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1

Substructured multibody molecular dynamics.  

SciTech Connect

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

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

2006-11-01T23:59:59.000Z

2

Millisecond-scale molecular dynamics simulations on Anton  

Science Conference Proceedings (OSTI)

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

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

2009-11-01T23:59:59.000Z

3

Multiscale FEM-MD schema  

Science Conference Proceedings (OSTI)

... coupling finite element modeling (FEM) to atomistic Molecular Dynamics (MD) 1 ... for using extremely high (very unrealistic) indentation rates that are ...

2013-06-27T23:59:59.000Z

4

Molecular dynamics simulations of ordered alkane chains physisorbed on graphite  

E-Print Network (OSTI)

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

Peters, Achim

5

Molecular dynamics simulation of Li surface erosion and bubble formation  

E-Print Network (OSTI)

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

Harilal, S. S.

6

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

Science Conference Proceedings (OSTI)

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

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

2011-05-01T23:59:59.000Z

7

Anton, a special-purpose machine for molecular dynamics simulation  

Science Conference Proceedings (OSTI)

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

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

2008-07-01T23:59:59.000Z

8

Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems  

Science Conference Proceedings (OSTI)

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

Matt Chiu; Martin C. Herbordt

2010-11-01T23:59:59.000Z

9

Adaptive-boost molecular dynamics simulation of carbon diffusion in iron  

E-Print Network (OSTI)

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

Ishii, Akio

10

Molecular dynamics simulation of displacement cascades in FeCr alloys  

E-Print Network (OSTI)

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

11

Molecular Dynamics Simulations of Microscale Fluid Transport  

E-Print Network (OSTI)

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

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

1998-01-01T23:59:59.000Z

12

Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters  

Science Conference Proceedings (OSTI)

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

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

2011-07-01T23:59:59.000Z

13

Anton, a special-purpose machine for molecular dynamics simulation  

Science Conference Proceedings (OSTI)

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

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

2007-06-01T23:59:59.000Z

14

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

Science Conference Proceedings (OSTI)

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

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

2013-11-01T23:59:59.000Z

15

Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit  

E-Print Network (OSTI)

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

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

2010-01-21T23:59:59.000Z

16

A Molecular Dynamics  

Science Conference Proceedings (OSTI)

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

17

A Molecular Dynamic Study  

Science Conference Proceedings (OSTI)

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

18

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

Science Conference Proceedings (OSTI)

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

W. Andreoni; A. Curioni; T. Mordasini

2001-05-01T23:59:59.000Z

19

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

Science Conference Proceedings (OSTI)

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

Panagiotis Angelikopoulos; Costas Papadimitriou; Petros Koumoutsakos

2012-01-01T23:59:59.000Z

20

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

E-Print Network (OSTI)

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

Zhigilei, Leonid V.

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


21

The implementation of polarizable and flexible models in molecular dynamics simulations  

Science Conference Proceedings (OSTI)

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

Shihao Wang; Natalie M. Cann

2009-06-01T23:59:59.000Z

22

Introduction to Accelerated Molecular Dynamics  

SciTech Connect

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

Perez, Danny [Los Alamos National Laboratory

2012-07-10T23:59:59.000Z

23

Introduction to Accelerated Molecular Dynamics  

SciTech Connect

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

Perez, Danny [Los Alamos National Laboratory

2012-07-10T23:59:59.000Z

24

Harvesting graphics power for MD simulations  

E-Print Network (OSTI)

We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a congruential shift random number generator are presented. The performance of the GPU's is compared to their main processor counterpart. We achieve speedups of up to 80, 40 and 150 fold, respectively. With newest generation of GPU's one can run standard MD simulations at 10^7 flops/$.

J. A. van Meel; A. Arnold; D. Frenkel; S. F. Portegies Zwart; R. G. Belleman

2007-09-20T23:59:59.000Z

25

Molecular dynamics simulations and drug discovery  

E-Print Network (OSTI)

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

Durrant, Jacob D; McCammon, J Andrew

2011-01-01T23:59:59.000Z

26

Fluctuations in molecular dynamics simulations  

Science Conference Proceedings (OSTI)

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

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

2010-03-01T23:59:59.000Z

27

Stochastic Event-Driven Molecular Dynamics  

Science Conference Proceedings (OSTI)

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

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

2008-02-01T23:59:59.000Z

28

Langevin molecular dynamics derived from Ehrenfest dynamics  

E-Print Network (OSTI)

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

Szepessy, Anders

2007-01-01T23:59:59.000Z

29

Gas-Phase Molecular Dynamics  

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

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

30

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

E-Print Network (OSTI)

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

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

2009-01-22T23:59:59.000Z

31

A Molecular Dynamics Simulation  

Science Conference Proceedings (OSTI)

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

32

Ab-Initio Molecular Dynamics  

E-Print Network (OSTI)

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

Kühne, Thomas D

2012-01-01T23:59:59.000Z

33

Molecular Statics and Molecular Dynamics Simulations of the ...  

Science Conference Proceedings (OSTI)

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

34

Accelerated Molecular Dynamics Methods  

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

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

35

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

Science Conference Proceedings (OSTI)

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

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

2011-10-01T23:59:59.000Z

36

GAS PHASE MOLECULAR DYNAMICS  

SciTech Connect

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

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

1999-06-09T23:59:59.000Z

37

Gas Phase Molecular Dynamics  

Science Conference Proceedings (OSTI)

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

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

1999-05-21T23:59:59.000Z

38

Langevin molecular dynamics derived from Ehrenfest dynamics  

E-Print Network (OSTI)

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

Anders Szepessy

2007-12-21T23:59:59.000Z

39

Molecular Dynamics Simulations of Thermoset Polymers for ...  

Science Conference Proceedings (OSTI)

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

40

Stochastic Event-Driven Molecular Dynamics  

Science Conference Proceedings (OSTI)

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

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

2008-02-01T23:59:59.000Z

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


41

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

SciTech Connect

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

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

2012-01-01T23:59:59.000Z

42

A thread calculus with molecular dynamics  

Science Conference Proceedings (OSTI)

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

J. A. Bergstra; C. A. Middelburg

2010-07-01T23:59:59.000Z

43

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

Science Conference Proceedings (OSTI)

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

Paolo Valentini; Thomas E. Schwartzentruber

2009-12-01T23:59:59.000Z

44

Radiation in molecular dynamic simulations  

DOE Green Energy (OSTI)

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

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

2008-10-13T23:59:59.000Z

45

Enhanced molecular dynamics for simulating porous interphase layers in batteries.  

DOE Green Energy (OSTI)

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

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

2009-10-01T23:59:59.000Z

46

Force spectroscopy of polymer desorption: Theory and Molecular Dynamics simulation  

E-Print Network (OSTI)

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

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

2013-10-14T23:59:59.000Z

47

Molecular Dynamics of Martenstic Phase Transitions  

Science Conference Proceedings (OSTI)

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

48

Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films  

E-Print Network (OSTI)

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

Kim, Bo Hung

2009-05-01T23:59:59.000Z

49

Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen  

DOE Green Energy (OSTI)

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

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

2008-02-14T23:59:59.000Z

50

Molecular dynamics simulation of hydrogen diffusion in titanium  

National Nuclear Security Administration (NNSA)

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

51

Lightweight computational steering of very large scale molecular dynamics simulations  

Science Conference Proceedings (OSTI)

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

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

1996-09-01T23:59:59.000Z

52

Structural Modeling and Molecular Dynamics Simulation of the Actin Filament  

DOE Green Energy (OSTI)

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

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

2011-01-01T23:59:59.000Z

53

Surface detection, meshing and analysis during large molecular dynamics simulations  

SciTech Connect

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

Dupuy, L M; Rudd, R E

2005-08-01T23:59:59.000Z

54

Molecular Dynamics Study of Krypton Isotopes Physisorbed on Graphite  

E-Print Network (OSTI)

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

Bader, Karson

2012-01-01T23:59:59.000Z

55

Md. Saifur Rahaman Md. Saifur Rahaman  

E-Print Network (OSTI)

of Chemical and Environmental Engineering "Environmental Applications of Nanotechnology" Advisor: ProfMd. Saifur Rahaman Resume 1 Md. Saifur Rahaman Department of Chemical and Environmental Engineering from Wastewater through Struvite Crystallization in a Fluidized Bed Reactor: Kinetics, Hydrodynamics

Elimelech, Menachem

56

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

E-Print Network (OSTI)

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

Tiezheng Qian; Xiao-Ping Wang; Ping Sheng

2005-02-26T23:59:59.000Z

57

Local Restaurants - Gaithersburg, MD  

Science Conference Proceedings (OSTI)

... Subway 16 Bureau Dr. Gaithersburg, MD (301) 527-8988. Thai Tanium 657 Center Point Way Gaithersburg, MD (301) 990-3699. ...

2013-07-25T23:59:59.000Z

58

The molecular dynamics simulation of ion-induced ripple growth  

Science Conference Proceedings (OSTI)

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

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

2009-11-28T23:59:59.000Z

59

Phonostat: Thermostatting phonons in molecular dynamics simulations  

E-Print Network (OSTI)

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

Raghunathan, Rajamani

60

Molecular dynamics calculation of free energy  

Science Conference Proceedings (OSTI)

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

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

1988-01-01T23:59:59.000Z

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61

Molecular Dynamics Study of Nucleation during Crystallization  

Science Conference Proceedings (OSTI)

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

62

LAMMPS Molecular Dynamics Simulator - TMS  

Science Conference Proceedings (OSTI)

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

63

Fermionic Molecular Dynamics for nuclear dynamics and thermodynamics  

E-Print Network (OSTI)

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

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

2008-12-02T23:59:59.000Z

64

Phase-field Simulations/Molecular Dynamics  

Science Conference Proceedings (OSTI)

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

65

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

Science Conference Proceedings (OSTI)

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

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

2007-08-01T23:59:59.000Z

66

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

Science Conference Proceedings (OSTI)

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

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

2007-08-01T23:59:59.000Z

67

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

Science Conference Proceedings (OSTI)

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

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

2007-07-30T23:59:59.000Z

68

Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron  

E-Print Network (OSTI)

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

Leone, Stephen R.

2010-01-01T23:59:59.000Z

69

Molecular dynamics simulation of UO2 nanocrystals melting  

E-Print Network (OSTI)

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

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

2011-01-01T23:59:59.000Z

70

OpenAtom -- Ab initio molecular dynamics package  

Science Conference Proceedings (OSTI)

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

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

2008-01-01T23:59:59.000Z

71

MOLECULAR DYNAMICS STUDY OF THE THERMAL CONDUCTIVITY OF AMORPHOUS NANOPOROUS SILICA  

E-Print Network (OSTI)

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

Coquil, Thomas; Fang, Jin; Pilon, Laurent

2011-01-01T23:59:59.000Z

72

Application of optimal prediction to molecular dynamics  

SciTech Connect

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

Barber IV, John Letherman

2004-12-01T23:59:59.000Z

73

DYNAMICAL ANALYSIS OF HIGHLY EXCITED MOLECULAR SPECTRA  

SciTech Connect

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

Michael E. Kellman

2005-06-17T23:59:59.000Z

74

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

E-Print Network (OSTI)

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

Heinz, Stefan

75

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

SciTech Connect

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

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

2003-02-01T23:59:59.000Z

76

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase  

Science Conference Proceedings (OSTI)

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

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

2012-05-09T23:59:59.000Z

77

Molecular Dynamics Method in Microscale Heat Transfer Shigeo Maruyama  

E-Print Network (OSTI)

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

Maruyama, Shigeo

78

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

DOE Green Energy (OSTI)

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

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

2010-10-14T23:59:59.000Z

79

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

E-Print Network (OSTI)

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

Djurabekova, Flyura; Pohjonen, Aarne; Nordlund, Kai

2011-01-01T23:59:59.000Z

80

Molecular Dynamics Simulation of Cavitation in Metallic Glass  

Science Conference Proceedings (OSTI)

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

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


81

GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES  

SciTech Connect

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

MUCKERMAN,J.T.

1999-06-09T23:59:59.000Z

82

Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules  

SciTech Connect

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

Muckerman, J.T.

1999-05-21T23:59:59.000Z

83

Molecular Dynamics Simulation of Thermoset Fracture with ...  

Science Conference Proceedings (OSTI)

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

84

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

Science Conference Proceedings (OSTI)

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

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

2010-06-22T23:59:59.000Z

85

Molecular dynamics simulation of deuterium trapping and bubble formation in tungsten  

E-Print Network (OSTI)

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

Harilal, S. S.

86

Can Dynamic Contact Angle Be Measured Using Molecular Modeling?  

E-Print Network (OSTI)

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

Malani, Ateeque A. A. G.

87

Molecular Dynamics Simulations of Vacancy and Oxygen Diffusion ...  

Science Conference Proceedings (OSTI)

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

88

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

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

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

89

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

E-Print Network (OSTI)

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

Schlegel, H. Bernhard

90

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

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

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

91

Order parameter prediction from molecular dynamics simulations in proteins  

E-Print Network (OSTI)

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

Perilla, Juan R

2011-01-01T23:59:59.000Z

92

Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps  

E-Print Network (OSTI)

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

Volkovich, Roie

2010-01-01T23:59:59.000Z

93

Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps  

E-Print Network (OSTI)

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

Roie Volkovich; Uri Peskin

2010-12-01T23:59:59.000Z

94

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

Science Conference Proceedings (OSTI)

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

Ross C. Walker; Levi Pierce; Romelia Salomon

2012-07-01T23:59:59.000Z

95

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

SciTech Connect

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

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

2013-01-01T23:59:59.000Z

96

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

E-Print Network (OSTI)

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

Hirunsit, Pussana

2007-05-01T23:59:59.000Z

97

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

SciTech Connect

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

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

1995-09-01T23:59:59.000Z

98

Contents 1 Molecular Dynamics Simulation of Argon 1  

E-Print Network (OSTI)

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

unknown authors

2010-01-01T23:59:59.000Z

99

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

SciTech Connect

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

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

2009-10-27T23:59:59.000Z

100

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

SciTech Connect

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

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

2012-01-01T23:59:59.000Z

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


101

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

SciTech Connect

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

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

2013-01-01T23:59:59.000Z

102

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

Science Conference Proceedings (OSTI)

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

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

2008-01-01T23:59:59.000Z

103

Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron  

SciTech Connect

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

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

2010-03-14T23:59:59.000Z

104

Quantum dynamics of bio-molecular systems in noisy environments  

E-Print Network (OSTI)

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

M. B. Plenio; S. F. Huelga

2012-02-05T23:59:59.000Z

105

Molecular dynamics study of sodium using a model pseudopotential  

Science Conference Proceedings (OSTI)

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

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

1981-01-01T23:59:59.000Z

106

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

E-Print Network (OSTI)

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

Goddard III, William A.

107

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

Science Conference Proceedings (OSTI)

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

Gerald Paul

2007-02-01T23:59:59.000Z

108

Molecular Dynamics Simulations to Compute the Bulk Response of Amorphous PMMA  

E-Print Network (OSTI)

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

Goddard III, William A.

109

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine  

E-Print Network (OSTI)

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

Rapaport, D C

2009-01-01T23:59:59.000Z

110

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

SciTech Connect

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

Hall, G.E.

2011-05-31T23:59:59.000Z

111

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

SciTech Connect

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

Hall G. E.; Goncharov, V.

2012-05-29T23:59:59.000Z

112

Dynamic Properties of Molecular Motors in Burnt-Bridge Models  

E-Print Network (OSTI)

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

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

2007-05-04T23:59:59.000Z

113

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

SciTech Connect

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

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

2009-04-03T23:59:59.000Z

114

Molecular dynamics studies of interfacial water at the alumina surface.  

DOE Green Energy (OSTI)

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

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

2011-01-01T23:59:59.000Z

115

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

Science Conference Proceedings (OSTI)

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

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

2012-05-29T23:59:59.000Z

116

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

SciTech Connect

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

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

2010-06-01T23:59:59.000Z

117

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

DOE Green Energy (OSTI)

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

Kannan, Srinivasaraghavan; Zacharias, Martin W.

2007-11-01T23:59:59.000Z

118

Category:Baltimore, MD | Open Energy Information  

Open Energy Info (EERE)

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

119

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

SciTech Connect

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

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

2012-12-15T23:59:59.000Z

120

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

Science Conference Proceedings (OSTI)

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

Dang, Liem X.; Chang, Tsun-Mei

2012-01-19T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
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121

Prototyping Bio-Nanorobots using Molecular Dynamics Simulation  

E-Print Network (OSTI)

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

Hamdi, Mustapha; Ferreira, A; Mavroidis, Constantinos

2007-01-01T23:59:59.000Z

122

A multiscale Molecular Dynamics approach to Contact Mechanics  

E-Print Network (OSTI)

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

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

2005-08-10T23:59:59.000Z

123

Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite  

E-Print Network (OSTI)

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

unknown authors

2005-01-01T23:59:59.000Z

124

Molecular dynamics simulation of strongly coupled QCD plasmas  

E-Print Network (OSTI)

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

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

2006-01-06T23:59:59.000Z

125

A First Principles Molecular Dynamics Study Of Calcium Ion In Water  

SciTech Connect

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

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

2005-01-28T23:59:59.000Z

126

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

E-Print Network (OSTI)

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

Zhigilei, Leonid V.

