSTI)

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

    2014-01-01

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

  18. Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

    SciTech Connect (OSTI)

    Fattebert, J.-L.; Richards, D.F.; Glosli, J.N.

    2012-12-01

    We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·106 particles on 65,536 MPI tasks.

  19. Modeling and simulation of consumer response to dynamic pricing.

    SciTech Connect (OSTI)

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

    2012-08-01

    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.

  20. Molecular dynamics study of the stability of a carbon nanotube atop a catalytic nanoparticle

    E-Print Network [OSTI]

    Verkhovtsev, Alexey V; Solov'yov, Andrey V

    2014-01-01

    The stability of a single-walled carbon nanotube placed on top of a catalytic nickel nanoparticle is investigated by means of molecular dynamics simulations. As a case study, we consider the $(12,0)$ nanotube consisting of 720 carbon atoms and the icosahedral Ni$_{309}$ cluster. An explicit set of constant-temperature simulations is performed in order to cover a broad temperature range from 400 to 1200 K, at which a successful growth of carbon nanotubes has been achieved experimentally by means of chemical vapor deposition. The stability of the system depending on parameters of the involved interatomic interactions is analyzed. It is demonstrated that different scenarios of the nanotube dynamics atop the nanoparticle are possible depending on the parameters of the Ni-C potential. When the interaction is weak the nanotube is stable and resembles its highly symmetric structure, while an increase of the interaction energy leads to the abrupt collapse of the nanotube in the initial stage of simulation. In order t...

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

    SciTech Connect (OSTI)

    Pratt, L. R.; Eckert, J.

    1989-06-15

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

  2. Dynamical QCD+QED simulation with staggered quarks

    E-Print Network [OSTI]

    Ran Zhou; Steven Gottlieb

    2014-11-15

    Electromagnetic effects play an important role in many phenomena such as isospin-symmetry breaking in the hadron spectrum and the hadronic contributions to g-2. We have generalized the MILC QCD code to include the electromagnetic field. In this work, we focus on simulations including charged sea quarks using the RHMC algorithm. We show details of the dynamical QCD+QED simulation algorithm with compact QED. We analyze the code performance and results for hadron-spectrum observables.

  3. Numerical simulation of undersea cable dynamics

    SciTech Connect (OSTI)

    Ablow, C.M.; Schechter, S.

    1983-01-01

    A fully three-dimensional code has been written to compute the motion of a towed cable. The code is based on a robust and stable finite difference approximation to the differential equations derived from basic dynamics. A 3500-ft cable pulled at 18.5 knots (hr/sup -1/) through a circular turn of 700 yd radius has been computed in about half of the real time of the maneuver. The computed displacements are close to the measured ones; the changes in depth are within 2%.

  4. MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR WATER -METHANE AND WATER -ETHANE MIXTURES

    E-Print Network [OSTI]

    1 MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR WATER - METHANE AND WATER - ETHANE MIXTURES Jeffrey were used to calculate water - methane and water - ethane phase equilibria over a wide range

  5. Molecular dynamics evidences of the full graphitization of a nanodiamond annealed at 1500 K

    E-Print Network [OSTI]

    Powles, Rebecca

    Molecular dynamics evidences of the full graphitization of a nanodiamond annealed at 1500 K J The annealing of a small nanodiamond cluster at 1500 K is studied by molecular dynamics. The transformation nanodiamond clusters (NDC) [7] is probably the most pop- ular, as it allows the production of onions

  6. Energy-transfer dynamics of high-pressure rovibrationally excited molecular H2

    E-Print Network [OSTI]

    Augustine, Mathew P.

    Energy-transfer dynamics of high-pressure rovibrationally excited molecular H2 David J. Saiki 2005; published online 14 September 2005 The energy-transfer dynamics of high-pressure molecular H2 gas energy transfer is described and used to fit the experimental Raman scattering results obtained

  7. Chemistry 231 Fall 2013 Chemistry 231, Chemical Kinetics and Molecular Reaction Dynamics

    E-Print Network [OSTI]

    Continetti, Robert E.

    Chemistry 231 Fall 2013 Chemistry 231, Chemical Kinetics and Molecular Reaction Dynamics Dept chemical kinetics, the connection between chemical kinetics and molecular reaction dynamics as well as some and Hase, Prentice Hall (1999) 4. Chemical Kinetics, K.J. Laidler, McGraw Hill (1965) 5. Gas Phase Reaction

  8. Electronic processes in fast thermite chemical reactions: A first-principles molecular dynamics study

    E-Print Network [OSTI]

    Southern California, University of

    Electronic processes in fast thermite chemical reactions: A first-principles molecular dynamics composites. We have investigated the thermite reaction of Fe2O3 with aluminum by molecular dynamics as thermite reaction, is widely utilized in the synthesis and processing of materials 1 . In addition

  9. Adaptive Multiscale Molecular Dynamics of Macromolecular Fluids Steven O. Nielsen,1

    E-Print Network [OSTI]

    Nielsen, Steven O.

    diffusion in polymer electrolytes, signal transduction be- tween proteins, nanostructure formationAdaptive Multiscale Molecular Dynamics of Macromolecular Fluids Steven O. Nielsen,1 Preston B 2010; published 3 December 2010) Until now, adaptive atomistic­coarse-grain (A/CG) molecular dynamics

  10. Mesoscale simulations of polymer dynamics in microchannel flows

    E-Print Network [OSTI]

    L. Cannavacciuolo; R. G. Winkler; G. Gompper

    2007-09-24

    The non-equilibrium structural and dynamical properties of flexible polymers confined in a square microchannel and exposed to a Poiseuille flow are investigated by mesoscale simulations. The chain length and the flow strength are systematically varied. Two transport regimes are identified, corresponding to weak and strong confinement. For strong confinement, the transport properties are independent of polymer length. The analysis of the long-time tumbling dynamics of short polymers yields non-periodic motion with a sublinear dependence on the flow strength. We find distinct differences for conformational as well as dynamical properties from results obtained for simple shear flow.

  11. Analytical Rescaling of Polymer Dynamics from Mesoscale Simulations

    E-Print Network [OSTI]

    I. Y. Lyubimov; J. McCarty; A. Clark; M. G. Guenza

    2011-03-10

    We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse-graining affects entropy and dissipation, two factors enter the rescaling: inclusion of intramolecular vibrational degrees of freedom, and rescaling of the friction coefficient. Because our approach is analytical, it is general and transferable. Translational and rotational diffusion of unentangled and entangled polyethylene melts, predicted from mesoscale simulations of coarse-grained polymer melts using our rescaling procedure, are in quantitative agreement with united atom simulations and with experiments.

  12. Detachment of semiflexible polymer chains from a substrate - a Molecular Dynamics investigation

    E-Print Network [OSTI]

    J. Paturej; A. Erbas; A. Milchev; V. G. Rostiashvili

    2014-11-24

    Using Molecular Dynamics simulations, we study the force-induced detachment of a coarse-grained model polymer chain from an adhesive substrate. One of the chain ends is thereby pulled at constant speed off the attractive substrate and the resulting saw-tooth profile of the measured mean force $$ vs height $D$ of the end-segment over the plane is analyzed for a broad variety of parameters. It is shown that the observed characteristic oscillations in the $$-$D$ profile depend on the bending and not on the torsional stiffness of the detached chains. Allowing for the presence of hydrodynamic interactions (HI) in a setup with explicit solvent and DPD-thermostat, rather than the case of Langevin thermostat, one finds that HI have little effect on the $$-$D$ profile. Also the change of substrate affinity with respect to the solvent from solvophilic to solvophobic is found to play negligible role in the desorption process. In contrast, a changing ratio $\\epsilon_s^A / \\epsilon_s^B$ of the binding energies of $A$- and $B$-segments in the detachment of an $AB$-copolymer from adhesive surface strongly changes the $$-$D$ profile whereby the $B$-spikes vanish when $\\epsilon_s^A / \\epsilon_s^B < 0.15$. Eventually, performing an atomistic simulation of a (bio)-polymer {\\it polyglycine}, we demonstrate that the simulation results, derived from our coarse-grained model, comply favorably with those from the all-atom simulation.

  13. NUMERICAL SIMULATION OF AIR POLLUTION DYNAMICS DUE TO

    E-Print Network [OSTI]

    Olszewski Jr., Edward A.

    spots. ­ Global weather patterns effected. ­ CO2 and other pollutant emissions contributing to globalNUMERICAL SIMULATION OF AIR POLLUTION DYNAMICS DUE TO POINT SOURCE EMISSIONS FROM AN INDUSTRIAL, and ultimately effects the global climate balance. · About 60% of emissions from point sources · Major pollutants

  14. Dynamic Simulation of DFIG Wind Turbines on FPGA Boards

    E-Print Network [OSTI]

    Zambreno, Joseph A.

    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

  15. SIMULATING MARKET TRANSFORMATION DYNAMICS USING A HYBRID ENERGY ECONOMY MODEL

    E-Print Network [OSTI]

    ii SIMULATING MARKET TRANSFORMATION DYNAMICS USING A HYBRID ENERGY ECONOMY MODEL: A LOOK the likely effects of alternative policies, potential adoption rates of clean technologies, and costs to society in the long run. My goal was to use a "hybrid" energy economy model (CIMS), which combines

  16. Dynamically Adaptive Partition-based Interest Management in Distributed Simulation

    E-Print Network [OSTI]

    Kumova, Bora

    Dynamically Adaptive Partition-based Interest Management in Distributed Simulation Bora . Kumova on the effectiveness of the employed interest management (IM) schema that aims at reducing the overall computational the processing load from overloaded areas of the shared data to less loaded hosts, the partition-based technique

  17. DYNAMIC IMAGE SIMULATIONS FOR ADAPTIVE SENSOR PERFORMANCE PREDICTIONS

    E-Print Network [OSTI]

    Kerekes, John

    devices such as MEMS-based micromirrors can be modeled, but the desired overall sensor application oftenDYNAMIC IMAGE SIMULATIONS FOR ADAPTIVE SENSOR PERFORMANCE PREDICTIONS Michael D. Presnara,b , John is necessary for predicting real-life performance of adaptive sensor models. Physics-based modeling

  18. Bottom baryons from a dynamical lattice QCD simulation

    E-Print Network [OSTI]

    Randy Lewis; R. M. Woloshyn

    2009-01-12

    Bottom baryon masses are calculated based on a 2+1 flavor dynamical lattice QCD simulation. The gauge field configurations were computed by the CP-PACS and JLQCD collaborations using an improved clover action. The bottom quark is described using lattice NRQCD. Results are presented for single and double-b baryons at one lattice spacing. Comparison with experimental values is discussed.

