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1

PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs  

SciTech Connect (OSTI)

We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.

Kylasa, S.B., E-mail: skylasa@purdue.edu [Department of Elec. and Comp. Eng., Purdue University, West Lafayette, IN 47907 (United States); Aktulga, H.M., E-mail: hmaktulga@lbl.gov [Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, MS 50F-1650, Berkeley, CA 94720 (United States); Grama, A.Y., E-mail: ayg@cs.purdue.edu [Department of Computer Science, Purdue University, West Lafayette, IN 47907 (United States)

2014-09-01T23:59:59.000Z

2

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

E-Print Network [OSTI]

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

Liu, Hongyi

2013-01-01T23:59:59.000Z

3

Substructured multibody molecular dynamics.  

SciTech Connect (OSTI)

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

4

Introduction to Molecular Dynamics and Accelerated Molecular Dynamics  

SciTech Connect (OSTI)

We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

Perez, Danny [Los Alamos National Laboratory

2012-06-25T23:59:59.000Z

5

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

E-Print Network [OSTI]

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

Brenner, Donald W.

6

Mapping molecular dynamics computations to hypercubes  

E-Print Network [OSTI]

December 1993 Major Subject: ('omputer Science MAPPING MOLECULAR DYNAMICS COMPUTATIONS TO HYPERCUBES A Thesis by VAMSEE IvRISHNA LAIvAMSANI Submitted to Texas AX. 'M University in partial fnlfillment of the requirements for the degree of lv... for systematic modeling, mapping and perfornianrc analysis of a Grand Challenge application problein in computational biology called Moleru- lar Dynamics S&tnufat&un uj Proteins Molecular Dynamics (MD) is an important techn&que used m computational...

Lakamsani, Vamsee Krishna

1993-01-01T23:59:59.000Z

7

Accelerated molecular dynamics methods  

SciTech Connect (OSTI)

The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.

Perez, Danny [Los Alamos National Laboratory

2011-01-04T23:59:59.000Z

8

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

9

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

E-Print Network [OSTI]

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

Southern California, University of

10

Why are MD simulated protein folding times wrong? Dmitry Nerukh  

E-Print Network [OSTI]

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

Nerukh, Dmitry

11

Path Integral Monte Carlo and Density Functional Molecular Dynamics Simulations of Hot, Dense Helium  

E-Print Network [OSTI]

Path Integral Monte Carlo and Density Functional Molecular Dynamics Simulations of Hot, Dense integral Monte Carlo (PIMC) and density func- tional molecular dynamics (DFT-MD), are applied to study hot excitation mecha- nisms that determine their behavior at high temperature. The helium atom has two ionization

Militzer, Burkhard

12

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

E-Print Network [OSTI]

Molecular dynamics simulations of the elastic properties of polymer/carbon nanotube composites Yue composite. However, improvements in properties are by no means guaranteed, and the results are often in the composite. In this paper, we present classical molecular dynamics (MD) simulations of model polymer

Elliott, James

13

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

E-Print Network [OSTI]

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

Maruyama, Shigeo

14

Introduction to Accelerated Molecular Dynamics  

SciTech Connect (OSTI)

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

15

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

E-Print Network [OSTI]

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

Han, Kunwoo

2009-06-02T23:59:59.000Z

16

Trillion-atom molecular dynamics becomes a reality  

SciTech Connect (OSTI)

By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD{_}render.

Kadau, Kai [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory

2008-01-01T23:59:59.000Z

17

Molecular dynamics simulation of chains mobility in polyethylene crystal  

E-Print Network [OSTI]

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

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

2014-01-17T23:59:59.000Z

18

Molecular Dynamics Simulations of Solutions at Constant Chemical Potential  

E-Print Network [OSTI]

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

Perego, Claudio; Parrinello, Michele

2015-01-01T23:59:59.000Z

19

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

E-Print Network [OSTI]

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

Steinhoff, Heinz-Jürgen

20

A molecular dynamics study of polymer/graphene interfacial systems  

SciTech Connect (OSTI)

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

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

2014-05-15T23:59:59.000Z

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

Modeling Molecular Dynamics from Simulations  

SciTech Connect (OSTI)

Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.

Hinrichs, Nina Singhal (University of Chicago) [University of Chicago

2009-01-28T23:59:59.000Z

22

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

23

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

SciTech Connect (OSTI)

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

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

2014-01-01T23:59:59.000Z

24

Accelerated Molecular Dynamics Simulation of Thermal Desorption.  

E-Print Network [OSTI]

??Desorption is a process ubiquitous in phenomena involving surfaces. However, it has rarely been simulated on the molecular level. Molecular dynamics simulation can provide the… (more)

Becker, Kelly

2008-01-01T23:59:59.000Z

25

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

SciTech Connect (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

26

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

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

DFT calculations on molecular clusters and electrode surfaces, reactive molecular dynamics simulations allowing modeling of SEI formation, and classical molecular dynamics...

27

Molecular dynamics simulation of threshold displacement energies...  

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

experimental estimates in ceramics. Citation: Moreira PA, R Devanathan, J Yu, and WJ Weber.2009."Molecular dynamics simulation of threshold displacement energies in...

28

Molecular dynamics simulation studies of electrolytes andelectrolyte...  

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

Merit Review and Peer Evaluation Meeting, May 18-22, 2009 -- Washington D.C. es40smith.pdf More Documents & Publications Molecular Dynamics Simulation Studies of...

29

A Molecular Dynamics Investigation of Hydrolytic Polymerization...  

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

Hydrolytic Polymerization in a Metal-Hydroxide Gel. A Molecular Dynamics Investigation of Hydrolytic Polymerization in a Metal-Hydroxide Gel. Abstract: The early stages of the...

30

Accelerated molecular dynamics methods: introduction and recent developments  

SciTech Connect (OSTI)

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

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

2009-01-01T23:59:59.000Z

31

Optimal prediction in molecular dynamics  

E-Print Network [OSTI]

Optimal prediction approximates the average solution of a large system of ordinary differential equations by a smaller system. We present how optimal prediction can be applied to a typical problem in the field of molecular dynamics, in order to reduce the number of particles to be tracked in the computations. We consider a model problem, which describes a surface coating process, and show how asymptotic methods can be employed to approximate the high dimensional conditional expectations, which arise in optimal prediction. The thus derived smaller system is compared to the original system in terms of statistical quantities, such as diffusion constants. The comparison is carried out by Monte-Carlo simulations, and it is shown under which conditions optimal prediction yields a valid approximation to the original system.

Benjamin Seibold

2008-08-22T23:59:59.000Z

32

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

E-Print Network [OSTI]

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

Zhigilei, Leonid V.

33

Minor Groove Deformability of DNA: A Molecular Dynamics Free...  

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

Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study. Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study. Abstract:...

34

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

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

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

35

Molecular Dynamics Simulation of the AgCl/Electrolyte Interfacial...  

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

Simulation of the AgClElectrolyte Interfacial Capacity. Molecular Dynamics Simulation of the AgClElectrolyte Interfacial Capacity. Abstract: Molecular dynamics simulation of the...

36

Comparative molecular dynamics analysis of tapasin-dependent...  

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

molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles. Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I...

37

Molecular Dynamics Simulation of Thermodynamic Properties in Uranium Dioxide  

SciTech Connect (OSTI)

In the present study, we investigated the thermodynamic properties of uranium dioxide (UO2) by molecular dynamics (MD) simulations. As for solid UO2, the lattice parameter, density, and enthalpy obtained by MD simulations were in good agreement with existing experimental data and previous theoretical predictions. The calculated thermal conductivities matched the experiment results at the midtemperature range but were underestimated at very low and very high temperatures. The calculation results of mean square displacement represented the stability of uranium at all temperatures and the high mobility of oxygen toward 3000 K. By fitting the diffusivity constant of oxygen with the Vogel-Fulcher-Tamman law, we noticed a secondary phase transition near 2006.4 K, which can be identified as a ‘‘strong’’ to ‘‘fragile’’ supercooled liquid or glass phase transition in UO2. By fitting the oxygen diffusion constant with the Arrhenius equation, activation energies of 2.0 and 2.7 eV that we obtained were fairly close to the recommended values of 2.3 to 2.6 eV. Xiangyu Wang, Bin Wu, Fei Gao, Xin Li, Xin Sun, Mohammed A. Khaleel, Ademola V. Akinlalu and Li Liu

Wang, Xiangyu; Wu, Bin; Gao, Fei; Li, Xin; Sun, Xin; Khaleel, Mohammad A.; Akinlalu, Ademola V.; Liu, L.

2014-03-01T23:59:59.000Z

38

Hydration structure of salt solutions from ab initio molecular dynamics  

SciTech Connect (OSTI)

The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L. [Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122 (United States)

2013-01-07T23:59:59.000Z

39

Combined 3D-QSAR, molecular docking and molecular dynamics study on thyroid hormone activity of hydroxylated polybrominated diphenyl ethers to thyroid receptors ?  

SciTech Connect (OSTI)

Several recent reports suggested that hydroxylated polybrominated diphenyl ethers (HO-PBDEs) may disturb thyroid hormone homeostasis. To illuminate the structural features for thyroid hormone activity of HO-PBDEs and the binding mode between HO-PBDEs and thyroid hormone receptor (TR), the hormone activity of a series of HO-PBDEs to thyroid receptors ? was studied based on the combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) methods. The ligand- and receptor-based 3D-QSAR models were obtained using Comparative Molecular Similarity Index Analysis (CoMSIA) method. The optimum CoMSIA model with region focusing yielded satisfactory statistical results: leave-one-out cross-validation correlation coefficient (q{sup 2}) was 0.571 and non-cross-validation correlation coefficient (r{sup 2}) was 0.951. Furthermore, the results of internal validation such as bootstrapping, leave-many-out cross-validation, and progressive scrambling as well as external validation indicated the rationality and good predictive ability of the best model. In addition, molecular docking elucidated the conformations of compounds and key amino acid residues at the docking pocket, MD simulation further determined the binding process and validated the rationality of docking results. -- Highlights: ? The thyroid hormone activities of HO-PBDEs were studied by 3D-QSAR. ? The binding modes between HO-PBDEs and TR? were explored. ? 3D-QSAR, molecular docking, and molecular dynamics (MD) methods were performed.

Li, Xiaolin [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China)] [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China); Ye, Li [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China)] [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China); Wang, Xiaoxiang [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China)] [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China); Wang, Xinzhou [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China)] [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China); Liu, Hongling [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China)] [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China); Zhu, Yongliang [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China)] [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China); Yu, Hongxia, E-mail: hongxiayu01@yahoo.com.cn [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China)] [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China)

2012-12-15T23:59:59.000Z

40

An Analysis of the Interactions between the Sem-5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations,  

E-Print Network [OSTI]

to the construction of van der Waals interaction energy profiles for each ligand as well as for wild-type and mutant Dynamics, Free Energy Calculations, and Sequence Analysis Wei Wang, Wendell A. Lim,, Araz Jakalian,§,# Jian the interactions between Sem-5 and its ligands using molecular dynamics (MD), free energy calculations

Wang, Wei

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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to obtain the most current and comprehensive results.


41

9/28/98 9:58:58 am, Journal of Non-Crystalline Solids MOLECULAR DYNAMICS SIMULATION OF VITREOUS SILICA STRUCTURES  

E-Print Network [OSTI]

Dynamics (MD) techniques to simulate glass structures has become a valuable tool for gaining insight1 9/28/98 9:58:58 am, Journal of Non-Crystalline Solids MOLECULAR DYNAMICS SIMULATION OF VITREOUS SILICA STRUCTURES Norman T. Huff*, Owens Corning Science and Technology Center, 2790 Columbus Road

Goddard III, William A.

42

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

SciTech Connect (OSTI)

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

Krishna, Rajamani; van Baten, Jasper M

2011-01-01T23:59:59.000Z

43

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

44

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

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

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

45

Dynamics of a globular protein and its hydration water studied by neutron scattering and MD simulations  

E-Print Network [OSTI]

This review article describes our neutron scattering experiments made in the past four years for the understanding of the single-particle (hydrogen atom) dynamics of a protein and its hydration water and the strong coupling ...

Chen, Sow-Hsin

2010-01-01T23:59:59.000Z

46

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

SciTech Connect (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 of the algorithm, and moving all the major computation parts into GPU, we have reached a speed of 12 s per molecular dynamics (MD) step for a 512 atom system using 256 GPU cards. This is about 20 times faster than the CPU version of the code regardless of the number of CPU cores used. Our tests and analysis on different GPU platforms and configurations shed lights on the optimal GPU deployments for PWP-DFT calculations. An 1800 step MD simulation is used to study the liquid phase properties of GaInP.

Jia, Weile, E-mail: jiawl@sccas.cn [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China) [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing (China); Fu, Jiyun, E-mail: fujy@sccas.cn [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China) [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing (China); Cao, Zongyan, E-mail: zycao@sccas.cn [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China)] [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China); Wang, Long, E-mail: wangl@sccas.cn [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China)] [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China); Chi, Xuebin, E-mail: chi@sccas.cn [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China)] [Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No. 4 South 4th Street, ZhongGuanCun, Beijing 100190 (China); Gao, Weiguo, E-mail: wggao@fudan.edu.cn [School of Mathematical Sciences, Fudan University, 220 Handan Road, Shanghai 200433 (China) [School of Mathematical Sciences, Fudan University, 220 Handan Road, Shanghai 200433 (China); MOE Key Laboratory of Computational Physical Sciences, Fudan University, Shanghai (China); Wang, Lin-Wang, E-mail: lwwang@lbl.gov [Material Science Division, Lawrence Berkeley National Laboratory, One Cyclotron Road Mail Stop 50F Berkeley, CA 94720 (United States)] [Material Science Division, Lawrence Berkeley National Laboratory, One Cyclotron Road Mail Stop 50F Berkeley, CA 94720 (United States)

2013-10-15T23:59:59.000Z

47

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

SciTech Connect (OSTI)

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

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

2013-12-02T23:59:59.000Z

48

Reaction dynamics in polyatomic molecular systems  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

49

Molecular Dynamics Simulations of Supported Pt Nanoclusters  

E-Print Network [OSTI]

¤Introduction and Background ¤Constructing a Physical Model ¤Details of the Simulation ¤Results and Conclusions · Petroleum reformation · Gasification of biomass for biofuels #12;Previous Investigation of NanoclustersMolecular Dynamics Simulations of Supported Pt Nanoclusters Jeffrey Moore #12;A Brief Outline

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

50

Molecular Dynamics Study of the Proposed Proton Transport Pathways...  

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

Dynamics Study of the Proposed Proton Transport Pathways in FeFe-Hydrogenase. Molecular Dynamics Study of the Proposed Proton Transport Pathways in FeFe-Hydrogenase. Abstract:...

51

OpenAtom -- Ab initio molecular dynamics package  

SciTech Connect (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

2008-01-01T23:59:59.000Z

52

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

E-Print Network [OSTI]

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

Cai, Wei

53

A molecular dynamics study of nuclear quantum effect on the diffusion of hydrogen in condensed phase  

SciTech Connect (OSTI)

In this paper, the quantum effect of hydrogen molecule on its diffusivity is analyzed using Molecular Dynamics (MD) method. The path integral centroid MD (CMD) method is applied for the reproduction method of time evolution of the molecules. The diffusion coefficient of liquid hydrogen is calculated using the Green-Kubo method. The simulation is performed at wide temperature region and the temperature dependence of the quantum effect of hydrogen molecule is addressed. The calculation results are compared with those of classical MD results. As a result, it is confirmed that the diffusivity of hydrogen molecule is changed depending on temperature by the quantum effect. It is clarified that this result can be explained that the dominant factor by quantum effect on the diffusivity of hydrogen changes from the swollening the potential to the shallowing the potential well around 30 K. Moreover, it is found that this tendency is related to the temperature dependency of the ratio of the quantum kinetic energy and classical kinetic energy.