127

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

E-Print Network (OSTI)

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

Neff, Jason

128

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

E-Print Network (OSTI)

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

129

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

E-Print Network (OSTI)

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

Mavroidis, Constantinos

130

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

Science Conference Proceedings (OSTI)

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

Bing-Yang Cao; Ruo-Yu Dong

2012-06-01T23:59:59.000Z

131

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

SciTech Connect

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

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

2011-07-10T23:59:59.000Z

132

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

E-Print Network (OSTI)

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

Alznauer, Tobias

2012-01-01T23:59:59.000Z

133

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

DOE Data Explorer (OSTI)

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

Plimpton, Steve; Thompson, Aidan; Crozier, Paul

134

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

E-Print Network (OSTI)

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

de Groot, Bert

135

Nanoaggregation and solubility of crude oil asphaltenes from molecular dynamics simulations  

Science Conference Proceedings (OSTI)

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

Francesco Frigerio

2009-12-01T23:59:59.000Z

136

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

SciTech Connect

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

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

2010-01-01T23:59:59.000Z

137

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

E-Print Network (OSTI)

of Infectious Diseases, Ft. Detrick, MD, USA 2 Biotechnology High Performance Computing Software Applications

138

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

E-Print Network (OSTI)

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

Voigt, Chris

139

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

SciTech Connect

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

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

2012-05-31T23:59:59.000Z

140

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

Science Conference Proceedings (OSTI)

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

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

2012-12-21T23:59:59.000Z

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


141

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

SciTech Connect

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

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

2013-01-01T23:59:59.000Z

142

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

E-Print Network (OSTI)

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

Han, Kunwoo

2006-08-01T23:59:59.000Z

143

Molecular dynamics simulation of montmorillonite and mechanical and thermodynamic properties calculations  

E-Print Network (OSTI)

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

Atilhan, Selma

2007-05-01T23:59:59.000Z

144

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

E-Print Network (OSTI)

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

Nigel Cundy; Weonjong Lee

2011-10-10T23:59:59.000Z

145

Molecular dynamics analysis of PVA-AgnP composites by dielectric spectroscopy  

Science Conference Proceedings (OSTI)

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

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

2012-01-01T23:59:59.000Z

146

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

E-Print Network (OSTI)

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

Utah, University of

147

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

E-Print Network (OSTI)

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

Esfarjani, Keivan

148

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

Science Conference Proceedings (OSTI)

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

Rafal Metkowski; Piotr Bala; Terry W. Clark

2001-09-01T23:59:59.000Z

149

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

Science Conference Proceedings (OSTI)

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

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

2009-01-01T23:59:59.000Z

150

Large-scale Excited Electron Molecular Mechanics/Dynamics  

Science Conference Proceedings (OSTI)

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

151

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

E-Print Network (OSTI)

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

Carey, Ralph

2012-05-01T23:59:59.000Z

152

Crossed molecular beam studies of atmospheric chemical reaction dynamics  

SciTech Connect

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

Zhang, Jingsong

1993-04-01T23:59:59.000Z

153

I12: Quantum Chemical Molecular Dynamics Simulations on ...  

Science Conference Proceedings (OSTI)

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

154

Molecular dynamics on distributed-memory MIMD computers with load balancing  

Science Conference Proceedings (OSTI)

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

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

1994-12-31T23:59:59.000Z

155

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

DOE R&D Accomplishments (OSTI)

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

Lee, Y. T.

1973-09-00T23:59:59.000Z

156

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

E-Print Network (OSTI)

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

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

2006-10-19T23:59:59.000Z

157

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

E-Print Network (OSTI)

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

de Gispert, Adrià

158

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

E-Print Network (OSTI)

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

Harilal, S. S.

159

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

E-Print Network (OSTI)

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

Gaddamanugu, Dhatri

2009-05-01T23:59:59.000Z

160

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

E-Print Network (OSTI)

We present an efficient general approach to first principles molecular dynamics simulations based on extended Lagrangian Born-Oppenheimer molecular dynamics in the limit of vanishing self-consistent field optimization. The reduction of the optimization requirement reduces the computational cost to a minimum, but without causing any significant loss of accuracy or longterm energy drift. The optimization-free first principles molecular dynamics requires only one single diagonalization per time step and yields trajectories at the same level of accuracy as "exact", fully converged, Born-Oppenheimer molecular dynamics simulations. The optimization-free limit of extended Lagrangian Born-Oppenheimer molecular dynamics therefore represents an ideal starting point for a robust and efficient formulation of a new generation first principles quantum mechanical molecular dynamics simulation schemes.

Souvatzis, Petros

2013-01-01T23:59:59.000Z

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While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
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161

Dynamic Coherence in Excitonic Molecular Complexes under Various Excitation Conditions  

E-Print Network (OSTI)

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

Chenu, Aurélia; Mancal, Tomáš

2013-01-01T23:59:59.000Z

162

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

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

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

163

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

Science Conference Proceedings (OSTI)

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

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

2010-08-14T23:59:59.000Z

164

Dynamic fluorescence imaging with molecular agents for cancer detection  

E-Print Network (OSTI)

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

Kwon, Sun Kuk

2006-12-01T23:59:59.000Z

165

Spontaneous fission of /sup 259/Md  

SciTech Connect

The mass and kinetic energy distributions of fission fragments from the spontaneous fission of th newly discovered nuclide /sup 259/Md were obtained. /sup 259/Md was identified as the E. C. daughter of /sup 259/No, and was found to decay entirely (> 95%) by spontaneous fission with a 95-min half-life. From the kinetic energies measured for 397 pairs of coincident fragments, a mass distribution was derived that is symmetric with sigma = 13 amu. /sup 259/Md, together with /sup 258/Fm and /sup 259/Fm, form a select group of three nuclides whose mass division in spontaneous fission is highly symmetric. Unlike the total-kinetic-energy (TKE) distributions of /sup 258/Fm and /sup 259/Fm, which peak at approx. = to 240 MeV, this distribution for /sup 259/Md is broad and is 50 MeV lower in energy. Analysis of the mass and energy distributions shows that events near mass symmetry also exhibit a broad TKE distribution, with one-third of the symmetric events having TKEs less than 200 MeV. The associated of low TKEs with symmetric mass division in the fission of very heavy actinides is anomalous and inconsistent with theories based upon the emergence of fragment shells near the scission point. Either three-body fragmentation or peculiar fragment shapes are assumed as the cause for the large consumption of Coulomb energy observed for a significant fraction of symmetric fissions in /sup 259/Md. 6 figures.

Hulet, E.K.; Wild, J.F.; Lougheed, R.W.; Baisden, P.A.; Landrum, J.H.; Dougan, R.J.; Mustafa, M.; Ghiorso, A.; Nitschke, J.M.

1979-05-04T23:59:59.000Z

166

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

E-Print Network (OSTI)

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

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

2004-03-13T23:59:59.000Z

167

Molecular Dynamics Simulation of Solidification in Cu50Zr50 Alloy  

Science Conference Proceedings (OSTI)

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

168

Processed Splitting Algorithms for Rigid-Body Molecular Dynamics Simulations  

E-Print Network (OSTI)

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

Igor P. Omelyan

2008-05-15T23:59:59.000Z

169

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

E-Print Network (OSTI)

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

Chen, Liao Y.

170

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

E-Print Network (OSTI)

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

Maruyama, Shigeo

171

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

Science Conference Proceedings (OSTI)

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

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

2013-10-01T23:59:59.000Z

172

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

Science Conference Proceedings (OSTI)

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

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

2010-06-01T23:59:59.000Z

173

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

E-Print Network (OSTI)

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

Meirovitch, Hagai

174

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

Science Conference Proceedings (OSTI)

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

175

Compute Node MD3000 Storage Array  

E-Print Network (OSTI)

Compute Node MD3000 Storage Array Dell 2950 Head Node 24-Port Switch Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node 24-Port Switch Dell 2950

Weber, David J.

176

Heart Failure Jason Ryan, MD, MPH  

E-Print Network (OSTI)

1 Heart Failure Jason Ryan, MD, MPH Director, UCONN Heart Failure Center University of Connecticut,084,000 $34.8 billion Background on Heart Failure Heart failure (HF) is a major public health problem resulting in substantial morbidity and mortality 1American Heart Association.2008 Heart and Stroke

Oliver, Douglas L.

177

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

E-Print Network (OSTI)

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

Cambridge, University of

178

New amorphous forms of solid CO2 from ab initio molecular dynamics  

E-Print Network (OSTI)

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

Plašienka, Dušan

2013-01-01T23:59:59.000Z

179

Molecular Approaches to Understanding C & N Dynamics in MArine Sediments  

Science Conference Proceedings (OSTI)

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

Arturo Massol; James Tiedje; Jizhong Zhou; Allan Devol

2007-05-16T23:59:59.000Z

180

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

Office of Legacy Management (LM)

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

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


181

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

E-Print Network (OSTI)

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

H. Feldmeier; J. Schnack

1998-06-02T23:59:59.000Z

182

Free Energy Calculation in MD Simulation  

E-Print Network (OSTI)

Free Energy Calculation in MD Simulation #12;Basic Thermodynamics Helmoholtz free energy A = U ­ TS + i Ni dA = wrev (reversible, const N V T) eq (22.9) McQuarrie & Simon Gibbs free energy G = U;Implication of Free Energy A B Keq = [A]/[B] Keq = exp (-G0 /RT) G0 = -RT ln Keq G = G0 + RT ln Q G > 0

Nielsen, Steven O.

183

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

DOE Green Energy (OSTI)

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

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

2008-11-01T23:59:59.000Z

184

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

DOE Green Energy (OSTI)

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

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

2004-01-01T23:59:59.000Z

185

Density Functional Theory and Molecular Dynamics Studies on Energetics and Kinetics for Electro-Active Polymers: PVDF and P(VDF-TrFE)  

E-Print Network (OSTI)

We use first principles methods to study static and dynamical mechanical properties of the ferroelectric polymer Poly(vinylidene fluoride) (PVDF) and its copolymer with trifluoro ethylene (TrFE). We use density functional theory [within the generalized gradient approximation (DFT-GGA)] to calculate structures and energetics for various crystalline phases for PVDF and P(VDF-TrFE). We find that the lowest energy phase for PVDF is a non-polar crystal with a combination of trans (T) and gauche (G) bonds; in the case of the copolymer the role of the extra (bulkier) F atoms is to stabilize T bonds. This leads to the higher crystallinity and piezoelectricity observed experimentally. Using the MSXX first principles-based force field (FF) with molecular dynamics (MD), we find that the energy barrier necessary to nucleate a kink (gauche pairs separated by trans bonds) in an all-T crystal is much lower (14.9 kcal/mol) in P(VDF-TrFE) copolymer than in PVDF (24.8 kcal/mol). This correlates with the observation that the polar phase of the copolymer exhibits a solid-solid a transition to a non-polar phase under heating while PVDF directly melts. We also studied the mobility of an interface between a polar and non-polar phases under uniaxial stress; we find a lower threshold stress and a higher mobility in the copolymer as compared with PVDF. Finally, considering plastic deformation under applied shear, we find that the chains for P(VDF-TrFE) have a very low resistance to sliding, particularly along the chain direction. The atomistic characterization of these "unit mechanisms" provides essential input to mesoscopic or macroscopic models of electro-active polymers.

H. B. Su; Alejandro Strachan; William A. Goddard III

2004-08-09T23:59:59.000Z

186

Molecular studies of the structural properties of hydrogen gas in bulk water.  

DOE Green Energy (OSTI)

We report on our studies of the structural properties of a hydrogen molecule dissolved in liquid water. The radial distribution function, coordination number and coordination number distribution are calculated using different representations of the interatomic forces within molecular dynamics (MD), Monte Carlo (MC) and ab initio molecular dynamics (AIMD) simulation frameworks. Although structural details differ in the radial distribution functions generated from the different force fields, all approaches agree that the average and most probable number of water molecules occupying the inner hydration sphere around hydrogen is 16. Furthermore, all results exclude the possibility of clathrate-like organization of water molecules around the hydrophobic molecular hydrogen solute.

Rempe, Susan L.; Sabo, Dubravko; Greathouse, Jeffery A.; Martin, Marcus Gary

2006-02-01T23:59:59.000Z

187

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

Science Conference Proceedings (OSTI)

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

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

2013-01-01T23:59:59.000Z

188

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

DOE Green Energy (OSTI)

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

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

2001-11-21T23:59:59.000Z

189

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

Office of Legacy Management (LM)

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

190

Connecting the Molecular and the Continuum Scales  

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

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

191

Nuclear liquid-gas phase transition studied with antisymmetrized molecular dynamics  

E-Print Network (OSTI)

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

Takuya Furuta; Akira Ono

2003-05-19T23:59:59.000Z

192

Molecular dynamic studies on anisotropic explosion of laser irradiated Xe cluster  

Science Conference Proceedings (OSTI)

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

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

2012-09-15T23:59:59.000Z

193

Visualization of parallel molecular dynamics simulation on a remote visualization platform  

SciTech Connect

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

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

1994-09-01T23:59:59.000Z

194

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

SciTech Connect

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

Germann, T. C. (Timothy C.)

2001-06-01T23:59:59.000Z

195

A new battery-charging method suggested by molecular dynamics simulations  

E-Print Network (OSTI)

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

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

2010-01-01T23:59:59.000Z

196

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

E-Print Network (OSTI)

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

Khotimah, Siti Nurul; Widayani,; Waris, Abdul

2011-01-01T23:59:59.000Z

197

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

Science Conference Proceedings (OSTI)

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

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

2012-06-06T23:59:59.000Z

198

A molecular dynamics simulation of DNA damage induction by ionizing radiation  

E-Print Network (OSTI)

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

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

2013-01-01T23:59:59.000Z

199

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

Science Conference Proceedings (OSTI)

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

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

2012-01-01T23:59:59.000Z

200

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

DOE Green Energy (OSTI)

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

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

2004-09-03T23:59:59.000Z

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201

Oral Histories: Pathologist Clarence Lushbaugh, M.D.  

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

3 HUMAN RADIATION STUDIES: REMEMBERING THE EARLY YEARS Oral History of Pathologist Clarence Lushbaugh, M.D. Conducted October 5, 1994 United States Department of Energy Office of...

202

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

Science Conference Proceedings (OSTI)

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

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

2011-05-01T23:59:59.000Z

203

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

Office of Legacy Management (LM)

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

204

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

E-Print Network (OSTI)

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

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

2013-07-24T23:59:59.000Z

205

Net Zero Residential Test Facility Gaithersburg, MD Solar Photovoltaic Panels  

E-Print Network (OSTI)

1 Net Zero Residential Test Facility Gaithersburg, MD Solar Photovoltaic Panels Solar Thermal R-35 Rim Joist Area 5" open cell spray foam 2" mineral wool insulation blanket R-10 Basement Slab electric WH #12;NZERTF Gaithersburg, MD Solar Photovoltaic Array Roof Mounted South half of main roof

Oak Ridge National Laboratory

206

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

E-Print Network (OSTI)

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

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

2011-01-01T23:59:59.000Z

207

Molecular dynamics simulation of interaction of H with vacancy in W  

DOE Green Energy (OSTI)

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

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

2009-09-15T23:59:59.000Z

208

Molecular dynamics simulation of high strain-rate void nucleation and growth in copper  

Science Conference Proceedings (OSTI)

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

Belak, J.

1997-07-01T23:59:59.000Z

209

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

SciTech Connect

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

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

2013-01-01T23:59:59.000Z

210

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

SciTech Connect

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

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

2012-12-07T23:59:59.000Z

211

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

E-Print Network (OSTI)

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

Fu, Xuebing

2008-08-01T23:59:59.000Z

212

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

E-Print Network (OSTI)

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

Zhigilei, Leonid V.

213

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

E-Print Network (OSTI)

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

Maruyama, Shigeo

214

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

Office of Legacy Management (LM)

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

215

Dynamics  

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

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

216

MD. SAIFUR RAHAMAN 9 Hillhouse Ave., Environmental Engineering Program  

E-Print Network (OSTI)

of Chemical Engineering, Yale University Project: "Environmental implications and applications of engineeredMD. SAIFUR RAHAMAN 9 Hillhouse Ave., Environmental Engineering Program Department of Chemical Crystallization in a Fluidized Bed Reactor: Kinetics, Hydrodynamics and Performance" Supervisor: Professor Donald

Elimelech, Menachem

217

Cove Point, MD Natural Gas Liquefied Natural Gas Imports from...  

Gasoline and Diesel Fuel Update (EIA)

Trinidad and Tobago (Million Cubic Feet) Cove Point, MD Natural Gas Liquefied Natural Gas Imports from Trinidad and Tobago (Million Cubic Feet) Year Jan Feb Mar Apr May Jun Jul Aug...

218

Cove Point, MD Natural Gas Liquefied Natural Gas Imports from...  

Annual Energy Outlook 2012 (EIA)

Norway (Million Cubic Feet) Cove Point, MD Natural Gas Liquefied Natural Gas Imports from Norway (Million Cubic Feet) Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 2011...

219

Cove Point, MD Natural Gas Liquefied Natural Gas Imports from...  

Annual Energy Outlook 2012 (EIA)

Nigeria (Million Cubic Feet) Cove Point, MD Natural Gas Liquefied Natural Gas Imports from Nigeria (Million Cubic Feet) Year Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 2011...

220

Cove Point, MD Natural Gas Liquefied Natural Gas Imports from...  

U.S. Energy Information Administration (EIA) Indexed Site

Algeria (Million Cubic Feet) Cove Point, MD Natural Gas Liquefied Natural Gas Imports from Algeria (Million Cubic Feet) Decade Year-0 Year-1 Year-2 Year-3 Year-4 Year-5 Year-6...

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221

Cove Point, MD Natural Gas Liquefied Natural Gas Imports from...  

U.S. Energy Information Administration (EIA) Indexed Site

Egypt (Million Cubic Feet) Cove Point, MD Natural Gas Liquefied Natural Gas Imports from Egypt (Million Cubic Feet) Decade Year-0 Year-1 Year-2 Year-3 Year-4 Year-5 Year-6 Year-7...