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

    SciTech Connect (OSTI)

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

    1998-09-15

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

  20. Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion

    E-Print Network [OSTI]

    Latombe, Jean-Claude

    Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular pathways. We introduce Stochastic Roadmap Simulation (SRS), a new approach for exploring the ki- netics a roadmap. A roadmap is computed by sampling a molecule's conformation space at random. The computation does

  1. Molecular dynamics study of interfacial confinement effects of aqueous NaCl brines in nanoporous carbon

    SciTech Connect (OSTI)

    Wander, M. C. F.; Shuford, K. L.

    2010-12-09

    In this paper, studies of aqueous electrolyte solutions in contact with a family of porous carbon geometries using classical molecular dynamics simulations are presented. These simulations provide an atomic scale depiction of ion transport dynamics in different environments to elucidate power of aqueous electrolyte supercapacitors. The electrolyte contains alkali metal and halide ions, which allow for the examination of size trends within specific geometries as well as trends in concentration. The electrode pores are modeled as planar graphite sheets and carbon nanotubes with interstices ranging from one to four nanometers. Ordered layers form parallel to the carbon surface, which facilitates focused ion motion under slightly confining conditions. As a result, the ion’s diffusivities are enhanced in the direction of the slit or pore. Further confining the system leads to decreased ion diffusivities. The ions are fully hydrated in all but the smallest slits and pores with those sizes showing increased ion pairing. There is strong evidence of charge separation perpendicular to the surface at all size scales, concentrations, and ion types, providing a useful baseline for examining differential capacitance behavior and future studies on energy storage. These systems show promise as high-power electrical energy storage devices.

  2. Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations

    E-Print Network [OSTI]

    G. L. Giorgi; M. Roncaglia; F. A. Raffa; M. Genovese

    2015-07-13

    During the long course of evolution, nature has learnt how to exploit quantum effects. In fact, recent experiments reveal the existence of quantum processes whose coherence extends over unexpectedly long time and space ranges. In particular, photosynthetic processes in light-harvesting complexes display a typical oscillatory dynamics ascribed to quantum coherence. Here, we consider the simple model where a dimer made of two chromophores is strongly coupled with a quasi-resonant vibrational mode. We observe the occurrence of wide oscillations of genuine quantum correlations, between electronic excitations and the environment, represented by vibrational bosonic modes. Such a quantum dynamics has been unveiled through the calculation of the negativity of entanglement and the discord, indicators widely used in quantum information for quantifying the resources needed to realize quantum technologies. We also discuss the possibility of approximating additional weakly-coupled off-resonant vibrational modes, simulating the disturbances induced by the rest of the environment, by a single vibrational mode. Within this approximation, one can show that the off-resonant bath behaves like a classical source of noise.

  3. Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics with reaction

    E-Print Network [OSTI]

    Lisal, Martin

    Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics. R. Smith, J. Chem. Phys. 125, 16490 2006 , a mesoscale simulation technique for studying polymer

  4. A molecular dynamics study of the effect of a substrate on catalytic metal clusters in nucleation process of single-walled carbon nanotubes

    E-Print Network [OSTI]

    Maruyama, Shigeo

    process of single-walled carbon nanotubes Yasushi Shibuta1 *, Shigeo Maruyama2 1 Department of Materials of the substrate on catalytic metal clusters in nucleation process of single-walled carbon nanotubes was studied by classical molecular dynamics (MD) simulation. The melting point of a nickel cluster decreased

  5. Generic solar photovoltaic system dynamic simulation model specification.

    SciTech Connect (OSTI)

    Ellis, Abraham; Behnke, Michael Robert; Elliott, Ryan Thomas

    2013-10-01

    This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intended to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.

  6. Molecular Structure and Dynamics in Thin Water Films at the Silica and Graphite Surfaces

    SciTech Connect (OSTI)

    Argyris, Dr. Dimitrios [University of Oklahoma; Tummala, Dr. Naga Rajesh [University of Oklahoma; StrioloDr., A [Vanderbilt University; Cole, David R [ORNL

    2008-01-01

    The structure and dynamic properties of interfacial water at the graphite and silica solid surfaces were investigated using molecular dynamics simulations. The effect of surface properties on the characteristics of interfacial water was quantified by computing density profiles, radial distribution functions, surface density distributions, orientation order parameters, and residence and reorientation correlation functions. In brief, our results show that the surface roughness, chemical heterogeneity, and surface heterogeneous charge distribution affect the structural and dynamic properties of the interfacial water molecules, as well as their rate of exchange with bulk water. Most importantly, our results indicate the formation of two distinct water layers at the SiO2 surface covered by a large density of hydroxyl groups. Further analysis of the data suggests a highly confined first layer where the water molecules assume preferential hydrogen-down orientation and a second layer whose behavior and characteristics are highly dependent on those of the first layer through a well-organized hydrogen bond network. The results suggest that water-water interactions, in particular hydrogen bonds, may be largely responsible for macroscopic interfacial properties such as adsorption and contact angle.

  7. Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water

    SciTech Connect (OSTI)

    Kobayashi, Kazuya; Liang, Yunfeng E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp; Matsuoka, Toshifumi E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp; Sakka, Tetsuo

    2014-04-14

    The NaCl salt–solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt–solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt–solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemical potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules.

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

    E-Print Network [OSTI]

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

    2014-02-19

    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 fundamental requirements 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 to simulate efficiently complex fluid-fluid interfaces. We demonstrate how this approach can be used to study a wide class of challenging problems. Several examples are given, with an accent on bicontinuous phases formation in polyelectrolyte solutions and ferrofluid emulsions. We also show 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.

  9. Dislocation dynamics simulations of plasticity at small scales

    SciTech Connect (OSTI)

    Zhou, Caizhi

    2010-12-15

    As metallic structures and devices are being created on a dimension comparable to the length scales of the underlying dislocation microstructures, the mechanical properties of them change drastically. Since such small structures are increasingly common in modern technologies, there is an emergent need to understand the critical roles of elasticity, plasticity, and fracture in small structures. Dislocation dynamics (DD) simulations, in which the dislocations are the simulated entities, offer a way to extend length scales beyond those of atomistic simulations and the results from DD simulations can be directly compared with the micromechanical tests. The primary objective of this research is to use 3-D DD simulations to study the plastic deformation of nano- and micro-scale materials and understand the correlation between dislocation motion, interactions and the mechanical response. Specifically, to identify what critical events (i.e., dislocation multiplication, cross-slip, storage, nucleation, junction and dipole formation, pinning etc.) determine the deformation response and how these change from bulk behavior as the system decreases in size and correlate and improve our current knowledge of bulk plasticity with the knowledge gained from the direct observations of small-scale plasticity. Our simulation results on single crystal micropillars and polycrystalline thin films can march the experiment results well and capture the essential features in small-scale plasticity. Furthermore, several simple and accurate models have been developed following our simulation results and can reasonably predict the plastic behavior of small scale materials.

  10. Thermal decomposition of RDX from reactive molecular dynamics Alejandro Strachana)

    E-Print Network [OSTI]

    Goddard III, William A.

    efficient way. Typical HE materials, such as TNT, RDX, HMX, TATB, and PETN, are complex organic molecular

  11. Simulating the Dynamic Coupling of Market and Physical System Operations

    SciTech Connect (OSTI)

    Widergren, Steven E.; Roop, Joseph M.; Guttromson, Ross T.; Huang, Zhenyu

    2004-06-01

    Abstract-As energy trading products cover shorter time periods and demand response programs move toward real-time pricing, financial market-based activity impacts ever more directly the physical operation of the system. To begin to understand the complex interactions between the market-driven operation signals, the engineered controlled schemes, and the laws of physics, new system modeling and simulation techniques must be explored. This discussion describes requirements for new simulation tools to address such market transaction control interactions and an approach to capture the dynamic coupling between energy markets and the physical operation of the power system appropriate for dispatcher reaction time frames.

  12. Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics with reaction ensemble Monte Carlo.

    E-Print Network [OSTI]

    Lisal, Martin

    Mesoscale simulation of polymer reaction equilibrium: Combining dissipative particle dynamics a mesoscale simulation technique, called the reaction ensemble dissipative particle dynamics RxDPD method. Coarse-grained, particle- based mesoscale models that retain only the most essential features

  13. Molecular dynamics simulations of threshold displacement energies in Fe

    E-Print Network [OSTI]

    Nordlund, Kai

    , 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

  14. Tribological behavior of polymers simulated by molecular dynamics

    E-Print Network [OSTI]

    North Texas, University of

    of high mechanical strength, stiffness, and elongation at break of the spider silk dragline structure.13

  15. Nanofluidic Osmotic Diodes: Theory and Molecular Dynamics Simulations

    E-Print Network [OSTI]

    Picallo, Clara

    Osmosis describes the flow of water across semipermeable membranes powered by the chemical free energy extracted from salinity gradients. While osmosis can be expressed in simple terms via the van ’t Hoff ideal gas formula ...

  16. Mechanical Properties of Glassy Polyethylene Nanofibers via Molecular Dynamics Simulations

    E-Print Network [OSTI]

    Buell, Sezen

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

  17. Molecular dynamics simulation of nanoporous graphene for selective gas separation

    E-Print Network [OSTI]

    Au, Harold (Harold S.)

    2012-01-01

    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 ...

  18. Molecular Dynamics Simulations to Study Protein Folding and Unfolding

    E-Print Network [OSTI]

    Caflisch, Amedeo

    and results are essential in validating the force fields (V7 10/11 13:29) VCH/G J-1079 Buchner I PMU: WSL

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

    E-Print Network [OSTI]

    Luo, Tengfei

    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 ...

  20. Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.

    E-Print Network [OSTI]

    2015-01-01

    Based Materials for Organic Solar Cells. Dyes Pigm. 2013,organic electronic devices, such as transistors and solar cells.

  1. Brownian dynamics simulations of fine-scale molecular models

    E-Print Network [OSTI]

    Burmenko, Irina

    2005-01-01

    One of the biggest challenges in non-Newtonian fluid mechanics is calculating the polymer contribution to the stress tensor, which is needed to calculate velocity and pressure fields as well as other quantities of interest. ...

  2. Molecular dynamics simulations of boronnitride nanotubes embedded in

    E-Print Network [OSTI]

    Burstedde, Carsten

    study the properties of a ceramics composite material made from Si 3 B 3 N 7 matrix and BN nanotubes. We calculate stress­strain curves for the composite to predict the rates of reinforcement of the matrix due­B­N ceramics, composites, elastic moduli PACS: 02.70.Ns, 62.20.Dc, 62.25.+g, 81.05.Je, 83.10.Rs

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

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

    2 DOE Hydrogen and Fuel Cells Program and Vehicle Technologies Program Annual Merit Review and Peer Evaluation Meeting es058bedrov2012p.pdf More Documents & Publications High...