Nagashima, Hiroki; Tokumasu, Takashi [Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi (Japan); Tsuda, Shin-ichi [Shinshu University, 77-7 Minamibori, Nagano, Nagano (Japan); Tsuboi, Nobuyuki [Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu, Fukuoka (Japan); Koshi, Mitsuo [Yokohama National University, 79-7 Tokiwadai, Hodogaya, Yokohama, Kanagawa (Japan); Hayashie, A. Koichi [AoyamaGakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa (Japan)

2014-10-06T23:59:59.000Z

54

Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics  

E-Print Network [OSTI]

1 Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision University, Raleigh, NC 27695 Abstract Violation of energy conservation in Poisson-Boltzmann molecular is the observed violation of energy conservation in Poisson-Boltzmann molecular dynamics, in part due to its

Zhao, Hongkai

55

Molecular gas and the dynamics of galaxies  

E-Print Network [OSTI]

In this review, I discuss some highlights of recent research on molecular gas in galaxies; large-scale CO maps of nearby galaxies are being made, which extend our knowledge on global properties, radial gradients, and spiral structure of the molecular ISM. Very high resolution are provided by the interferometers, that reveal high velocity gradients in galaxy nuclei, and formation of embedded structures, like bars within bars. Observation of the CO and other lines in starburst galaxies have questioned the H2-to-CO conversion factor. Surveys of dwarfs have shown how the conversion factor depends on metallicity. The molecular content is not deficient in galaxy clusters, as is the atomic gas. Galaxy interactions are very effective to enhance gas concentrations and trigger starbursts. Nuclear disks or rings are frequently observed, that concentrate the star formation activity. Since the density of starbursting galaxies is strongly increasing with redshift, the CO lines are a privileged tool to follow evolution of galaxies and observe the ISM dynamics at high redshift: due to the high excitation of the molecular gas, the stronger high-$J$ CO lines are redshifted into the observable band, which facilitates the detection.

F. Combes

1999-02-01T23:59:59.000Z

56

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

SciTech Connect (OSTI)

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

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

2014-01-01T23:59:59.000Z

57

Molecular beam studies of reaction dynamics  

SciTech Connect (OSTI)

Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.

Lee, Y.T.

1987-03-01T23:59:59.000Z

58

Accelerated Molecular Dynamics Methods | Department of Energy  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious Rank EERE:YearRound-Up fromDepartment of Energy 601Department ofEnergyDeploymentMolecular Dynamics

59

Molecular dynamics simulation of hydration in myoglobin  

SciTech Connect (OSTI)

This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After salvation of the protein, energy minimization and equilibration of the system, 50 pico seconds of Newtonian dynamics was performed. This data showed that only 4 water molecules are continously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water.

Gu, Wei [New Mexico Univ., Albuquerque, NM (United States). Dept. of Biochemistry; Schoenborn, B.P. [Los Alamos National Lab., NM (United States)

1995-09-01T23:59:59.000Z

60

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

E-Print Network [OSTI]

.1063/1.1669063 Ferroelectric lithium niobate (LiNbO3) has emerged as an important material in surface acoustic wave devices1 the structure and properties of materials. Indeed, atomic-level simulations have been used previously-dynamics MD simulations described here we treat the Coulomb interactions using a direct summation method

Gopalan, Venkatraman

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


61

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

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

Program, and Vehicle Technologies Program Annual Merit Review and Peer Evaluation es058smith2011o.pdf More Documents & Publications Molecular Dynamics Simulation Studies of...

62

Molecular dynamics study of interfacial confinement effects of...  

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

Molecular dynamics study of interfacial confinement effects of aqueous NaCl brines in nanoporous carbon Re-direct Destination: In this paper, studies of aqueous electrolyte...

63

Molecular Dynamics Investigation of Ferrous-Ferric Electron Transfer...  

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

Electron Transfer in a Hydrolyzing Aqueous Solution: Calculation of the pH Molecular Dynamics Investigation of Ferrous-Ferric Electron Transfer in a Hydrolyzing Aqueous Solution:...

64

Molecular Dynamics Simulation Studies of Electrolytes and Electrolyte...  

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

and is lower than the barrier for opening EC cyclic radical. ReaxFF molecular dynamics simulations show similar barriers in gas and condensed phases for these reactions....

65

Molecular dynamics simulations of ion range profiles for heavy...  

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

simulations of ion range profiles for heavy ions in light targets. Molecular dynamics simulations of ion range profiles for heavy ions in light targets. Abstract: The determination...

66

Molecular Dynamics Simulations of Uranyl and Uranyl Carbonate...  

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

Simulations of Uranyl and Uranyl Carbonate Adsorption at Alumino-silicate Surfaces. Molecular Dynamics Simulations of Uranyl and Uranyl Carbonate Adsorption at Alumino-silicate...

67

accurate dynamic molecular: Topics by E-print Network  

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

18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 How accurate is molecular dynamics? Mathematical Physics (arXiv) Summary: Born-Oppenheimer dynamics is shown to provide...

68

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

E-Print Network [OSTI]

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

Goddard III, William A.

69

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

SciTech Connect (OSTI)

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

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

2009-08-14T23:59:59.000Z

70

animated molecular dynamics: Topics by E-print Network  

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

animated molecular dynamics First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Molecular dynamics of B DNA...

71

atom molecular dynamics: Topics by E-print Network  

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

atom molecular dynamics First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Billion Atom Molecular Dynamics...

72

Molecular beam studies of reaction dynamics  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

73

Molecular beam studies of reaction dynamics  

SciTech Connect (OSTI)

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

Lee, Yuan T.

1991-03-01T23:59:59.000Z

74

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

E-Print Network [OSTI]

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

Cai, Wei

75

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

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

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

76

Molecular Dynamics Simulations of Uranyl and Uranyl Carbonate Adsorption at Alumino-silicate Surfaces  

SciTech Connect (OSTI)

Adsorption at mineral surfaces is a critical factor controlling the mobility of uranium(VI) in aqueous environments. Therefore, molecular dynamics (MD) simulations were performed to investigate uranyl(VI) adsorption onto two neutral alumino-silicate surfaces, namely the orthoclase (001) surface and the octahedral aluminum sheet of the kaolinite (001) surface. Although uranyl preferentially adsorbed as a bi-dentate innersphere complex on both surfaces, the free energy of adsorption at the orthoclase surface (-15 kcal mol-1) was significantly more favorable than that at the kaolinite surface (-3 kcal mol-1), which was attributed to differences in surface functional groups and to the ability of the orthoclase surface to dissolve a surface potassium ion upon uranyl adsorption. The structures of the adsorbed complexes compared favorably with X-ray absorption spectroscopy results. Simulations of the adsorption of uranyl complexes with up to three carbonate ligands revealed that uranyl complexes coordinated to up to 2 carbonate ions are stable on the orthoclase surface whereas uranyl carbonate surface complexes are unfavored at the kaolinite surface. Combining the MD-derived equilibrium adsorption constants for orthoclase with aqueous equilibrium constants for uranyl carbonate species indicates the presence of adsorbed uranium complexes with one or two carbonates in alkaline conditions, in support of current uranium(VI) surface complexation models.

Kerisit, Sebastien N.; Liu, Chongxuan

2014-03-03T23:59:59.000Z

77

Considerations and Recent Advances in Molecular Dynamics Introduction  

E-Print Network [OSTI]

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

78

Molecular Dynamics - Solvated Interaction Energy Studies of Protein-Protein Interactions; The MP1-p14 Scaffolding Complex  

SciTech Connect (OSTI)

Using the MP1-p14 scaffolding complex from the mitogen-activated protein kinase signaling pathway as model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. Hot spots are located by virtual alanine-scanning consensus predictions over three different energy functions and two different single-structure representations of the complex. Refined binding affinity predictions for select hot-spot mutations are carried out by applying first-principle methods such as the molecular mechanics generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) to the molecular dynamics (MD) trajectories for mutated and wild-type complexes. Here, predicted hot-spot residues were actually mutated to alanine, and crystal structures of the mutated complexes were determined. Two mutated MP1-p14 complexes were investigated, the p14(Y56A)-mutated complex and the MP1(L63A, L65A)-mutated complex. Alternative ways to generate MD ensembles for mutant complexes, not relying on crystal structures for mutated complexes, were also investigated. The SIE function, fitted on protein-ligand binding affinities, gave absolute binding affinity predictions in excellent agreement with experiment and outperformed standard MM-GBSA predictions when tested on the MD ensembles of Ras-Raf and Ras-RalGDS protein-protein complexes. For wild-type and mutant MP1-p14 complexes, SIE predictions of relative binding affinities were supported by a yeast two-hybrid assay that provided semiquantitative relative interaction strengths. Results on the MP1-mutated complex suggested that SIE predictions deteriorate if mutant MD ensembles are approximated by just mutating the wild-type MD trajectory. The SIE data on the p14-mutated complex indicated feasibility for generating mutant MD ensembles from mutated wild-type crystal structure, despite local structural differences observed upon mutation. For energetic considerations, this would circumvent costly needs to produce and crystallize mutated complexes. The sensitized protein-protein interface afforded by the p14(Y56A) mutation identified here has practical applications in screening-based discovery of first-generation small-molecule hits for further development into specific modulators of the mitogen-activated protein kinase signaling pathway.

Cui,Q.; Sulea, T.; Schrag, J.; Munger, C.; Hung, M.; Naim, M.; Cygler, M.; Purisima, E.

2008-01-01T23:59:59.000Z

79

Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene  

E-Print Network [OSTI]

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

Yi, Peng

80

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

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

than the ions on lattice sites in perfect MO2. Citation: Xiao HY, Y Zhang, and WJ Weber.2012."Ab Initio Molecular Dynamics Simulations of Low-Energy Recoil Eventsin ThO2,...

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

Molecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion  

E-Print Network [OSTI]

. Lozano June 2010 SSL # 6-10 #12;#12;Molecular Dynamics Modeling of Ionic Liquids in Electrospray Propulsion Nanako Takahashi, Paulo C. Lozano June 2010 SSL # 6-10 This work is based on the unaltered text

82

CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS  

SciTech Connect (OSTI)

This is the final progress report for Award DE-SC0004920, entitled 'Characterizing coupled charge transport with multi scale molecular dynamics'. The technical abstract will be provided in the uploaded report.

Swanson, Jessica

2011-08-31T23:59:59.000Z

83

Molecular Dynamics Simulation Studies of Electrolytes andElectrolyte...  

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

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

84

Ab initio molecular dynamics simulations of low energy recoil...  

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

of low energy recoil events in ceramics . Ab initio molecular dynamics simulations of low energy recoil events in ceramics . Abstract: The recent progress in the use of large-scale...

85

antisymmetrized molecular dynamics: Topics by E-print Network  

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

antisymmetrized molecular dynamics First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Superdeformed ?...

86

Dynamic transition in an atomic glass former: a molecular dynamics evidence  

E-Print Network [OSTI]

We find that a Lennard-Jones mixture displays a dynamic phase transition between an active regime and an inactive one. By means of molecular dynamics simulations and of a finite-size study, we show that the space time dynamics in the supercooled regime coincides with a dynamic first order transition point.

Estelle Pitard; Vivien Lecomte; Frédéric Van Wijland

2011-11-28T23:59:59.000Z

87

Dynamic Load Balancing for the Distributed Mining of Molecular Structures  

E-Print Network [OSTI]

Dynamic Load Balancing for the Distributed Mining of Molecular Structures Giuseppe Di Fatta, Member the data mining community, where algorithms to find frequent graphs have received increasing attention over a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular

Berthold, Michael R.

88

Molecular dynamics simulation of Li surface erosion and bubble formation  

E-Print Network [OSTI]

.49.Sf Keywords: Liquid metal; Lithium; Ion-surface interactions 1. Introduction Bombardment Structure and dynamical properties of liquid Li containing He atoms were studied by the Molecular Dynamics characteristics of light low-energy ions on a liquid Li surface and their diffusion properties have attracted much

Harilal, S. S.

89

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

90

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

SciTech Connect (OSTI)

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

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

2008-01-01T23:59:59.000Z

91

Dynamical analysis of highly excited molecular spectra  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

92

First principles molecular dynamics without self-consistent field optimization  

SciTech Connect (OSTI)

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

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

2014-01-28T23:59:59.000Z

93

Interaction of Polar and Nonpolar Organic Pollutants with Soil Organic Matter: Sorption Experiments and Molecular Dynamics Simulation  

E-Print Network [OSTI]

The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question How organic pollutants interact with SOM? is lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model followed by carrying out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), representing the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and the theoretical outcomes explored four major points regarding sorption of SAA and HCB on soil. 1. The interaction depends on the SOM chemical composition mo...

Ahmed, Ashour A; Aziz, Saadullah G; Hilal, Rifaat H; Elroby, Shaaban A; Al-Youbi, Abdulrahman O; Leinweber, Peter; Kühn, Oliver

2014-01-01T23:59:59.000Z

94

Molecular simulation study of homogeneous crystal nucleation in n-alkane melts  

E-Print Network [OSTI]

This work used molecular dynamics (MD) and Monte Carlo (MC) method to study the homogeneous crystal nucleation in the melts of n-alkanes, the simplest class of chain molecules. Three n-alkanes with progressive chain length ...

Yi, Peng, Ph. D. Massachusetts Institute of Technology

2011-01-01T23:59:59.000Z

95

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

E-Print Network [OSTI]

Myoglobin-CO Substate Structures and Dynamics: Multidimensional Vibrational Echoes and Molecular to establishing the relationships between protein structure and protein function.1-5 Protein dynamics occur structural specificity to assign these dynamics to particular atomic motions. Computational tech- niques

Fayer, Michael D.

96

Plasticity of metallic nanostructures : molecular dynamics simulations   

E-Print Network [OSTI]

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

Healy, Con

2014-11-27T23:59:59.000Z

97

State-to-state dynamics of molecular energy transfer  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

98

Last Name First Name Degree Abookire Susan MD, MPH  

E-Print Network [OSTI]

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

Paulsson, Johan

99

Multiple time step integrators in ab initio molecular dynamics  

SciTech Connect (OSTI)

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

Luehr, Nathan; Martínez, Todd J. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States) [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); The PULSE Institute, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Markland, Thomas E. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)] [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

2014-02-28T23:59:59.000Z

100

VUV studies of molecular photofragmentation dynamics  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

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

Massively parallel molecular dynamics simulations of  

E-Print Network [OSTI]

experimental studies pioneered by Dobson and coworkers have shown that amyloids and fibrils can be formed of their three- dimensional (3D) structure and dynamics at the atomic level. This understanding can not only from the traditional beta-amyloid peptides but also from almost any proteins, such as lysozyme

Berne, Bruce J.

102

DYNAMICS OF INFRARED MULTIPHOTON DISSOCIATION OF SF6 BY MOLECULAR BEAM METHOD  

E-Print Network [OSTI]

molecular beam apparatus has been adapted to study the dynamics of excitationdynamics of molecular decomposition and the degree of vibrational excitation,

Grant, E.R.

2010-01-01T23:59:59.000Z

103

Optical pumpterahertz probe spectroscopy of dyes in solutions: Probing the dynamics of liquid solvent or solid precipitate?  

E-Print Network [OSTI]

dynamics simulations to investigate ultrafast dynamics following electronic excitation of Coumarin 153 and dynamics, preferably at a molecular level of reso- lution. In particular, solvent relaxation following body of time-resolved spectro- scopic studies, as well as molecular dynamics MD simula- tions have been

KuÂ?el, Petr

104

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine  

E-Print Network [OSTI]

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

Rapaport, Dennis C.

105

A Molecular Dynamics Simulation of Hydrogen Storage with SWNTs  

E-Print Network [OSTI]

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

Maruyama, Shigeo

106

Molecular dynamics simulations of boronnitride nanotubes embedded in  

E-Print Network [OSTI]

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

Ferrari, Patrik L.

107

MOLECULAR DYNAMICS SIMULATION OF THERMAL BOUNDARY CONDUCTANCE BETWEEN SWNT AND  

E-Print Network [OSTI]

MOLECULAR DYNAMICS SIMULATION OF THERMAL BOUNDARY CONDUCTANCE BETWEEN SWNT AND SURROUNDING FLUIDS JinHyeok Cha, Shohei Chiashi, Junichiro Shiomi, and Shigeo Maruyama* Department of Mechanical applications. In particular, the thermal boundary conductance (TBC) K between an SWNT and surrounding fluid

Maruyama, Shigeo

108

Molecular Dynamics of Methanol Monocation (CH3OH+ ) in Strong  

E-Print Network [OSTI]

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

Schlegel, H. Bernhard

109

Molecular Determinants and Dynamics of Hepatitis C Virus Secretion  

E-Print Network [OSTI]

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

110

Hydrogen Raman shifts in carbon nanotubes from molecular dynamics simulation  

E-Print Network [OSTI]

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

Brenner, Donald W.