222

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

E-Print Network (OSTI)

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

Diddo Diddens; Andreas Heuer

2012-11-14T23:59:59.000Z

223

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

SciTech Connect

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

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

2012-01-01T23:59:59.000Z

224

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

SciTech Connect

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

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

2012-01-01T23:59:59.000Z

225

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

E-Print Network (OSTI)

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

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

2003-01-01T23:59:59.000Z

226

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

SciTech Connect

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

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

2012-08-02T23:59:59.000Z

227

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

SciTech Connect

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

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

2006-05-15T23:59:59.000Z

228

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

SciTech Connect

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

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

2012-09-01T23:59:59.000Z

229

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

E-Print Network (OSTI)

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

Baty, Austin Alan

2013-05-01T23:59:59.000Z

230

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

E-Print Network (OSTI)

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

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

2013-06-04T23:59:59.000Z

231

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

SciTech Connect

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

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

2011-01-01T23:59:59.000Z

232

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

E-Print Network (OSTI)

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

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

2004-01-01T23:59:59.000Z

233

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

Science Conference Proceedings (OSTI)

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

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

2009-12-14T23:59:59.000Z

234

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

Science Conference Proceedings (OSTI)

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

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

2012-07-01T23:59:59.000Z

235

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

SciTech Connect

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

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

2011-01-01T23:59:59.000Z

236

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

SciTech Connect

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

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

2011-07-15T23:59:59.000Z

237

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

SciTech Connect

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

Furuhama, Ayako; Dupuis, Michel; Hirao, Kimihiko

2008-05-29T23:59:59.000Z

238

Security Standards for the Global Information Grid Gary Buda, Booz Allen & Hamilton, Linthicum, MD 21090  

E-Print Network (OSTI)

, Telcordia Technologies, Morristown, NJ 07960 Chris Kubic, Department of Defense, Ft. Meade, MD, 20755

Lee, Ruby B.

239

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

DOE Green Energy (OSTI)

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

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

2009-10-01T23:59:59.000Z

240

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

Office of Legacy Management (LM)

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

Note: This page contains sample records for the topic "molecular dynamics md" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
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241

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

E-Print Network (OSTI)

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

Rich, Sarah Celeste

2008-01-01T23:59:59.000Z

242

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

Science Conference Proceedings (OSTI)

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

Sukky Jun; Tenzin Tashi; Harold S. Park

2011-01-01T23:59:59.000Z

243

Function and dynamics of aptamers: A case study on the malachite green aptamer  

Science Conference Proceedings (OSTI)

Aptamers are short single-stranded nucleic acids that can bind to their targets with high specificity and high affinity. To study aptamer function and dynamics, the malachite green aptamer was chosen as a model. Malachite green (MG) bleaching, in which an OH- attacks the central carbon (C1) of MG, was inhibited in the presence of the malachite green aptamer (MGA). The inhibition of MG bleaching by MGA could be reversed by an antisense oligonucleotide (AS) complementary to the MGA binding pocket. Computational cavity analysis of the NMR structure of the MGA-MG complex predicted that the OH{sup -} is sterically excluded from the C1 of MG. The prediction was confirmed experimentally using variants of the MGA with changes in the MG binding pocket. This work shows that molecular reactivity can be reversibly regulated by an aptamer-AS pair based on steric hindrance. In addition to demonstrate that aptamers could control molecular reactivity, aptamer dynamics was studied with a strategy combining molecular dynamics (MD) simulation and experimental verification. MD simulation predicted that the MG binding pocket of the MGA is largely pre-organized and that binding of MG involves reorganization of the pocket and a simultaneous twisting of the MGA terminal stems around the pocket. MD simulation also provided a 3D-structure model of unoccupied MGA that has not yet been obtained by biophysical measurements. These predictions were consistent with biochemical and biophysical measurements of the MGA-MG interaction including RNase I footprinting, melting curves, thermodynamic and kinetic constants measurement. This work shows that MD simulation can be used to extend our understanding of the dynamics of aptamer-target interaction which is not evident from static 3D-structures. To conclude, I have developed a novel concept to control molecular reactivity by an aptamer based on steric protection and a strategy to study the dynamics of aptamer-target interaction by combining MD simulation and experimental verification. The former has potential application in controlling metabolic reactions and protein modifications by small reactants and the latter may serve as a general approach to study the dynamics of aptamer-target interaction for new insights into mechanisms of aptamer-target recognition.

Wang, Tianjiao

2008-12-01T23:59:59.000Z

244

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

E-Print Network (OSTI)

and the atmosphere from biomass burning.  Climatic Change Introduction to pyrolysis of biomass.  J.  Anal.  Appl.  Molecular Structure of Plant Biomass-derived Black Carbon (

Keiluweit, M.

2010-01-01T23:59:59.000Z

245

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

SciTech Connect

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

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

2012-10-15T23:59:59.000Z

246

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

SciTech Connect

We give the details of a new partitioning scheme of the kinetic energy in molecular dynamics. The scheme utilizes instantaneous internal coordinates and atomic velocities, and at the lowest level separates the kinetic energy into solute and solvent (or bath) contributions. We illustrate its application in an analysis of the short-time dynamics of ‘cyclic’ and ‘branched’ water tetramers after an ionization event. The analysis supports the partitioning of the tetrameric systems into two subsystems, a ‘reactive trimer’ and a ‘solvent’ molecule. The partitioned kinetic energy exhibits two features, a broad peak assigned to the interaction between the two sub-systems and a sharper peak arising from the proton transfer that occurs upon ionization. It is found that the stability of the hydroxyl radical formed upon ionization is sensitive to the instantaneous configuration of the water molecules around the ionized water. Michel Dupuis was supported in part by the Division of Chemical Sciences, Office of Basic Energy Sciences, of the U.S. Department of Energy (DOE). This research was performed in part using the Molecular Science Computing Facility in the he William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the PNNL. The EMSL is funded by DOE’s Office of Biological and Environmental Research. PNNL is operated by Battelle for DOE.

Furuhama, Ayako; Dupuis, Michel; Hirao, Kimihiko

2008-02-15T23:59:59.000Z

247

Medical Scholars (BS/MD) Program Expectations and Requirements  

E-Print Network (OSTI)

Medical Scholars (BS/MD) Program Expectations and Requirements Undergraduate portion semester GPAs lower than 3.5 will trigger an automatic review by the Medical Scholars Committee of the Medical Scholars Committee, to delay their entry to medical school by one year to broaden their education

Fernandez, Eduardo

248

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

Office of Legacy Management (LM)

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

249

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

Office of Legacy Management (LM)

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

250

Spectroscopic studies beyond N = 152 neutron gap : decay of {sup 255 ovr sub 101}Md and {sup 256 ovr sub 101}Md.  

Science Conference Proceedings (OSTI)

The isotopes {sup 255}Md and {sup 256}Md were produced by the irradiation of {sup 253}Es with 35-45 MeV {alpha} particles by ({alpha},n) and ({alpha},2n) reactions and were removed from the target by a helium jet system. {alpha}, {gamma}, and {alpha}-{gamma} coincidence spectra were measured with Si and Ge(Li) detectors. From the EC decays of {sup 255}Md and {sup 256}Md, levels in {sup 255}Fm and {sup 256}Fm were deduced. Favored {alpha} decay of {sup 255}Md was found to populate the 7/2{sup -}[514] single-particle state in {sup 251}Es, thus establishing the 7/2{sup -}[514] as the {sup 255}Md ground state. Several {gamma} rays were observed in the {sub 256}Md {alpha}-{gamma} coincidence spectrum. {sup 256}Fm is the heaviest nucleus in which excited intrinsic states have been identified.

Ahmad, I.; Chasman, R. R.; Fields, P. R.

2000-01-01T23:59:59.000Z

251

Spectroscopic studies beyond the N=152 neutron gap: Decay of {sub 101}{sup 255}Md and {sub 101}{sup 256}Md  

Science Conference Proceedings (OSTI)

The isotopes {sup 255}Md and {sup 256}Md were produced by the irradiation of {sup 253}Es with 35-45 MeV {alpha} particles by ({alpha},n) and ({alpha},2n) reactions and were removed from the target by a helium jet system. {alpha}, {gamma}, and {alpha}-{gamma} coincidence spectra were measured with Si and Ge(Li) detectors. From the EC decays of {sup 255}Md and {sup 256}Md, levels in {sup 255}Fm and {sup 256}Fm were deduced. Favored {alpha} decay of {sup 255}Md was found to populate the 7/2{sup -}[514] single-particle state in {sup 251}Es, thus establishing the 7/2{sup -}[514] as the {sup 255}Md ground state. Several {gamma} rays were observed in the {sup 256}Md {alpha}-{gamma} coincidence spectrum. {sup 256}Fm is the heaviest nucleus in which excited intrinsic states have been identified. (c) 2000 The American Physical Society.

Ahmad, I. [Argonne National Laboratory, Argonne, Illinois 60439 (United States); Chasman, R. R. [Argonne National Laboratory, Argonne, Illinois 60439 (United States); Fields, P. R. [Argonne National Laboratory, Argonne, Illinois 60439 (United States)

2000-04-01T23:59:59.000Z

252

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

DOE Green Energy (OSTI)

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

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

2005-01-28T23:59:59.000Z

253

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

Science Conference Proceedings (OSTI)

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

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

2011-11-08T23:59:59.000Z

254

Revealing molecular structure and dynamics through high-order harmonic generation driven by mid-IR fields  

SciTech Connect

High-order harmonic generation (HHG) from molecules produces spectra that are modulated by interferences that encode both the static structure and the electron dynamics initiated by interaction with the laser field. Using a midinfrared (mid-IR) laser at 1300 nm, we are able to study the region of the harmonic spectrum containing such interferences in CO{sub 2} over a wide range of intensities. This allows for isolation and characterization of interference minima arising due to subcycle electronic dynamics triggered by the laser field, which had previously been identified but not systematically separated. Our experimental and theoretical results demonstrate important steps toward combining attosecond temporal and angstrom-scale spatial resolution in molecular HHG imaging.

Torres, R.; Siegel, T.; Brugnera, L.; Ivanov, M. Yu.; Marangos, J. P. [Blackett Laboratory, Imperial College London, Prince Consort Road, London SW7 2BW (United Kingdom); Procino, I. [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Underwood, Jonathan G. [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX (United Kingdom); Altucci, C.; Velotta, R. [Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia and Dipartimento di Scienze Fisiche, Universita di Napoli 'Federico II', Naples (Italy); Springate, E.; Froud, C.; Turcu, I. C. E. [Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Chilton, Didcot, Oxon OX11 0QX (United Kingdom); Patchkovskii, S. [Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6 (Canada); Smirnova, O. [Max-Born-Institute, 2a Max-Born-Strasse, Berlin D-12489 (Germany)

2010-05-15T23:59:59.000Z

255

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

E-Print Network (OSTI)

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

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

2011-07-11T23:59:59.000Z

256

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

SciTech Connect

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

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

2008-09-28T23:59:59.000Z

257

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

DOE Green Energy (OSTI)

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

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

2010-12-09T23:59:59.000Z

258

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

E-Print Network (OSTI)

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

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

2007-01-12T23:59:59.000Z

259

Molecular dynamics of gases and vapors in nanoporous solids. Final LDRD project report  

DOE Green Energy (OSTI)

This report provides a study of gases in microporous solids using molecular modeling. The theory of gas transport in porous materials as well as the molecular modeling literature is briefly reviewed. Work complete is described and analyzed with retard to the prevailing theory. The work covers two simple subjects, construction of porous solid models and diffusion of He, H{sub 2}, Ar and CH{sub 4} down a pressure gradient across the material models as in typical membrane permeation experiments. The broader objective is to enhance our capability to efficiently and accurately develop, produce and apply microporous materials.

Pohl, P.I.

1996-08-01T23:59:59.000Z

260

Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule  

DOE Green Energy (OSTI)

Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.

Dardi, P.S.

1984-11-01T23:59:59.000Z

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


261

Real Time Dynamics of Laser Activated Interface Processes at the Molecular Scale  

SciTech Connect

Nanotechnology is one of the most interesting and challenging frontiers of science and technology. We are motivated by the belief that progress will come from improved understanding and control of structure, dynamics and reactivity at interfaces. First, we provide a summary of our projects and key findings. The following pages provide a more detailed account.

Eric Borguet

2007-12-30T23:59:59.000Z

262

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

Science Conference Proceedings (OSTI)

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

Paulo F. B. Goncalves; Hubert Stassen

2005-01-01T23:59:59.000Z

263

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

E-Print Network (OSTI)

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

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

2011-01-01T23:59:59.000Z

264

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

Science Conference Proceedings (OSTI)

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

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

2005-12-01T23:59:59.000Z

265

Molecular beams studies of the energetics and dynamics of elementary chemical reactions  

DOE Green Energy (OSTI)

Quantum mechanical effects on the angular distribution of HF products from the F + H/sub 2/ reaction were studied using crossed atomic and molecular beams with a rotatable mass spectrometer detector and time-of-flight velocity analysis. Measurement of the singlet-triplet splitting of CH/sub 2/ from the recoil velocities of fragments from ketene photodissociation in a molecular beam is also reported. Partial center-of-mass angular distributions, and velocity flux contour maps have been derived for individual vibrational states of the HF product from the F + H/sub 2/ reaction at collision energies of 2 and 3 kcal/mole. The center-of-mass distributions were obtained by analysis of laboratory angular and time-of-flight measurements of the reactive scattering. The results are consistent with recent three dimensional quantum mechanical scattering calculations, which predict that resonance effects should appear in the product angular distributions in this energy range. The photofragmentation of ketene in a molecular beam was used to measure the singlet-triplet splitting in CH/sub 2/. A rare gas halide excimer laser operating at 351 nm (XeF) and 308 nm (XeCl) dissociated the ketene. Time-of-flight measurements of the fragment velocities allowed determination of the energetics of the dissociation. The /sup 1/A/sub 1/ - /sup 3/B/sub 1/ splitting in CH/sub 2/ was found to be 8.5 +- 0.8 kcal/mole. This agrees with many experimental results, but not with the value of 19.5 kcal/mole derived from recent photodetachment experiments on CH/sub 2//sup -/.

Hayden, C.C.

1982-05-01T23:59:59.000Z

266

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

SciTech Connect

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

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

2009-11-15T23:59:59.000Z

267

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

E-Print Network (OSTI)

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

Chen, Liuxi

2012-08-01T23:59:59.000Z

268

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

E-Print Network (OSTI)

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

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

2005-12-23T23:59:59.000Z

269

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

E-Print Network (OSTI)

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

Herman, Agnieszka

2011-01-01T23:59:59.000Z

270

QAARM: Quasi-anharmonic auto-regressive model reveals molecular recognition pathways in ubiquitin  

SciTech Connect

Molecular dynamics (MD) simulations have dramatically improved the atomistic understanding of protein motions, energetics and function. These growing datasets have necessitated a corresponding emphasis on trajectory analysis methods for characterizing simulation data, particularly since functional protein motions and transitions are often rare and/or intricate events. Observing that such events give rise to long-tailed spatial distributions, we recently developed a higher-order statistics based dimensionality reduction method, called quasi-anharmonic analysis (QAA), for identifying biophysically-relevant reaction coordinates and substates within MD simulations. Further characterization of conformation space should consider the temporal dynamics specific to each identified substate. Our model uses hierarchical clustering to learn energetically coherent substates and dynamic modes of motion from a 0.5 {mu}s ubiqutin simulation. Autoregressive (AR) modeling within and between states enables a compact and generative description of the conformational landscape as it relates to functional transitions between binding poses. Lacking a predictive component, QAA is extended here within a general AR model appreciative of the trajectory's temporal dependencies and the specific, local dynamics accessible to a protein within identified energy wells. These metastable states and their transition rates are extracted within a QAA-derived subspace using hierarchical Markov clustering to provide parameter sets for the second-order AR model. We show the learned model can be extrapolated to synthesize trajectories of arbitrary length.

Ramanathan, Arvind [ORNL; Agarwal, Pratul K [ORNL

2011-01-01T23:59:59.000Z

271

Oral Histories: Oncologist Helen Vodopick, M.D.  

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

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

272

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

SciTech Connect

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

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

2009-10-20T23:59:59.000Z

273

Persistent dynamic entanglement from classical motion: How bio-molecular machines can generate non-trivial quantum states  

E-Print Network (OSTI)

Very recently [Phys. Rev. E 82, 021921 (2010)] a simple mechanism was presented by which a molecule subjected to forced oscillations, out of thermal equilibrium, can maintain quantum entanglement between two of its quantum degrees of freedom. Crucially, entanglement can be maintained even in the presence of very intense noise, so intense that no entanglement is possible when the forced oscillations cease. This mechanism may allow for the presence of non-trivial quantum entanglement in biological systems. Here we significantly enlarge the study of this model. In particular, we show that the persistent generation of dynamic entanglement is not restricted to the bosonic heat bath model, but it can also be observed in other decoherence models, e.g. the spin gas model, and in non-Markovian scenarios. We also show how conformational changes can be used by an elementary machine to generate entanglement even in unfavorable conditions. In biological systems, similar mechanisms could be exploited by more complex molecular machines or motors.

Gian Giacomo Guerreschi; Jianming Cai; Sandu Popescu; Hans J. Briegel

2011-11-09T23:59:59.000Z

274

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

Science Conference Proceedings (OSTI)

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

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

2012-08-21T23:59:59.000Z

275

Dynamic  

Office of Legacy Management (LM)

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

276

From Molecular Computing to Molecular Programming  

E-Print Network (OSTI)

From Molecular Computing to Molecular Programming Masami Hagiya Graduate School of Science of the Japanese Molecular Computer Project, and foresee the future of the #12;eld. In addition to describing the major achievements of the project, Suyama's Dynamic Programming Molecular Computer and Sakamoto

Hagiya, Masami

277

Soham Al Snih Al Snih, MD., PhD. Curriculum Vitae CURRICULUM VITAE  

E-Print Network (OSTI)

Soham Al Snih Al Snih, MD., PhD. Curriculum Vitae 1 CURRICULUM VITAE NAME: Soham Al Snih Al Snih, M at the Sealy Center on Aging, University of Texas Medical Branch, Galveston, TX. #12;Soham Al Snih Al Snih, MD arthritis. B. Grant Support Current Grant Support: 1R03 AG029959-01A2 (Al Snih ­PI) Period: 06

Wood, James B.