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankADVANCED MANUFACTURING OFFICESpecialAPPENDIX F Wetlandsof Energy ModelSEI LayerManufactured

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankADVANCED MANUFACTURING OFFICESpecialAPPENDIX F Wetlandsof Energy ModelSEI

  6. Sandia Energy - Molecular Dynamics Simulations Predict Fate of Uranium in

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis ofSampleLignin-Feasting MicrobeMesaAnalysis

  7. Molecular Dynamics Simulations of Gas Selectivity in Amorphous Porous

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTechtail.Theory ofDid you notHeatMaRIEdioxide capture |GE PutsgovSitesMobileTechnologies

  8. Dynamics of Molecular Clouds: Observations, Simulations, and NIF

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(Journal Article) | SciTech Connect

  9. Dynamics of Molecular Clouds: Observations, Simulations, and NIF

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfate Reducing(Journal Article) | SciTech ConnectExperiments (Conference) | SciTech Connect

  10. Nonequilibrium molecular dynamics simulations of confined fluids in contact

    Office of Scientific and Technical Information (OSTI)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTech Connect Nanomechanical switch for|Connect Non-Large Hadronelectronwith the bulk

  11. Computer simulations of adsorption and molecular recognition phenomena in molecularly imprinted polymers 

    E-Print Network [OSTI]

    Dourado, Eduardo Manuel de Azevedo

    2011-11-22

    Molecularly imprinted polymers (MIPs) are a novel, promising family of porous materials with potential applications ranging from separations, chemical sensing and catalysis to drug delivery and artificial immunoassays. The ...

  12. Optimum protein-excipient interactions using molecular docking simulations

    E-Print Network [OSTI]

    Tarar, Haider

    2014-04-01

    , two commonly used excipients, the sugars sucrose and mannitol, have been investigated so far. Some of the surfactants which will be looked at as excipients in the future include Octyl glucoside, Tween 40 and Tween 80. Molecular docking... toolkit (http://cactus.nci.nih.gov/translate/). Docking Using ADT (Pokphanh, 2011). Fig. 4: A docking conformation of Octyl Glucoside with Myoglobin in Autodock. Summer 2013 – Spring 2014 | 73 ————————— References Dimitrov Dimiter S., 2012...

  13. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    E-Print Network [OSTI]

    Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

  14. Nonadiabatic ab initio molecular dynamics of photoisomerization in bridged azobenzene

    SciTech Connect (OSTI)

    Gao Aihua; Li Bin; Zhang Peiyu; Han Keli [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China)

    2012-11-28

    The photoisomerization mechanisms of bridged azobenzene are investigated by means of surface hopping dynamics simulations based on the Zhu-Nakamura theory. In the geometry optimizations and potential energy surface calculations, four minimum-energy conical intersections between the ground state and the lowest excited state are found to play important roles in the trans-cis and cis-trans isomerization processes. The trans-cis photoisomerization proceeds through two minimum-energy conical intersections. Ultrafast pedal motion of the N atoms and twisting of phenyl rings around their N-C bonds allows the molecule to move to a minimum-energy conical intersection, after which surface hopping from S{sub 1} to S{sub 0} occurs. In the S{sub 0} state, further rotation occurs around the N=N bond and two N-C bonds until the azo moiety and phenyl rings complete their isomerization. Finally, the cis form is achieved by subsequent adjustment of the ethylene bridge. In the cis-trans photodynamics, there is one rotational pathway, in the middle of which two CIs are responsible for the surface hopping to the S{sub 0} state. After the nonadiabatic transition, the molecule reaches the trans form through a barrierless pathway and the two phenyl rings and the additional bridge complete their reorientation almost at the same time.

  15. Microwave Heating of Water, Ice and Saline Solution: Molecular Dynamics Study

    E-Print Network [OSTI]

    Motohiko Tanaka; Motoyasu Sato

    2006-09-24

    In order to study the heating process of water by the microwaves of 2.5-20GHz frequencies, we have performed molecular dynamics simulations by adopting a non-polarized water model that have fixed point charges on rigid-body molecules. All runs are started from the equilibrated states derived from the I$_{c}$ ice with given density and temperature. In the presence of microwaves, the molecules of liquid water exhibit rotational motion whose average phase is delayed from the microwave electric field. Microwave energy is transferred to the kinetic and inter-molecular energies of water, where one third of the absorbed microwave energy is stored as the latter energy. The water in ice phase is scarcely heated by microwaves because of the tight hydrogen-bonded network of water molecules. Addition of small amount of salt to pure water substantially increases the heating rate because of the weakening by defects in the water network due to sloshing large-size negative ions.

  16. Lennard-Jones systems near solid walls: Computing interfacial free energies from molecular simulation methods

    E-Print Network [OSTI]

    Ronald Benjamin; Jürgen Horbach

    2013-06-03

    Different computational techniques in combination with molecular dynamics computer simulation are used to to determine the wall-liquid and the wall-crystal interfacial free energies of a modified Lennard-Jones (LJ) system in contact with a solid wall. Two different kinds of solid walls are considered: a flat structureless wall and a structured wall consisting of an ideal crystal with the particles rigidly attached to fcc lattice sites. Interfacial free energies are determined by a thermodynamic integration scheme, the anisotropy of the pressure tensor, the non-equilibrium work method based on Bennett acceptance criteria, and a method using Cahn's adsorption equations based on the interfacial thermodynamics of Gibbs. For the flat wall, interfacial free energies as a function of different densities of the LJ liquid and as a function of temperature along the coexistence curve are calculated. In case of a structured wall, the interaction strength between the wall and the LJ system and the lattice constant of the structured wall are varied. Using the values of the wall-liquid and wall-crystal interfacial energies along with the value for the crystal-liquid interfacial free energy determined previously for the same system by the "cleaving potential method", we obtain the contact angle as a function of various parameters; in particular the conditions are found under which partial wetting occurs.

  17. RUMD: A general purpose molecular dynamics package optimized to utilize GPU hardware down to a few thousand particles

    E-Print Network [OSTI]

    Bailey, Nicholas P; Hansen, Jesper Schmidt; Veldhorst, Arno A; Bøhling, Lasse; Lemarchand, Claire A; Olsen, Andreas E; Bacher, Andreas K; Larsen, Heine; Dyre, Jeppe C; Schrøder, Thomas B

    2015-01-01

    RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating small to medium system sizes (roughly from a few thousand up to hundred thousand particles). It has a performance that is comparable to other GPU-MD codes at large system sizes and substantially better at smaller sizes.RUMD is open-source and consists of a library written in C++ and the CUDA extension to C, an easy-to-use Python interface, and a set of tools for set-up and post-simulation data analysis. The paper describes RUMD's main features, optimizations and performance benchmarks.

  18. Matrix-assisted pulsed laser evaporation of polymeric materials: a molecular dynamics study

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Matrix-assisted pulsed laser evaporation of polymeric materials: a molecular dynamics study Tatiana Matrix-assisted pulsed laser evaporation (MAPLE) has been recently developed to deposit high-quality thin is modeled as a solution of polymer molecules in a molecular matrix. The breathing sphere model is used

  19. Properties of gravitationally equilibrated Yukawa systems—A molecular dynamics study

    SciTech Connect (OSTI)

    Charan, Harish; Ganesh, Rajaraman Joy, Ashwin

    2014-04-15

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

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

    E-Print Network [OSTI]

    M. Ebrahim Foulaadvand; Neda Ojaghlou

    2014-09-27

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

  1. Why are MD simulated protein folding times wrong? Dmitry Nerukh

    E-Print Network [OSTI]

    Nerukh, Dmitry

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

  2. BP205 Molecular Dynamics of the Cell Problem Set 3

    E-Print Network [OSTI]

    Voigt, Chris

    -small molecule interactions? Now, produce a MATLAB simulation of the system ­ represent the line of cells. First, set C=0 initially at all points. Simulate the system using one of MATLAB's ode solvers until C

  3. A time-dependent momentum-space density functional theoretical approach for electron transport dynamics in molecular devices

    E-Print Network [OSTI]

    Chu, Shih-I

    and structures PACS 85.65.+h ­ Molecular electronic devices PACS 71.15.Pd ­ Molecular dynamics calculations (Carr for electron transport dynamics in molecular devices Zhongyuan Zhou(a) and Shih-I Chu Department of Chemistry. The electron wave function is calculated by solving this equation in a finite P-space volume. This approach

  4. Impact of deformation on the atomic structures and dynamics of a Cu-Zr metallic glass: A molecular dynamics study

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

    Zhang, Y.; Mendelev, M. I.; Wang, C. Z.; Ott, R.; Zhang, F.; Besser, M. F.; Ho, K. M.; Kramer, M. J.

    2014-11-03

    Despite numerous studies on the atomic structures of Cu-Zr metallic glasses (MGs), their inherent structural ordering, e.g., medium-range order (MRO), remains difficult to describe. Specifically lacking is an understanding of how the MRO responds to deformation and the associated changes in atomic mobility. In this paper, we focus on the impact of deformation on MRO and associated effect on diffusion in a well-relaxed Cu64.5Zr35.5 MG by molecular dynamics simulations. The Cu-Zr MG exhibits a larger elastic limit of 0.035 and a yield stress of 3.5 GPa. The cluster alignment method was employed to characterize the icosahedral short-range order (ISRO) andmore »Bergman-type medium-range order (BMRO) in the models upon loading and unloading. From this analysis, we find the disruption of both ISRO and BMRO occurs as the strain reaches about 0.02, well below the elastic limit. Within the elastic limit, the total fractions of ISRO or BMRO can be fully recovered upon unloading. The diffusivity increases six to eight times in regions undergoing plastic deformation, which is due to the dramatic disruption of the ISRO and BMRO. As a result, by mapping the spatial distributions of the mobile atoms, we demonstrate the increase in atomic mobility is due to the extended regions of disrupted ISRO and more importantly BMRO.« less

  5. Impact of deformation on the atomic structures and dynamics of a Cu-Zr metallic glass: A molecular dynamics study

    SciTech Connect (OSTI)

    Zhang, Y.; Mendelev, M. I.; Wang, C. Z.; Ott, R.; Zhang, F.; Besser, M. F.; Ho, K. M.; Kramer, M. J.