111

MD user's manual  

SciTech Connect (OSTI)

MD is the S-1 Mark IIA machine debugger. It is the hardware equivalent of a software symbolic debugger. It consists of a user-level program which executes on a VAX computer running Berkeley UNIX and a device driver which resides within the UNIX kernel. It communicates with the S-1 Mark IIA through a front-end interface attached to the UNIBUS of the VAX. The first section of this report describes MD's user interface and command set. The second section describes the virtual machine interface through which MD and the UNIX device driver communicate.

Correll, S.

1988-04-01T23:59:59.000Z

112

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

E-Print Network [OSTI]

Calculation of heat capacities of light and heavy water by path-integral molecular dynamics-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water

Nielsen, Steven O.

113

A Molecular Dynamics Investigation of the Titration of a TrivalentAque...  

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

the Titration of a TrivalentAqueous Ion. A Molecular Dynamics Investigation of the Titration of a TrivalentAqueous Ion. Abstract: We carried out a series of molecular dynamics...

114

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

E-Print Network [OSTI]

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

Hinrichs, Nina Singhal

115

Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method  

SciTech Connect (OSTI)

The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

Nakata, Hiroya [Tokyo Institute of Technology; Schmidt, Michael W [Ames Laboratory; Fedorov, Dmitri G [National Institute of Advanced Industrial Science and Technology (AIST); Kitaura, Kazuo [Kobe University; Nakamura, Shinichiro [Nakamura Lab; Gordon, Mark S [Ames Laboratory

2014-10-16T23:59:59.000Z

116

Study of the subpicosecond rotational molecular dynamics in liquids  

SciTech Connect (OSTI)

The parameters of the femtosecond vibration-rotation molecular dynamics of liquid acetonitrile CH{sub 3}CN, trimethylacetonitrile (CH{sub 3}){sub 3}CCN, propionitrile CH{sub 3}CH{sub 2}CN, fluoroform CHF{sub 3}, and chloroform CHCl{sub 3} are found by analysing the ultrafast optical Kerr effect. The influence of the molecular structure on the features of rotational (diffusion and libration) motions is studied. It is shown that the distribution of libration frequencies is described by the Maxwell distribution. (laser applications and other topics in quantum electronics)

Nikiforov, V G; Lobkov, Vladimir S [E.K.Zavoisky Physical-Technical Institute, Kazan Scientific Center, Russian Academy of Sciences, Kazan (Russian Federation)

2006-10-31T23:59:59.000Z

117

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

E-Print Network [OSTI]

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

Maruyama, Shigeo

118

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

E-Print Network [OSTI]

January 2004; accepted 11 March 2004 Ultrafast photoinduced dynamics of electronic excitation in molecularElectron-nuclear correlations for photo-induced dynamics in molecular dimers Dmitri S. Kilin, Yuri dimers is drastically affected by the dynamic reorganization of inter- and intra- molecular nuclear

119

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

SciTech Connect (OSTI)

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

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

2013-11-15T23:59:59.000Z

120

Prediction of Thermal Conductivity for Irradiated SiC/SiC Composites by Informing Continuum Models with Molecular Dynamics Data  

SciTech Connect (OSTI)

This article proposes a new method to estimate the thermal conductivity of SiC/SiC composites subjected to neutron irradiation. The modeling method bridges different scales from the atomic scale to the scale of a 2D SiC/SiC composite. First, it studies the irradiation-induced point defects in perfect crystalline SiC using molecular dynamics (MD) simulations to compute the defect thermal resistance as a function of vacancy concentration and irradiation dose. The concept of defect thermal resistance is explored explicitly in the MD data using vacancy concentrations and thermal conductivity decrements due to phonon scattering. Point defect-induced swelling for chemical vapor deposited (CVD) SiC as a function of irradiation dose is approximated by scaling the corresponding MD results for perfect crystal ?-SiC to experimental data for CVD-SiC at various temperatures. The computed thermal defect resistance, thermal conductivity as a function of grain size, and definition of defect thermal resistance are used to compute the thermal conductivities of CVD-SiC, isothermal chemical vapor infiltrated (ICVI) SiC and nearly-stoichiometric SiC fibers. The computed fiber and ICVI-SiC matrix thermal conductivities are then used as input for an Eshelby-Mori-Tanaka approach to compute the thermal conductivities of 2D SiC/SiC composites subjected to neutron irradiation within the same irradiation doses. Predicted thermal conductivities for an irradiated Tyranno-SA/ICVI-SiC composite are found to be comparable to available experimental data for a similar composite ICVI-processed with these fibers.

Nguyen, Ba Nghiep; Gao, Fei; Henager, Charles H.; Kurtz, Richard J.

2014-05-01T23:59:59.000Z

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.


121

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

122

Fast parallel algorithms for short-range molecular dynamics  

SciTech Connect (OSTI)

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a subset of atoms; the second assigns each a subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently -- those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 10,000,000 atoms on three parallel supercomputers, the nCUBE 2, Intel iPSC/860, and Intel Delta. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and the Intel Delta performs about 30 times faster than a single Y-MP processor and 12 times faster than a single C90 processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Plimpton, S.

1993-05-01T23:59:59.000Z

123

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

SciTech Connect (OSTI)

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

Hall, G.E.

2011-05-31T23:59:59.000Z

124

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

SciTech Connect (OSTI)

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

Hall G. E.; Goncharov, V.

2012-05-29T23:59:59.000Z

125

Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films  

E-Print Network [OSTI]

is almost a constant for ??f /? 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...

Kim, Bo Hung

2010-07-14T23:59:59.000Z

126

A molecular understanding of the dynamic mechanism of aquaporin osmosis  

E-Print Network [OSTI]

AQPs (aquaporins), the rapid water channels of cells, play a key role in maintaining osmotic equilibrium of cells. In this paper, we reported the dynamic mechanism of AQP osmosis at the molecular level. A theoretical model based on molecular dynamics was carried out and verified by the published experimental data. The reflection coefficients ({\\sigma}) of neutral molecules are mainly decided by their relative size with AQPs, and increase with a third power up to a constant value 1. This model also indicated that the reflection coefficient of a complete impermeable solute can be smaller than 1. The H+ concentration of solution can influence the driving force of the AQPs by changing the equivalent diameters of vestibules surrounded by loops with abundant polar amino acids. In this way, pH of solution can regulate water permeability of AQPs. Therefore, an AQP may not only work as a switch to open or close, but as a rapid response molecular valve to control its water flow. The vestibules can prevent the channel blockage of AQPs by a primary screening before their constriction region. This model also provides a prediction tool to the structure of AQPs by the {\\sigma}s of special solutes. The puzzling variance between {\\sigma} to erythrocytes AQP1 and {\\sigma} to oocytes-expressing AQP1 was also explained.

Liangsuo Shua; Suyi Huang; Xin Qian; Xiyun Wanga; Yixin Lin; Kai Tan; Chaohui Shu; Shiping Jin

2014-03-31T23:59:59.000Z

127

Structure and dynamics of nonaqueous mixtures of dipolar liquids. II. Molecular dynamics simulations  

E-Print Network [OSTI]

2000 Molecular dynamics simulations have been used to study mixtures of acetone/methanol, acetonitrile/ methanol, and acetone/acetonitrile over their entire composition range. Using the effective pair potentials in these two papers is on the nonaqueous dipolar liquid mixtures of acetone/methanol, acetonitrile

128

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

SciTech Connect (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

129

Dynamics of Functionalized Surface Molecular Monolayers Studied with Ultrafast Infrared Vibrational Spectroscopy  

E-Print Network [OSTI]

Dynamics of Functionalized Surface Molecular Monolayers Studied with Ultrafast Infrared Vibrational by excitation transfer and molecular reorientation. The HDTG experiments show no evidence of anisotropy decay of molecular monolayers depend on the structure and dynamics of the surface-attached molecules. New tools

Fayer, Michael D.

130

The coupling of dynamics and molecular chemistry in galaxies  

E-Print Network [OSTI]

While the best tracer of the molecular component and its dynamics in galaxies is the CO molecule, which excitation is revealed by its isotopic and (2-1)/(1-0) ratios, the denser gas is revealed by molecules such as HCN, HNC, HCO+ or CN, which are now widely used to probe star formation regions, or to quantify the impact of the nuclear activity on the interstellar medium. This paper reviews recent observations in nearby galaxies, where these molecular line ratios serve as diagnostic tools of the physical conditions of the gas and also of its chemical properties. Those differ significantly according to the proximity of an AGN or of a starburst. The origin of the differences is not yet well known and could be due to different densities, temperatures, chemical abundances or non-collisional excitation of the gas (e.g. Aalto et al 2007, Krips et al 2007). HCN or HNC line enhancements can be caused not only by higher gas densities/temperatures, but also UV/X-ray radiation, and global IR pumping. The chemistry can be dominated by PDR regions near a starburst, or X-ray dominated in a molecular torus surrounding an AGN (XDR regions). The molecular line ratios expected in those regions vary according to the different models (Meijerink et al. 2007).

F. Combes

2007-09-24T23:59:59.000Z

131

Simulation studies of slow dynamics of hydration water in lysozyme : hydration level dependence and comparison with experiment using new time domain analysis  

E-Print Network [OSTI]

A series of Molecular Dynamics (MD) simulations using the GROMACS® package has been performed in this thesis. It is used to mimic and simulate the hydration water in Lysozyme with three different hydration levels (h = 0.3, ...

Kim, Chansoo, S.M. Massachusetts Institute of Technology

2008-01-01T23:59:59.000Z

132

Large-Scale Molecular Dynamics Simulations for Highly Parallel Infrastructures  

E-Print Network [OSTI]

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

Pazúriková, Jana

2014-01-01T23:59:59.000Z

133

Higher-order symplectic Born-Oppenheimer molecular dynamics  

SciTech Connect (OSTI)

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

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

2009-01-01T23:59:59.000Z

134

Generalized Extended Lagrangian Born-Oppenheimer Molecular Dynamics  

E-Print Network [OSTI]

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

Niklasson, Anders M N

2014-01-01T23:59:59.000Z

135

Large scale molecular dynamics modeling of materials fabrication processes  

SciTech Connect (OSTI)

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

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

1994-02-01T23:59:59.000Z

136

Molecular nonlinear dynamics and protein thermal uncertainty quantification  

SciTech Connect (OSTI)

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

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

2014-03-15T23:59:59.000Z

137

Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite  

E-Print Network [OSTI]

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.

A. Ito; H. Nakamura

2006-04-26T23:59:59.000Z

138

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

E-Print Network [OSTI]

Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole chemical re- action. In this paper we report the first application of molecular dynamics simulation methods to model the excited state double-proton transfer dynamics involved in the tau- tomerization reaction

Miller, William H.

139

High temperature phonon dispersion in graphene using classical molecular dynamics  

SciTech Connect (OSTI)

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

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

2014-04-24T23:59:59.000Z

140

Equilibration of experimentally determined protein structures for molecular dynamics simulation Emily B. Walton and Krystyn J. VanVliet*  

E-Print Network [OSTI]

Equilibration of experimentally determined protein structures for molecular dynamics simulation well studied, ranging from refinements of static x-ray crystallog- raphy structures to dynamic Preceding molecular dynamics simulations of biomolecular interactions, the molecule of interest is often

Van Vliet, Krystyn 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.


141

Predictors of cavitation in glassy polymers under tensile strain: a coarse grained molecular dynamics  

E-Print Network [OSTI]

Predictors of cavitation in glassy polymers under tensile strain: a coarse grained molecular the cavity position before the cavitation occurs. Even if the localization of a cavity is not directly: Cavitation, Plasticity, Computational modeling, Molecular dynamics simulation, Mechanical properties. 1

Paris-Sud XI, Université de

142

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

SciTech Connect (OSTI)

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

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

2014-01-07T23:59:59.000Z

143

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

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

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

Plimpton, Steve; Thompson, Aidan; Crozier, Paul

144

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

E-Print Network [OSTI]

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

Liao, Jun-min

2006-01-01T23:59:59.000Z

145

E-Print Network 3.0 - accelerated molecular dynamics Sample Search...  

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

77 Summary: . The molecular synchrotron1 is analogous to charged-particle accelerators. It borrows the techniques of high... electronic potentials governing the dynamics...

146

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

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

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

147

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

SciTech Connect (OSTI)

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

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

2014-04-21T23:59:59.000Z

148

Spatially resolved dynamic structure factor of finite systems from molecular dynamics simulations  

SciTech Connect (OSTI)

The dynamical response of metallic clusters up to 10{sup 3} atoms is investigated using the restricted molecular dynamics simulations scheme. Exemplarily, a sodium like material is considered. Correlation functions are evaluated to investigate the spatial structure of collective electron excitations and the optical response of laser-excited clusters. In particular, the spectrum of bilocal correlation functions shows resonances representing different modes of collective excitations inside the nano plasma. The spatial structure, the resonance energy, and the width of the eigenmodes have been investigated for various values of electron density, temperature, cluster size, and ionization degree. Comparison with bulk properties is performed and the dispersion relation of collective excitations is discussed.

Raitza, Thomas; Roepke, Gerd; Reinholz, Heidi; Morozov, Igor [Institut fuer Physik, Universitaet Rostock, D-18051 Rostock (Germany); Institut fuer Theoretische Physik, Johannes-Kepler-Universitaet Linz, A-4040 Linz, Austria and Institute of Physics, University of Western Australia, Perth, WA 6009 (Australia); Joint Institute for High Temperatures of RAS, 13 Izhorskaya Street, Building 2, Moscow RU-125412 (Russian Federation)

2011-09-15T23:59:59.000Z

149

Molecular Dynamics Study of Vibrational Excitation Dynamics and Desorption in Solid O2 Lukasz Dutkiewicz,*, Robert E. Johnson, Akos Vertes, and Roman Pedrys  

E-Print Network [OSTI]

Molecular Dynamics Study of Vibrational Excitation Dynamics and Desorption in Solid O2 LukaszVed: September 8, 1998 Molecular dynamics calculations were performed to describe vibrational to translational is the conversion of internal energy to lattice motion and desorption. Therefore, we use molecular dynamics

Vertes, Akos

150

Mechanical unfolding of a beta-hairpin using molecular dynamics  

SciTech Connect (OSTI)

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

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

1999-10-16T23:59:59.000Z

151

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

SciTech Connect (OSTI)

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

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

2014-10-15T23:59:59.000Z

152

A Molecular Dynamics Simulation of Hydrogen Storage by SWNTs Tatsuto Kimuraa  

E-Print Network [OSTI]

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

Maruyama, Shigeo

153

Molecular Dynamics Simulation of Hydrogen Storage with Single Walled Carbon Nanotubes  

E-Print Network [OSTI]

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

Maruyama, Shigeo

154

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

155

AB INITIO MOLECULAR-DYNAMICS SIMULATIONS OF DYE MOLECULES ON SURFACES  

E-Print Network [OSTI]

AB INITIO MOLECULAR-DYNAMICS SIMULATIONS OF DYE MOLECULES ON SURFACES M. SUGIHARA1 , H. MEYER2 , P, Austria We have performed ab initio total energy calculations and molecular-dynamics sim- ulations of dye molecules on NaCl(100) surfaces and in water. The flat dye molecule trimethine, [C19H17N2O2]+, which forms

Entel, P.