278

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

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

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

279

Molecular Dynamics Simulations II  

Science Conference Proceedings (OSTI)

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

280

Molecular Dynamics Simulations I  

Science Conference Proceedings (OSTI)

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

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281

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

SciTech Connect

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

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

2012-03-15T23:59:59.000Z

282

Images in Neuroscience Carol A. Tamminga, M.D., Editor  

E-Print Network (OSTI)

is delivered to the brain region of interest using a fiberoptic-based system or a light-emitting diode (LED-sensitive, molecular, neu- ronal activity "switches." These "switches" are microbial, light- sensitive ion conductance-regulat- ing activity of these "switches" can be controlled externally with light pulses. ChR2 is a cation

Deisseroth, Karl

283

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

Office of Science (SC) Website

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

284

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

Office of Science (SC) Website

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

285

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

Office of Science (SC) Website

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

286

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

Office of Science (SC) Website

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

287

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

Office of Science (SC) Website

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

288

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

Office of Science (SC) Website

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

289

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

Office of Science (SC) Website

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

290

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

Office of Science (SC) Website

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

291

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

Office of Science (SC) Website

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

292

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

Office of Science (SC) Website

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

293

Price of Cove Point, MD Natural Gas LNG Imports from Algeria...  

Gasoline and Diesel Fuel Update (EIA)

Algeria (Dollars per Thousand Cubic Feet) Price of Cove Point, MD Natural Gas LNG Imports from Algeria (Dollars per Thousand Cubic Feet) Decade Year-0 Year-1 Year-2 Year-3 Year-4...

294

Price of Cove Point, MD Natural Gas LNG Total Imports (Dollars...  

Gasoline and Diesel Fuel Update (EIA)

Total Imports (Dollars per Thousand Cubic Feet) Price of Cove Point, MD Natural Gas LNG Total Imports (Dollars per Thousand Cubic Feet) Decade Year-0 Year-1 Year-2 Year-3 Year-4...

295

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

U.S. Energy Information Administration (EIA) Indexed Site

Egypt (Nominal Dollars per Thousand Cubic Feet) Price of Cove Point, MD Natural Gas LNG Imports from Egypt (Nominal Dollars per Thousand Cubic Feet) Decade Year-0 Year-1 Year-2...

296

LDRD Final Report (08-ERD-037): Important Modes to Drive Protein MD Simulations to the Next Conformational Level  

SciTech Connect

Every action in biology is performed by dynamic proteins that convert between multiple states in order to engage their functions. Often binding to various ligands is essential for the rates of desired transitions to be enhanced. The goal of computational biology is to study these transitions and discover the different states to fully understand the protein's normal and diseased function, design drugs to target/bias specific states, and understand all of the interactions in between. We have developed a new methodology that is capable of calculating the absolute free energy of proteins while taking into account all the interactions with the solvent molecules. The efficiency of the new scheme is an order of magnitude greater than any existing technique. This method is now implemented in the massively parallel popular MD program package NAMD. This now makes it possible to calculate the relative stability of different conformational states of biological macromolecules as well as their binding free energies to various ligands.

Sadigh, B

2011-04-07T23:59:59.000Z

297

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

E-Print Network (OSTI)

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

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

2013-01-01T23:59:59.000Z

298

Tautomerism in liquid 1,2,3-triazole: a combined Energy-Dispersive X-Ray Diffraction, Molecular Dynamics and FTIR study  

E-Print Network (OSTI)

In this work, we report a multitechnique (energy-dispersive X-Ray diffraction, computational methods and FT-IR spectroscopy) study of the tautomeric equilibrium of 1,2,3-triazole, one of the few small nitrogen-containing eterocycles liquid at room temperature. The T-2H form (C2v symmetry) is found to be strongly favored in gas and solid phases, whereas the neat liquid gives diffraction patterns that can be interpreted satisfactorily with the structure functions calculated from some molecular dynamics results for both T-2H and T-1H tautomers, although the T-2H form gives a slightly better agreement.

Marco Bellagamba; Luigi Bencivenni; Lorenzo Gontrani; Leonardo Guidoni; Claudia Sadun

2013-01-18T23:59:59.000Z

299

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

E-Print Network (OSTI)

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

Leung, Kevin; 10.1039/B925853A

2010-01-01T23:59:59.000Z

300

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

E-Print Network (OSTI)

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

A. Marco Saitta; Michael L. Klein

1999-09-01T23:59:59.000Z

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


301

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

Science Conference Proceedings (OSTI)

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

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

2012-06-06T23:59:59.000Z

302

Homogeneous Non-Equilibrium Molecular Dynamics Methods for Calculating the Heat Transport Coefficient of Solids and Mixtures  

E-Print Network (OSTI)

of flexible molecules - Butane. Molecular Physics, 81(6):in polyatomic fluids: n-Butane as an illustration. Chemicalfor two models of liquid Butane. Chemical Physics, 198(1-2):

Mandadapu, Kranthi Kiran

2011-01-01T23:59:59.000Z

303

Partition-of-unity finite-element method for large scale quantum molecular dynamics on massively parallel computational platforms  

Science Conference Proceedings (OSTI)

Over the course of the past two decades, quantum mechanical calculations have emerged as a key component of modern materials research. However, the solution of the required quantum mechanical equations is a formidable task and this has severely limited the range of materials systems which can be investigated by such accurate, quantum mechanical means. The current state of the art for large-scale quantum simulations is the planewave (PW) method, as implemented in now ubiquitous VASP, ABINIT, and QBox codes, among many others. However, since the PW method uses a global Fourier basis, with strictly uniform resolution at all points in space, and in which every basis function overlaps every other at every point, it suffers from substantial inefficiencies in calculations involving atoms with localized states, such as first-row and transition-metal atoms, and requires substantial nonlocal communications in parallel implementations, placing critical limits on scalability. In recent years, real-space methods such as finite-differences (FD) and finite-elements (FE) have been developed to address these deficiencies by reformulating the required quantum mechanical equations in a strictly local representation. However, while addressing both resolution and parallel-communications problems, such local real-space approaches have been plagued by one key disadvantage relative to planewaves: excessive degrees of freedom (grid points, basis functions) needed to achieve the required accuracies. And so, despite critical limitations, the PW method remains the standard today. In this work, we show for the first time that this key remaining disadvantage of real-space methods can in fact be overcome: by building known atomic physics into the solution process using modern partition-of-unity (PU) techniques in finite element analysis. Indeed, our results show order-of-magnitude reductions in basis size relative to state-of-the-art planewave based methods. The method developed here is completely general, applicable to any crystal symmetry and to both metals and insulators alike. We have developed and implemented a full self-consistent Kohn-Sham method, including both total energies and forces for molecular dynamics, and developed a full MPI parallel implementation for large-scale calculations. We have applied the method to the gamut of physical systems, from simple insulating systems with light atoms to complex d- and f-electron systems, requiring large numbers of atomic-orbital enrichments. In every case, the new PU FE method attained the required accuracies with substantially fewer degrees of freedom, typically by an order of magnitude or more, than the current state-of-the-art PW method. Finally, our initial MPI implementation has shown excellent parallel scaling of the most time-critical parts of the code up to 1728 processors, with clear indications of what will be required to achieve comparable scaling for the rest. Having shown that the key remaining disadvantage of real-space methods can in fact be overcome, the work has attracted significant attention: with sixteen invited talks, both domestic and international, so far; two papers published and another in preparation; and three new university and/or national laboratory collaborations, securing external funding to pursue a number of related research directions. Having demonstrated the proof of principle, work now centers on the necessary extensions and optimizations required to bring the prototype method and code delivered here to production applications.

Pask, J E; Sukumar, N; Guney, M; Hu, W

2011-02-28T23:59:59.000Z

304

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

Science Conference Proceedings (OSTI)

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

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

1991-03-07T23:59:59.000Z

305

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

E-Print Network (OSTI)

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

Kalinichev, Andrey G.

306

BERAC Meeting September 5 2008 Gaithersburg MD | U.S. DOE Office of Science  

Office of Science (SC) Website

September 5 2008 Gaithersburg MD September 5 2008 Gaithersburg MD Biological and Environmental Research Advisory Committee (BERAC) BERAC Home Meetings BERAC Minutes BERAC Minutes Archive Members Charges/Reports Charter .pdf file (40KB) BER Committees of Visitors BER Home Meetings BERAC Meeting September 5 2008 Gaithersburg MD Print Text Size: A A A RSS Feeds FeedbackShare Page BER September 5, 2008 Arlington, VA Agenda Presentations Peg Riley .ppt file (357KB), Life and Medical Sciences Division Committee of Visitors Report Patricia Dehmer .ppt file (2.6MB), Report from the Office of Science Todd Anderson .ppt file (1.2MB), Scientific Focus Area (SFA) Rollout & Discussion Robert Dickinson .ppt file (6.1MB), Report on Climate Research Grand Challenges Mike Kuperberg .ppt file (975KB), Climate & Environmental Sciences

307

REVIEW ARTICLE Molecular Anions  

E-Print Network (OSTI)

REVIEW ARTICLE Molecular Anions Jack Simons Chemistry Department, Henry Eyring Center ReceiVed: February 28, 2008 The experimental and theoretical study of molecular anions has undergone on the experimental front. Theoretical developments on the electronic structure and molecular dynamics fronts now

Simons, Jack

308

DEVELOPMENTAL DYNAMICS 235:1738–1752, 2006 REVIEWS–A PEER REVIEWED FORUM Molecular Genetic Cascades for External Genitalia Formation: An Emerging  

E-Print Network (OSTI)

External genitalia are anatomical structures located at the posterior embryonic region as part of several urogenital/reproductive organs. The embryonic anlage of the external genitalia, the genital tubercle (GT) develops as a bud-shaped structure with an initial urethral plate and later urethra. Embryonic external genitalia are considered to be one of the appendages. Recent experiments suggest that essential regulatory genes possess similar functions for the outgrowth regulation of the GT and limb appendages. The transient embryonic epithelia located in the distal GT are called the distal urethral epithelium (DUE) regulating, at least in part, the (distal) GT development. This review covers the available data about early patterning of GT and discusses the molecular developmental similarities and points of divergence between the different appendages. Development of the male and female external genitalia is also reviewed. Developmental Dynamics

H. Kataoka; A. Kuroiwa; Y. Chen

2006-01-01T23:59:59.000Z

309

Mar. Drugs 2013, 11, 3350-3371; doi:10.3390/md11093350 marine drugs  

E-Print Network (OSTI)

Mar. Drugs 2013, 11, 3350-3371; doi:10.3390/md11093350 marine drugs ISSN 1660-3397 www% cytotoxicity was observed at the highest concentration tested (5 µg mL-1 ). However, OPEN ACCESS #12;Mar. Drugs Pinna had first been implicated in food poisoning in China in 1990 [1]. Pinnatoxin A (Pn

Recanati, Catherine

310

A coupled RISM/MD or MC simulation methodology for solvation free energies  

E-Print Network (OSTI)

A coupled RISM/MD or MC simulation methodology for solvation free energies Holly Freedman, Thanh N methods for determination of solvation free energies. We employ the RISM formulation of solvation free-netted chain equations. We apply this approach to determining free energies of solvation for several small

Truong, Thanh N.

311

MD Study of Phase Change of Water inside a Carbon Nanotube Tatsuto KIMURA and Shigeo MARUYAMA  

E-Print Network (OSTI)

into ice crystal at 220 K or 200 K. In the case of phase change at 220 K, octagonal ice nanotube MD Study of Phase Change of Water inside a Carbon Nanotube * Tatsuto KIMURA and Shigeo MARUYAMA Dept. of Mech. Eng., The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 Phase change

Maruyama, Shigeo

312

Ira Helfand, MD International Physicians for the Prevention of Nuclear War  

E-Print Network (OSTI)

of studies have shown that a limited, regional nuclear war between India and Pakistan would cause significantIra Helfand, MD International Physicians for the Prevention of Nuclear War Physicians for Social Responsibility NUCLEAR FAMINE: A BILLION PEOPLE AT RISK Global Impacts of Limited Nuclear War on Agriculture

Robock, Alan

313

14th international symposium on molecular beams  

SciTech Connect

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

Not Available

1992-09-01T23:59:59.000Z

314

14th international symposium on molecular beams  

Science Conference Proceedings (OSTI)

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

Not Available

1992-01-01T23:59:59.000Z

315

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

Science Conference Proceedings (OSTI)

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

Rasha A. Azzam; Tarek M. Madkour

2008-12-01T23:59:59.000Z

316

Molecular Simulation Study of Diverting Materials Used in Matrix Acidizing  

E-Print Network (OSTI)

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

Sultan, Abdullah S.

2009-08-01T23:59:59.000Z

317

THE DYNAMICS OF DENSE CORES IN THE PERSEUS MOLECULAR CLOUD. II. THE RELATIONSHIP BETWEEN DENSE CORES AND THE CLOUD  

Science Conference Proceedings (OSTI)

We utilize the extensive data sets available for the Perseus molecular cloud to analyze the relationship between the kinematics of small-scale dense cores and the larger structures in which they are embedded. The kinematic measures presented here can be used in conjunction with those discussed in our previous work as strong observational constraints that numerical simulations (or analytic models) of star formation should match. We find that dense cores have small motions with respect to the {sup 13}CO gas, about one third of the {sup 13}CO velocity dispersion along the same line of sight. Within each extinction region, the core-to-core velocity dispersion is about half of the total ({sup 13}CO) velocity dispersion seen in the region. Large-scale velocity gradients account for roughly half of the total velocity dispersion in each region, similar to what is predicted from large-scale turbulent modes following a power spectrum of P(k) {proportional_to} k {sup -4}.

Kirk, Helen; Johnstone, Doug [Department of Physics and Astronomy, University of Victoria, Victoria, BC, V8P 1A1 (Canada); Pineda, Jaime E.; Goodman, Alyssa, E-mail: hkirk@cfa.harvard.ed [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

2010-11-01T23:59:59.000Z

318

Ceramic Composites, Inc. 1110 Benfield Blvd, Ste Q, Millersville, MD 21108  

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

Composites, Inc. Composites, Inc. 1110 Benfield Blvd, Ste Q, Millersville, MD 21108 A subsidiary of Technology Assessment and Transfer, Inc. 410-987-3435 fax 410-987-7172 www.techassess.com AGENCY: DOE / NETL CONTRACT: DE-FG02-03ER83627 TITLE: Enhanced Performance Carbon Foam Heat Exchanger for Power Plant Cooling REPORT: Final Technical Report PERIOD: 21 July 2003 - 13 July 2007 TPOC: Barbara Carney carney@netl.doe.gov PHONE: 304-285-4671 PI: Steven Seghi steve@techassess.com PHONE: 410-987-3435 COMPANY: Ceramic Composites, Inc. 133 Defense Hwy, Ste 212 Annapolis, MD 21401 SBIR/STTR Rights Notice These SBIR/STTR data are furnished with SBIR/STTR rights under Grant No. DE-FG02- 03ER83627. For a period of 4 years after the acceptance of all items to be delivered under this

319

FINDING OF MD SIGNIFICANT IMPACT FORMERLY UTILIZED HED/AEC SITES REMEDIAL ACTION PROGRAM:  

Office of Legacy Management (LM)

FINDING OF MD SIGNIFICANT IMPACT FINDING OF MD SIGNIFICANT IMPACT FORMERLY UTILIZED HED/AEC SITES REMEDIAL ACTION PROGRAM: BAY0 CANYONS, NEW MEXICO Under the Formerly Utilized Sites Remedial Action Program (FUSRAP), the U.S. Department of Energy (DOE) has proposed to carry out rcmedfrl action at a site located in Bayo Canyon, Los Alamos County, New Mexico. Although the site as partially decontaminated and decommissioned in the 196Os, there remain above-background amounts of radionuclides. DOE has determined that strontium-90 in excess of DDE's proposed remedial- action criterir exists in subsurface materials underlying an area of about 0.6 ha (1.5 acres) at the Bayo Canyon site. The proposed action is to demarcate this are8 and restrict its use to activities that will not disturb this sub-

320

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

SciTech Connect

We report new molecular dynamics results elucidating the structure of the electrical double layer (EDL) on smectite surfaces contacting mixed NaCl-CaCl{sup 2} electrolyte solutions in the range of concentrations relevant to pore waters in geologic repositories for CO{sub 2} or high-level radioactive waste (0.34-1.83 mol{sub c} dm{sup -3}). Our results confirm the existence of three distinct ion adsorption planes (0-, {beta}-, and d-planes), often assumed in EDL models, but with two important qualifications: (1) the location of the {beta}- and d-planes are independent of ionic strength or ion type and (2) 'indifferent electrolyte' ions can occupy all three planes. Charge inversion occurred in the diffuse ion swarm because of the affinity of the clay surface for CaCl{sup +} ion pairs. Therefore, at concentrations 0.34 mol{sub c} dm{sup -3}, properties arising from long-range electrostatics at interfaces (electrophoresis, electro-osmosis, co-ion exclusion, colloidal aggregation) will not be correctly predicted by most EDL models. Co-ion exclusion, typically neglected by surface speciation models, balanced a large part of the clay mineral structural charge in the more concentrated solutions. Water molecules and ions diffused relatively rapidly even in the first statistical water monolayer, contradicting reports of rigid 'ice-like' structures for water on clay mineral surfaces.

Bourg, I.C.; Sposito, G.

2011-04-01T23:59:59.000Z

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


321

Level structure and production cross section of {sub {Xi}}{sup 12} Be studied with coupled-channels antisymmetrized molecular dynamics  

SciTech Connect

A theoretical framework of coupled-channels antisymmetrized molecular dynamics that describes the multistrangeness system with mixing between different baryon species is developed and applied to {sub {Lambda}}{sup 12}C and {sub {Xi}}{sup 12}Be. By introducing a minor modification to the YN G-matrix interaction derived from the Nijmegen model-D, the low-lying level structure and production cross section of {sub {Lambda}}{sup 12}C are reasonably described. It is found that the low-lying states of {sub {Xi}}{sup 12}Be are dominated by the {sup 11}B {circle_times} {Xi}{sup -} channel and their order strongly depends on {Xi}N effective interactions used in the calculation. The calculated peak position of the production cross section depends on the {Xi}N effective interaction and the magnitude of spin-flip and non-spin-flip cross sections of K{sup -}p{yields}K{sup +}{Xi}{sup -} elemental processes. We suggest that the {sup 12}C(K{sup -},K{sup +}){sub {Xi}}{sup 12}Be reaction possibly provides us information about the {Xi}N interaction.