    2014-11-03

    Despite numerous studies on the atomic structures of Cu-Zr metallic glasses (MGs), their inherent structural ordering, e.g., medium-range order (MRO), remains difficult to describe. Specifically lacking is an understanding of how the MRO responds to deformation and the associated changes in atomic mobility. In this paper, we focus on the impact of deformation on MRO and associated effect on diffusion in a well-relaxed Cu64.5Zr35.5 MG by molecular dynamics simulations. The Cu-Zr MG exhibits a larger elastic limit of 0.035 and a yield stress of 3.5 GPa. The cluster alignment method was employed to characterize the icosahedral short-range order (ISRO) and Bergman-type medium-range order (BMRO) in the models upon loading and unloading. From this analysis, we find the disruption of both ISRO and BMRO occurs as the strain reaches about 0.02, well below the elastic limit. Within the elastic limit, the total fractions of ISRO or BMRO can be fully recovered upon unloading. The diffusivity increases six to eight times in regions undergoing plastic deformation, which is due to the dramatic disruption of the ISRO and BMRO. As a result, by mapping the spatial distributions of the mobile atoms, we demonstrate the increase in atomic mobility is due to the extended regions of disrupted ISRO and more importantly BMRO.

  6. Computational mechanics of molecular systems: Quantifying high-dimensional dynamics by distribution of Poincare recurrence times

    E-Print Network [OSTI]

    Nerukh, Dmitry

    Computational mechanics of molecular systems: Quantifying high- dimensional dynamics computational mechanics as a bridge between deterministic chaos in nonlinear dynamical systems with few degrees-Hakodate, School of Systems Information Science, Department of Complex System, 116-2 Kamedanakano-cho, Hakodate

  7. Molecular-dynamics study of incoherent quasielastic neutron-scattering spectra of supercooled water

    E-Print Network [OSTI]

    Sciortino, Francesco

    Molecular-dynamics study of incoherent quasielastic neutron-scattering spectra of supercooled water neutron-scattering experiments. Second, we explore the possibility of an alterna- tive method of analysis of high-resolution quasielastic neutron-scattering spectra, taking into account the slow dynamics

  8. Molecular dynamics studies of brittle fracture in vitreous silica: Review and recent progress

    E-Print Network [OSTI]

    Deymier, Pierre

    Molecular dynamics studies of brittle fracture in vitreous silica: Review and recent progress, Gainesville, FL 32611, USA Abstract The dynamics of brittle fracture in vitreous silica has been a subject surrounding the voids. Ó 2005 Elsevier B.V. All rights reserved. 1. Introduction Fracture in brittle materials

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

    E-Print Network [OSTI]

    Nigel Cundy; Weonjong Lee

    2012-02-27

    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.

  10. COMPILED HARDWARE ACCELERATION OF MOLECULAR DYNAMICS CODE Jason Villarreal and Walid A. Najjar

    E-Print Network [OSTI]

    Najjar, Walid A.

    diffraction) or nuclear magnetic resonance (NMR) data. The force field is based on a potential energy function in a given biomolecular environment. These simulations are very demanding computa- tionally, where environment. MD simulations are based upon the use of a molecular mechanics force field and the availability

  11. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    SciTech Connect (OSTI)

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-08-21

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} ? f(x{sub (i?1})]{sub i} {sub =1,M} = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H{sub 2}O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

  12. Molecular simulations of hydrogen and methane permeation through pore mouth modified zeolite Sang Eun Jeea

    E-Print Network [OSTI]

    McGaughey, Alan

    Molecular simulations of hydrogen and methane permeation through pore mouth modified zeolite]. Inorganic membranes have the potential to play an important role in these separations if membranes than CO2 or CH4, two typical gases present during H2 production. Experiments that have been performed

  13. Investigations of Solar Prominence Dynamics Using Laboratory Simulations

    SciTech Connect (OSTI)

    Paul M Bellan

    2008-05-28

    Laboratory experiments simulating many of the dynamical features of solar coronal loops have been carried out. These experiments manifest collimation, kinking, jet flows, and S-shapes. Diagnostics include high-speed photography and x-ray detectors. Two loops having opposite or the same magnetic helicity polarities have been merged and it is found that counter-helicity merging provides much greater x-ray emission. A non-MHD particle orbit instability has been discovered whereby ions going in the opposite direction of the current flow direction can be ejected from a magnetic flux tube.

  14. Description of waste pretreatment and interfacing systems dynamic simulation model

    SciTech Connect (OSTI)

    Garbrick, D.J.; Zimmerman, B.D.

    1995-05-01

    The Waste Pretreatment and Interfacing Systems Dynamic Simulation Model was created to investigate the required pretreatment facility processing rates for both high level and low level waste so that the vitrification of tank waste can be completed according to the milestones defined in the Tri-Party Agreement (TPA). In order to achieve this objective, the processes upstream and downstream of the pretreatment facilities must also be included. The simulation model starts with retrieval of tank waste and ends with vitrification for both low level and high level wastes. This report describes the results of three simulation cases: one based on suggested average facility processing rates, one with facility rates determined so that approximately 6 new DSTs are required, and one with facility rates determined so that approximately no new DSTs are required. It appears, based on the simulation results, that reasonable facility processing rates can be selected so that no new DSTs are required by the TWRS program. However, this conclusion must be viewed with respect to the modeling assumptions, described in detail in the report. Also included in the report, in an appendix, are results of two sensitivity cases: one with glass plant water recycle steams recycled versus not recycled, and one employing the TPA SST retrieval schedule versus a more uniform SST retrieval schedule. Both recycling and retrieval schedule appear to have a significant impact on overall tank usage.

  15. Molecular simulation of a model of dissolved organic matter

    SciTech Connect (OSTI)

    Sutton, Rebecca; Sposito, Garrison; Diallo, Mamadou S.; Schulten,Hans-Rolf

    2004-11-08

    A series of atomistic simulations was performed to assess the ability of the Schulten dissolved organic matter (DOM) molecule, a well-established model humic molecule, to reproduce the physical and chemical behavior of natural humic substances. The unhydrated DOM molecule had a bulk density value appropriate to humic matter, but its Hildebrand solubility parameter was lower than the range of current experimental estimates. Under hydrated conditions, the DOM molecule went through conformational adjustments that resulted in disruption of intramolecular hydrogen bonds (H-bonds), although few water molecules penetrated the organic interior. The radius of gyration of the hydrated DOM molecule was similar to those measured for aquatic humic substances. To simulate humic materials under aqueous conditions with varying pH levels, carboxyl groups were deprotonated, and hydrated Na{sup +} or Ca{sup 2+} were added to balance the resulting negative charge. Because of intrusion of the cation hydrates, the model metal- humic structures were more porous, had greater solvent-accessible surface areas, and formed more H-bonds with water than the protonated, hydrated DOM molecule. Relative to Na{sup +}, Ca{sup 2+} was both more strongly bound to carboxylate groups and more fully hydrated. This difference was attributed to the higher charge of the divalent cation. The Ca-DOM hydrate, however, featured fewer H-bonds than the Na-DOM hydrate, perhaps because of the reduced orientational freedom of organic moieties and water molecules imposed by Ca{sup 2+}. The present work is, to our knowledge, the first rigorous computational exploration regarding the behavior of a model humic molecule under a range of physical conditions typical of soil and water systems.

  16. Bulk and Surface Molecular Orientation Distribution in Injection-molded Liquid Crystalline Polymers: Experiment and Simulation

    SciTech Connect (OSTI)

    Fang, J.; Burghardt, W; Bubeck, R; Burgard, S; Fischer, D

    2010-01-01

    Bulk and surface distributions of molecular orientation in injection-molded plaques of thermotropic liquid crystalline polymers (TLCPs) have been studied using a combination of techniques, coordinated with process simulations using the Larson-Doi 'polydomain' model. Wide-angle X-ray scattering was used to map out the bulk orientation distribution. Fourier Transform Infrared Attenuated Total Reflectance (FTIR-ATR) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) were utilized to probe the molecular orientation states to within about {approx}5 {micro}m and {approx}2 nm, respectively, of the sample surface. These noninvasive, surface-sensitive techniques yield reasonable self-consistency, providing complementary validation of the robustness of these methods. An analogy between Larson-Doi and fiber orientation models has allowed the first simulations of TLCP injection molding. The simulations capture many fine details in the bulk orientation distribution across the sample plaque. Direct simulation of surface orientation at the level probed by FTIR-ATR and NEXAFS was not possible due to the limited spatial resolution of the simulations. However, simulation results extracted from the shear-dominant skin region are found to provide a qualitatively accurate indicator of surface orientation. Finally, simulations capture the relation between bulk and surface orientation states across the different regions of the sample plaque.

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

    E-Print Network [OSTI]

    Fringer, Oliver B.

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

  18. How to obtain thermostatted ring polymer molecular dynamics from exact quantum dynamics and when to use it

    E-Print Network [OSTI]

    Timothy J. H. Hele

    2015-08-24

    We obtain thermostatted ring polymer molecular dynamics (TRPMD) from exact quantum dynamics via Matsubara dynamics, a recently-derived form of linearization which conserves the quantum Boltzmann distribution. Performing a contour integral in the complex quantum Boltzmann distribution of Matsubara dynamics, replacement of the imaginary Liouvillian which results with a Fokker-Planck term gives TRPMD. We thereby provide error terms between TRPMD and quantum dynamics and predict the systems in which they are likely to be small. Using a harmonic analysis we show that careful addition of friction causes the correct oscillation frequency of the higher ring-polymer normal modes in a harmonic well, which we illustrate with calculation of the position-squared autocorrelation function. However, no physical friction parameter will produce the correct fluctuation dynamics for a parabolic barrier. The results in this paper are consistent with previous numerical studies and advise the use of TRPMD for the computation of spectra.

  19. How to obtain thermostatted ring polymer molecular dynamics from exact quantum dynamics and when to use it

    E-Print Network [OSTI]

    Hele, Timothy J H

    2015-01-01

    We obtain thermostatted ring polymer molecular dynamics (TRPMD) from exact quantum dynamics via Matsubara dynamics, a recently-derived form of linearization which conserves the quantum Boltzmann distribution. Performing a contour integral in the complex quantum Boltzmann distribution of Matsubara dynamics, replacement of the imaginary Liouvillian which results with a Fokker-Planck term gives TRPMD. We thereby provide error terms between TRPMD and quantum dynamics and predict the systems in which they are likely to be small. Using a harmonic analysis we show that careful addition of friction causes the correct oscillation frequency of the higher ring-polymer normal modes in a harmonic well, which we illustrate with calculation of the position-squared autocorrelation function. However, no physical friction parameter will produce the correct fluctuation dynamics for a parabolic barrier. The results in this paper are consistent with previous numerical studies and advise the use of TRPMD for the computation of spe...