156

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

E-Print Network [OSTI]

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

Bjørnstad, Ottar Nordal

157

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

E-Print Network [OSTI]

Exceptional tools for studying the structure and dynamics of materials at the molecular level, complementary to x-rays, in under- standing the structure and dynamics of materials at the molecular level · Soft matter · Magnetism and superconductivity · Life sciences · Structural biology · Complex fluids

158

A dynamical definition of quasibound molecular clusters Sarah A. Harris and Ian J. Forda)  

E-Print Network [OSTI]

A dynamical definition of quasibound molecular clusters Sarah A. Harris and Ian J. Forda of a quasibound cluster are identified through a retrospective dynamical definition. The trajectory of a molecular is satisfied, however, at the instant that the energy of the departing molecule in the center of mass frame

Ford, Ian

159

Photoexcited breathers in conjugated polyenes: An excited-state molecular dynamics study  

E-Print Network [OSTI]

for the simulation of excited- state molecular dynamics in extended molecular systems with sizes up to hundreds cells (9), display panels (10­12), photovoltaic cells (13­15), photodetectors (16­18), transistors (19 of -conjugated molecular systems is challenging because of electronic correlation effects and strong electron

Tretiak, Sergei

160

Shell Model Dynamics of HCl on the MgO(001) Surface Terrace Andreas Markmann,1  

E-Print Network [OSTI]

are then used to aid the analysis of MD calculations. After equilibrium dynamics, a sudden excitation of the OH of molecular dynamics using specially tailored laser fields. The reaction of hydrogen chloride moleculesShell Model Dynamics of HCl on the MgO(001) Surface Terrace Andreas Markmann,1 Jacob L. Gavartin,2

Markmann, Andreas

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


161

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

E-Print Network [OSTI]

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

Tuscia, Università Degli Studi Della

162

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

SciTech Connect (OSTI)

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

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

2010-01-01T23:59:59.000Z

163

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

SciTech Connect (OSTI)

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

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

2014-03-28T23:59:59.000Z

164

Molecular dynamics simulation studies of structural and dynamical properties of rapidly quenched Al  

SciTech Connect (OSTI)

The structural and dynamical properties of rapidly quenched Al are studied by molecular dynamics simulations. The pair-correlation function of high temperature liquid Al agrees well with the experimental results. Different cooling rates are applied with high cooling rates leading to glass formation, while low cooling rates leading to crystallization. The local structures are characterized by Honeycutt–Andersen indices and Voronoi tessellation analysis. The results show that for high cooling rates, the local structures of the liquid and glassy Al are predominated by icosahedral clusters, together with considerable amount of face-centered cubic and hexagonal close packed short-range orders. These short-range order results are further confirmed using the recently developed atomic cluster alignment method. Moreover, the atomic cluster alignment clearly shows the crystal nucleation process in supercooled liquid of Al. Finally, the mean square displacement for the liquid is also analyzed, and the corresponding diffusion coefficient as a function of temperature is calculated.

Shen, B. [Fudan University; Liu, C. Y. [Zhengzhou University; Jia, Y. [Zhengzhou University; Yue, G. Q. [Fudan University; Ke, F. S. [Fudan University; Zhao, H. B. [Fudan University; Chen, L. Y. [Fudan University; Wang, S. Y. [Ames Laboratory; Wang, Cai-Zhuang [Ames Laboratory; Ho, Kai-Ming [Ames Laboratory

2013-06-11T23:59:59.000Z

165

A time-dependent momentum-space density functional theoretical approach for electron transport dynamics in molecular devices  

E-Print Network [OSTI]

for electron transport dynamics in molecular devices Zhongyuan Zhou(a) and Shih-I Chu Department of Chemistry and structures PACS 85.65.+h ­ Molecular electronic devices PACS 71.15.Pd ­ Molecular dynamics calculations (Carr) approach in momentum (P) space for the study of electron transport in molecular devices under arbitrary

Chu, Shih-I

166

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

E-Print Network [OSTI]

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

D. C. Rapaport

2014-11-13T23:59:59.000Z

167

Achieving energy conservation in PoissonBoltzmann molecular dynamics: Accuracy and precision with finite-difference algorithms  

E-Print Network [OSTI]

Achieving energy conservation in Poisson­Boltzmann molecular dynamics: Accuracy and precision t Violation of energy conservation in Poisson­Boltzmann molecular dynamics, due to the limited accuracy method. One of the issues is the observed violation of energy conservation in PB molecular dynamics

Zhao, Hongkai

168

Semiclassical Molecular Dynamics Simulations of the Excited State Photodissociation Dynamics of H2O in the A1B1 Band  

E-Print Network [OSTI]

Semiclassical Molecular Dynamics Simulations of the Excited State Photodissociation Dynamics of H2O modeled in terms of classical molecular dynamics simulations.9,12 However, the photodissociation from The photodissociation dynamics of H2O in the A1 B1 band is investigated by implementing a recently developed time

Wu, Yinghua

169

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

SciTech Connect (OSTI)

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

170

Molecular Dynamics Simulations of CO2 Formation in Interstellar Ices  

E-Print Network [OSTI]

CO2 ice is one of the most abundant components in ice-coated interstellar ices besides H2O and CO, but the most favorable path to CO2 ice is still unclear. Molecular dynamics calculations on the ultraviolet photodissociation of different kinds of CO-H2O ice systems have been performed at 10 K in order to demonstrate that the reaction between CO and an OH molecule resulting from H2O photodissociation through the first excited state is a possible route to form CO2 ice. However, our calculations, which take into account different ice surface models, suggest that there is another product with a higher formation probability ((3.00+-0.07)x10-2), which is the HOCO complex, whereas the formation of CO2 has a probability of only (3.6+-0.7)x10-4. The initial location of the CO is key to obtain reaction and form CO2: the CO needs to be located deep into the ice. The HOCO complex becomes trapped in the cold ice surface in the trans-HOCO minimum because it quickly loses its internal energy to the surrounding ice, preventi...

Arasa, Carina; van Dishoeck, Ewine F; Kroes, Geert-Jan

2013-01-01T23:59:59.000Z

171

Molecular Simulation of Reaction and Adsorption in Nanochemical Devices  

E-Print Network [OSTI]

Reaction Ensemble Molecular Dynamics (DCC- RxMD) method, allows for the calculation of both equilibrium a nanoscale reactor in the presence of a semipermeable nanomembrane modelling silicalite. We studied in all the nanoscale membrane reactor systems considered. The results of this work demonstrate

Lisal, Martin

172

CANCELLED Molecular dynamics simulations of noble gases in liquidwater: Solvati on structure, self-diffusion, and kinetic isotopeeffect  

SciTech Connect (OSTI)

Despite their great importance in low-temperaturegeochemistry, self-diffusion coefficients of noble gas isotopes in liquidwater (D) have been measured only for the major isotopes of helium, neon,krypton and xenon. Data on the self-diffusion coefficients of minor noblegas isotopes are essentially non-existent and so typically are estimatedby a kinetic theory model in which D varies as the inverse square root ofthe isotopic mass (m): D proportional to m-0.5. To examine the validityof the kinetic theory model, we performed molecular dynamics (MD)simulations of the diffusion of noble gases in ambient liquid water withan accurate set of noble gas-water interaction potentials. Our simulationresults agree with available experimental data on the solvation structureand self-diffusion coefficients of the major noble gas isotopes in liquidwater and reveal for the first time that the isotopic mass-dependence ofall noble gas self-diffusion coefficients has the power-law form Dproportional to m-beta with 0

Bourg, I.C.; Sposito, G.

2007-05-25T23:59:59.000Z

173

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

E-Print Network [OSTI]

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

Kyoko K. Tanaka; Akio Kawano; Hidekazu Tanaka

2014-02-26T23:59:59.000Z

174

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

E-Print Network [OSTI]

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

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

2011-07-24T23:59:59.000Z

175

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

SciTech Connect (OSTI)

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

Pokorna, Sarka; Jurkiewicz, Piotr; Hof, Martin, E-mail: martin.hof@jh-inst.cas.cz [J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic); Vazdar, Mario [Division of Organic Chemistry and Biochemistry, Rudjer Boškovi? Institute, P.O.B. 180, HR-10002 Zagreb (Croatia); Cwiklik, Lukasz [J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8 (Czech Republic); Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic); Jungwirth, Pavel [Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic); Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere (Finland)

2014-12-14T23:59:59.000Z

176

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

E-Print Network [OSTI]

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

Southern California, University of

177

Dynamics of excess electrons in atomic and molecular clusters  

E-Print Network [OSTI]

Time-Resolved Dynamics in Acetonitrile Cluster Anions (CH 3Time-resolved dynamics in acetonitrile clusters anions (CH 3resolved dynamics in acetonitrile clusters anions (CH 3 CN)

Young, Ryan Michael

2011-01-01T23:59:59.000Z

178

Susan P. Taylor, MD Shorewood, Wisconsin  

E-Print Network [OSTI]

Noxapater, Mississippi Corey W. Gilliland, MD Mesa, Arizona Jeanne V. Hamel, MD Elk Grove, California Steven Manhattan, Kansas Dean Afif Shoucair, DO Frankfort, Illinois John Mitchell Simson, MD Albuquerque, New

179

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

SciTech Connect (OSTI)

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

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

2013-12-21T23:59:59.000Z

180

Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics  

E-Print Network [OSTI]

The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 K and 400 K. Density-functional theory, paired with a modern exchange-correlation functional (PBE), provides an excellent agreement for the structural properties and binding energy of the water monomer and dimer. On the other hand, the structural and dynamical properties of the bulk liquid show a clear enhancement of the local structure compared to experimental results; a distinctive transition to liquid-like diffusion occurs in the simulations only at the elevated temperature of 400 K. Extensive runs of up to 50 picoseconds are needed to obtain well-converged thermal averages; the use of ultrasoft or norm-conserving pseudopotentials and the larger plane-wave sets associated with the latter choice had, as expected, only negligible effects on the final result. Finite-size effects in the liquid state are found to be mostly negligible for systems as small as 32 molecules per unit cell.

P. H-L. Sit; Nicola Marzari

2005-04-08T23:59:59.000Z

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.


181

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

E-Print Network [OSTI]

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

Gaddamanugu, Dhatri

2010-07-14T23:59:59.000Z

182

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

E-Print Network [OSTI]

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...

Baty, Austin Alan

2013-02-06T23:59:59.000Z

183

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

E-Print Network [OSTI]

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

Smith, Bradley D.

184

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

E-Print Network [OSTI]

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

Zhang, Luzheng

185

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

E-Print Network [OSTI]

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

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

2014-12-15T23:59:59.000Z

186

The role of the molecular dynamics in the local intensity instabilities of large aperture dye lasers  

E-Print Network [OSTI]

The role of the molecular dynamics in the local intensity instabilities of large aperture dye fluctuations of large aperture dye lasers, and find dependencies on solvent viscosity and active molecular size dye lasers are used in a great deal of practical applications, from isotope enrichment to photody

Rey Juan Carlos, Universidad

187

Intramolecular vibronic dynamics in molecular solids: C60 L. Kjeldgaard,1,  

E-Print Network [OSTI]

Intramolecular vibronic dynamics in molecular solids: C60 L. Kjeldgaard,1, * T. Käämbre,1, J RPES and resonant inelastic x-ray scattering RIXS . Excitation as a function of energy within the lowest unoccupied molecular orbital resonance yielded strong oscillations in intensity and dispersion

Schnadt, Joachim

188

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

E-Print Network [OSTI]

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

Sawyer, Wallace

189

ab-initio molecular dynamics: Topics by E-print Network  

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

ab-initio molecular dynamics First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Ab-Initio Molecular...

190

ab initio molecular-dynamics: Topics by E-print Network  

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

ab initio molecular-dynamics First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Ab-Initio Molecular...

191

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

SciTech Connect (OSTI)

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

Krishna, Rajamani; van Baten, Jasper M.

2011-01-01T23:59:59.000Z

192

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

E-Print Network [OSTI]

Where to find the mind: Identifying the scale of cognitive dynamics Luke Conlin, Department as occurring within individual minds and those that treat it as irreducibly distributed or situated in material and social contexts. We contend that accounts of individual minds as complex systems are theoretically

Hammer, David

193

Crossed molecular beam studies of atmospheric chemical reaction dynamics  

SciTech Connect (OSTI)

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

Zhang, Jingsong

1993-04-01T23:59:59.000Z

194

Glassy dynamics, aging in mobility, and structural relaxation of strongly adsorbed polymer films: Corrugation or confinement?  

E-Print Network [OSTI]

Glassy dynamics, aging in mobility, and structural relaxation of strongly adsorbed polymer films of Western Ontario, London, Ontario N6A 5B7, Canada Abstract. A molecular dynamics simulation (MD. The model reproduces many experimentally observed features such as logarithmic aging of structural

Mueser, Martin

195

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

E-Print Network [OSTI]

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

Rapaport, Dennis C.

196

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

E-Print Network [OSTI]

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

Hammes-Schiffer, Sharon

197

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

SciTech Connect (OSTI)

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

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

2013-09-21T23:59:59.000Z

198

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

E-Print Network [OSTI]

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

Ulm, Universität

199

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

E-Print Network [OSTI]

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

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

2006-12-20T23:59:59.000Z

200

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

SciTech Connect (OSTI)

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

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

1994-12-01T23:59:59.000Z

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


201

Influence of temperature and viscosity on anthracene rotational diffusion in organic solvents: Molecular dynamics simulations and fluorescence anisotropy study  

E-Print Network [OSTI]

Molecular dynamics simulations and fluorescenceanisotropy decay measurements are used to investigate the rotational diffusion of anthracene in two organic solvents—cyclohexane and 2-propanol—at several temperatures. Molecular ...

Jas, Gouri S.; Wang, Yan; Pauls, Steven W.; Johnson, Carey K.; Kuczera, Krzysztof

1997-01-01T23:59:59.000Z

202

Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: a non-equilibrium molecular dynamics study  

E-Print Network [OSTI]

The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear is investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity and normal stress differences of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid. The corresponding molecular structure is studied at the same shear rates and temperatures. The Cooee bitumen is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. The nanoaggregates are shown to break up at very high shear rates, leading only to a minor effect on the viscosity of the mixture. At low shear rates, bitumen can be seen as a colloidal suspension of nanoaggregates in a solvent. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified...

Lemarchand, Claire A; Todd, Billy D; Daivis, Peter J; Hansen, Jesper S

2015-01-01T23:59:59.000Z

203

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

SciTech Connect (OSTI)

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

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

2013-12-07T23:59:59.000Z

204

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

E-Print Network [OSTI]

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

Lisal, Martin

205

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

E-Print Network [OSTI]

The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and/or crystal growth) becoming small- thus a matter of kinetics. However there is evidence, dating back to the empirics of coal briquetting for maximum trucking efficiency, that ellipsoids pack efficiently when disordered. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids or spherocylinders (diatomics excepted) into the world of molecules with attractive forces, we have made a molecular dynamics MD study of crystal melting and glass formation on the Gay- Berne (G-B) model of ellipsoidal objects across the aspect ratio range of the hard ellipsoid studies. Here we report that, in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states, that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers" - single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. The existence of crystal-free routes to the glassy state removes any precrystalline fluctuation perspective from the "glass problem". Unexpectedly we find that liquids with aspect ratios in the "crystallophobic" range also behave in an unusual (non-hysteritic) way during temperature cycling through the glass transition. We link this to the highly volume fraction-sensitive ("fragile") behavior observed in recent hard dumbbell studies at similar length/diameter ratios.

Vitaliy Kapko; Dmitry V. Matyushov; C. Austen Angell

2011-06-07T23:59:59.000Z

206

The Dynamical Structure and Evolution of Giant Molecular Clouds  

E-Print Network [OSTI]

Giant molecular clouds (GMCs) are the sites of star formation in the Galaxy. Many of their properties can be understood in terms of a model in which the GMCs and the star-forming clumps within them are in approximate pressure equilibrium, with turbulent motions treated as a separate pressure component.

Christopher F. McKee

1999-01-26T23:59:59.000Z

207

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

SciTech Connect (OSTI)

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

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

2010-08-14T23:59:59.000Z

208

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

E-Print Network [OSTI]

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

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

2014-06-13T23:59:59.000Z

209

Resonant behavior in heat transfer across weak molecular interfaces  

SciTech Connect (OSTI)

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

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

2013-12-21T23:59:59.000Z

210

Theoretical aspects of gas-phase molecular dynamics  

SciTech Connect (OSTI)

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

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

1993-12-01T23:59:59.000Z

211

Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation  

SciTech Connect (OSTI)

Lignin, a major polymeric component of plant cell walls, forms aggregates in vivo and poses a barrier to cellulosic ethanol production. Here, neutron scattering experiments and molecular dynamics simulations reveal that lignin aggregates are characterized by a surface fractal dimension that is invariant under change of scale from ~1 1000 . The simulations also reveal extensive water penetration of the aggregates and heterogeneous chain dynamics corresponding to a rigid core with a fluid surface.