Matsumiya, H.; Tsubakihara, K.; Kimura, M.; Dote, A.; Ohnishi, A. [Department of Cosmosciences, Graduate School of Science, Hokkaido University, Sapporo 001-0021 (Japan); Creative Research Institution (CRIS), Hokkaido University, Sapporo 060-0810 (Japan); Institute of Particle and Nuclear Studies, KEK, Tsukuba, Ibaraki 305-0801 (Japan); Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto 606-8502 (Japan)

2011-02-15T23:59:59.000Z

322

Medication Safety in Older Adults: Home-Based Practice Patterns Joshua P. Metlay, MD, PhD,wzz  

E-Print Network (OSTI)

Medication Safety in Older Adults: Home-Based Practice Patterns Joshua P. Metlay, MD, Ph-reported sources of in- formation on current medications as well as home-based practices for organizing medication

Hennessy, Sean

323

Mesoscale Molecular Dynamics with LAMMPS  

Science Conference Proceedings (OSTI)

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

324

Molecular-Frame Angular Distributions of Resonant Auger Electrons  

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

new insights in the dynamic world of molecular phenomena. The molecular frame is the natural reference frame for the study of molecules and their interaction with electromagnetic...

325

Turbulent molecular clouds  

E-Print Network (OSTI)

Stars form within molecular clouds but our understanding of this fundamental process remains hampered by the complexity of the physics that drives their evolution. We review our observational and theoretical knowledge of molecular clouds trying to confront the two approaches wherever possible. After a broad presentation of the cold interstellar medium and molecular clouds, we emphasize the dynamical processes with special focus to turbulence and its impact on cloud evolution. We then review our knowledge of the velocity, density and magnetic fields. We end by openings towards new chemistry models and the links between molecular cloud structure and star--formation rates.

Hennebelle, Patrick

2012-01-01T23:59:59.000Z

326

High Temperature Nanoindentation of Ni-Base Superalloys  

Science Conference Proceedings (OSTI)

molecular dynamics (MD) and dislocation dynamics models are often used to quantify the ...... Engineering: A, Volume 253, Number 1, 30. September 1998 , pp .

327

A Molecular Based Model for Polymer Viscoelasticity: Intra-and Inter-Molecular  

E-Print Network (OSTI)

A Molecular Based Model for Polymer Viscoelasticity: Intra- and Inter-Molecular Variability H viscoelasticity based on a stick-slip continuum molecular-based model. The model developed is a continuum tube-system is composed of long molecular chains. The dynamics of these molecular chains are developed by modeling them

328

MD-Predicted Phase diagrams for Pattern Formation due to Ion Irradiation  

E-Print Network (OSTI)

Energetic particle irradiation of solids can cause surface ultra-smoothening, self-organized nanoscale pattern formation, or degradation of the structural integrity of nuclear reactor components. Periodic patterns including high-aspect ratio quantum dots, with occasional long-range order and characteristic spacing as small as 7 nm, have stimulated interest in this method as a means of sub-lithographic nanofabrication. Despite intensive research there is little fundamental understanding of the mechanisms governing the selection of smooth or patterned surfaces, and precisely which physical effects cause observed transitions between different regimes has remained a matter of speculation. Here we report the first prediction of the mechanism governing the transition from corrugated surfaces to flatness, using only parameter-free molecular dynamics simulations of single-ion impact induced crater formation as input into a multi-scale analysis, and showing good agreement with experiment. Our results overturn the paradigm attributing these phenomena to the removal of target atoms via sputter erosion. Instead, the mechanism dominating both stability and instability is shown to be the impact-induced redistribution of target atoms that are not sputtered away, with erosive effects being essentially irrelevant. The predictions are relevant in the context of tungsten plasma-facing fusion reactor walls which, despite a sputter erosion rate that is essentially zero, develop, under some conditions, a mysterious nanoscale topography leading to surface degradation. Our results suggest that degradation processes originating in impact-induced target atom redistribution effects may be important, and hence that an extremely low sputter erosion rate is an insufficient design criterion for morphologically stable solid surfaces under energetic particle irradiation.

Scott A. Norris; Juha Samela; Laura Bukonte; Marie Backman; Djurabekova Flyura; Kai Nordlund; Charbel S. Madi; Michael P. Brenner; Michael J. Aziz

2010-12-23T23:59:59.000Z

329

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

DOE Green Energy (OSTI)

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

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

2006-11-30T23:59:59.000Z

330

Molecular Foundry  

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

Theory of Nanostructured Materials Theory of Nanostructured Materials The Theory of Nanostructured Materials Facility at the Molecular Foundry is focused on expanding our understanding of materials at the nanoscale. Our research connects the structural and dynamical properties of materials to their functions, such as electrical conductivity and storage, light-harvesting for electricity and fuel, or gas separation and sequestration. We develop and employ a broad range of tools, including advanced electronic-structure theory, excited-state methods, model Hamiltonians, and statistical mechanical models. This combination of approaches reveals how materials behave at the nanoscale, in pursuit of materials and devices that meet global energy and sustainability needs. Electronic structure of complex materials and interfaces for energy

331

ANL/ALCF/ESP-13/14 NAMD - The Engine for Large-Scale Classical MD  

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

4 4 NAMD - The Engine for Large-Scale Classical MD Simulations of Biomolecular Systems Based on a Polarizable Force Field ALCF-2 Early Science Program Technical Report Argonne Leadership Computing Facility About Argonne National Laboratory Argonne is a U.S. Department of Energy laboratory managed by UChicago Argonne, LLC under contract DE-AC02-06CH11357. The Laboratory's main facility is outside Chicago, at 9700 South Cass Avenue, Argonne, Illinois 60439. For information about Argonne and its pioneering science and technology programs, see www.anl.gov. Availability of This Report This report is available, at no cost, at http://www.osti.gov/bridge. It is also available on paper to the U.S. Department of Energy and its contractors, for a processing fee, from:

332

DOE Challenge Home Case Study, Nexus EnergyHomes, Frederick, MD, Production  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Nexus Nexus EnergyHomes Frederick, MD BUILDING TECHNOLOGIES OFFICE DOE Challenge Home builders are in the top 1% of builders in the country meeting the extraordinary levels of excellence and quality specifi ed by the U.S. Department of Energy. Every DOE Challenge Home starts with ENERGY STAR for Homes Version 3 for an energy-effi cient home built on a solid foundation of building science research. Then, even more advanced technologies are designed in for a home that goes above and beyond current code to give you the superior quality construction, HVAC, appliances, indoor air quality, safety, durability, comfort, and solar-ready components along with ultra-low or no utility bills. This provides homeowners with a quality home that will last for generations to come.

333

DEPARTMENT OF HEALTH AN~~.N~dtAN, MD. Y.P.H.  

Office of Legacy Management (LM)

,' ,...- ,' ,...- -., -.- . . we#lnty..: - DEPARTMENT OF HEALTH AN~~.N~dtAN, MD. Y.P.H. April 30, 1979 . _-- _' . U.S.E.P.A. Radiation Branch 26 Federal Plaz;a, Boom 9079 New York, N. Y. 10007 Attention: Miss Feldman:, Gentlemen: In accordance with your request to Calvin E. Weber, P.E., Assistant Commissioner of Health for Environmental Quality, I am forwarding a copy of a report prepared by him concerning a radiation survey conducted in the vicinity of the former Canadian Radium and Uranium Corpora+on plant on Railroad Avenue in the Village of Mount Kisco, Westchester County, New Yor Please transmit any comments you may have regarding this matter directly to Mr. Weber. Very truly Yours, Conmissioner of Health xc:rr cc: Sherwood Davies, P.E. lbm Cashman

334

Recipient: County of Howard, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA COMPLIANCE FORM  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

2 2 Recipient: County of Howard, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA COMPLIANCE FORM Activities Determination/ Categorical Exclusion Reviewer's Specific Instructions and Rationale (Restrictions and Allowable Activity) Electric Pick-up truck for on- site use at Alpha Ridge Landfill B5.1 None Landfill Forced Draft Heater A9 This CX applies to preliminary engineering and design tasks only. Additional information is required to make a NEPA determination for construction and operation tasks. Diesel Hybrid Truck B5.1 None Home Energy Audits A9 None Park Ballfield Lights Energy Efficiency B5.1 Waste Stream Clause Energy Efficiency Analysis via Monitoring of Sub-Meters Installation B5.1 None Energy Management Consultant A9 None High Efficiency Lighting - Rec & Parks B5.1

335

Recipient. County of Baltimore, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

0 0 Recipient. County of Baltimore, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA COMPLIANCE FORM Activities Determination/ Categorical Exclusion Reviewer's Specific Instructions and Rationale (Restrictions and Allowable Activity) Renovation for the Green Resource Center B5.1 All administrative activities, audits, outreach, and technical advice should be CX'd. All EE activities are subject to the Waste Stream Clause, Historic Preservation clause, and Engineering clause. Energy Audits for Business & Government Structures A9, All, B5.1 None Revolving Loan Fund A9, All, B5.1 All administrative activities, audits, outreach, and technical advice should be CX'd. All EE activities are subject to the Waste Stream Clause, Historic Preservation clause, and Engineering clause.

336

Oral Histories: Dr. John W. Gofman, M.D., Ph.D.  

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

7 7 HUMAN RADIATION STUDIES: REMEMBERING THE EARLY YEARS Oral History of Dr. John W. Gofman, M.D., Ph.D. Conducted December 20, 1994 United States Department of Energy Office of Human Radiation Experiments June 1995 CONTENTS Foreword Short Biography Oberlin College, Enrollment in Western Reserve Medical School To University of California, Berkeley to Study Physical Chemistry Assisting Seaborg's Research, Discovery of Uranium-233 The Manhattan Project From Research to Laboratory Production of Plutonium Joe Hamilton's Cavalier Approach to Radiation Medical Treatments With Radioactive Phosphorus (32P) Conflict Between University of California San Francisco and Berkeley Reflections on Ernest Lawrence Heart Disease Studies AEC Support for Heart Disease Studies Heparin and Lipoprotein Research With Human Subjects

337

Oral Histories: Oral History of Radiologist Henry I. Kohn, M.D., Ph.D.  

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

1 1 HUMAN RADIATION STUDIES: REMEMBERING THE EARLY YEARS Oral History of Radiologist Henry I. Kohn, M.D., Ph.D. Conducted September 13, 1994 United States Department of Energy Office of Human Radiation Experiments June 1995 CONTENTS Foreword Short Biography Studying the Effects of X Rays on Animal Blood Chemistry at Oak Ridge Work at UCSF's Radiological Laboratory Advantages of Yeast Cells for Studying Radiation Effects Reflections on Bert Low-Beer and Joseph Hamilton Radiation Genetics Experiments on Mice Reflections on Reynold Brown and Henry Kaplan Establishment of Harvard's Joint Center for Radiation Therapy (Mid '60s) Radiological Assessment for the National Academy of Science Survey of Nuclear and Alternative Energy (1975–79) Biologist and Physicist Perspectives on Radiological Effects

338

Felix F? Camacho Governor Michael W. Cruz, M.D. Lieutenant Governor  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

O. Box 2950 Haghiia, Guam 96932 O. Box 2950 Haghiia, Guam 96932 TEL: (671) 472-8931 FAX: (671) 477-4826 EMAIL: governo@mail.gov.gu Felix F? Camacho Governor Michael W. Cruz, M.D. Lieutenant Governor 0 6 MAW 2009 The Honorable Steven Chu Secretary U.S. Department of Energy 1000 Independence Avenue, S. W. Washington, D.C. 20585 Re: State Energy Program Assurances Dear Secretary Chu: As a condition of receiving Guam's share of the $3.1 billion funding for the State Energy Program (SEP) under the American Recovery and Renewal Act of 2009 (H.R. l)(ARRA), I am providing the following assurances. I have written to the Consolidated Commission on Utilities, Guam's public utility commission, and requested that they consider additional actions to promote energy efficiency, consistent with the Federal

339

Molecular Nanosprings for Protein-Based Nanorobotics  

E-Print Network (OSTI)

Molecular Nanosprings for Protein-Based Nanorobotics Mustapha Hamdi 1 , Antoine Ferreira 1 antoine.ferreira@ensi-bourges.fr , mavro@coe.neu.edu This paper presents a molecular mechanics study using a molecular dynamics software (NAMD2) for characterization of molecular elastic joints for bio nanorobotic

Mavroidis, Constantinos

340

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

E-Print Network (OSTI)

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

Buehler, Markus J.

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


341

DL_POLY Molecular Simulation Package  

Science Conference Proceedings (OSTI)

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

342

California Health eQuality Advisory Committee Kenneth W. Kizer, M.D., M.P.H. -Chair  

E-Print Network (OSTI)

California Health eQuality Advisory Committee Kenneth W. Kizer, M.D., M.P.H. - Chair Distinguished Association (IHA) Ellen Wu, M.P.H. Executive Director California Pan-Ethnic Health Network Pamela L. Lane, M.S., RHIA, CPHIMS, Ex officio Deputy Secretary, HIE California Health & Human Services Agency Linette T

California at Davis, University of

343

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

E-Print Network (OSTI)

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

Zhang, Luzheng

344

Assessment of Molecular Modeling & Simulation  

Science Conference Proceedings (OSTI)

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

None

2002-01-03T23:59:59.000Z

345

Oral Histories: Physician James S. Robertson, M.D., Ph.D.  

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

8 8 HUMAN RADIATION STUDIES: REMEMBERING THE EARLY YEARS Oral History of Physician James S. Robertson, M.D., Ph.D. Conducted January 20, 1995 United States Department of Energy Office of Human Radiation Experiments September 1995 CONTENTS Foreword Short Biography Education Research on Human Subjects at Berkeley Invited to Join the New Lab at Brookhaven (1950) Boron Neutron Capture Therapy Other AEC Biomedical Programs Brookhaven Human Use Committee Castle Bravo Atomic Weapon Test (March 1, 1954) Studies on Marshallese at Brookhaven Modern BNCT Treatment Leaves Brookhaven for the Mayo Clinic (1975) Joins the Department of Energy (1983) Work at the Naval Radiological Defense Laboratory (1953–55) Controversial Treatments and the "Crackpot File" FOREWORD I n December 1993, U.S. Secretary of Energy Hazel R. O'Leary announced her Openness Initiative. As part of this initiative, the Department of Energy undertook an effort to identify and catalog historical documents on radiation experiments that had used human subjects. The Office of Human Radiation Experiments coordinated the Department's search for records about these experiments. An enormous volume of historical records has been located. Many of these records were disorganized; often poorly cataloged, if at all; and scattered across the country in holding areas, archives, and records centers.

346

Transport coefficients of n-butane into and through the surface of silicalite-1 from non-equilibrium molecular dynamics study  

E-Print Network (OSTI)

Transport coefficients of n-butane into and through the surface of silicalite-1 from non dynamics Non-equilibrium thermodynamics Silicalite-1 n-Butane adsorption a b s t r a c t We have studied coupled heat and mass transfer of n-butane through a membrane of silicalite-1. A description

Kjelstrup, Signe

347

Kinetic energy deficit in the symmetric fission of /sup 259/Md. [Light particle emission in /sup 256/Fm fission  

Science Conference Proceedings (OSTI)

The fragment energies of about 725 coincidence events have now been observed in the spontaneous fission (SF) decay of 105-min /sup 259/Md since its discovery in 1977. The fission of /sup 259/Md is characterized by a symmetric mass distribution, similar to those of /sup 258/Fm and /sup 259/Fm, but with a broad total kinetic energy (anti TKE) distribution which peaks at about 195 MeV, in contrast to those of /sup 258/Fm and /sup 259/Fm, for which the anti TKE is about 240 MeV. This kinetic energy deficit, approx. 40 MeV, has been postulated to be due to the emission of hydrogen-like particles by /sup 259/Md at the scission point in a large fraction of the fissions, leaving the residual fissioning nucleus with 100 protons. The residual nucleus would then be able to divide into two ultrastable tin-like fission fragments, but with less kinetic energy than that observed in the SF of /sup 258/Fm and /sup 259/Fm, because of binding-energy losses and a reduction in the Coulomb repulsion of the major fragments. To test this hypothesis, counter-telescope experiments aimed at detecting and identifying these light particles were performed. In 439 SF events 3 + 3 protons of the appropriate energy were observed, too few to account for the kinetic energy deficit in the fission of /sup 259/Md. There seems to be no explanation for this problem within the framework of current fission theory. These results are discussed along with preliminary measurements of light-particle emission in the SF of /sup 256/Fm. 5 figures.

Hulet, E.K.; Wild, J.F.; Lougheed, R.W.; Baisden, P.A.; Dougan, R.J.; Mustafa, M.G.

1980-10-01T23:59:59.000Z

348

Magnetismo Molecular (Molecular Magentism)  

SciTech Connect

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

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

2010-07-01T23:59:59.000Z

349

Molecular Foundry  

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

The People of the Molecular Foundry In addition to state-of-the-art instrumentation, Users at the Molecular Foundry benefit from the unique in-house expertise of its researchers....

350

Evaluation of Generic EBS Design Concepts and Process Models...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

temperatures and pressures; 4) thermodynamic modeling and database development; 5) Molecular Dynamics (MD) study of clay hydration at ambient and elevated temperatures; and 6)...