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

    E-Print Network [OSTI]

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

    2013-10-02

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

  1. Strategies for coupling energy simulation and computational fluid dynamics programs

    E-Print Network [OSTI]

    Zhai, Zhiqiang; Chen, Qingyan; Klems, Joseph H.; Haves, Philip

    2001-01-01

    2000. “EnergyPlus: Energy Simulation Program” . ASHRAEA Coupled Airflow-and-Energy Simulation Program for IndoorSTRATEGIES FOR COUPLING ENERGY SIMULATION AND COMPUTATIONAL

  2. NUMERICAL SIMULATION OF ELECTROMECHANICAL DYNAMICS IN PACED CARDIAC TISSUE Xiaopeng Zhao

    E-Print Network [OSTI]

    Zhao, Xiaopeng

    NUMERICAL SIMULATION OF ELECTROMECHANICAL DYNAMICS IN PACED CARDIAC TISSUE Henian Xia Xiaopeng Zhao of Tennessee Knoxville, TN 37996 kwong@utk.edu ABSTRACT We study electromechanical dynamics in paced cardiac physics fields are integrated, including electrophysiology, electromechanics, and mechanoelectrical

  3. A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

    SciTech Connect (OSTI)

    Sun, Hui-Yong [Shandong University of Technology, Zibo 255049 (China)] [Shandong University of Technology, Zibo 255049 (China); Ji, Feng-Qin, E-mail: fengqinji@mail.hzau.edu.cn [National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070 (China) [National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070 (China); Center for Bioinformatics, Huazhong Agricultural University, Wuhan 430070 (China)

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer The study revealed the detailed resistance mechanism of the non-active mutation C1156Y in ALK. Black-Right-Pointing-Pointer C1156Y leads to crizotinib displacement and conformational changes in the binding cavity. Black-Right-Pointing-Pointer The conformations cause a decline in the vdW and electrostatic energy between crizotinib and ALK. -- Abstract: Crizotinib is an anaplastic lymphoma kinase (ALK) inhibitor that has recently been approved in the US for the treatment of non-small cell lung carcinoma (NSCLC). Despite its outstanding safety and efficacy, several resistant mutations against crizotinib have been detected in the treatment of NSCLC. However, in contrast to the widely accepted mechanism of steric hindrance by mutations at the active site, the mechanism by which the C1156Y non-active site mutation confers resistance against crizotinib remains unclear. In the present study, the resistance mechanism of C1156Y in ALK was investigated using molecular dynamics simulations. The results suggest that despite the non-active site mutation, C1156Y causes the dislocation of crizotinib as well as the indirect conformational changes in the binding cavity, which results in a marked decrease in the van der Waals and electrostatic interactions between crizotinib and ALK. The obtained results provide a detailed explanation of the resistance caused by C1156Y and may give a vital clue for the design of drugs to combat crizotinib resistance.

  4. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    E-Print Network [OSTI]

    Hua Y. Geng

    2014-12-19

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of $r_{s}=0.912$.

  5. A molecular dynamics study of nuclear quantum effect on the diffusion of hydrogen in condensed phase

    SciTech Connect (OSTI)

    Nagashima, Hiroki; Tokumasu, Takashi; Tsuda, Shin-ichi; Tsuboi, Nobuyuki; Koshi, Mitsuo; Hayashie, A. Koichi

    2014-10-06

    In this paper, the quantum effect of hydrogen molecule on its diffusivity is analyzed using Molecular Dynamics (MD) method. The path integral centroid MD (CMD) method is applied for the reproduction method of time evolution of the molecules. The diffusion coefficient of liquid hydrogen is calculated using the Green-Kubo method. The simulation is performed at wide temperature region and the temperature dependence of the quantum effect of hydrogen molecule is addressed. The calculation results are compared with those of classical MD results. As a result, it is confirmed that the diffusivity of hydrogen molecule is changed depending on temperature by the quantum effect. It is clarified that this result can be explained that the dominant factor by quantum effect on the diffusivity of hydrogen changes from the swollening the potential to the shallowing the potential well around 30 K. Moreover, it is found that this tendency is related to the temperature dependency of the ratio of the quantum kinetic energy and classical kinetic energy.

  6. Sediment Dynamics Simulation via Cellular Automata Artificial Intelligence -SYNOPSIS 1.0 Dr. Juan M. Restrepo

    E-Print Network [OSTI]

    Fatkullin, Ibrahim

    Sediment Dynamics Simulation via Cellular Automata Artificial Intelligence - SYNOPSIS 1.0 Dr. Juan dynamics and artificial intelligence. Sediment Dynamics Sediment dynamics is the physics of sedimentary's work, and proved to be quite a task indeed. Artificial Intelligence Because this research project

  7. Theoretical aspects of gas-phase molecular dynamics

    SciTech Connect (OSTI)

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

    1993-12-01

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

  8. Discontinuous Shear Thickening in Brownian Suspensions By Dynamic Simulation

    E-Print Network [OSTI]

    Mari, Romain; Morris, Jeffrey F; Denn, Morton M

    2015-01-01

    Dynamic particle-scale numerical simulations are used to show that the shear thickening observed in dense colloidal, or Brownian, suspensions is of a similar nature to that observed in non-colloidal suspensions, i.e., a stress-induced transition from a flow of lubricated near-contacting particles to a flow of a frictionally contacting network of particles. Abrupt (or discontinuous) shear thickening is found to be a geometric rather than hydrodynamic phenomenon; it stems from the strong sensitivity of the jamming volume fraction to the nature of contact forces between suspended particles. The thickening obtained in a colloidal suspension of purely hard frictional spheres is qualitatively similar to experimental observations. However the agreement cannot be made quantitative with only hydrodynamics, frictional contacts and Brownian forces. Therefore the role of a short-range repulsive potential mimicking the stabilization of actual suspensions on the thickening is studied. The effects of Brownian and repulsive ...

  9. Simulation of Molecular Signaling in Blood Vessels: Software Design and Application to Atherogenesis

    E-Print Network [OSTI]

    Luca Felicetti; Mauro Femminella; Gianluca Reali

    2013-06-01

    This paper presents a software platform, named BiNS2, able to simulate diffusion-based molecular communications with drift inside blood vessels. The contribution of the paper is twofold. First a detailed description of the simulator is given, under the software engineering point of view, by highlighting the innovations and optimizations introduced. Their introduction into the previous version of the BiNS simulator was needed to provide to functions for simulating molecular signaling and communication potentials inside bounded spaces. The second contribution consists of the analysis, carried out by using BiNS2, of a specific communication process happening inside blood vessels, the atherogenesis, which is the initial phase of the formation of atherosclerotic plaques, due to the abnormal signaling between platelets and endothelium. From a communication point of view, platelets act as mobile transmitters, endothelial cells are fixed receivers, sticky to the vessel walls, and the transmitted signal is made of bursts of molecules emitted by platelets. The simulator allows evaluating the channel latency and the footprint on the vessel wall of the transmitted signal as a function of the transmitter distance from the vessels wall, the signal strength, and the receiver sensitivity.

  10. Calculation of the crystal-melt interfacial free energy of succinonitrile from molecular simulation

    E-Print Network [OSTI]

    Feng, Xiaobing; Laird, Brian Bostian

    2006-01-30

    purpose of the current work is to determine whether the interfacial free energy of a molecular material can be accurately calculated by computer simulation. We have chosen SCN as a test candidate because experimental values for both the magnitude...;#1;7.9±0.8#2;#1;10?3 613 #1;2003#2;#4;, but is about 20% lower than the earlie obtained by Schaefer et al. #3;Philos. Mag. 32, 725 #1; calculated anisotropy of the interfacial free energy o addition, the Turnbull coefficient from our simulation work demonstrates...

  11. Free energy and molecular dynamics calculations for the cubic-tetragonal phase transition in zirconia

    E-Print Network [OSTI]

    Paxton, Anthony T.

    in zirconia Stefano Fabris,* Anthony T. Paxton, and Michael W. Finnis Atomistic Simulation Group, Department zirconia is studied by molecu- lar dynamics MD simulations and within the framework of the Landau theory solutions of zirconia (ZrO2) with cubic stabilizing oxides like Y2O3, MgO or CeO, and are generally called

  12. Photoionization analysis of chemo-dynamical dwarf galaxies simulations

    E-Print Network [OSTI]

    Melekh, B; Hensler, G; Buhajenko, O

    2015-01-01

    Photoionization modelling allows to follow the transport, the emergence, and the absorption of photons taking into account all important processes in nebular plasmas. Such modelling needs the spatial distribution of density, chemical abundances and temperature, that can be provided by chemo-dynamical simulations (ChDS) of dwarf galaxies. We perform multicomponent photoionization modelling (MPhM) of the ionized gas using 2-D ChDSs of dwarf galaxies. We calculate emissivity maps for important nebular emission lines. Their intensities are used to derive the chemical abundance of oxygen by the so-called Te- and R23-methods. Some disagreements are found between oxygen abundances calculated with these methods and the ones coming from the ChDSs. We investigate the fraction of ionizing radiation emitted in the star-forming region which is able to leak out the galaxy. The time- and direction-averaged escape fraction in our simulation is 0.35-0.4. Finally, we have calculated the total Halpha lumi- nosity of our model g...

  13. RECENT PROGRESS IN DYNAMIC PROCESS SIMULATION OF CRYOGENIC REFRIGERATORS

    SciTech Connect (OSTI)

    Kuendig, A. [Linde Kryotechnik AG, Dattlikonerstrasse 5, CH-8422 Pfungen (Switzerland)

    2008-03-16

    At the CEC 2005 a paper with the title 'Helium refrigerator design for pulsed heat load in Tokamaks' was presented. That paper highlighted the control requirements for cryogenic refrigerators to cope with the expected load variations of future nuclear fusion reactors. First dynamic computer simulations have been presented.In the mean time, the computer program is enhanced and a new series of process simulations are available. The new program considers not only the heat flows and the temperature variations within the heat exchangers, but also the variation of mass flows and pressure drops. The heat transfer numbers now are calculated in dependence of the flow speed and the gas properties. PI-controllers calculate the necessary position of specific valves for maintaining pressures, temperatures and the rotation speed of turbines.Still unsatisfactory is the fact, that changes in the process arrangement usually are attended by adjustments in the program code. It is the main objective of the next step of development a more flexible code which enables that any user defined process arrangements can be assembled by input data.