Petridis, Loukas [ORNL; Pingali, Sai Venkatesh [ORNL; Urban, Volker S [ORNL; Heller, William T [ORNL; O'Neill, Hugh Michael [ORNL; Foston, Marcus [Georgia Institute of Technology; Ragauskas, A J [Georgia Institute of Technology; Smith, Jeremy C [ORNL

2011-01-01T23:59:59.000Z

212

Electron Transfer Dynamics in Efficient Molecular Solar Cells  

SciTech Connect (OSTI)

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

Meyer, Gerald John

2014-10-01T23:59:59.000Z

213

Molecular dynamics simulation of threshold displacement energies in zircon.  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: VegetationEquipment SurfacesResource ProgramModification and ApplicationMolecular StructureMolecularand|

214

Molecular Dynamics Simulations of Gas Selectivity in Amorphous Porous  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May Jun Jul(Summary)morphinanInformation Desert Southwest Regionat Cornell Batteries & Fuel CellsModels from BigMolecular

215

Molecular dynamics simulations of coherent optical photon emission from shock waves in Evan J. Reed,1,2,  

E-Print Network [OSTI]

Molecular dynamics simulations of coherent optical photon emission from shock waves in crystals, 013904 2006 . In this work, we present analysis and molecular dynamics simulations of shock waves subject to a shock wave or solitonlike propagating excitation E. J. Reed et al., Phys. Rev. Lett. 96

Soljaèiæ, Marin

216

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

E-Print Network [OSTI]

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

Alfè, Dario

217

Ab initio molecular-dynamics study of the structural, vibrational, and electronic properties of glassy GeSe 2  

E-Print Network [OSTI]

Ab initio molecular-dynamics study of the structural, vibrational, and electronic properties We present results of an ab initio molecular-dynamics study of glassy GeSe2 using a 216 atom model static structure factors, and ring structures. The total static structure factor and first sharp

Drabold, David

218

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

E-Print Network [OSTI]

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

Truhlar, Donald G

219

Interaction potentials for alumina and molecular dynamics simulations of amorphous and liquid alumina  

E-Print Network [OSTI]

Interaction potentials for alumina and molecular dynamics simulations of amorphous and liquid for preventing crystalliza- tion and giving chemical stability and durability to a glaze, for instance. Due been identified.4 A review of these crystal structures and their pre- cursors can be found in the work

Southern California, University of

220

Accelerated, energy-conserving BornOppenheimer molecular dynamics via Fock matrix extrapolation  

E-Print Network [OSTI]

Accelerated, energy-conserving Born­Oppenheimer molecular dynamics via Fock matrix extrapolation iterations per time step, without sacrificing energy conservation. In test calculations for C2F4, (H2O)4 � , (H2O)6, and [Fe(H2O)6]21 , we demonstrate energy-conserving Fock matrix extrapolation that reduces

Herbert, John

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


221

Molecular Dynamics Simulation of Amyloid b Dimer Formation B. Urbanc,* L. Cruz,* F. Ding,*y  

E-Print Network [OSTI]

of amyloid plaques. Hence, finding the conformation of these oligo- meric forms of Ab may be important; Thompson, 2003). The most common view is that Ab(1­40) and Ab(1­ 42) in fibrils form parallel bMolecular Dynamics Simulation of Amyloid b Dimer Formation B. Urbanc,* L. Cruz,* F. Ding,*y D

Stanley, H. Eugene

222

Non-adiabatic molecular dynamics simulation of ultrafast solar cell electron transfer  

E-Print Network [OSTI]

confinement devices [1­5]. Solar cells of the Graetzel type [6,7] are based on dye sensitized nanocrystalline in solar cells, photocatalysis and photoelectrolysis. The electronic structure of the dye cell; Ultrafast electron transfer; Non-adiabatic molecular dynamics simulation; Dye sensitized titanium

223

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 energy evaluation is a central issue in atomistic modeling.1­5 When the free energy is known, equilibrium

Meirovitch, Hagai

224

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.

225

Fermionic Molecular Dynamics: Multifragmentation in heavy-ion collisions and in excited nuclei  

E-Print Network [OSTI]

Within Fermionic Molecular Dynamics we investigate fragmentation of a compound system which was created in a heavy-ion collision at a beam energy in the Fermi energy domain and the decay of excited iron nuclei. We show that in FMD many-body correlations play an important role in the formation of fragments.

H. Feldmeier; J. Schnack

1997-03-17T23:59:59.000Z

226

Nonadiabatic transition state theory and multiple potential energy surface molecular dynamics of infrequent events  

E-Print Network [OSTI]

Nonadiabatic transition state theory and multiple potential energy surface molecular dynamics in the vicinity of the energy barrier, i.e., in the region of the transition state or bottleneck. In general, TST 07974 Received 7 July 1995; accepted 17 August 1995 Classical transition state theory TST provides

Hammes-Schiffer, Sharon

227

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

E-Print Network [OSTI]

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

Southern California, University of

228

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

E-Print Network [OSTI]

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

229

A Combined Molecular Dynamics and Diffusion Model of Single Proton Conduction through Gramicidin  

E-Print Network [OSTI]

A Combined Molecular Dynamics and Diffusion Model of Single Proton Conduction through Gramicidin through the gramicidin pore is described by a potential of mean force and diffusion coefficient obtained in the hydrogen bonding structure of pore waters without an excess proton. Proton entrance and exit were

Schumaker, Mark

230

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

E-Print Network [OSTI]

Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes YASUSHI SHIBUTA, SHIGEO MARUYAMA Nucleation process of single-walled carbon nanotubes by the catalytic chemical of a cap-structure of a nanotube. When the catalytic cluster reaches saturation with carbon atoms

Maruyama, Shigeo

231

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

E-Print Network [OSTI]

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

Saiz, Leonor

232

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

E-Print Network [OSTI]

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

Bryant, Zev

233

Molecular Simulation of Multistate Peptide Dynamics: A Comparison Between Microsecond Timescale Sampling  

E-Print Network [OSTI]

, Alberta T2N 1N4, Canada 2 Centre for Biomolecular Interdisciplinary Studies and Industrial ApplicationsMolecular Simulation of Multistate Peptide Dynamics: A Comparison Between Microsecond Timescale energy landscape and the kinetics of the equilibrium is high- lighted by principal component analysis

Sorin, Eric J.

234

Molecular dynamics in liquid cyclopropane. Raman and magnetic nuclear resonance studies  

E-Print Network [OSTI]

723 Molecular dynamics in liquid cyclopropane. II. 2014 Raman and magnetic nuclear resonance as a function of temperature (155, 300 K) and pressure (up to 3 kilobars). 13C and 2H nuclear magnetic resonance experiments are performed in the same temperature range. The isotropic and anisotropic Raman profiles

Boyer, Edmond

235

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

E-Print Network [OSTI]

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

236

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

E-Print Network [OSTI]

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

Maruyama, Shigeo

237

accelerating bio-molecular dynamics: Topics by E-print Network  

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

accelerating bio-molecular dynamics First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Charge transport...

238

Molecular dynamics of gas phase hydrogen-bonded complexes  

E-Print Network [OSTI]

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

Wofford, Billy Alan

2012-06-07T23:59:59.000Z

239

Graphics processing units accelerated semiclassical initial value representation molecular dynamics  

SciTech Connect (OSTI)

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

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

2014-05-07T23:59:59.000Z

240

Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations  

E-Print Network [OSTI]

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

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

2015-01-30T23:59:59.000Z

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.


241

Isomorphic classical molecular dynamics model for an excess electronin a supercritical fluid  

SciTech Connect (OSTI)

Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path integral statistics through the use of analytical continuation techniques. At low fluid densities, the RPMD model substantially underestimates the contribution of delocalized states to the dynamics of the excess electron. However, with increasing solvent density, the RPMD model improves, nearly satisfying analytical continuation constraints at densities approaching those of typical liquids. In the high density regime, quantum dispersion substantially decreases the self-diffusion of the solvated electron. In this regime where the dynamics of the electron is strongly coupled to the dynamics of the atoms in the fluid, trajectories that can reveal diffusive motion of the electron are long in comparison to {beta}{h_bar}.

Miller III, Thomas F.

2008-08-04T23:59:59.000Z

242

Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow: a non-equilibrium molecular dynamics study  

E-Print Network [OSTI]

The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear is investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity and normal stress differences of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid. The corresponding molecular structure is studied at the same shear rates and temperatures. The Cooee bitumen is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. The nanoaggregates are shown to break up at very high shear rates, leading only to a minor effect on the viscosity of the mixture. At low shear rates, bitumen can be seen as a colloidal suspension of nanoaggregates in a solvent. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. The alignment of docosane molecules due to form and intrinsic birefringence and its effect on the rheological properties of the mixture are discussed. The stress optical rule is shown to be valid only in a limited range of shear rates at high temperatures, because this rule neglects the presence of other molecule types than docosane at high shear rates and the effect of intermolecular alignment, which gets more pronounced at high shear rates.

Claire A. Lemarchand; Nicholas P. Bailey; Billy D. Todd; Peter J. Daivis; Jesper S. Hansen

2015-01-03T23:59:59.000Z

243

Abington Abington Pediatrics* 360 Brockton Avenue, Suite 102, MA 02351 Yara Fernandez, MD 781-792-1999 781-792-1990 Laurie Massey, MD  

E-Print Network [OSTI]

Andrea Reilly, MD Milton Pediatric Associates - MGH 10 Hawthorne Place, Suite 110, MA 02114 JonathanCullough, MD Rebecca Niloff, MD Cara O'Reilly, MD Scott Paul, MD Jonathon Brenner, MD John Robinson, MD Heidi-643-8120 Elizabeth Turnock, MD Pediatric Group Practice 55 Fruit Street, YAW 6D, MA 02114 Ronald Benz, MD 617

Mootha, Vamsi K.

244

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

E-Print Network [OSTI]

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

V. A. Levashov

2014-06-23T23:59:59.000Z

245

Parallel implementation of three-dimensional molecular dynamic simulation for laser-cluster interaction  

SciTech Connect (OSTI)

The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of the experiments reported in the literature. Scaling laws for the computational time is established by varying the number of processor cores and number of macroparticles used. The capabilities of the code are highlighted by implementing various diagnostic tools. To study the dynamics of the laser-cluster interactions, the executable version of the code is available from the author.

Holkundkar, Amol R. [Department of Physics, Birla Institute of Technology and Science, Pilani-333 031 (India)] [Department of Physics, Birla Institute of Technology and Science, Pilani-333 031 (India)

2013-11-15T23:59:59.000Z

246

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

SciTech Connect (OSTI)

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

Lu, Gui [Key Laboratory for Thermal Science and Power Engineering of MOE, Beijing Key Laboratory for CO2 Utilization and Reduction Technology, Tsinghua University, Beijing 100084 (China) [Key Laboratory for Thermal Science and Power Engineering of MOE, Beijing Key Laboratory for CO2 Utilization and Reduction Technology, Tsinghua University, Beijing 100084 (China); Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104 (United States); Hu, Han; Sun, Ying, E-mail: yyduan@tsinghua.edu.cn, E-mail: ysun@coe.drexel.edu [Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104 (United States)] [Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104 (United States); Duan, Yuanyuan, E-mail: yyduan@tsinghua.edu.cn, E-mail: ysun@coe.drexel.edu [Key Laboratory for Thermal Science and Power Engineering of MOE, Beijing Key Laboratory for CO2 Utilization and Reduction Technology, Tsinghua University, Beijing 100084 (China)] [Key Laboratory for Thermal Science and Power Engineering of MOE, Beijing Key Laboratory for CO2 Utilization and Reduction Technology, Tsinghua University, Beijing 100084 (China)

2013-12-16T23:59:59.000Z

247

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

SciTech Connect (OSTI)

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

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

2014-04-07T23:59:59.000Z

248

Lattice thermal conductivity of UO{sub 2} using ab-initio and classical molecular dynamics  

SciTech Connect (OSTI)

We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000?K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500?K.

Kim, Hyoungchul [Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109 (United States); High-Temperature Energy Materials Research Center, Korea Institute of Science and Technology, Seoul 136–791 (Korea, Republic of); Kim, Moo Hwan [Division of Advanced Nuclear Engineering, Pohang University of Science and Technology, Pohang 790-784 (Korea, Republic of); Kaviany, Massoud, E-mail: kaviany@umich.edu [Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109 (United States); Division of Advanced Nuclear Engineering, Pohang University of Science and Technology, Pohang 790-784 (Korea, Republic of)

2014-03-28T23:59:59.000Z

249

Quantum molecular dynamics simulation of shock-wave experiments in aluminum  

SciTech Connect (OSTI)

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

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

2014-06-14T23:59:59.000Z

250

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

SciTech Connect (OSTI)

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

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

2011-09-01T23:59:59.000Z

251

Quantum wave packet ab initio molecular dynamics: An approach to study quantum dynamics in large systems  

E-Print Network [OSTI]

of computational methods in gas-phase1 and condensed phase quantum dynamics.2 In many cases the Born robust by using adaptive grids to achieve optimized sampling. One notable feature of the approach

Iyengar, Srinivasan S.

252

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

E-Print Network [OSTI]

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

Maruyama, Shigeo

253

Semiclassical analysis of quantum dynamics  

E-Print Network [OSTI]

Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using trajectories have achieved great successes in the computer simulations of various systems, but it is difficult to incorporate quantum effects in a robust way. Therefore, improving quantum wavepacket dynamics and incorporating nonadiabatic transitions and quantum effects into classical and semi-classical molecular dynamics is critical as well as challenging. In this paper, we present a MD scheme in which a new set of equations of motion (EOM) are proposed to effectively propagate nuclear trajectories while conserving quantum mechanical energy which is critical for describing quantum effects like tunneling. The new quantum EOM is tested on a one-state one-dimensional and a two-state two-dimensional model nonadiabatic systems. The global quantum force experienced by each trajectory promotes energy redistribution among the bundle of trajectories, and thus helps the individual trajectory tunnel through the potential barrier higher than the energy of the trajectory itself. Construction of the new quantum force and EOM also provides a better way to treat the issue of back-reaction in mixed quantum-classical (MQC) methods, i.e. self-consistency between quantum degrees of freedom (DOF) and classical DOF.

Siyang Yang

2011-11-15T23:59:59.000Z

254

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

E-Print Network [OSTI]

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

Silva Hernandez, Carlos Ardenis A.

2011-08-08T23:59:59.000Z

255

Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors  

SciTech Connect (OSTI)

In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW{sub 12}O{sub 40}{sup 3?}, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

Balliou, A., E-mail: aballiou@imel.demokritos.gr [Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Aghia Paraskevi, Athens 15310 (Greece); Department of Chemical Engineering, NTUA, Zographou Campus, Athens 15773 (Greece); Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N. [Institute of Nanoscience and Nanotechnology, NCSR Demokritos, Aghia Paraskevi, Athens 15310 (Greece); Tsikritzis, D.; Kennou, S. [Department of Chemical Engineering, University of Patras, University Campus, Patras 26504 (Greece)

2014-10-14T23:59:59.000Z

256

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

SciTech Connect (OSTI)

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

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

2013-11-07T23:59:59.000Z

257

Influencing Strong Field Excitation Dynamics through Molecular Structure Noel P. Moore, Alexei N. Markevitch, and Robert J. Levis*  

E-Print Network [OSTI]

LETTERS Influencing Strong Field Excitation Dynamics through Molecular Structure Noel P. Moore,cm-2 ) excitation in a series of polyatomic molecules of increasing characteristic length1-4 report the effect of molecular size on the coupling and partitioning of intense laser radiation

Levis, Robert J.