351

Molecular Foundry  

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

The Molecular Foundry The Molecular Foundry Lawrence Berkeley National Laboratory One Cyclotron Road Building 67 Berkeley, CA 94720 Screen reader users: click here for plain HTML Go to Google Maps Home Molecular Foundry, Berkeley, CA Loading... Map Sat Ter Did you mean a different: Did you mean a different: Did you mean a different: Add Destination - Show options Hide options Get Directions Note: Public transit coverage may not be available in this area. Molecular Foundry, Berkeley, CA A Molecular Foundry 67 Cyclotron Rd, Berkeley, CA ‎ foundry.lbl.gov 3 reviews · "Berkeley Lab. About the Foundry. What is the Molecular Foundry? Research Themes; Foundry Careers; Media Gallery; Other User Facilities external link; Contact Us" - lbl.gov Directions Search nearby more See all 14 results for Molecular Foundry, Berkeley, CA

352

Photoconduction efficiencies and dynamics in GaN nanowires grown by chemical vapor deposition and molecular beam epitaxy: A comparison study  

Science Conference Proceedings (OSTI)

The normalized gains, which determines the intrinsic photoconduction (PC) efficiencies, have been defined and compared for the gallium nitride (GaN) nanowires (NWs) grown by chemical vapor deposition (CVD) and molecular beam epitaxy (MBE). By excluding the contributions of experimental parameters and under the same light intensity, the CVD-grown GaN NWs exhibit the normalized gain which is near two orders of magnitude higher than that of the MBE-ones. The temperature-dependent time-resolved photocurrent measurement further indicates that the higher photoconduction efficiency in the CVD-GaN NWs is originated from the longer carrier lifetime induced by the higher barrier height ({phi}{sub B} = 160 {+-} 30 mV) of surface band bending. In addition, the experimentally estimated barrier height at 20 {+-} 2 mV for the MBE-GaN NWs, which is much lower than the theoretical value, is inferred to be resulted from the lower density of charged surface states on the non-polar side walls.

Chen, R. S. [Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Tsai, H. Y. [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Huang, Y. S. [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Department of Electronic Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan (China); Chen, Y. T. [Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan (China); Chen, L. C. [Center for Condensed Matter Sciences, National Taiwan University, Taipei 10617, Taiwan (China); Chen, K. H. [Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan (China); Center for Condensed Matter Sciences, National Taiwan University, Taipei 10617, Taiwan (China)

2012-09-10T23:59:59.000Z

353

Structure and Dynamics of Forsterite-scCO2/H2O Interfaces as a Function of Water Content  

Science Conference Proceedings (OSTI)

Molecular dynamics (MD) simulations of forsterite surfaces in contact with supercritical carbon dioxide (scCO2) fluids of varying water content were performed to determine the partition of water between the scCO2 fluid and the mineral surface, the nature of CO2 and H2O bonding at the interface, and the regions of the interface that may be conducive to HxCO3(2-x)- formation. Calculations of the free energy of the associative adsorption of water onto the (010) forsterite surface from the scCO2 phase indicated that the formation of a water film up to three-monolayer thick can be exothermic even for water contents below the water saturation concentration of the scCO2 fluid. In MD simulations of scCO2/H2O mixtures in contact with the (010) forsterite surface, H2O was found to readily displace CO2 at the surface and, therefore, CO2 directly contacted the surface only for water coverages below two monolayers. For thicker water films, a two-monolayer hydration layer formed that CO2 could not penetrate. Simulations of the hydroxylated (010) surface and of the (011) surface suggested that this conclusion can be extended to forsterite surfaces with different surface structures and/or compositions. The density, diffusion, and degree of hydration of CO2 as well as the extent of CO2/H2O mixing at the interface were all predicted to depend strongly on the thickness of the water-rich film, i.e., on the water content of the scCO2 fluid.

Kerisit, Sebastien N.; Weare, John H.; Felmy, Andrew R.

2012-05-01T23:59:59.000Z

354

Molecular Foundry  

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

SEMINARS ARCHIVE The Molecular Foundry regularly offers seminars and events that feature compelling research and information for those who investigate at the nanoscale. Seminars...

355

Molecular Foundry  

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

EVENTS ARCHIVE The Molecular Foundry regularly offers seminars and events that feature compelling research and information for those who investigate at the nanoscale. Seminars...

356

Molecular Foundry  

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

efficient energy storage and conversion. Electron donors and acceptors at interfaces Molecular level design and synthesis has created tailor-made electron donors and acceptors...

357

Molecular Foundry  

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

Careers Information about current openings at the Molecular Foundry and complete application information is available from LBNL Human Resources. Please follow the application...

358

Molecular Foundry  

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

the Future, Atom by Atom Organized into six interdependent research Facilities, The Molecular Foundry, along with Berkeley Lab's additional User programs and affiliated research...

359

Molecular Foundry  

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

Sign-Up (Resource Database) Weekly Seminars Users' Executive Committee (UEC) The Molecular Foundry Users' Association is composed of all Foundry Users. Upon beginning work on...

360

Molecular Foundry  

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

Management Code of Conduct Conflict Resolution Beginning your project Access to the Molecular Foundry is free of charge for approved, non-proprietary research. (Proprietary...

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


361

Molecular Foundry  

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

SEMINARS The Molecular Foundry regularly offers seminars and events that feature compelling research and information for those who investigate at the nanoscale. Seminars occur on...

362

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

Office of Science (SC) Website

(CPIMS) research emphasizes molecular understanding of chemical, physical, and electron-driven processes in aqueous media and at interfaces. Studies of reaction dynamics at...

363

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

Science Conference Proceedings (OSTI)

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

364

Molecular Science and Technology (MST) Program The Taiwan International Graduate Program (TIGP), Academia Sinica  

E-Print Network (OSTI)

Molecular Science and Technology (MST) Program The Taiwan International Graduate Program (TIGP), Academia Sinica Research Topics The following research fields constitute the spectrum of the Molecular Science and Technology (MST) graduate program: (1)Chemical dynamics and molecular spectroscopy: This topic

365

Molecular nanocomposites.  

Science Conference Proceedings (OSTI)

The goals of this project are to understand the fundamental principles that govern the formation and function of novel nanoscale and nanocomposite materials. Specific scientific issues being addressed include: design and synthesis of complex molecular precursors with controlled architectures, controlled synthesis of nanoclusters and nanoparticles, development of robust two or three-dimensionally ordered nanocomposite materials with integrated functionalities that can respond to internal or external stimuli through specific molecular interactions or phase transitions, fundamental understanding of molecular self-assembly mechanisms on multiple length scales, and fundamental understanding of transport, electronic, optical, magnetic, catalytic and photocatalytic properties derived from the nanoscale phenomena and unique surface and interfacial chemistry for DOE's energy mission.

Voigt, James A.

2010-03-01T23:59:59.000Z

366

Molecular Foundry  

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

is equipped with a variety of tools to aid in work with biomolecules, microbes, molecular biology techniques and cell culture. These tools include: a BioFlo fermentor (14 L),...

367

Molecular fountain.  

SciTech Connect

A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

Strecker, Kevin E.; Chandler, David W.

2009-09-01T23:59:59.000Z

368

Application of optimal prediction to molecular dynamics  

E-Print Network (OSTI)

Heat Capacity calculated viaHeat Capacity calculated via the Galerkinfriction . . . . . . . . . . . . . . . . . Heat Capacity

Barber IV, John Letherman

2004-01-01T23:59:59.000Z

369

Nonequilibrium Molecular Dynamics Simulations of the Rheology...  

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

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

370

Iterative Energy Minimization for Quantum Molecular Dynamics  

E-Print Network (OSTI)

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

Southern California, University of

371

A Molecular Dynamics Investigation of Graphene  

Science Conference Proceedings (OSTI)

About this Abstract. Meeting, Materials Science & Technology 2013. Symposium, Materials Tribology: Fundamentals, Applications and Solutions. Presentation ...

372

Reactive Molecular Dynamics Simulations of Switching in ...  

Science Conference Proceedings (OSTI)

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

373

Molecular Science Research Center 1992 annual report  

Science Conference Proceedings (OSTI)

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

Knotek, M.L.

1994-01-01T23:59:59.000Z

374

I The sat (Sl md.re#t IR) inpuFs OyaCIjdo  

E-Print Network (OSTI)

aH a * input cQhrd8&mr: bc;ch ktpm tyva the paeMitv in&rtor to vvhen"b ' is low, the activehDgh outpu? is forced high; when "R " is low, the active-high output is forced low. Although normally the aotive-low output is drs complement of DUAL DTYPE RIP-FLOP e J-K master/slave The duat D-type flip-flop shown in Figura I of two imht D-tr.pe flip-flops with inputs on the left and flipflops: W mn&h w?U sxta mfy for as long as both "8 ' and "R " wo brcl low. The flip-flop will return to some indeterminate state when both " S and "R " go high. FIGURE 2. Four-Bit Bistable Latch input. tion is derived as follows:- The "DC " input has an AND relationship with the "C " input w shown by the subswipted "C". Therefore, Data passas through "Dc" only when "6 ' is active trua- Input "C " is sensitive to transition, or sensitive as shown by:he ed % (dynamic indicator) symbol.- Absence of the polarity indicator on input "C " means that the MORE E level is true. Therefore, ive true on a low-to-hi& tramis# * and when "C " is active true as stated &over data is passed through and active low outputs are by the abseme/presence of tarritvindicator {-P 1. FOUR-BIT BISTABLE LATCH The fourbit bistable latch shown in Figure 2 consists of four independent D-type flip-flops. FFI and FF2 are controlled by the 61 dock input, and FF3 and FF4 are controlled by the C2 clock input. This is evident by the subscripted C1 and C2 on the input data lines. Information present at a data (Dc) input is transferred to the active-high and active-low outputs when the associated clock input is high: the outputs will follow the data as long as the clock remains high. When the clock goes low, the information that was present at the data input when t4e transition occurred is retained at the outputs until the dock returns high. WWW.HPARCHIVE.COM-flops. Inputs to the master section on the left side are controlled by the gate (G) pulse. The gate pulse also controls the state of the coupling transistors (not shown) wh connect the mmw aprd dm

unknown authors

1976-01-01T23:59:59.000Z

375

83.10.Mj – Molecular dynamics, Brownian dynamics  

E-Print Network (OSTI)

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

Y. Visell (a

2011-01-01T23:59:59.000Z

376

Molecular Foundry  

NLE Websites -- All DOE Office Websites

Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE Berkeley Lab Berkeley Lab A-Z Index Phone Book Jobs Search DOE About the Foundry What is the Molecular Foundry? Research Themes Foundry Careers Media Gallery Other User Facilities external link Contact Us Go News & Highlights Users People Facilities Imaging and Manipulation Nanofabrication Theory Inorganic Biological Organic NCEM external link Seminars & Events Publications The Molecular Foundry is a Department of Energy-funded nanoscience research facility that provides users from around the world with access to cutting-edge expertise and instrumentation in a collaborative, multidisciplinary environment. Call for Proposals: The next deadline for standard proposals is Through March 31, 2014 Find out more information about becoming a Molecular Foundry facilities User. 2013 Annual User Meeting Postponed - Date TBD

377

Molecular motors interacting with their own tracks Max N. Artyomov  

E-Print Network (OSTI)

Molecular motors interacting with their own tracks Max N. Artyomov Department of Chemistry; published 17 April 2008 Dynamics of molecular motors that move along linear lattices and interact with them exactly solvable discrete-state "burnt- bridge" models. Molecular motors are viewed as diffusing particles

378

Molecular correlations in a supercooled liquid L. Fabbian,1  

E-Print Network (OSTI)

Molecular correlations in a supercooled liquid L. Fabbian,1 A. Latz,2 R. Schilling,2 F. Sciortino,1 1998; revised manuscript received 22 March 2000 We present static and dynamic properties of molecular effort in the direction of solving the molecular mode-coupling theory MMCT equations for supercooled

Sciortino, Francesco

379

GPU-accelerated molecular visualization on petascale supercomputing platforms  

Science Conference Proceedings (OSTI)

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

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

2013-11-01T23:59:59.000Z

380

Dynamic nuclear polarization for NMR : applications and hardware development  

E-Print Network (OSTI)

solid State NMR (SSNMR) can determine molecular as well as supermolecular structure and dynamics. The low signal intensities make many of these experiments prohibitively long. Dynamic Nuclear Polarization provides a method ...

Casey, Andrew (Andrew Byron)

2008-01-01T23:59:59.000Z

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


381

Ultrafast Core-Hole Induced Dynamics in Water  

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

molecular level, you will find a surprisingly turbulent, dynamic universe. The water molecules constantly form and break bonds under the influence of several weak interactions,...

382

Molecular Foundry  

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

See the Foundry's full equipment list See the Foundry's full equipment list Organic and Macromolecular Synthesis Capabilities & Tools Major Instruments and Capabilities AB SCIEX TF4800 MALDI TOF-TOF Mass Spectrometer This instrument is the tandem time-of-flight mass spectrometer systems, providing the excellent level of molecular mass coverage in the range of molecular masses 500 and 150,000 Da, high throughput, and confidence in both qualitative and quantitative analyses. The analyzer combines all of the advantages of MALDI in a flexible, easy-to-use, ultra-high-performance mass spectrometer with all the advanced capabilities of software. On-axis laser provides high sensitivity to identify and quantitate low-abundance compounds in complex samples. High-resolution precursor ion selection lets

383

Early maturation processes in coal. Part 2: Reactive dynamics simulations using the ReaxFF reactive force field on Morwell Brown coal structures  

E-Print Network (OSTI)

Early maturation processes in coal. Part 2: Reactive dynamics simulations using the ReaxFF reactive force field on Morwell Brown coal structures Elodie Salmon a , Adri C.T. van Duin b , François Lorant Brown coal using the ReaxFF reactive force field. We find that these reactive MD simulations

Goddard III, William A.

384

NEWTON's Molecular Biology Videos  

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

Molecular Biology Videos Do you have a great molecular biology video? Please click our Ideas page. Featured Videos: University of Berkeley - Molecular Biology Lectures University...

385

Better HMC integrators for dynamical simulations  

SciTech Connect

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

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

2010-06-01T23:59:59.000Z

386

Molecular Phylogeny Reconstruction  

E-Print Network (OSTI)

Molecular Phylogeny Reconstruction Sudhir Kumar, Arizona State University, Tempe, Arizona, USA Alan Filipski, Arizona State University, Tempe, Arizona, USA Molecular phylogenetics deals with the inference molecular data. By modelling patterns of molecular change in protein and deoxyribonucleic acid (DNA

Kumar, Sudhir

387

Near quantitative agreement of model free DFT- MD predictions with XAFS observations of the hydration structure of highly charged transition metal ions  

Science Conference Proceedings (OSTI)

DFT-MD simulations (PBE96 and PBE0) with MD-XAFS scattering calculations (FEFF9) show near quantitative agreement with new and existing XAFS measurements for a comprehensive series of transition metal ions which interact with their hydration shells via complex mechanisms (high spin, covalency, charge transfer, etc.). This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the U.S. DOE by Battelle. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the U.S. DOE's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Fulton, John L.; Bylaska, Eric J.; Bogatko, Stuart A.; Balasubramanian, Mahalingam; Cauet, Emilie L.; Schenter, Gregory K.; Weare, John H.

2012-09-20T23:59:59.000Z

388

Surface Chemical Dynamics  

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

Surface Chemical Dynamics Surface Chemical Dynamics The goal of the Surface Chemical Dynamics Program is to elucidate the underlying physical processes that determine the products (selectivity) and yield (efficiency) of chemical transformations relevant to energy-related chemistry on catalytic and nanostructured surfaces. Achieving this end requires understanding the evolution of the reactant-molecule/surface complex as molecules adsorb, bonds dissociate, surface species diffuse, new bonds form and products desorb. The pathways and time scales of these processes are ultimately determined by a multidimensional potential energy surface that is a function of the geometric and electronic structures of the surface and the reactant, product, intermediate and transition-state molecular and atomic species.

389

Atomic, Molecular & Optical Sciences  

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

Atomic, Molecular and Optical Sciences Atomic, Molecular and Optical Sciences The goal of the program is to understand the structure and dynamics of atoms and molecules using photons and ions as probes. The current program is focussed on studying inner-shell photo-ionization and photo-excitation of atoms and molecules, molecular orientation effects in slow collisions, slowing and cooling molecules, and X-ray photo-excitation of laser-dressed atoms. The experimental and theoretical efforts are designed to break new ground and to provide basic knowledge that is central to the programmatic goals of the Department of Energy (DOE). Unique LBNL facilities such as the Advanced Light Source (ALS), the ECR ion sources at the 88-inch cyclotron, and the National Energy Research Scientific Computing Center (NERSC) are

390

Electron Trapping by Molecular Vibration  

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

Electron Trapping by Molecular Vibration Print Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping, giving rise to a broad feature in the photoelectron spectrum known as a shape resonance. This process represents a novel type of symmetry-breaking phenomenon that has not been observed previously but appears to be widespread. Such coupling between electronic motion and nuclear motion becomes increasingly important as scientists learn more about the geometry and dynamics of novel chemical structures such as those found in nanodevices and transient chemical species, and the results have implications for studies that use photoelectron spectroscopy as a diagnostic tool.

391

Electron Trapping by Molecular Vibration  

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

Electron Trapping by Molecular Vibration Print Electron Trapping by Molecular Vibration Print In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping, giving rise to a broad feature in the photoelectron spectrum known as a shape resonance. This process represents a novel type of symmetry-breaking phenomenon that has not been observed previously but appears to be widespread. Such coupling between electronic motion and nuclear motion becomes increasingly important as scientists learn more about the geometry and dynamics of novel chemical structures such as those found in nanodevices and transient chemical species, and the results have implications for studies that use photoelectron spectroscopy as a diagnostic tool.