  14. Discontinuous Shear Thickening in Brownian Suspensions By Dynamic Simulation

    E-Print Network [OSTI]

    Romain Mari; Ryohei Seto; Jeffrey F. Morris; Morton M. Denn

    2015-08-05

    Dynamic particle-scale numerical simulations are used to show that the shear thickening observed in dense colloidal, or Brownian, suspensions is of a similar nature to that observed in non-colloidal suspensions, i.e., a stress-induced transition from a flow of lubricated near-contacting particles to a flow of a frictionally contacting network of particles. Abrupt (or discontinuous) shear thickening is found to be a geometric rather than hydrodynamic phenomenon; it stems from the strong sensitivity of the jamming volume fraction to the nature of contact forces between suspended particles. The thickening obtained in a colloidal suspension of purely hard frictional spheres is qualitatively similar to experimental observations. However the agreement cannot be made quantitative with only hydrodynamics, frictional contacts and Brownian forces. Therefore the role of a short-range repulsive potential mimicking the stabilization of actual suspensions on the thickening is studied. The effects of Brownian and repulsive forces on the onset stress can be combined in an additive manner. The simulations including Brownian and stabilizing forces show excellent agreement with experimental data for the viscosity $\\eta$ and the second normal stress difference $N_2$.

  15. Electron Transfer Dynamics in Efficient Molecular Solar Cells

    SciTech Connect (OSTI)

    Meyer, Gerald John

    2014-10-01

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

  16. Sandia Energy - Atomistic Molecular Dynamics of Ion-Containing Polymers

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-Throughput Analysis ofSample SULI ProgramPhysical Society NamesAtomistic Molecular

  17. SIMULATION OF HENs This chapter describes how dynamic simulations of HENs can be carried out. The type and

    E-Print Network [OSTI]

    Skogestad, Sigurd

    be carried out. The type and complexity of the model of each heat exchanger significantly affect the efforts required for HEN simulation, and focus is on the development of a general heat exchanger model countercurrent heat exchangers are briefly described, and the chapter closes by explaining how dynamic simulation

  18. The formulation of quantum statistical mechanics based on the Feynman path centroid density. IV. Algorithms for centroid molecular dynamics

    E-Print Network [OSTI]

    Cao, Jianshu

    . Algorithms for centroid molecular dynamics Jianshu Cao and Gregory A. Voth Department of Chemistry 1994) Numerical algorithms are developed for the centroid molecular dynamics (centroid MD) method to carry out a direct calculation of the force on the centroid variables in the centroid MD algorithm

  19. Statistical-Temperature Monte Carlo and Molecular Dynamics Algorithms Jaegil Kim,* John E. Straub, and Thomas Keyes

    E-Print Network [OSTI]

    Straub, John E.

    Statistical-Temperature Monte Carlo and Molecular Dynamics Algorithms Jaegil Kim,* John E. Straub. A novel molecular dynamics algorithm (STMD) applicable to complex systems and a Monte Carlo algorithmRevLett.97.050601 PACS numbers: 05.10.ÿa, 02.70.Rr, 87.18.Bb The Wang-Landau (WL) Monte Carlo (MC) algorithm

  20. STOCK: Structure mapper and online coarse-graining kit for molecular simulations

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

    Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

    2015-03-15

    We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be providedmore »by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.« less

  1. Molecular dynamics study of non-equilibrium energy transport from a cylindrical track: Part II

    E-Print Network [OSTI]

    Johnson, Robert E.

    Molecular dynamics study of non-equilibrium energy transport from a cylindrical track: Part II that it is the description of the radial transport and the absence of energy transport to the surface, rather than¯ects the nature of the energizing process rather than the energy transport. In this paper we describe the details

  2. Molecular dynamics study of non-equilibrium energy transport from a cylindrical track

    E-Print Network [OSTI]

    Johnson, Robert E.

    Molecular dynamics study of non-equilibrium energy transport from a cylindrical track I. Test were carried out to describe the kinetic energy transport in a low temper- ature, condensed-gas solid, equilibration competes with radial transport of energy from the cylindrically excited region. The radial

  3. Proton-coupled electron transfer reactions in solution: Molecular dynamics with quantum transitions for model systems

    E-Print Network [OSTI]

    Hammes-Schiffer, Sharon

    Proton-coupled electron transfer reactions in solution: Molecular dynamics with quantum transitions A general minimal model for proton-coupled electron transfer PCET reactions in solution is presented. This model consists of three coupled degrees of freedom that represent an electron, a proton, and a solvent

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

    E-Print Network [OSTI]

    Neff, Jason

    Decomposition Carbon Pyrolysis-GC/MS Disturbance 1. Introduction Soil organic matter (SOM) is an importantMolecular C dynamics downstream: The biochemical decomposition sequence and its impact on soil in spectroscopic and other chemical methods have greatly enhanced our ability to characterize soil organic matter

  5. A Molecular Dynamics Approach to the Structural Characterization of Amyloid Aggregation

    E-Print Network [OSTI]

    Caflisch, Amedeo

    may be common to all amyloidogenic polypeptides. The ability of a polypeptide chain to self-assembleA Molecular Dynamics Approach to the Structural Characterization of Amyloid Aggregation M. Cecchini polypeptides. The strategy is based on the decomposition of the sequence into overlapping stretches

  6. Investigating a Back Door Mechanism of Actin Phosphate Release by Steered Molecular Dynamics

    E-Print Network [OSTI]

    Wriggers, Willy

    - dependent self-assembly in the cell cytoplasm plays an important role in processes involving cell motility.1Investigating a Back Door Mechanism of Actin Phosphate Release by Steered Molecular Dynamics Willy-Champaign, Urbana, Illinois ABSTRACT In actin-based cell motility, phos- phate (Pi) release after ATP hydrolysis

  7. Brine Rejection from Freezing Salt Solutions: A Molecular Dynamics Study Lubos Vrbka and Pavel Jungwirth*

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Brine Rejection from Freezing Salt Solutions: A Molecular Dynamics Study Lubos Vrbka and Pavel process of brine rejection from freezing salt solutions is investigated with atomic resolution using. The presence of salt slows down the freezing process, which leads to the formation of an almost neat ice next

  8. Accelerated, energy-conserving BornOppenheimer molecular dynamics via Fock matrix extrapolation

    E-Print Network [OSTI]

    Herbert, John

    in order to accelerate convergence of the electronic structure calculations, can suffer from systematic­Oppenheimer molecular dynamics calculations, especially those that exploit information retained from previous time steps, on a potential energy surface obtained by ``on-the-fly'' solution of the quantum-mechanical electronic structure

  9. Identification of the protein folding transition state from molecular dynamics trajectories

    E-Print Network [OSTI]

    Caflisch, Amedeo

    Identification of the protein folding transition state from molecular dynamics trajectories S. Muff The rate of protein folding is governed by the transition state so that a detailed characterization of its. INTRODUCTION Proteins fold from the heterogeneous set of denatured conformations to the structurally well

  10. Molecular Dynamics of Methylamine, Methanol, and Methyl Fluoride Cations in Intense 7 Micron Laser Fields

    E-Print Network [OSTI]

    Schlegel, H. Bernhard

    Molecular Dynamics of Methylamine, Methanol, and Methyl Fluoride Cations in Intense 7 Micron Laser of methylamine (CH3NH2 + ), methanol (CH3OH+ ), and methyl fluoride (CH3F+ ) cations by short, intense laser 7 m laser pulses. This work is motivated by recent studies of methanol cations by Yamanouchi and co

  11. Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics

    E-Print Network [OSTI]

    Sargent, Edward H. "Ted"

    Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics Andrei Buin halide perovskites have recently attracted tremen- dous attention at both the experimental. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius

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

    E-Print Network [OSTI]

    Chen, Liao Y.

    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

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

    E-Print Network [OSTI]

    Meirovitch, Hagai

    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 energy evaluation is a central issue in atomistic modeling.1­5 When the free energy is known, equilibrium

  14. Molecular Dynamics modelling of the adhesive interaction between fine F. A. Gilabert

    E-Print Network [OSTI]

    Krivtsov, Anton M.

    Molecular Dynamics modelling of the adhesive interaction between fine particles F. A. Gilabert the frictionless adhesive interaction force between two fine cohesive polymer grains. The model consists of three a higher resolution near the contact area. Secondly, the cohesion strength (i.e., the work of adhesion

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

    E-Print Network [OSTI]

    of the nuclear equilibrium upon photoexcitation. In the limiting case of resonance between the electronic energy with the overall nuclear wave packet width. The demonstrated quantum relaxation features of the photoinduced dynamics in molecular systems, which play domi- nant roles in a variety of problems in physics, technology

  16. Nonadiabatic transition state theory and multiple potential energy surface molecular dynamics of infrequent events

    E-Print Network [OSTI]

    Hammes-Schiffer, Sharon

    Nonadiabatic transition state theory and multiple potential energy surface molecular dynamics in the vicinity of the energy barrier, i.e., in the region of the transition state or bottleneck. In general, TST 07974 Received 7 July 1995; accepted 17 August 1995 Classical transition state theory TST provides

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

    E-Print Network [OSTI]

    Saiz, Leonor

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

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

    E-Print Network [OSTI]

    Martin, Jan M.L.

    energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407 , which leads to two equivalent ``hydrogen bonding contacts,'' is extremely close in energy on an overall flatFrom ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding

  19. Size and Temperature Effects on the Fracture Mechanisms of Silicon Nanowires: Molecular Dynamics

    E-Print Network [OSTI]

    Cai, Wei

    Size and Temperature Effects on the Fracture Mechanisms of Silicon Nanowires: Molecular Dynamics. The fracture behavior of the NWs depends both on temperature and NW diameter. For NWs of di- ameter larger than 4 nm, cleavage fracture on the transverse (1 1 0) plane are predominantly observed at temperatures

  20. Correlations and Symmetry of Interactions Influence Collective Dynamics of Molecular Motors

    E-Print Network [OSTI]

    Celis-Garza, Daniel; Kolomeisky, Anatoly B

    2015-01-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In ad...

  1. Microscopic Mechanisms and Dynamics Simulations of S3/2) Reacting with Methane

    E-Print Network [OSTI]

    1 Microscopic Mechanisms and Dynamics Simulations of O+ (4 S3/2) Reacting with Methane Lipeng Sun: The reaction O+ (4 S3/2) + methane is studied as a benchmark for developing the theory of polymer erosion by O;2 Microscopic Mechanisms and Dynamics Simulations of O+ (4 S3/2) Reacting with Methane spacecraft,3 surprisingly

  2. Graphics processing units accelerated semiclassical initial value representation molecular dynamics

    SciTech Connect (OSTI)

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

    2014-05-07

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

  3. Collective Molecular Dynamics of a Floating Water Bridge

    E-Print Network [OSTI]

    Emilio Del Giudice; Elmar C. Fuchs; Giuseppe Vitiello

    2010-04-06

    When a high voltage is applied to pure water filling two beakers kept close to each other, a connection forms spontaneously, giving the impression of a floating water bridge. This phenomenon is of special interest, since it comprises a number of phenomena currently tackled in modern water science. The formation and the main properties of this floating water bridge are analyzed in the conceptual framework of quantum electrodynamics. The necessary conditions for the formation are investigated as well as the time evolution of the dynamics. The predictions are found in agreement with the observations.