258

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

E-Print Network [OSTI]

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

Maruyama, Shigeo

259

Structure of excited states of Be-11 studied with Antisymmetrized Molecular Dynamics  

E-Print Network [OSTI]

The structures of the ground and excited states of Be-11 were studied with a microscopic method of antisymmetrized molecular dynamics. The theoretical results reproduce the abnormal parity of the ground state and predict various kinds of excited states. We suggest a new negative-parity band with a well-developed clustering structure which reaches high-spin states. Focusing on a $2\\alpha$ clustering structure, we investigated structure of the ground and excited states. We point out that molecular orbits play important roles for the intruder ground state and the low-lying $2\\hbar \\omega$ states. The features of the breaking of $\\alpha$ clusters were also studied with the help of data for Gamow-Teller transitions.

Y. Kanada-En'yo; H. Horiuchi

2002-04-15T23:59:59.000Z

260

Spectroscopy and intruder configurations of $^{33}$Mg and $^{31}$Ne studied with antisymmetrized molecular dynamics  

E-Print Network [OSTI]

Excitation spectra and neutron single particle configurations of $^{33}$Mg and $^{31}$Ne are investigated by using antisymmetrized molecular dynamics combined with generator coordinate method. It is shown that both nuclei have strongly deformed $3/2^-$ ground state with a $3p2h$ configuration. The excitation spectra are qualitatively understood in terms of the Nilsson model and the calculation has shown the coexistence of different intruder configurations within small excitation energy. The calculated one neutron separation energy of $^{31}$Ne is rather small ($S_n=250$ keV) and implies a p-wave one neutron halo with a strongly deformed core.

M. Kimura

2011-05-17T23:59:59.000Z

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261

Structure of Excited States of 10Be studied with Antisymmetrized Molecular Dynamics  

E-Print Network [OSTI]

We study structure of excited states of 10Be with the method of variation after spin parity projection in the framework of antisymmetrized molecular dynamics. Present calculations describe many excited states and reproduce the experimental data of E2 and E1 transitions and the new data of the $\\beta$ transition strength successfully. We make systematic discussions on the molecule-like structures of light unstable nuclei and the important role of the valence neutrons based on the results obtained with the framework which is free from such model assumptions as the existence of inert cores and clusters.

Y. Kanada-En'yo; H. Horiuchi; A. Dote

1999-05-21T23:59:59.000Z

262

Cluster Structures of the Ground and Excited States of 12Be Studied with Antisymmetrized Molecular Dynamics  

E-Print Network [OSTI]

The structures of the ground and excited states of 12Be were studied with antisymmetrized molecular dynamics. The ground state was found to be a state with a developed 2-alpha core with two neutrons occupying the intruder orbits. The energy levels of the newly measured spin-assigned states were described well, except for the $1^-_1$ state. The calculations indicated that many exotic cluster structures appear in the low-energy region. The widths concerning alpha and 6He decays were discussed by using reduced width amplitudes.

Yoshiko Kanada-En'yo; Hisashi Horiuchi

2003-04-28T23:59:59.000Z

263

Variation after Angular Momentum Projection for the Study of Excited States Based on Antisymmetrized Molecular Dynamics  

E-Print Network [OSTI]

In order to study the structure of excited states we perform a variational calculation after spin parity projection (VAP) within the framework of Antisymmetrized Molecular Dynamics (AMD). The framework is proven to be a new powerful approach for the study of the various structures of excited states because it is free from model assumptions such as inert cores, existence of clusters, and the axial symmetry. By using finite range interactions with a density dependent term we reproduce well all the energy levels below 15 MeV in $^{12}$C. This is the first theoretical model that reproduces many $E2$ transition rates and $\\beta$ decays to $^{12}$C successfully.

Y. Kanada-En'yo

2002-04-15T23:59:59.000Z

264

Antisymmetrized Molecular Dynamics with Coherent State Pion and Its Application to Excited Spectrum of 12C  

E-Print Network [OSTI]

We have introduced coherent state neutral pion into Antisymmetrized Molecular Dynamics. With the aid of coherent state technique, it becomes possible to calculate transition matrix elements of the pion field operator and to study excited states containing pions. For large pion-nucleon coupling fpiN > 1.6, pions have a finite expectation value and bring large energy gain in 12C. We discuss two aspects of pionic effects in spectroscopy; the LS interaction like effect and the mixing of different nucleon parity states, which would modify low energy nuclear levels.

Akinori Isshiki; Kenichi Naito; Akira Ohnishi

2005-07-13T23:59:59.000Z

265

Peeling back the layers: a molecular dynamics investigation into heterogeneous ice nucleation  

E-Print Network [OSTI]

Coarse grained molecular dynamics simulations are presented in which the sensitivity of the ice nucleation rate to the hydrophilicity of a graphene nanoflake is investigated. We find that an optimal interaction strength for promoting ice nucleation exists, which coincides with that found previously for an FCC (111) surface. We further investigate the role that the layering of interfacial water plays in heterogeneous ice nucleation, and demonstrate that the extent of layering is not a good indicator of ice nucleating ability for all surfaces. Our results suggest that to be an efficient ice nucleating agent, a surface should not bind water too strongly if it is able to accommodate high coverages of water.

Cox, Stephen J; Slater, Ben; Michaelides, Angelos

2015-01-01T23:59:59.000Z

266

Solvent-Driven Preferential Association of Lignin with Regions of Crystalline Cellulose in Molecular Dynamics Simulation  

SciTech Connect (OSTI)

The precipitation of lignin onto cellulose after pretreatment of lignocellulosic biomass is an obstacle to economically viable cellulosic ethanol production. Here, 750 ns nonequilibrium molecular dynamics simulations are reported of a system of lignin and cellulose in aqueous solution. Lignin is found to strongly associate with itself and the cellulose. However, noncrystalline regions of cellulose are observed to have a lower tendency to associate with lignin than crystalline regions, and this is found to arise from stronger hydration of the noncrystalline chains. The results suggest that the recalcitrance of crystalline cellulose to hydrolysis arises not only from the inaccessibility of inner fibers but also due to the promotion of lignin adhesion.

Lindner, Benjamin [ORNL] [ORNL; Petridis, Loukas [ORNL] [ORNL; Schulz, Roland [ORNL] [ORNL; Smith, Jeremy C [ORNL] [ORNL

2013-01-01T23:59:59.000Z

267

Molecular Dynamics Simulations of Tri-n-butyl-phosphate/n-Dodecane Mixture: Thermophysical Properties and Molecular Structure  

SciTech Connect (OSTI)

Molecular dynamics simulations of tri-n-butyl-phosphate (TBP)/n-dodecane mixture in the liquid phase have been carried out using two recently developed TBP force field models (J. Phys. Chem. B 2012, 116, 305) in combination with the all-atom optimized potentials for liquid simulations (OPLS-AA) force field model for n-dodecane. Specifically, the electric dipole moment of TBP, mass density of the mixture, and the excess volume of mixing were computed with TBP mole fraction ranging from 0 to 1. It is found that the aforementioned force field models accurately predict the mass density of the mixture in the entire mole fraction range. Commensurate with experimental measurements, the electric dipole moment of the TBP was found to slightly increase with the mole fraction of TBP in the mixture. Also, in accord with experimental data, the excess volume of mixing is positive in the entire mole fraction range, peaking at TBP mole fraction range 0.3 0.5. Finally, a close examination of the spatial pair correlation functions between TBP molecules, and between TBP and n-dodecane molecules, revealed formation of TBP dimers through self-association at close distance, a phenomenon with ample experimental evidence.

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

2014-01-01T23:59:59.000Z

268

On the dynamic and static manifestation of molecular absorption in thin films probed by a microcantilever  

SciTech Connect (OSTI)

Mechanical resonators shaped like microcantilevers have been demonstrated as a platform for very sensitive detection of chemical and biological analytes. However, its use as an analytical tool will require fundamental understanding of the molecular absorption-induced effects in the static and dynamic sensor response. The effect of absorption-induced surface stress on the microcantilever response is here investigated using palladium hydride formation. It is shown that the resonance and deformation states of the cantilever monitored simultaneously exhibit excellent correlation with the phase of the hydride formation. However, the associated frequency shifts and quasistatic bending are observed to be independent during solid solution phase. Importantly, absorption-induced changes in the elastic parameters of the palladium film are found to play a dominant role in the static and dynamic response. The presented results help in discerning the parameters that control the cantilever response as well as the relationships between these parameters.

Finot, Eric [Institut CARNOT de Bourgogne] [Institut CARNOT de Bourgogne; Fabre, Arnaud [French Atomic Energy Commission (CEA), Centre de Valduc, Is-sur-Tille] [French Atomic Energy Commission (CEA), Centre de Valduc, Is-sur-Tille; Passian, Ali [ORNL] [ORNL; Thundat, Thomas [University of Alberta, Edmonton, Canada] [University of Alberta, Edmonton, Canada

2014-01-01T23:59:59.000Z

269

The dynamics of cargo driven by molecular motors in the context of asymmetric simple exclusion processes  

E-Print Network [OSTI]

We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of an asymmetric simple exclusion processes (ASEP). The model is formulated to account for i) excluded volume interactions, ii) the observed asymmetry of the stochastic movement of individual motors and iii) interactions between motors and cargo. Items (i) and (ii) form the basis of ASEP models and have already been considered in the literature to study the behavior of motor density profile [Parmeggiani 03]. Item (iii) is new. It is introduced here as an attempt to describe explicitly the dependence of cargo movement on the dynamics of motors. The steady-state solutions of the model indicate that the system undergoes a phase transition of condensation type as the motor density varies. We study the consequences of this transition to the properties of cargo velocity.

Carla Goldman; Elisa T. Sena

2008-10-07T23:59:59.000Z

270

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

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

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

271

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

E-Print Network [OSTI]

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

Alford, Simon

272

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

SciTech Connect (OSTI)

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

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

2013-07-28T23:59:59.000Z

273

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

274

Quantum molecular dynamics simulations of transport properties in liquid and dense-plasma plutonium  

SciTech Connect (OSTI)

We have calculated the viscosity and self-diffusion coefficients of plutonium in the liquid phase using quantum molecular dynamics (QMD) and in the dense-plasma phase using orbital-free molecular dynamics (OFMD), as well as in the intermediate warm dense matter regime with both methods. Our liquid metal results for viscosity are about 40% lower than measured experimentally, whereas a previous calculation using an empirical interatomic potential (modified embedded-atom method) obtained results 3-4 times larger than the experiment. The QMD and OFMD results agree well at the intermediate temperatures. The calculations in the dense-plasma regime for temperatures from 50 to 5000 eV and densities about 1-5 times ambient are compared with the one-component plasma (OCP) model, using effective charges given by the average-atom code inferno. The inferno-OCP model results agree with the OFMD to within about a factor of 2, except for the viscosity at temperatures less than about 100 eV, where the disagreement is greater. A Stokes-Einstein relationship of the viscosities and diffusion coefficients is found to hold fairly well separately in both the liquid and dense-plasma regimes.

Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2011-02-15T23:59:59.000Z

275

Laser Control of Dissipative Two-Exciton Dynamics in Molecular Aggregates  

E-Print Network [OSTI]

There are two types of two-photon transitions in molecular aggregates, that is, non-local excitations of two monomers and local double excitations to some higher excited intra-monomer electronic state. As a consequence of the inter-monomer Coulomb interaction these different excitation states are coupled to each other. Higher excited intra-monomer states are rather short-lived due to efficient internal conversion of electronic into vibrational energy. Combining both processes leads to the annihilation of an electronic excitation state, which is a major loss channel for establishing high excitation densities in molecular aggregates. Applying theoretical pulse optimization techniques to a Frenkel exciton model it is shown that the dynamics of two-exciton states in linear aggregates (dimer to tetramer) can be influenced by ultrafast shaped laser pulses. In particular, it is studied to what extent the decay of the two-exciton population by inter-band transitions can be transiently suppressed. Intra-band dynamics is described by a dissipative hierarchy equation approach, which takes into account strong exciton-vibrational coupling in the non-Markovian regime.

Yun-an Yan; Oliver Kühn

2012-07-09T23:59:59.000Z

276

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

SciTech Connect (OSTI)

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

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

2014-09-07T23:59:59.000Z

277

DOCTOR'S HEART George Stetten, M.D.  

E-Print Network [OSTI]

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

Stetten, George

278

David Brick, MD, FAAP, FACC Image credit  

E-Print Network [OSTI]

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

279

Lessons Learned Tracy Glauser, M.D.  

E-Print Network [OSTI]

Lessons Learned Tracy Glauser, M.D. Cincinnati Children's Hospital Medical Center #12;Overview 1. Lessons Learned a. NeuroNEXT Executive Committee b. NINDS clinical trials (NSD-K) study section c. PI

280

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]

Dynamics with Born-Oppenheimer and Extended Lagrangian Methods Using Atom Centered Basis Functions H calculations. For Born-Oppenheimer methods, the electronic structure calculations are converged, whereas trajectory calculations, Born-Oppenheimer dynamics, Extended Lagrangian dynamics, ADMP Introduction

Schlegel, H. Bernhard

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While these samples are representative of the content of NLEBeta,
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We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Simulations of the dissociation of small helium clusters with ab initio molecular dynamics in electronically excited states  

SciTech Connect (OSTI)

The dynamics resulting from electronic excitations of helium clusters were explored using ab initio molecular dynamics. The simulations were performed with configuration interaction singles and adiabatic classical dynamics coupled to a state-following algorithm. 100 different configurations of He{sub 7} were excited into the 2s and 2p manifold for a total of 2800 trajectories. While the most common outcome (90%) was complete fragmentation to 6 ground state atoms and 1 excited state atom, 3% of trajectories yielded bound, He {sub 2}{sup *}, and <0.5% yielded an excited helium trimer. The nature of the dynamics, kinetic energy release, and connections to experiments are discussed.

Closser, Kristina D.; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Department of Chemistry, University of California Berkeley, Berkeley, California 94720 (United States) [Department of Chemistry, University of California Berkeley, Berkeley, California 94720 (United States); Ultrafast X-Ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Gessner, Oliver [Ultrafast X-Ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)] [Ultrafast X-Ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

2014-04-07T23:59:59.000Z

282

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

SciTech Connect (OSTI)

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

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

2011-01-01T23:59:59.000Z

283

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

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

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

284

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

E-Print Network [OSTI]

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...

Hirunsit, Pussana

2009-05-15T23:59:59.000Z

285

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

SciTech Connect (OSTI)

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

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

2009-10-19T23:59:59.000Z

286

Pygmy and Giant Dipole Resonances by Coulomb Excitation using a Quantum Molecular Dynamics model  

E-Print Network [OSTI]

Pygmy and Giant Dipole Resonance (PDR and GDR) in Ni isotopes have been investigated by Coulomb excitation in the framework of the Isospin-dependent Quantum Molecular Dynamics model (IQMD). The spectra of $\\gamma$ rays are calculated and the peak energy, the strength and Full Width at Half Maximum (FWHM) of GDR and PDR have been extracted. Their sensitivities to nuclear equation of state, especially to its symmetry energy term are also explored. By a comparison with the other mean-field calculations, we obtain the reasonable values for symmetry energy and its slope parameter at saturation, which gives an important constrain for IQMD model. In addition, we also studied the neutron excess dependence of GDR and PDR parameters for Ni isotopes and found that the energy-weighted sum rule (EWSR) $PDR_{m_1}/GDR_{m_1}%$ increases linearly with the neutron excess.