392

Molecular Foundry  

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

See the Foundry's full equipment list See the Foundry's full equipment list Nanofabrication Capabilities & Tools Major Capabilities: Instruments and Labs Zeiss Crossbeam 1540 EsB The Molecular Foundry Zeiss Cross-beam is one of the most versatile lithographic and inspection tools allowing fabrication of complex prototypes for nanoelectronics, nano-optical antenna, modifying scanning probe tips, rapid electrical contacting and many other applications. The 1500XB Cross Beam combines the Gemini field emission column (FESEM) with the Orsay Physics focused ion beam (FIB). In addition, the instrument offers a multi-channel gas injection system to allow ion and electron beam induced deposition (IBID and EBID) and chemically assisted ion beam etching (CAIBE). The tool can be used for lithographic patterning of materials or

393

Applying Computational Science to Education: The Molecular Workbench Paradigm  

Science Conference Proceedings (OSTI)

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

Robert F. Tinker; Qian Xie

2008-01-01T23:59:59.000Z

394

Molecular Biology DEGREE PROGRAMME  

E-Print Network (OSTI)

BSc (Hons) Molecular Biology DEGREE PROGRAMME GUIDE 2013-2014 #12;BSc (Hons) Molecular Biology - Year 2 - Year 3 - Year 4 Introduction Molecular biology aims to understand living systems by focusing on the molecular components upon which they are built. Molecular biology is one of great successes of 20th century

Siddharthan, Advaith

395

Bad seeds sprout perilous dynamics: stochastic thermostat induced trajectory synchronization in biomolecules  

SciTech Connect

Molecular dynamics simulations starting from different initial conditions are commonly used to mimic the behavior of an experimental ensemble. We show in this article that when a Langevin thermostat is used to maintain constant temperature during such simulations, extreme care must be taken when choosing the random number seeds used in order to prevent statistical correlation among the MD trajectories. While recent studies have shown that stochastically thermostatted trajectories evolving within a single potential basin with identical random number seeds tend to synchronize, we show that there is a synchronization effect even for complex, biologically relevant systems. We demonstrate this effect in simulations of Alanine trimer and pentamer and in a simulation of a temperature-jump experiment for peptide folding of a 14-residue peptide. Even in replica-exchange simulations, in which the trajectories are at different temperatures, we find partial synchronization occurring when the same random number seed is employed. We explain this by extending the recent derivation of the synchronization effect for two trajectories in a harmonic well to the case in which the trajectories are at two different temperatures. Our results suggest several ways in which mishandling selection of a pseudo random number generator initial seed can lead to corruption of simulation data. Simulators can fall into this trap in simple situations such as neglecting to specifically indicate different random seeds in either parallel or sequential restart simulations, utilizing a simulation package with a weak pseudorandom number generator, or using an advanced simulation algorithm that hasn't been programmed to distribute initial seeds.

Voter, A F [Los Alamos National Laboratory; Sindhikara, Daniel J [UNIV OF FLORIDA; Kim, Seonah [UNIV OF CALIFORNIA; Roitberg, Adrian E [UNIV OF FLORIDA

2009-01-01T23:59:59.000Z

396

Dynamic Protonation Equilibrium of Solvated Acetic Acid  

Science Conference Proceedings (OSTI)

For the first time, the dynamic protonation equilibrium between an amino acid side chain analogue and bulk water as well as the diffusion properties of the excess proton were successfully reproduced through unbiased computer simulations. During a 50 ns Q-HOP MD simulation, two different regimes of proton transfer were observed. Extended phases of frequent proton swapping between acetic acid and nearby water were separated by phases where the proton freely diffuses in the simulation box until it is captured again by acetic acid. The pKa of acetic acid was calculated around 3.0 based on the relative population of protonated and deprotonated states and the diffusion coefficient of excess proton was computed from the average mean squared displacement in the simulation. Both calculated values agree well with the experimental measurements.

Gu, Wei; Frigato, Tomaso; Straatsma, TP; Helms, Volkhard H.

2007-04-13T23:59:59.000Z

397

Photoionization of excited molecular states  

DOE Green Energy (OSTI)

Rapid advances in laser and detector technologies are making it possible to investigate molecular photophysics and photochemistry in powerful new ways. For example, resonantly enhanced multiphoton ionization (REMPI) measurements, in which the total (or the mass selected) ion current is monitored as a function of laser wavelength, have yielded extensive and often novel information on the spectroscopy of the resonant intermediate states. With the addition of photoelectron spectrometry (PES) to analyze the kinetic energy of the ejected electrons, it is possible to determine the branching ratios into different electronic, vibrational, and rotational levels of the product ion and to focus directly on both the dynamics of the multiphoton ionization process and the photoionization of excited state species. In the present paper, we report several REMPI/PES studies of H/sub 2/ and N/sub 2/. The results reflect both the spectroscopy and the dynamics of photoionization of excited molecular states and are discussed in terms of the selection rules for photoionization and the relative probabilities of photoionization from Rydberg and valence states. In some cases, in accordance with the Franck-Condon principle, the results demonstrate that resonant multiphoton ionization through Rydberg states may be a powerful technique for the production of electronic, vibrational, and rotational state selected ions. However, in other cases, systematic departures from Franck-Condon behavior are observed, which reflect the more subtle dynamics of excited state photoionization.

Dehmer, P.M.; Dehmer, J.L.; Pratt, S.T.

1984-01-01T23:59:59.000Z

398

RussiaSNL2-web.indd  

National Nuclear Security Administration (NNSA)

During Dynamic Crack Propagation During Dynamic Crack Propagation Principal Investigators: E.P. (Tony) Chen (SNL) and Alexander Selezenev (VNIIEF) Project Description This project involves conducting molecular dynamics (MD) simulation of micro-crack propagation in materials. It will use MD simulation to study phonon generation mecha- nisms during initiation and propagation of a micro-crack; the MD simulation will be per- formed in 2-D and 3-D geometries. Initially 2-D and 3-D crystal structures will be built using parallel computers. SageMD code will be parallelized and used in MD simulations. Details of the MD simulations will be defi ned. With MD simulation, the sample will be loaded with boundary conditions specifi ed under which initially the crack extension proceeds in the direction perpendicular to the crack

399

Dislocation Dynamics  

Science Conference Proceedings (OSTI)

Mar 7, 2013 ... Recent Progress in Dislocation Dynamics: Sylvie Aubry1; Athanasios Arsenlis1; Wei Cai2; Steve Fitzgerald3; 1LLNL; 2Stanford University; ...

400

Large Scale Computing Requirements for Basic Energy Sciences (An BES / ASCR / NERSC Workshop) Hilton Washington DC/Rockville Meeting Center, Rockville MD 3D Geophysical Imaging  

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

Requirements Requirements for Basic Energy Sciences (An BES / ASCR / NERSC Workshop) Hilton Washington DC/Rockville Meeting Center, Rockville MD 3D Geophysical Modeling and Imaging G. A. Newman Lawrence Berkeley National Laboratory February 9 - 10 , 2010 Talk Outline * SEAM Geophysical Modeling Project - Its Really Big! * Geophysical Imaging (Seismic & EM) - Its 10 to 100x Bigger! - Reverse Time Migration - Full Waveform Inversion - 3D Imaging & Large Scale Considerations - Offshore Brazil Imaging Example (EM Data Set) * Computational Bottlenecks * Computing Alternatives - GPU's & FPGA's - Issues Why ? So that the resource industry can tackle grand geophysical challenges (Subsalt imaging, land acquisition, 4-D, CO2, carbonates ......) SEAM Mission Advance the science and technology of applied

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


401

The Molecular Foundry  

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

PEOPLE JOB OPPORTUNITIES USER'S ASSOCIATION CONTACT US Foundry Intranet DOE Basic Energy Sciences User Facilities Molecular Foundry Seminar "Tuning Phonons in Molecular...

402

NEWTON's Molecular Biology Archive  

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

Molecular Biology Archive: Loading Most Recent Molecular Biology Questions: Cytoplasm pH DNA Extract and Cold Alcohol Albino Gene Loci Male Development Candy and Bacteria Revisited...

403

Dudley Herschbach: Chemical Reactions and Molecular Beams  

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

Dudley Herschbach: Dudley Herschbach: Chemical Reactions and Molecular Beams Resources with Additional Information Dudley Herschbach Courtesy of Texas A&M University As a co-recipient of the 1986 Nobel Prize in Chemistry, 'Dudley Herschbach was cited for "providing a much more detailed understanding of how chemical reactions take place". Using molecular beams, he studied elementary reactions such as K + CH3I and K + Br2, where it became possible to correlate reaction dynamics with the electronic structures of reactants and products. Exchanges proceeded through a persistent complex that lasted for many rotational periods, with product angular distributions reflecting the degree of reagent entanglement. Later this work was extended to H + Cl2, Cl + HI, halogen substitution reactions with vinyl and allyl halides, as well as such systems as Xe + Ar2 → XeAr + Ar. Herschbach has been a pioneer in the measurement and theoretical interpretation of vector properties of reaction dynamics, a field known as "molecular stereodynamics".

404

Electron Trapping by Molecular Vibration  

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

Electron Trapping by Molecular Electron Trapping by Molecular Vibration Electron Trapping by Molecular Vibration Print Wednesday, 27 April 2005 00:00 In photoelectron spectroscopy experiments performed at the ALS, a group of researchers has found that electronic transitions normally thought to be forbidden can in fact be excited in conjunction with certain types of molecular vibrations. Specifically, they found that when the symmetry of a linear triatomic molecule is broken by asymmetric vibrational modes, photoelectrons can become temporarily trapped by the molecule before ultimately escaping, giving rise to a broad feature in the photoelectron spectrum known as a shape resonance. This process represents a novel type of symmetry-breaking phenomenon that has not been observed previously but appears to be widespread. Such coupling between electronic motion and nuclear motion becomes increasingly important as scientists learn more about the geometry and dynamics of novel chemical structures such as those found in nanodevices and transient chemical species, and the results have implications for studies that use photoelectron spectroscopy as a diagnostic tool.

405

Cytoskeleton dynamics: Fluctuations within the network  

Science Conference Proceedings (OSTI)

Out-of-equilibrium systems, such as the dynamics of a living cytoskeleton (CSK), are inherently noisy with fluctuations arising from the stochastic nature of the underlying biochemical and molecular events. Recently, such fluctuations within the cell were characterized by observing spontaneous nano-scale motions of an RGD-coated microbead bound to the cell surface [Bursac et al., Nat. Mater. 4 (2005) 557-561]. While these reported anomalous bead motions represent a molecular level reorganization (remodeling) of microstructures in contact with the bead, a precise nature of these cytoskeletal constituents and forces that drive their remodeling dynamics are largely unclear. Here, we focused upon spontaneous motions of an RGD-coated bead and, in particular, assessed to what extent these motions are attributable to (i) bulk cell movement (cell crawling), (ii) dynamics of focal adhesions, (iii) dynamics of lipid membrane, and/or (iv) dynamics of the underlying actin CSK driven by myosin motors.

Bursac, Predrag [Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115 (United States); Sports Medicine Group, Regeneration Technologies Inc., Alachua, FL 32616 (United States); Fabry, Ben [Department of Physics, Erlangen University, Erlangen (Germany); Trepat, Xavier [Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115 (United States); Lenormand, Guillaume [Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115 (United States); Butler, James P. [Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115 (United States); Wang, Ning [Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115 (United States); Fredberg, Jeffrey J. [Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115 (United States); An, Steven S. [Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115 (United States); Division of Physiology, Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 (United States); E-mail: san@jhsph.edu

2007-04-06T23:59:59.000Z

406

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

E-Print Network (OSTI)

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

Rice, Andrew Patrick

2011-01-01T23:59:59.000Z

407

Molecular biology, a widely used expression for a changeable meaning Gabriel Gachelin  

E-Print Network (OSTI)

1 Molecular biology, a widely used expression for a changeable meaning Gabriel Gachelin Centre de to introduce the round table on the dynamics of molecular biology and to take the opportunity to express my personal view on that question. "Molecular biology" is a widely accepted term. Numerous excellent studies

Paris-Sud XI, Université de

408

Transport and Self-Assembly in Molecular Nanosystems  

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

Transport and Transport and Self-Assembly in Molecular Nanosystems Transport and Self-Assembly in Molecular Nanosystems Key Challenges: Use classical molecular dynamics and coarse grain molecular dynamics to enable "bottom-up" material design of a wide variety of nanostructures possessing a wealth of unique properties. The goal is to guide and inform synthetic investigations and understand molecular and electronic transport, self-assembly, catalysis, and other phenomena. Ab-initio electronic structure and quantum transport methods are also used. The modeling often involves large systems (500,000 atoms) and cooperative use of several codes such as Gaussian and NAMD. Free-energy calculations typically require good ensemble averaging and therefore, must be performed

409

Molecular mean field theory for liquid water  

E-Print Network (OSTI)

Attractive bonding interactions between molecules typically have inherent conservation laws which influence the statistical properties of such systems in terms of corresponding sum rules. We considered lattice water as an example and enunciated the consequences of the sum rule through a general computational procedure called "Molecular mean field" theory. Fluctuations about mean field are computed and many of the liquid properties have been deduced and compared with Monte Carlo simulation, molecular dynamics and experimental results. Large correlation lengths are seen to be a consequence of the sum rule in liquid phase. Long range Coulomb interactions are shown to have minor effects on our results.

Jampa Maruthi Pradeep Kanth; Ramesh Anishetty

2010-04-09T23:59:59.000Z

410

A molecular mechanics force field for lignin  

DOE Green Energy (OSTI)

A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials and bonded parameters are obtained by optimizing vibrational frequencies and normal modes. Finally, the force field is validated by performing a molecular dynamics simulation of a crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this lignin force field will enable full simulations of lignocellulose.

Petridis, Loukas [ORNL; Smith, Jeremy C [ORNL

2009-02-01T23:59:59.000Z

411

Molecular Cell Short Article  

E-Print Network (OSTI)

Molecular Cell Short Article Nucleosome Organization Affects the Sensitivity of Gene Expression to Promoter Mutations Gil Hornung,1 Moshe Oren,2 and Naama Barkai1,* 1Department of Molecular Genetics 2Department of Molecular Cell Biology Weizmann Institute of Science, Rehovot, Israel *Correspondence: naama

Barkai, Naama

412

DYNAMIC SCREENING IN SOLAR PLASMA  

Science Conference Proceedings (OSTI)

In the hot, dense plasma of solar and stellar interiors, Coulomb potentials are screened, resulting in increased nuclear reaction rates. Although Salpeter's approximation for static screening is widely accepted and used in stellar modeling, the question of screening in nuclear reactions has been revisited. In particular, the issue of dynamic effects has been raised by Shaviv and Shaviv who apply the techniques of molecular dynamics to the conditions in the Sun's core in order to numerically determine the effect of screening. By directly calculating the motion of ions and electrons due to Coulomb interactions, the simulations are used to compute the effect of screening without the mean field assumption inherent in Salpeter's approximation. In this paper, we reproduce their numerical analysis of the screening energy in the plasma of the solar core and conclude that the effects of dynamic screening are relevant and should be included when stellar nuclear reaction rates are computed.

Mao, Dan; Daeppen, Werner [Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089 (United States); Mussack, Katie [Institute of Astronomy, University of Cambridge, Cambridge CB3 0HA (United Kingdom)], E-mail: mussack@ast.cam.ac.uk

2009-08-20T23:59:59.000Z

413

Dynamic screening in solar plasma  

E-Print Network (OSTI)

In the hot, dense plasma of solar and stellar interiors, Coulomb potentials are screened, resulting in increased nuclear reaction rates. Although Salpeter's approximation for static screening is widely accepted and used in stellar modeling, the question of screening in nuclear reactions has been revisited. In particular the issue of dynamic effects has been raised by Shaviv and Shaviv who apply the techniques of molecular dynamics to the conditions in the Sun's core in order to numerically determine the effect of screening. By directly calculating the motion of ions and electrons due to Coulomb interactions, the simulations are used to compute the effect of screening without the mean-field assumption inherent in Salpeter's approximation. In this paper we reproduce their numerical analysis of the screening energy in the plasma of the solar core and conclude that the effects of dynamic screening are relevant and should be included when stellar nuclear reaction rates are computed.

Mao, Dan; Däppen, Werner

2009-01-01T23:59:59.000Z

414

Computer simulation and topological modeling of radiation effects in zircon  

E-Print Network (OSTI)

The purpose of this study is to understand on atomic level the structural response of zircon (ZrSiO4) to irradiation using molecular dynamics (MD) computer simulations, and to develop topological models that can describe ...

Zhang, Yi, 1979-

2006-01-01T23:59:59.000Z

415

Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models  

E-Print Network (OSTI)

Molecular dynamics (MD) simulations can now predict ms-timescale folding processes of small proteins; however, this presently requires hundreds of thousands of CPU hours and is primarily applicable to short peptides with ...

Waldispühl, Jerome

416

Proposal of a critical test of the Navier-Stokes-Fourier paradigm for compressible fluid continua  

E-Print Network (OSTI)

A critical, albeit simple experimental and/or molecular-dynamic (MD) simulation test is proposed whose outcome would, in principle, establish the viability of the Navier-Stokes-Fourier (NSF) equations for compressible fluid ...

Brenner, Howard

417

Adsorption sites of hydrogen atom on pure and Mg-doped multi-walled carbon nanotubes  

Science Conference Proceedings (OSTI)

Hydrogen adsorption sites on pure multiwalled carbon nanotube (MWCNT) and Mg-doped MWCNTs material system have been investigated using molecular dynamics (MD) simulations as well as quantum chemical calculations. Through combining MWCNTs with Mg, the ...

A. A. Al-Ghamdi, E. Shalaan, F. S. Al-Hazmi, Adel S. Faidah, S. Al-Heniti, M. Husain

2012-01-01T23:59:59.000Z

418

Transport modeling of simple fluids and nano-colloids : thermal conduction mechanisms and coarse projection  

E-Print Network (OSTI)

In the first part of this thesis, the modes of microscopic energy fluctuations governing heat flow in nano-colloids are quantitatively assessed by combining linear response theory with molecular dynamics (MD) simulations. ...

Eapen, Jacob, 1968-

2006-01-01T23:59:59.000Z

419

Molecular Science Research Center, 1991 annual report  

SciTech Connect

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

Knotek, M.L.

1992-03-01T23:59:59.000Z

420

NCNR Scaling of Membrane Phase Dynamics  

Science Conference Proceedings (OSTI)

... Authors. L. Porcar Oak Ridge National Laboratory Oak Ridge, TN 37831-6393 Present address: University of Maryland College Park, MD 20742. ...