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

    E-Print Network [OSTI]

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

    2007-01-12

    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.

  5. Combining quantum wavepacket ab initio molecular dynamics with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical

    E-Print Network [OSTI]

    Iyengar, Srinivasan S.

    : Implementation blending ONIOM and empirical valence bond theory Isaiah Sumner and Srinivasan S. Iyengara. All components of the methodology, namely, quantum dynamics and ONIOM molecular dynamics

  6. Molecular simulation study of role of polymer–particle interactions in the strain-dependent viscoelasticity of elastomers (Payne effect)

    SciTech Connect (OSTI)

    Chen, Yulong; Li, Ziwei; Wen, Shipeng; Zhang, Liqun; Yang, Qingyuan E-mail: LiuL@mail.buct.edu.cn; Zhong, Chongli; Liu, Li E-mail: LiuL@mail.buct.edu.cn

    2014-09-14

    The strain-amplitude dependence of viscoelastic behavior of model crosslinked elastomers containing various concentrations of spherical nanoparticles (NPs) was studied by non-equilibrium molecular dynamics simulation. All the filler NPs were in monodispersed state and the interactions between these particles were purely repulsive. The polymer–particle interactions were attractive and their interaction energies were tuned in a broad range. Through the computational study, many important features of the behavior of particle-reinforced elastomers observed in experiments, including the Payne effect, were successfully reproduced. It was shown that the magnitude of the Payne effect was found to depend on the polymer–particle interaction and the filler loading. By examining the microstructures of the simulation systems and their evolution during oscillatory shear, four different mechanisms for the role of the polymer–particle interactions in the Payne effect were revealed that consist of the debonding of polymer chains from NP surfaces, the breakage of polymer-shell-bridged NP network, the rearrangement of the NPs in the network into different layers and the shear-induced yielding of the rigid polymer shell in-between neighboring NPs.

  7. Molecular Dynamics Simulation of Microstructure and Molecular Mobilities in Swollen Nafion Membranes

    E-Print Network [OSTI]

    Muzzio, Fernando J.

    , for hydrogen and methanol fuel cells, which are seen today as the most promising energy suppliers for vehicles

  8. Molecular Dynamics Simulation of GaAs Molecular Beam Epitaxy D. A. Murdick,1

    E-Print Network [OSTI]

    Wadley, Haydn

    of Virginia, Charlottesville, Virginia 22904, USA 2 Department of Materials, University of Oxford, Oxford OX1 3PH, UK ABSTRACT The vapor deposition of epitaxial GaAs and (Ga,Mn)As thin films during far-temperature growth of Ga0.94Mn0.06As and the Mn clustering trends in as-grown films. INTRODUCTION GaAs is widely used

  9. The Momentum Cloud Method for Dynamic Simulation of Rigid Body Systems

    E-Print Network [OSTI]

    Sweetman, Bert

    is presented for a 6-body floating wind turbine system. CE Database subject headings: Simulation, Structural dynamics, Rigid-body dynamics, Wind power, Floating structures 1. Introduction and Background A multibody. Featherstone (Featherstone, 2008) investigates the dynamics formulation of a floating-base rigid-body system

  10. On theoretical issues of computer simulations sequential dynamical systems

    SciTech Connect (OSTI)

    Barrett, C.L.; Mortveit, H.S.; Reidys, C.M.

    1998-12-01

    The authors study a class of discrete dynamical systems that is motivated by the generic structure of simulations. The systems consist of the following data: (a) a finite graph Y with vertex set {l_brace}1,...,n{r_brace} where each vertex has a binary state, (b) functions F{sub i}:F{sub 2}{sup n} {r_arrow} F{sub 2}{sup n} and (c) an update ordering {pi}. The functions F{sub i} update the binary state of vertex i as a function of the state of vertex i and its Y-neighbors and leave the states of all other vertices fixed. The update ordering is a permutation of the Y-vertices. They derive a decomposition result, characterize invertible SDS and study fixed points. In particular they analyze how many different SDS that can be obtained by reordering a given multiset of update functions and give a criterion for when one can derive concentration results on this number. Finally, some specific SDS are investigated.

  11. Dynamics of pebbles in the vicinity of a growing planetary embryo: hydro-dynamical simulations

    E-Print Network [OSTI]

    Morbidelli, Alessandro

    2012-01-01

    Understanding the growth of the cores of giant planets is a difficult problem. Recently, Lambrechts and Johansen (2012; LJ12) proposed a new model in which the cores grow by the accretion of pebble-size objects, as the latter drift towards the star due to gas drag. Here, we investigate the dynamics of pebble-size objects in the vicinity of planetary embryos of 1 and 5 Earth masses and the resulting accretion rates. We use hydrodynamical simulations, in which the embryo influences the dynamics of the gas and the pebbles suffer gas drag according to the local gas density and velocities. The pebble dynamics in the vicinity of the planetary embryo is non-trivial, and it changes significantly with the pebble size. Nevertheless, the accretion rate of the embryo that we measure is within an order of magnitude of the rate estimated in LJ12 and tends to their value with increasing pebble-size. We conclude that the model by LJ12 has the potential to explain the rapid growth of giant planet cores. The actual accretion r...

  12. Molecular simulation study of polar order in orthogonal bent core smectic liquid crystals

    E-Print Network [OSTI]

    Stavros D. Peroukidis; Alexandros G. Vanakaras; Demetri J. Photinos

    2015-04-16

    We explore the phase behavior and structure of orthogonal smectic liquid crystals consisting of bent-core molecules (BCMs) by means of Monte Carlo molecular simulations. A simple athermal molecular model is introduced that describes the basic features of the BCMs. Phase transitions between uniaxial and biaxial (antiferroelectric) orthogonal smectics are obtained. The results indicate the presence of local in-plane polar correlations in the uniaxial smectic phase. The macroscopic uniaxial-biaxial transformation is rationalized in terms of local polar correlations giving rise to polar domains. The size of these polar domains grows larger under the action of an external vector field and their internal ordering is enhanced, leading to field-induced biaxial order-disorder transitions.

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

    SciTech Connect (OSTI)

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

    2011-02-22

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

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

    SciTech Connect (OSTI)

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

    2014-05-19

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

  15. On the correlation between the photoexcitation pathways and the critical energies required for ablation of poly(methyl methacrylate): A molecular dynamics study

    SciTech Connect (OSTI)

    Conforti, Patrick F.; Prasad, Manish; Garrison, Barbara J.

    2008-05-15

    The energetics initiating ablation in poly(methyl methacrylate) (PMMA) are studied using molecular dynamics (MD) simulation. The critical energy to initiate ablation in PMMA following the absorption of photons is investigated for two penetration depths along a range of fluences using a coarse-grained, hybrid Monte Carlo-MD scheme. Both heating and direct bond scission are simulated separately after photon absorption with additional transformation of material occurring via chemical reactions following the photochemical bond cleavage. For a given type of absorption and reaction channel, a critical energy can well describe the amount of energy required to initiate ablation. The simulations show a decrease in the critical energy when a greater amount of photochemistry is introduced in the system. The simulations complement experimental studies and elucidate how enhanced photochemistry lowers ablation thresholds in polymer substrates.

  16. Free Energy & Kinetics from Molecular Dynamics Objective: To give a presentation of about 60 minutes at the end of the week covering the key aspects of how to get kinetic

    E-Print Network [OSTI]

    Goldschmidt, Christina

    Free Energy & Kinetics from Molecular Dynamics 14.6.10 Objective: To give a presentation of about of determining macroscopic parameters by simulations. One of the most important examples would be free energy and rate constants. The above illustration is the standard description of free energy and rates of going

  17. From gyroscopic to thermal motion: a crossover in the dynamics of molecular superrotors

    E-Print Network [OSTI]

    Milner, A A; Rezaiezadeh, K; Milner, V

    2015-01-01

    Localized heating of a gas by intense laser pulses leads to interesting acoustic, hydrodynamic and optical effects with numerous applications in science and technology, including controlled wave guiding and remote atmosphere sensing. Rotational excitation of molecules can serve as the energy source for raising the gas temperature. Here, we study the dynamics of energy transfer from the molecular rotation to heat. By optically imaging a cloud of molecular superrotors, created with an optical centrifuge, we experimentally identify two separate and qualitatively different stages of its evolution. The first non-equilibrium "gyroscopic" stage is characterized by the modified optical properties of the centrifuged gas - its refractive index and optical birefringence, owing to the ultrafast directional molecular rotation, which survives tens of collisions. The loss of rotational directionality is found to overlap with the release of rotational energy to heat, which triggers the second stage of thermal expansion. The ...

  18. Design and Simulation of Molecular Nonvolatile Single-Electron Resistive Switches

    E-Print Network [OSTI]

    Simonian, Nikita; Likharev, Konstantin K

    2012-01-01

    We have carried out a preliminary design and simulation of a single-electron resistive switch based on a system of two linear, parallel, electrostatically-coupled molecules: one implementing a single-electron transistor and another serving as a single-electron trap. To verify our design, we have performed a theoretical analysis of this "memristive" device, based on a combination of ab-initio calculations of the electronic structures of the molecules and the general theory of single-electron tunneling in systems with discrete energy spectra. Our results show that such molecular assemblies, with a length below 10 nm and a footprint area of about 5 nm$^2$, may combine sub-second switching times with multi-year retention times and high ($> 10^3$) ON/OFF current ratios, at room temperature. Moreover, Monte Carlo simulations of self-assembled monolayers (SAM) based on such molecular assemblies have shown that such monolayers may also be used as resistive switches, with comparable characteristics and, in addition, b...