C. Tao; Y. G. Ma; G. Q. Zhang; X. G. Cao; D. Q. Fang. H. W. Wang

2013-02-01T23:59:59.000Z

287

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

SciTech Connect (OSTI)

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

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

2013-12-21T23:59:59.000Z

288

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

E-Print Network [OSTI]

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

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

2007-03-22T23:59:59.000Z

289

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

E-Print Network [OSTI]

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

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

2014-12-09T23:59:59.000Z

290

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

E-Print Network [OSTI]

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

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

2007-09-05T23:59:59.000Z

291

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

SciTech Connect (OSTI)

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

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

2008-06-01T23:59:59.000Z

292

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

SciTech Connect (OSTI)

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

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

2008-08-01T23:59:59.000Z

293

Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions  

E-Print Network [OSTI]

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

Nikolai V. Priezjev

2012-08-27T23:59:59.000Z

294

Multicomponent dynamics of coupled quantum subspaces and field-induced molecular ionizations  

SciTech Connect (OSTI)

To describe successive ionization steps of a many-electron atom or molecule driven by an ultrashort, intense laser pulse, we introduce a hierarchy of successive two-subspace Feshbach partitions of the N-electron Hilbert space, and solve the partitioned time-dependent Schrödinger equation by a short-time unitary algorithm. The partitioning scheme allows one to use different level of theory to treat the many-electron dynamics in different subspaces. We illustrate the procedure on a simple two-active-electron model molecular system subjected to a few-cycle extreme Ultra-Violet (XUV) pulse to study channel-resolved photoelectron spectra as a function of the pulse's central frequency and duration. We observe how the momentum and kinetic-energy distributions of photoelectrons accompanying the formation of the molecular cation in a given electronic state (channel) change as the XUV few-cycle pulse's width is varied, from a form characteristic of an impulsive ionization regime, corresponding to the limit of a delta-function pulse, to a form characteristic of multiphoton above-threshold ionization, often associated with continuous-wave infinitely long pulse.

Nguyen-Dang, Thanh-Tung; Viau-Trudel, Jérémy [Département de Chimie, Université Laval, Québec, Québec G1K 7P4 (Canada)] [Département de Chimie, Université Laval, Québec, Québec G1K 7P4 (Canada)

2013-12-28T23:59:59.000Z

295

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

SciTech Connect (OSTI)

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

296

Superdeformation and clustering in $^{40}$Ca studied with Antisymmetrized Molecular Dynamics  

E-Print Network [OSTI]

Deformed states in $^{40}$Ca are investigated with a method of antisymmetrized molecular dynamics. Above the spherical ground state, rotational bands arise from a normal deformation and a superdeformation as well as an oblate deformation. The calculated energy spectra and $E2$ transition strengths in the superdeformed band reasonably agree to the experimental data of the superdeformed band starting from the $0^+_3$ state at 5.213 MeV. By the analysis of single-particle orbits, it is found that the superdeformed state has particle-hole nature of an $8p$-$8h$ configuration. One of new findings is parity asymmetric structure with $^{12}$C+$^{28}$Si-like clustering in the superdeformed band. We predict that $^{12}$C+$^{28}$Si molecular bands may be built above the superdeformed band due to the excitation of inter-cluster motion. They are considered to be higher nodal states of the superdeformed state. We also suggest negative-parity bands caused by the parity asymmetric deformation.

Y. Kanada-En'yo; M. Kimura

2005-10-15T23:59:59.000Z

297

Molecular dynamics of excited state intramolecular proton transfer: 3-hydroxyflavone in solution  

SciTech Connect (OSTI)

The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 3-hydroxyflavone is investigated using classical molecular dynamics in conjunction with empirical valence bond (EVB) potentials for the description of intramolecular interactions, and a molecular mechanics and variable partial charge model, dependent on transferring proton position, for the description of solute-solvent interactions. A parallel multi-level genetic program was used to accurately fit the EVB potential energy surfaces to high level ab initio data. We have studied the excited state intramolecular proton transfer (ESIPT) reaction in three different solvent environments: methylcyclohexane, acetonitrile, and methanol. The effects of the environment on the proton transfer time and the underlying mechanisms responsible for the varied time scales of the ESIPT reaction rates are analyzed. We find that simulations with our EVB potential energy surfaces accurately reproduce experimentally determined reaction rates, fluorescence spectra, and vibrational frequency spectra in all three solvents. Furthermore, we find that the ultrafast ESIPT process results from a combination of ballistic transfer, and intramolecular vibrational redistribution, which leads to the excitation of a set of low frequency promoting vibrational modes. From this set of promoting modes, we find that an O-O in plane bend and a C-H out of plane bend are present in all three solvents, indicating that they are fundamental to the ultrafast proton transfer. Analysis of the slow proton transfer trajectories reveals a solvent mediated proton transfer mechanism, which is diffusion limited.

Bellucci, Michael A.; Coker, David F. [Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215 (United States)

2012-05-21T23:59:59.000Z

298

Local Dielectric Environment of B-DNA in Solution: Results from a 14 ns Molecular Dynamics Trajectory  

E-Print Network [OSTI]

Local Dielectric Environment of B-DNA in Solution: Results from a 14 ns Molecular Dynamics trajectory of B-DNA developed in a medium of explicit waters and sodium counterions with particle mesh Ewald around DNA are providing a reasonably accurate account of the local solution environment of a complicated

Jayaram, Bhyravabotla

299

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

E-Print Network [OSTI]

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

Apkarian, V. Ara

300

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

E-Print Network [OSTI]

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

Maruyama, Shigeo

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

Interaction potential for silicon carbide: A molecular dynamics study of elastic constants and vibrational density of states for crystalline  

E-Print Network [OSTI]

Interaction potential for silicon carbide: A molecular dynamics study of elastic constants and vibrational density of states for crystalline and amorphous silicon carbide Priya Vashishta,a Rajiv K. Kalia Silicon carbide SiC has been proposed for a wide range of technological applications

Southern California, University of

302

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

E-Print Network [OSTI]

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

Goddard III, William A.

303

hal-00170874,version1-10Sep2007 report number Ab initio molecular dynamics calculations of threshold  

E-Print Network [OSTI]

and optical properties of materials. For instance, a suitable ion irradiation may harden a material, lead: threshold displacement energies, ab initio molecular dynamics, silicon carbide 1 #12;Particle irradiation to a local oxydation state, or activate a magnetic order. The utility of ion irradiation is also well known

Paris-Sud XI, Université de

304

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

E-Print Network [OSTI]

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

305

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

E-Print Network [OSTI]

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

Brown, Michael F.

306

PHILOSOPHICAL MAGAZINE A, 1999, VOL. 79, NO. 6, 1321 1333 Molecular dynamics study on the structural changes of the  

E-Print Network [OSTI]

PHILOSOPHICAL MAGAZINE A, 1999, VOL. 79, NO. 6, 1321± 1333 Molecular dynamics study on the structural changes of the tilt grain boundary in aluminium W. Fan,Yizhen He and X. G. Gong Institute of Solid] Abstract The structure and physical properties of two Al tilt grain boundaries (GBs) at di erent

Gong, Xingao

307

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

SciTech Connect (OSTI)

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

Stoller, Roger E [ORNL] [ORNL

2013-01-01T23:59:59.000Z

308

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

SciTech Connect (OSTI)

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

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

2010-01-01T23:59:59.000Z

309

Molecular dynamics studies on spatial scale of low energy excitation in a simple polymer system  

E-Print Network [OSTI]

A molecular dynamics simulation is performed to investigate spatial scale of low energy excitation (LEE) in a single linear chain of united atoms. The self part of the dynamic structure function, $S_\\mathrm{S}(q,\\omega)$, is obtained in a wide range in frequency space ($\\omega$) and reciprocal space ($q$). A broad peak corresponding to the LEE is detected at $\\omega/2\\pi=2.5 \\times 10^{11} \\mathrm{s^{-1}}$ ($\\equiv \\omega_{\\mathrm{LEE}}/2\\pi$) on the contour maps of $S_\\mathrm{S}(q,\\omega)$, near and below the glass transition temperature ($T_{\\mathrm{g}}$=230 K). The $S_\\mathrm{S}(q,\\omega_{\\mathrm{LEE}})$ is symmetric around a maximum along the logarithm of $q$. The inverse of $q_{\\mathrm{max}}$, giving the maximum position of $S_\\mathrm{S}(q,\\omega_{\\mathrm{LEE}})$, depends on temperature as $2\\pi/q_{\\mathrm{max}}\\sim T^{0.52}$ for $60 \\mathrm{K}

Akira Koyama; Takashi Odagaki; Koji Fukao

2008-03-25T23:59:59.000Z

310

Molecular dynamics simulation of shock induced ejection on fused silica surface  

SciTech Connect (OSTI)

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

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

2014-05-21T23:59:59.000Z

311

Properties of liquid clusters in large-scale molecular dynamics nucleation simulations  

SciTech Connect (OSTI)

We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 10{sup 9} atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys. 139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ?kT = 0.1? for clusters with size i = 100. We find that the clusters deviate remarkably from spherical—with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%?30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates.

Angélil, Raymond; Diemand, Jürg [Institute for Theoretical Physics, University of Zurich, 8057 Zurich (Switzerland)] [Institute for Theoretical Physics, University of Zurich, 8057 Zurich (Switzerland); Tanaka, Kyoko K.; Tanaka, Hidekazu [Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819 (Japan)] [Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819 (Japan)

2014-02-21T23:59:59.000Z

312

Properties of gravitationally equilibrated Yukawa systems—A molecular dynamics study  

SciTech Connect (OSTI)

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

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

2014-04-15T23:59:59.000Z

313

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

SciTech Connect (OSTI)

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

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

2014-04-28T23:59:59.000Z

314

Quantify Water Extraction by TBP/Dodecane via Molecular Dynamics Simulations  

SciTech Connect (OSTI)

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

Khomami, Bamin [Univ. of Tennessee, Knoxville, TN (United States); Cui, Shengting [Univ. of Tennessee, Knoxville, TN (United States); de Almeida, Valmor F. [Oak Ridge National Lab., Oak Ridge, TN (United States); Felker, Kevin [Oak Ridge National Lab., Oak Ridge, TN (United States)

2013-05-16T23:59:59.000Z

315

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

SciTech Connect (OSTI)

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

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

2014-03-21T23:59:59.000Z

316

Heart Valve Disease James S. Gammie, MD  

E-Print Network [OSTI]

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

Weber, David J.

317

Strategic Plan Update Lydia Pleotis Howell MD  

E-Print Network [OSTI]

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

Leistikow, Bruce N.

318

Strategic Plan Update Lydia Pleotis Howell MD  

E-Print Network [OSTI]

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

Leistikow, Bruce N.

319

Marylee M. Rothschild, MD Louisville, Kentucky  

E-Print Network [OSTI]

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

320

NIST, Gaithersburg, MD Green Auditorium, Bldg101  

E-Print Network [OSTI]

MBE Summit NIST, Gaithersburg, MD Green Auditorium, Bldg101 Time Topic Speaker(s) 0830 Cauley, HII-Ingalls NIST MBE Activities Simon Frechette, NIST 0940-1010 Smart Manufacturing Overviews FY14 1100-1115 Partnership for Research & Innovation in Sustainable Manufacturing Process, & System

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321

Community Academic Profile Jon D. Fuller, MD  

E-Print Network [OSTI]

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

Ford, James

322

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

E-Print Network [OSTI]

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

M. Ebrahim Foulaadvand; Neda Ojaghlou

2014-09-27T23:59:59.000Z

323

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

SciTech Connect (OSTI)

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

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

2006-07-01T23:59:59.000Z

324

Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface  

E-Print Network [OSTI]

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of $r_{s}=0.912$.

Hua Y. Geng

2014-12-19T23:59:59.000Z

325

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

SciTech Connect (OSTI)

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

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

2014-05-15T23:59:59.000Z

326

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

SciTech Connect (OSTI)

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

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

2014-03-14T23:59:59.000Z

327

Structural changes in block copolymer solution under shear flow as determined by nonequilibrium molecular dynamics  

E-Print Network [OSTI]

A nonequilibrium molecular dynamics computer simulation on microsegregated solutions of symmetrical diblock copolymers is reported. As the polymer concentration increases, the system undergoes phase transitions in the following order: body centered cubic (BCC) micelles, hexagonal (HEX) cylinders, gyroid (GYR) bicontinuous networks, and lamellae (L), which are the same morphologies that have been reported for block copolymer melts. Structural classification is based on the patterns of the anisotropic static structure factor and characteristic 3-dimensional images. The systems in the BCC micellar ($\\rho\\sigma^{3}=0.3$) and HEX cylindrical ($\\rho\\sigma^{3}=0.4$) phases were then subjected to a steady planar shear flow. In weak shear flow, the segregated domains in both systems tend to rearrange into sliding parallel close-packed layers with their normal in the direction of the shear gradient. At higher shear rates both systems adopt a perpendicular lamellar structure with the normal along the neutral direction. A further increase in the shear rate results in a decrease in lamellar spacing without any further structural transitions. Two critical shear rate values that correspond to the demarcation of different structural behaviors were found.

Igor Rychkov; Kenichi Yoshikawa

2003-10-06T23:59:59.000Z

328

Dopant profile modeling by rare event enhanced domain-following molecular dynamics  

DOE Patents [OSTI]

A computer-implemented molecular dynamics-based process simulates a distribution of ions implanted in a semiconductor substrate. The properties of the semiconductor substrate and ion dose to be simulated are first initialized, including an initial set of splitting depths that contain an equal number of virtual ions implanted in each substrate volume determined by the splitting depths. A first ion with selected velocity is input onto an impact position of the substrate that defines a first domain for the first ion during a first timestep, where the first domain includes only those atoms of the substrate that exert a force on the ion. A first position and velocity of the first ion is determined after the first timestep and a second domain of the first ion is formed at the first position. The first ion is split into first and second virtual ions if the first ion has passed through a splitting interval. The process then follows each virtual ion until all of the virtual ions have come to rest. A new ion is input to the surface and the process repeats until all of the ion dose has been input. The resulting ion rest positions form the simulated implant distribution.

Beardmore, Keith M. (Santa Fe, NM); Jensen, Niels G. (Davis, CA)

2002-01-01T23:59:59.000Z

329

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

E-Print Network [OSTI]

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

Guido Tiana; Carlo Camilloni

2012-07-05T23:59:59.000Z

330

Alzheimer's amyloid-? and the disordered structural ensemble characterized using molecular dynamics and NMR spectroscopy  

E-Print Network [OSTI]

NL et al. (2008) Structure and dynamics of the Abeta(21-30)study of the structure and dynamics of the Alzheimer'sShaw DE (2012) Structure and dynamics of an unfolded protein

Ball, Katherine Aurelia

2013-01-01T23:59:59.000Z

331

Molecular dynamics simulation study of the high frequency sound waves in the fragile glass former ortho-terphenyl  

E-Print Network [OSTI]

Using a realistic flexible molecule model of the fragile glass former orthoterphenyl, we calculate via molecular dynamics simulation the collective dynamic structure factor, recently measured in this system by Inelastic X-ray Scattering. The comparison of the simulated and measured dynamic structure factor, and the study of its properties in an extended momentum, frequency and temperature range allows: i) to conclude that the utilized molecular model gives rise to a dynamic structure factor in agreement with the experimental data, for those thermodynamic states and momentum values where the latter are available; ii) to confirm the existence of a slope discontinuity on the T-dependence of the sound velocity that, at finite Q, takes place at a temperature T_x higher than the calorimetric glass transition temperature T_g; iii) to find that the values of T_x is Q-dependent and that its vanishing Q limit is consistent with T_g. The latter finding is interpreted within the framework of the current description of the dynamics of supercooled liquids in terms of exploration of the potential energy landscape.

S. Mossa; G. Monaco; G. Ruocco; M. Sampoli; F. Sette

2001-04-07T23:59:59.000Z

332

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

SciTech Connect (OSTI)

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

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

2013-01-28T23:59:59.000Z

333

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

SciTech Connect (OSTI)

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

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

2014-07-01T23:59:59.000Z

334

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

SciTech Connect (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

335

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

2013-02-20T23:59:59.000Z

336

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

SciTech Connect (OSTI)

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

Sibener, S. J.