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


421

Molecular Mechanism of Biological Proton Transport  

Science Conference Proceedings (OSTI)

Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

Pomes, R.

1998-09-01T23:59:59.000Z

422

Fast Flexible Modeling of RNA Structure Using Internal Coordinates  

Science Conference Proceedings (OSTI)

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. ... Keywords: Internal coordinate mechanics, molecular, structure, dynamics, RNA, modeling, prediction, linear, scaling.

Samuel Coulbourn Flores; Michael Sherman; Christopher M. Bruns; Peter Eastman; Russ B. Altman

2011-09-01T23:59:59.000Z

423

Condensed Phase and Interfacial Molecular Sciences | U.S. DOE Office of  

Office of Science (SC) Website

Condensed Phase and Interfacial Molecular Sciences Condensed Phase and Interfacial Molecular Sciences Chemical Sciences, Geosciences, & Biosciences (CSGB) Division CSGB Home About Research Areas Energy Frontier Research Centers (EFRCs) DOE Energy Innovation Hubs Scientific Highlights Reports & Activities Principal Investigators' Meetings BES Home Research Areas Condensed Phase and Interfacial Molecular Sciences Print Text Size: A A A RSS Feeds FeedbackShare Page Condensed Phase and Interfacial Molecular Science (CPIMS) research emphasizes molecular understanding of chemical, physical, and electron-driven processes in aqueous media and at interfaces. Studies of reaction dynamics at well-characterized metal and metal-oxide surfaces and clusters lead to the development of theories on the molecular origins of

424

Dynamic tariffs  

SciTech Connect

The general theoretical models of dynamic tariffs, such as spot pricing, are extended in this paper to include the issues of optimal response of industrial consumers and the effect of large scale penetration of these tariffs on the utility load curve. If such tariffs are to serve their purpose consumers need to acquire the ability for flexible and dynamic response. While the hardware for this is readily available the theoretical models and software systems are not. These issues are examined and correlated with industrial site studies. A systematic analysis of the effect of significant consumer response on the system load curve is next undertaken. A methodologically sound approach to system load and price forecasting is presented.

David, A.K.; Lee, Y.C.

1989-08-01T23:59:59.000Z

425

2010 Atomic & Molecular Interactions Gordon Research Conference  

SciTech Connect

The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

Todd Martinez

2010-07-23T23:59:59.000Z

426

Dynamics of H sub 2 elimination from unsaturated hydrocarbons  

DOE Green Energy (OSTI)

State-of-the-art laser and molecular beam techniques are used to study the dynamics of H{sub 2} elimination from 1,4-cyclohexadiene and ethylene. Information on the transition state configurations and the dynamics of the dissociation processes for these reactions is reported. 152 refs., 54 figs., 12 tabs.

Cromwell, E.F.

1991-02-01T23:59:59.000Z

427

Dissipative Particle Dynamics and Other Particle Methods for Multiphase Fluid Flow in Fractured and Porous Media  

Science Conference Proceedings (OSTI)

Particle methods are less computationally efficient than grid based numerical solution of the Navier Stokes equation. However, they have important advantages including rigorous mass conservation, momentum conservation and isotropy. In addition, there is no need for explicit interface tracking/capturing and code development effort is relatively low. We describe applications of three particle methods: molecular dynamics, dissipative particle dynamics and smoothed particle hydrodynamics. The mesoscale (between the molecular and continuum scales) dissipative particle dynamics method can be used to simulate systems that are too large to simulate using molecular dynamics but small enough for thermal fluctuations to play an important role.

Paul Meakin; Zhijie Xu

2009-08-01T23:59:59.000Z

428

Renewal processes and fluctuation analysis of molecular motor stepping  

E-Print Network (OSTI)

We model the dynamics of a processive or rotary molecular motor using a renewal processes, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation functions of the renewal process, which have applications to bead-assay experiments performed both with processive molecular motors, such as myosin V and kinesin, and rotary motors, such as F1-ATPase.

Jaime E. Santos; Thomas Franosch; Andrea Parmeggiani; Erwin Frey

2005-05-29T23:59:59.000Z

429

Rational Construction of Stochastic Numerical Methods for Molecular Sampling  

E-Print Network (OSTI)

In this article, we focus on the sampling of the configurational Gibbs-Boltzmann distribution, that is, the calculation of averages of functions of the position coordinates of a molecular $N$-body system modelled at constant temperature. We show how a formal series expansion of the invariant measure of a Langevin dynamics numerical method can be obtained in a straightforward way using the Baker-Campbell-Hausdorff lemma. We then compare Langevin dynamics integrators in terms of their invariant distributions and demonstrate a superconvergence property (4th order accuracy where only 2nd order would be expected) of one method in the high friction limit; this method, moreover, can be reduced to a simple modification of the Euler-Maruyama method for Brownian dynamics involving a non-Markovian (coloured noise) random process. In the Brownian dynamics case, 2nd order accuracy of the invariant density is achieved. All methods considered are efficient for molecular applications (requiring one force evaluation per times...

Leimkuhler, Benedict

2012-01-01T23:59:59.000Z

430

The Molecular Foundry  

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

LBNL Masthead A-Z Index Berkeley Lab masthead Phone Book Jobs Search The Molecular Foundry Home DOE - Office of Science ABOUT US FACILITIESCAPABILITIES RESEARCH BECOMING A USER...

431

The Molecular Foundry  

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

PEOPLE JOB OPPORTUNITIES USER'S ASSOCIATION CONTACT US Foundry Intranet DOE Basic Energy Sciences User Facilities Molecular Foundry Seminar "Atomic Structure and Applications...

432

The Molecular Foundry  

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

PEOPLE JOB OPPORTUNITIES USER'S ASSOCIATION CONTACT US Foundry Intranet DOE Basic Energy Sciences User Facilities Molecular Foundry Seminar Mineralization at the Organic...

433

The Molecular Foundry  

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

PEOPLE JOB OPPORTUNITIES USER'S ASSOCIATION CONTACT US Foundry Intranet DOE Basic Energy Sciences User Facilities Molecular Foundry Seminar "What Happens to Crystals When...

434

The Molecular Foundry  

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

Brett Helms, Berkeley Lab Title: Building Our Understanding of Nanocrystal Surface Structure Using Heterometallic Molecular Beacons Location: 67-3111 Chemla room View the Foundry...

435

A Molecular Simulation Study  

Science Conference Proceedings (OSTI)

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

436

The Molecular Foundry  

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

Seminar Schedule Abstract: The intriguing prospects of molecular electronics, nanotechnology, biomaterials, and the aim to close the gap between synthetic and biological...

437

Educational Molecular Biology Games  

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

Molecular Biology Games Do you have a great game? Please click our Ideas page. Featured Games: Biology Games fom biologyjunction.com Biology Games fom biologyjunction.com...

438

Molecular Hydrogen in Infrared Cirrus  

E-Print Network (OSTI)

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

Kristen Gillmon; J. Michael Shull

2005-07-25T23:59:59.000Z

439

Transport of Molecular Motor Dimers in Burnt-Bridge Models  

E-Print Network (OSTI)

Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic continuous-time burnt-bridge models. In these models the motion of molecular motors is viewed as a random walk along the lattices with periodically distributed weak links (bridges). When the particle crosses the weak link it can be destroyed with a probability $p$, driving the molecular motor motion in one direction. Dynamic properties and effective generated forces of dimer molecular motors are calculated exactly as a function of a concentration of bridges $c$ and burning probability $p$ and compared with properties of the monomer motors. It is found that the ratio of the velocities of the dimer and the monomer can never exceed 2, while the dispersions of the dimer and the monomer are not very different. The relative effective generated force of the dimer (as compared to the monomer) also cannot be larger than 2 for most sets of parameters. However, a very large force can be produced by the dimer in the special case of $c=1/2$ for non-zero shift between the lattices. Our calculations do not show the significant increase in the force generated by collagenase motor proteins in real biological systems as predicted by previous computational studies. The observed behavior of dimer molecular motors is discussed by considering in detail the particle dynamics near burnt bridges.

Alexander Yu. Morozov; Anatoly B. Kolomeisky

2007-09-21T23:59:59.000Z

440

Final Report: Integrated Multiscale Modeling of Molecular Computing Devices  

Science Conference Proceedings (OSTI)

The general theme of this research has been to expand the capabilities of a simulation technique, Kinetic Monte Carlo (KMC) and apply it to study self-assembled nano-structures on epitaxial thin films. KMC simulates thin film growth and evolution by replacing the detailed dynamics of the systemâ??s evolution, which might otherwise be studied using molecular dynamics, with an appropriate stochastic process.

Tim Schulze, University of Tennessee, Knoxville

2012-11-01T23:59:59.000Z

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441

Molecular models for explosives  

Science Conference Proceedings (OSTI)

Any fundamental understanding of detonations and explosives' behavior requires as a starting point a knowledge of molecular properties. Indeed, there is a sizable literature concerning observed decomposition kinetics, x-ray crystal structures, heats of formation, etc. for explosives. As a result of this extensive experimental work, a large and ever increasing number of observed properties of explosives are available. Given sufficient data, models for the prediction of molecular properties can be developed and calibrated. Nevertheless, many desirable molecular properties can be obtained with considerable effort and, in many cases, experimental measurements are not possible for practical reasons; e.g., bond dissociation energies are very difficult to obtain for explosives. Consequently, theoretical methods for obtaining these properties are quite desirable. In addition, it is oftentimes desired to estimate the properties of unknown molecules. Consequently, methods for the estimation of molecular properties, which might seem quite crude by other standards, can be of considerable practical value. We present in this paper some of our recent efforts at extending and developing molecular models for explosives. These efforts fall into three main areas: Estimation of crystal densities of organic nitrates and perchlorates by an entirely empirical group additivity method; calculation of molecular heats of formation and bond dissociation energies (BDE's) by a semi-empirical molecular orbital method (AM1); and the electronic structure of nitrobenzene as obtained from non-empirical (sometimes called ab initio molecular orbital calculations. 10 refs.

Ritchie, J.P.; Bachrach, S.M.

1987-01-01T23:59:59.000Z

442

Simple Dynamic Gasifier Model That Runs in Aspen Dynamics  

SciTech Connect

Gasification (or partial oxidation) is a vital component of 'clean coal' technology. Sulfur and nitrogen emissions can be reduced, overall energy efficiency is increased, and carbon dioxide recovery and sequestration are facilitated. Gasification units in an electric power generation plant produce a fuel for driving combustion turbines. Gasification units in a chemical plant generate gas, which can be used to produce a wide spectrum of chemical products. Future plants are predicted to be hybrid power/chemical plants with gasification as the key unit operation. The widely used process simulator Aspen Plus provides a library of models that can be used to develop an overall gasifier model that handles solids. So steady-state design and optimization studies of processes with gasifiers can be undertaken. This paper presents a simple approximate method for achieving the objective of having a gasifier model that can be exported into Aspen Dynamics. The basic idea is to use a high molecular weight hydrocarbon that is present in the Aspen library as a pseudofuel. This component should have the same 1:1 hydrogen-to-carbon ratio that is found in coal and biomass. For many plantwide dynamic studies, a rigorous high-fidelity dynamic model of the gasifier is not needed because its dynamics are very fast and the gasifier gas volume is a relatively small fraction of the total volume of the entire plant. The proposed approximate model captures the essential macroscale thermal, flow, composition, and pressure dynamics. This paper does not attempt to optimize the design or control of gasifiers but merely presents an idea of how to dynamically simulate coal gasification in an approximate way.

Robinson, P.J.; Luyben, W.L. [Lehigh University, Bethlehem, PA (United States). Dept. of Chemical Engineering

2008-10-15T23:59:59.000Z

443

Role of the Molecular Sublayer in the Melting or Freezing of Sea Ice  

Science Conference Proceedings (OSTI)

In an earlier paper, a second-moment turbulence closure model was applied to the problem of the dynamic and thermodynamic interaction of sea ice and the ocean surface mixed layer. An overly simplistic parameterization of the molecular sublayers ...

Michael Steele; George L. Mellor; Miles G. Mcphee

1989-01-01T23:59:59.000Z

444

Probing Core-Hole Localization in Molecular Nitrogen  

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

Probing Core-Hole Localization in Molecular Nitrogen Print Probing Core-Hole Localization in Molecular Nitrogen Print The behavior of the core hole created in molecular x-ray photoemission experiments has provided molecular scientists with a valuable window through which to probe the electronic structure and dynamics of molecules. But the answer to one fundamental quantum question-whether the core hole is localized or delocalized-has remained elusive for diatomic molecules in which both atoms are the same element. An international team of scientists from the University of Frankfurt in Germany, Berkeley Lab, Kansas State University, and Auburn University has now resolved the issue with an appropriate twist of quantum fuzziness. By means of coincident detection of the photoelectron ejected from molecular nitrogen and the Auger electron emitted femtoseconds later, the team found that how the measurements are done determines which description-localized or delocalized-is valid.

445

Probing Core-Hole Localization in Molecular Nitrogen  

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

Probing Core-Hole Localization in Molecular Nitrogen Print Probing Core-Hole Localization in Molecular Nitrogen Print The behavior of the core hole created in molecular x-ray photoemission experiments has provided molecular scientists with a valuable window through which to probe the electronic structure and dynamics of molecules. But the answer to one fundamental quantum question-whether the core hole is localized or delocalized-has remained elusive for diatomic molecules in which both atoms are the same element. An international team of scientists from the University of Frankfurt in Germany, Berkeley Lab, Kansas State University, and Auburn University has now resolved the issue with an appropriate twist of quantum fuzziness. By means of coincident detection of the photoelectron ejected from molecular nitrogen and the Auger electron emitted femtoseconds later, the team found that how the measurements are done determines which description-localized or delocalized-is valid.

446

Heart DiseaseHeart Disease--Learn to Love YourLearn to Love Your Michael McKee, M.D.Michael McKee, M.D.  

E-Print Network (OSTI)

Heart DiseaseHeart Disease-- Learn to Love YourLearn to Love Your HeartHeart Michael McKee, M.D.Michael McKee, M.D. March 19, 2010March 19, 2010 #12;GoalsGoals ·· Learn more about heart disease for yourself andLearn more about heart disease for yourself and for your studentsfor your students ·· Learn

Goldman, Steven A.

447

Dynamic stability of spindles controlled by molecular motor kinetics  

E-Print Network (OSTI)

We analyze the role of the force-dependent kinetics of motor proteins in the stability of antiparallel arrays of polar filaments, such as those in the mitotic spindle. We determine the possible stable structures and show that there exists an instability associated to the collective behavior of motors that leads to the collapse of the spindle. Our analysis provides a general framework to understand several experimental observations in eukaryotic cell division.

Otger Campas; Jaume Casademunt; Ignacio Pagonabarraga

2006-03-30T23:59:59.000Z

448

Molecular Dynamics Simulation on the Surface Melting and ...  

Science Conference Proceedings (OSTI)

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

449

Phase Field, Phase Field Crystal, Diffusive Molecular Dynamics  

Science Conference Proceedings (OSTI)

Mar 7, 2013... growth of quantum dots on thin membranes and the creation of superstructures (stripes, honeycomb and triangular) in ultrathin films of Cu on ...

450

Metallic Cluster Coalescence: Molecular Dynamics Simulations of Boundary Formation  

E-Print Network (OSTI)

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

Takahashi, A. R.

451

Molecular Dynamics Study of Voids and Bubbles in BCC Uranium  

Science Conference Proceedings (OSTI)

Many metallic nuclear fuels are body-centered cubic alloys of uranium that swell under fission conditions with the creation of fission product gases such as ...

452

Molecular Dynamics Simulation of Al Oxide Stress Corrosion Cracking  

Science Conference Proceedings (OSTI)

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

453

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

Science Conference Proceedings (OSTI)

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

454

Molecular dynamics simulation of nanoporous graphene for selective gas separation  

E-Print Network (OSTI)

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

Au, Harold (Harold S.)

2012-01-01T23:59:59.000Z

455

Attosecond X-Ray Pulses for Molecular Electronic Dynamics  

E-Print Network (OSTI)

of the neutral gas be tuned so that its positive dispersionpositive dispersion of the remaining neutral generation gas[

Abel, Mark Joseph

2010-01-01T23:59:59.000Z

456

Femtosecond Molecular Dynamics Studied with Vacuum Ultraviolet Pulse Pairs  

E-Print Network (OSTI)

and K. Osvay. Dispersion measurement of inert gases and gasone due to the dispersion of the noble gas atoms and one dueionization where dispersion due to the neutral gas atoms and

Allison III, Thomas K.

2010-01-01T23:59:59.000Z

457

CROSSED MOLECULAR BEAM STUDIES OF UN-IMOLECULAR REACTION DYNAMICS  

E-Print Network (OSTI)

released in carbon-chlorine bond formation to redistributeIn the reaction of chlorine and fluorine atoms with vinylthe reaction of The reaction chlorine atoms with 1, 2 and 3-

Buss, R.J.

2010-01-01T23:59:59.000Z

458

A Molecular Dynamics Study of the Austenite-Ferrite Interface ...  

Science Conference Proceedings (OSTI)

Proceedings Inclusion? Planned: A CD-only volume ... Studies on Vibrational Entropy in Alloys Using Inelastic Neutron Scattering at ORNL · Surface Prefreezing ...

459

Molecular dynamics simulation of hydrogen diffusion in titanium  

National Nuclear Security Administration (NNSA)

of hydrogen-metal systems for absorption of nuclear radiation, in neutron sources, for storage of hydrogen, or as catalyzers. This work is devoted to atomistic simulation of...

460

Molecular dynamics analysis of supercontraction in spider dragline silk  

E-Print Network (OSTI)

Spider dragline silk is a material that has evolved over millions of years to develop finely tuned mechanical properties. It is a protein-based fiber, used as the main structural component in spider webs and as a lifeline ...

Batty, Laura

2013-01-01T23:59:59.000Z