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

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

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

    2015-09-10

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

  20. Molecular imaging and dynamics at the LCLS John C H Spence*

    E-Print Network [OSTI]

    Crowther, Paul

    Molecular imaging and dynamics at the LCLS John C H Spence* ASU Physics/LBNL/NSF BioXFEL STC%summary%of%achievements%since% 12/2009%% %%%%%%%%The% LCLS near Stanford was the world s first hard X-ray laser. It produces 9 kV X ! No goniometer ! Our Liquid jet uses gas focusing to make a micron jet from bigger nozzle.. LCLS Rep Rate ~100 Hz

  1. Protein Molecular Dynamics With Electrostatic Force Entirely Determined by a Single Poisson-Boltzmann

    E-Print Network [OSTI]

    Lu, Benzhuo

    and Applied Physics, University of Science and Technology of China, Hefei, China 2 Center for Biomedical and compared with those obtained from 500-ps molecu- lar dynamics (MD) simulation with explicit water and a 500 of the BEM with macromol- ecule with "pinched" surface regions that are often found in deep crevices

  2. Dynamics of a globular protein and its hydration water studied by neutron scattering and MD simulations

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

    Chen, Sow-Hsin; Lagi, Marco; Chu, Xiang-qiang; Zhang, Yang; Kim, Chansoo; Faraone, Antonio; Fratini, Emiliano; Baglioni, Piero

    2010-01-01

    This review article describes our neutron scattering experiments made in the past four years for the understanding of the single-particle (hydrogen atom) dynamics of a protein and its hydration water and the strong coupling between them. We found that the key to this strong coupling is the existence of a fragile-to-strong dynamic crossover (FSC) phenomenon occurring at aroundTL= 225±5 K in the hydration water. On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the high density form (HDL), a more fluid state, to predominantly the low density form (LDL), a less fluidmore »state, derived from the existence of a liquid–liquid critical point at an elevated pressure. We show experimentally that this sudden switch in the mobility of hydration water on Lysozyme, B-DNA and RNA triggers the dynamic transition, at a temperatureTD= 220 K, for these biopolymers. In the glassy state, belowTD, the biopolymers lose their vital conformational flexibility resulting in a substantial diminishing of their biological functions. We also performed molecular dynamics (MD) simulations on a realistic model of hydrated lysozyme powder, which confirms the existence of the FSC and the hydration level dependence of the FSC temperature. Furthermore, we show a striking feature in the short time relaxation (?-relaxation) of protein dynamics, which is the logarithmic decay spanning 3 decades (from ps to ns). The long time?-relaxation shows instead a diffusive behavior, which supports the liquid-like motions of protein constituents. We then discuss our recent high-resolution X-ray inelastic scattering studies of globular proteins, Lysozyme and Bovine Serum Albumin. We were able to measure the dispersion relations of collective, intra-protein phonon-like excitations in these proteins for the first time. We found that the phonon energies show a marked softening and at the same time their population increases substantially in a certain wave vector range when temperature crosses over theTD. Thus the increase of biological activities aboveTDhas positive correlation with activation of slower and large amplitude collective motions of a protein.« less

  3. A model simulation of white-winged dove population dynamics in the Tamaulipan Biotic Province 

    E-Print Network [OSTI]

    Martinez, Cristina Ann

    2002-01-01

    I present the development, evaluation, and sensitivity analysis of a simulation model representing two components of population dynamics-natality and mortality-for the white-winged dove (Zenaida asiatica asiatica; WWDO). I also discuss the role...

  4. A Finite Element-Multibody Dynamics Co-simulation Methodology Applied to FAST 

    E-Print Network [OSTI]

    Suryakumar, Vishvas Samuel

    2013-05-02

    A co-simulation methodology is explored whereby a finite element code and a multi-body dynamics code featuring flexible cantilevered beams can be coupled and interactively executed. The floating frame of reference formulation is used to develop...

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

    E-Print Network [OSTI]

    Zhai, Zhiqiang, 1971-

    2003-01-01

    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 ...

  6. Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

    SciTech Connect (OSTI)

    Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

    2014-10-14

    In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW??O??³?, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

  7. Quantum Implementation of Unitary Coupled Cluster for Simulating Molecular Electronic Structure

    E-Print Network [OSTI]

    Yangchao Shen; Xiang Zhang; Shuaining Zhang; Jing-Ning Zhang; Man-Hong Yung; Kihwan Kim

    2015-06-01

    Quantum simulation represents an efficient solution to a certain classically intractable problem in various research area including quantum chemistry. The central problem of quantum chemistry is to determine the electronic structure and the ground-state energy of atoms and molecules. The exact classical calculation of the problem is demanding even for molecules with moderate size due to the "exponential catastrophe." To deal with such quantum chemistry problem, the coupled-cluster methods have been successfully developed, which are considered to be the current "gold standard" in classical computational chemistry. However, the coupled-cluster ansatz is built with non-unitary operation, which leads to drawbacks such as lacking variational bound of ground-state energy. The unitary version of the coupled-cluster methods would perfectly address the problem, whereas it is classically inefficient without proper truncation of the infinite series expansion. It has been a long-standing challenge to build an efficient computational scheme for the unitary coupled-cluster ansatz. Here we report an experimental realization of the unitary coupled cluster ansatz based on quantum simulation. The experiments are performed in a scalable platform containing a trapped multi-level \\Yb ion for simulating the electronic structure of a molecular ion (HeH$^+$); we experimentally compute ground-state the energy curve and simulate chemical-bond softening non-perturbatively, which clearly shows the quantum implementation of the unitary coupled-cluster method yields better ground-states energies than classical implementations with truncations. Furthermore, the energy measurements, one most time consuming part in the experiments, can be parallelized. Our experimental results provide a new and solid evidence of how quantum simulation can advance the field of quantum chemistry.

  8. Dynamical Simulation of Fluidized Beds --- Hydrodynamically Interacting Granular Particles

    E-Print Network [OSTI]

    Kengo Ichiki; Hisao Hayakawa

    1995-03-01

    A numerical simulation of a gas-fluidized bed is performed without introduction of any empirical parameters. Realistic bubbles and slugs are observed in our simulation. It is found that the convective motion of particles is important for the bubbling phase and there is no convection in the slugging phase. From the simulation results, non-Gaussian distributions are found in the particle velocities and the relation between the deviation from Gaussian and the local density of particles is suggested. It is also shown that the power spectra of particle velocities obey power laws. A brief explanation on the relationship between the simulation results and the Kolmogorov scaling argument is discussed.

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

    SciTech Connect (OSTI)

    Kipnusu, Wycliffe Kiprop; Kossack, Wilhelm; Iacob, Ciprian; Zeigermann, Philipp; Jasiurkowska, Malgorzata; Sangoro, Joshua R; Valiullin, Rustem; Kremer, Friedrich

    2013-01-01

    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.

  10. Magnetized Interstellar Molecular Clouds. I. Comparison Between Simulations and Zeeman Observations

    E-Print Network [OSTI]

    Li, Pak Shing; Klein, Richard I

    2015-01-01

    The most accurate measurements of magnetic fields in star-forming gas are based on the Zeeman observations analyzed by Crutcher et al. (2010). We show that their finding that the 3D magnetic field scales approximately as density$^{0.65}$ can also be obtained from analysis of the observed line-of-sight fields. We present two large-scale AMR MHD simulations of several thousand $M_\\odot$ of turbulent, isothermal, self-gravitating gas, one with a strong initial magnetic field (Alfven Mach number $M_{A,0}= 1$) and one with a weak initial field ($M_{A,0}=10$). We construct samples of the 100 most massive clumps in each simulation and show that they exhibit a power-law relation between field strength and density in excellent agreement with the observed one. Our results imply that the average field in molecular clumps in the interstellar medium is $ \\sim 42 n_{H,4}^{0.65} \\mu$G. Furthermore, the median value of the ratio of the line-of-sight field to density$^{0.65}$ in the simulations is within a factor of about (1....

  11. Dynamic properties of molecular motors in the divided-pathway model Rahul Kumar Das and Anatoly B. Kolomeisky*

    E-Print Network [OSTI]

    Dynamic properties of molecular motors in the divided-pathway model Rahul Kumar Das and Anatoly B on the web 9th April 2009 DOI: 10.1039/b901214a The mechanisms of molecular motors transport are important for understanding multiple biological processes. Recent single-molecule experiments indicate that motor proteins

  12. Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope

    E-Print Network [OSTI]

    Truhlar, Donald G

    Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum

  13. 2.13 HEAT TRANSFER & FLUID FLOW IN MICROCHANNELS 2.13.7-1 Molecular dynamics methods in

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

  14. Predicting alloy vibrational mode properties using lattice dynamics calculations, molecular dynamics simulations, and the virtual crystal

    E-Print Network [OSTI]

    McGaughey, Alan

    to their potentially low thermal conductivities, dis- ordered materials (e.g., alloys, amorphous solids, aerogels

  15. Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone

    E-Print Network [OSTI]

    Miller, William H.

    with the Chappuis band of ozone Victor S. Batista and William H. Millera) Department of Chemistry, University A ) of ozone following photoexcitation of the molecule in the gas phase with visible light. Our algorithm and recurrence events, as well as an interpretation of experimental studies of the Chappuis band of ozone

  16. Dynamical simulation of heavy-ion collisions in the energy range from a few tens MeV/A to a few hundreds MeV/A

    E-Print Network [OSTI]

    M. V. Garzelli

    2008-10-13

    The overlapping stage of heavy-ion reactions can be simulated by dynamical microscopical models, such as those built on the basis of the Molecular Dynamics (MD) approaches, allowing to study the fragment formation process. The present performances of the Quantum MD (QMD) code developed at the University of Milano are discussed, showing results concerning fragment and particle production at bombarding energies up to $\\lsim$ 700 MeV/A, as well as a preliminary analysis on the isoscaling behaviour of isotopic yield ratios for reactions with isospin composition N/Z in the (1 - 1.2) range, at a 45 MeV/A bombarding energy.

  17. Simulation of an atomistic dynamic field theory for monatomic liquids: Freezing and glass formation

    E-Print Network [OSTI]

    Grant, Martin

    Simulation of an atomistic dynamic field theory for monatomic liquids: Freezing and glass formation regime. The thermodynamics and dynamics of freezing and glass formation in this model system are studied.70.P , 64.70.D , 61.43. j, 81.05.Kf When a simple liquid is supercooled below its freezing temperature

  18. CFD Simulation of Dynamic Thrust and Radial Forces on a Vertical Axis Wind Turbine Blade

    E-Print Network [OSTI]

    Tullis, Stephen

    CFD Simulation of Dynamic Thrust and Radial Forces on a Vertical Axis Wind Turbine Blade K. Mc vibration source of a small scale vertical axis wind turbine. The dynamic loading on the blades of the turbine, as they rotate about the central shaft and travel through a range of relative angles of attack

  19. The `neighbor effect': Simulating dynamics in consumer preferences for new vehicle technologies

    E-Print Network [OSTI]

    to capture dynamics in consumer preferences. We estimate Canadians' preferences for new vehicle technologiesANALYSIS The `neighbor effect': Simulating dynamics in consumer preferences for new vehicle technologies Paulus Maua,1 , Jimena Eyzaguirrea,1 , Mark Jaccarda,, Colleen Collins-Doddb,2 , Kenneth

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

    E-Print Network [OSTI]

    Bretherton, Chris

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