2006-06-23T23:59:59.000Z

337

Anthropogenic and Climate Influences on Biogeochemical Dynamics and Molecular-Level Speciation of Soil Sulfur  

SciTech Connect (OSTI)

The soil environment is a primary component of the global biogeochemical sulfur (S) cycle, acting as a source and sink of various S species and mediating oxidation state changes. However, ecological significance of the various S forms and the impacts of human intervention and climate on the amount and structural composition of these compounds are still poorly understood. We investigated the long-term influences of anthropogenically mediated transitions from natural to managed ecosystems on molecular-level speciation, biogeochemical dynamics, and the apparent temperature sensitivity of S moieties in temperate, subtropical, and tropical environments with mean annual temperature (MAT) ranging from 5C to 21C, using elemental analysis and X-ray absorption near-edge structure (XANES) spectroscopy. Land-use and land-cover changes led to the depletion of total soil S in all three ecoregions over a period of up to 103 years. The largest decline occurred from tropical forest agroecosystems (67% Kakamega and 76% Nandi, Kenya), compared to losses from temperate (36% at Lethbridge, Canada, and 40% at Pendleton, USA) and subtropical (48% at South Africa) grassland agroecosystems. The total S losses correlated significantly with MAT. Anthropogenic interventions profoundly altered the molecular-level composition and resulted in an apparent shift in oxidation states of organic S from native ecosystems composed primarily of S moieties in intermediate and highly reduced oxidation states toward managed agroecosystems dominated by organic S rich in strongly oxidized functionalities. The most prominent change occurred in thiols and sulfides, the proportion of which decreased by 46% (Lethbridge) and 57% (Pendleton) in temperate agroecosystems, by 46% in subtropical agroecosystems, and by 79% (Nandi) and 81% (Kakamega) in tropical agroecosystems. The proportion of organic S directly linked to O increased by 81%, 168%, 40%, 92%, and 85%, respectively. Among the various organic S functionalities, thiols and sulfides seem to have higher apparent temperature sensitivity, and thus these organic S moieties may become prone to losses due to land-use changes, even from the cooler regions of the world if MAT of these regions rise in the future.

Solomon, D.; Lehmann, J; Kinyangi, J; Pell, A; Theis , J; Riha , S; Ngoze, S; Amelung, W; du Preez, C; et. al.

2009-01-01T23:59:59.000Z

338

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.

339

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

SciTech Connect (OSTI)

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

Stuart, Steven J.

2014-02-25T23:59:59.000Z

340

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

E-Print Network [OSTI]

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

Zhigilei, Leonid V.

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


341

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

SciTech Connect (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. 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 hexaaqua 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.

Sit, P H L.; Cococcioni, Matteo; Marzari, Nicola N.

2007-09-01T23:59:59.000Z

342

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

SciTech Connect (OSTI)

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

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

2012-10-15T23:59:59.000Z

343

Dynamical multi-breakup processes in the {sup 124}Sn+{sup 64}Ni system at 35 MeV/nucleon  

SciTech Connect (OSTI)

Multi-breakup processes for the {sup 124}Sn+{sup 64}Ni system at 35 MeV/nucleon have been studied with the forward part of the CHIMERA detector. An extensive comparison between experimental data corresponding to almost complete ternary events and constrained molecular dynamics (CoMD-II) calculations suggests different characteristic times in the selected processes. This is in agreement with previous studies of the same reaction already published concerning the prompt intermediate-mass-fragment emission. Stimulated by CoMD-II calculations, we investigate the existence of more complex dynamical multi-breakup processes occurring on the same time scale. A detailed study of the rotational dynamics leading to slower dynamical fission processes is also presented.

Papa, M.; Cardella, G.; De Filippo, E.; Giuliani, G.; Lanzano, G.; Pagano, A.; Pirrone, S.; Politi, G.; Porto, F.; Verde, G. [INFN, Sezione di Catania and Dipartimento di Fisica, Universita di Catania (Italy); Amorini, F.; Anzalone, A.; Bonasera, A.; Cavallaro, S.; Colonna, M.; Di Toro, M.; Giustolisi, F.; Iacono-Manno, M.; La Guidara, E.; Lanzalone, G. [INFN, Laboratori Nazionali del Sud and Dipartimento di Fisica, Universita di Catania (Italy)] (and others)

2007-05-15T23:59:59.000Z

344

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

E-Print Network [OSTI]

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

Lichtarge, Olivier

345

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

SciTech Connect (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

346

MOLECULAR DYNAMICS SIMULATION OF HETEROGENEOUS NUCLEATION OF LIQUID DROPLET ON SOLID SURFACE  

E-Print Network [OSTI]

such as the quantum dot generation. We have simulated the equilibrium liquid droplet on the solid surface simulation on the bubble nucleation process on the solid surface [2]. In the meantime, direct molecular

Maruyama, Shigeo

347

Molecular Dynamics Simulation of Damage Cascade Formation in Ion Bombarded Solids  

E-Print Network [OSTI]

/Molecular Massively Parallel Simulator). In one subtask, we studied damage cascade interactions caused by two 2 keV Si atoms simultaneously bombarding a crystalline Si substrate. We found that the enhanced displacement creation appears primarily in the thermal spike...

Chen, Di

2012-10-19T23:59:59.000Z

348

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

SciTech Connect (OSTI)

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

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

2014-09-30T23:59:59.000Z

349

Femtosecond Raman induced polarization spectroscopy studies of coherent rotational dynamics in molecular fluids  

SciTech Connect (OSTI)

We develop a polarization-sensitive femtosecond pump probe technique, Raman induced polarization spectroscopy (RIPS), to study coherent rotation in molecular fluids. By observing the collisional dephasing of the coherently prepared rotational states, we are able to extract information concerning the effects of molecular interactions on the rotational motion. The technique is quite sensitive because of the zero background detection method, and is also versatile due to its nonresonant nature.

Morgen, M.M. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; [Lawrence Berkeley National Lab., CA (United States)

1997-05-01T23:59:59.000Z

350

Recipient. County of Baltimore, MD ENERGY EFFICIENCY AND CONSERVATION...  

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

40 Recipient. County of Baltimore, MD ENERGY EFFICIENCY AND CONSERVATION BLOCK GRANTS NEPA COMPLIANCE FORM Activities Determination Categorical Exclusion Reviewer's Specific...

351

Evaluation of Powertrain Options and Component Sizing for MD...  

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

Sizing for MD and HD Applications on Real World Drive Cycles 2011 DOE Hydrogen and Fuel Cells Program, and Vehicle Technologies Program Annual Merit Review and Peer...

352

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

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

diffusion properties in electrode materials is important for designing rechargeable lithium-ion batteries with improved performance. In this work, the lithium dynamics in...

353

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

E-Print Network [OSTI]

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

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

2014-07-11T23:59:59.000Z

354

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

SciTech Connect (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

355

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

E-Print Network [OSTI]

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

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

2013-10-02T23:59:59.000Z

356

Role of entropy in the thermodynamic evolution of the time scale of molecular dynamics near the glass transition  

E-Print Network [OSTI]

In this Letter, we investigate how changes in the system entropy influence the characteristic time scale of the system molecular dynamics near the glass transition. Independently of any model of thermodynamic evolution of the time scale, against some previous suppositions, we show that the system entropy $S$ is not sufficient to govern the time scale defined by structural relaxation time $\\tau $. In the density scaling regime, we argue that the decoupling between $\\tau $ and $S$ is a consequence of different values of the scaling exponents $\\gamma $ and $\\gamma_S $ in the density scaling laws, $\\tau = f(\\rho ^\\gamma /T)$ and $S = h(\\rho ^{\\gamma_S}/T)$, where $\\rho $ and $T$ denote density and temperature, respectively. It implies that the proper relation between $\\tau $ and $S$ requires supplementing with a density factor, $u(\\rho)$, i.e.,$\\tau = g(u(\\rho)w(S))$. This meaningful finding additionally demonstrates that the density scaling idea can be successfully used to separate physically relevant contributions to the time scale of molecular dynamics near the glass transition. As an example, we revise the Avramov entropic model of the dependence $\\tau (T,\\rho)$, giving evidence that its entropic basis has to be extended by the density dependence of the maximal energy barrier for structural relaxation. We also discuss the excess entropy $S_{ex}$, the density scaling of which is found to mimic the density scaling of the total system entropy $S$.

K. Grzybowska; A. Grzybowski; S. Pawlus; J. Pionteck; M. Paluch

2014-10-23T23:59:59.000Z

357

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

358

Molecular Dynamics of Neutral Polymer Bonding Agent (NPBA) as Revealed by Solid-State NMR Spectroscopy  

E-Print Network [OSTI]

Neutral polymer bonding agent (NPBA) is one of the most promising polymeric materials, widely used in nitrate ester plasticized polyether (NEPE) propellant as bonding agent. The structure and dynamics of NPBA under different ...

Hu, Wei

359

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

E-Print Network [OSTI]

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

Southern California, University of

360

Hybrid Car-Parrinello/Molecular Mechanics Modelling of Transition Metal Complexes: Structure, Dynamics and Reactivity  

E-Print Network [OSTI]

Hybrid Car-Parrinello/Molecular Mechanics Modelling of Transition Metal Complexes: Structure). We have recently developed a QM/MM extension of a Car-Parrinello scheme [5]. These hybrid Car functional theory embedded in a classical force field description. The power of such a combined Car

Guidoni, Leonardo

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

The solvation of Cl , Br , and I in acetonitrile clusters: Photoelectron spectroscopy and molecular dynamics simulations  

E-Print Network [OSTI]

The solvation of Cl , Br , and I in acetonitrile clusters: Photoelectron spectroscopy and molecular in acetonitrile clusters CH3CN n with n 1­33, 1­40, and 1­55, respectively, taken with 7.9 eV photon energy. Anion simulations of halide­acetonitrile clusters reproduce the measured stabilization energies and generate full

Perera, Lalith

362

Defect production in tungsten: A comparison between field-ion microscopy and molecular-dynamics simulations  

E-Print Network [OSTI]

Defect production in tungsten: A comparison between field-ion microscopy and molecular defect production efficiencies obtained by FIM are a consequence of a surface effect, which greatly enhances defect production compared to that in the crystal interior. Comparison of clustering of vacancies

Nordlund, Kai

363

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

E-Print Network [OSTI]

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

364

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

E-Print Network [OSTI]

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

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

2008-04-10T23:59:59.000Z

365

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

E-Print Network [OSTI]

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

366

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

E-Print Network [OSTI]

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

Iyengar, Srinivasan S.

367

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

E-Print Network [OSTI]

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

Maruyama, Shigeo

368

Analysis of Photoreaction in the Delta Energy Region by the Quantum Molecular Dynamics Approach  

E-Print Network [OSTI]

We study the photoreaction in the delta energy region using the QMD approach. The proton and pion cross-sections are calculated and compared with experimental data. Through this work we examine the multistep contributions in the cross-sections and the {$\\pi - \\Delta$} dynamics.

Tomoyuki Maruyama; Koji Niita; Satoshi Chiba; Toshiki Maruyama; Akira Iwamoto

1997-05-02T23:59:59.000Z

369

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

SciTech Connect (OSTI)

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

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

2013-09-23T23:59:59.000Z

370

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

SciTech Connect (OSTI)

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

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

2014-05-19T23:59:59.000Z

371

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

SciTech Connect (OSTI)

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

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

2014-07-14T23:59:59.000Z

372

Molecular dynamics simulations of ion range profiles for heavy ions in  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: VegetationEquipment SurfacesResource ProgramModification and ApplicationMolecular

373

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

SciTech Connect (OSTI)

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

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

2009-11-15T23:59:59.000Z

374

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

E-Print Network [OSTI]

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

Maruyama, Shigeo

375

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

E-Print Network [OSTI]

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

Nordlund, Kai

376

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

E-Print Network [OSTI]

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

Richmond, Geraldine L.

377

Distance Restraints from Crosslinking Mass Spectrometry: Mining a Molecular Dynamics Simulation Database to Evaluate Lysine-Lysine Distances  

SciTech Connect (OSTI)

Integrative structural biology models the structures of protein complexes that are intractable by classical structural methods (because of extreme size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such method is chemical cross-linking mass spectrometry (XL-MS), in which cross-linked peptides, derived from a covalently cross-linked protein complex and identified by liquid chromatography-mass spectrometry, pinpoint protein residues close in three-dimensional space. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS3) have a linker arm that is 11.4 Å long when fully extended. However, XL-MS studies on proteins of known structure frequently report cross-links that exceed this distance. Typically, a tolerance of ~3 Å is added to the theoretical maximum to account for this observation, with little justification for the value chosen. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of all protein folds, to investigate the change in lysine-lysine distances resulting from native-state dynamics on the time-scale of tens of nanoseconds. We conclude that observed cross-links are consistent with a protein structure if the distance between cross-linked lysine N? atoms is less than the cross-linker length plus 11.3 Å. For DSS or BS3, this corresponds to a C? to C? distance of 30.4 Å. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures, and indicates the appropriate values of an XLMS derived distance constraint to use in structural modeling.

Merkley, Eric D.; Rysavy, Steven; Kahraman, Abdullah; Hafen, Ryan P.; Daggett, Valerie; Adkins, Joshua N.

2014-03-18T23:59:59.000Z

378

Dynamical Formation of the Dark Molecular Hydrogen Clouds around Diffuse HII Regions  

E-Print Network [OSTI]

We examine the triggering process of molecular cloud formation around diffuse HII regions. We calculate the time evolution of the shell as well as of the HII region in a two-phase neutral medium, solving the UV and FUV radiative transfer, the thermal and chemical processes in the time-dependent hydrodynamics code. In the cold neutral medium, the ambient gas is swept up in the cold (T \\sim 30-40K) and dense (n \\sim 10^3 cm^-3) shell around the HII region. In the shell, H_2 molecules are formed from the swept-up HI gas, but CO molecules are hardly formed. The reformation of H_2 molecules is more efficient with a higher-mass central star. The physical and chemical properties of gas in the shell are just intermediate between those of the neutral medium and molecular clouds observed by the CO emission. The dense shell with cold HI/H_2 gas easily becomes gravitationally unstable, and breaks up into small clouds. The cooling layer just behind the shock front also suffers from thermal instability, and will fragment into cloudlets with some translational motions. We suggest that the predicted cold ``dark'' HI/H_2 gas should be detected as the HI self-absorption (HISA) feature. We have sought such features in recent observational data, and found shell-like HISA features around the giant HII regions, W4 and W5. The shell-like HISA feature shows good spatial correlation with dust emission, but poor correlation with CO emission. Our quantitative analysis shows that the HISA cloud can be as cold as T \\sim a few x 10K. (abridged)

Takashi Hosokawa; Shu-ichiro Inutsuka

2007-04-05T23:59:59.000Z

379

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

E-Print Network [OSTI]

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

Yuichi Togashi; Alexander S. Mikhailov

2007-05-17T23:59:59.000Z

380

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

SciTech Connect (OSTI)

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

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

2014-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "molecular dynamics md" from the National Library of EnergyBeta (NLEBeta).
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381

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

SciTech Connect (OSTI)

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

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

2012-12-14T23:59:59.000Z

382

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution  

E-Print Network [OSTI]

The electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

Damian A. Scherlis; Jean-Luc Fattebert; Francois Gygi; Matteo Cococcioni; Nicola Marzari

2005-10-06T23:59:59.000Z

383

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

E-Print Network [OSTI]

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

Christoph Theis; Rolf Schilling

1998-08-07T23:59:59.000Z

384

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

385

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

SciTech Connect (OSTI)

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

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

2011-08-15T23:59:59.000Z

386

Coordination and Hydrolysis of Plutonium Ions in Aqueous Solution using Car-Parrinello Molecular Dynamics Free Energy Simulations  

SciTech Connect (OSTI)

Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics and the first hydrolysis constants of Pu3+, Pu4+, PuO2+ and PuO22+ ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with available experimental estimates. The hexavalent PuO22+ species is coordinated to 5 aquo ligands while the pentavalent PuO2+ complex is coordinated to 4 aquo ligands. The Pu3+ and Pu4+ ions are both coordinated to 8 water molecules. The first hydrolysis constants obtained for Pu3+ and PuO22+ are 6.65 and 5.70 respectively, all within 0.3 pH units of the experimental values (6.90 and 5.50 respectively). The hydrolysis constant of Pu4+, 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2+, 9.51, supports the experimental results of Bennett et al. (Radiochim. Act. 1992, 56, 15). A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.

Odoh, Samuel O.; Bylaska, Eric J.; De Jong, Wibe A.

2013-11-27T23:59:59.000Z

387

Length-scale dependent mechanical properties of Al-Cu eutectic alloy: Molecular dynamics based model and its experimental verification  

SciTech Connect (OSTI)

This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al{sub 2}Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al{sub 2}Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different length scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80?nm.

Tiwary, C. S., E-mail: cst.iisc@gmail.com; Chattopadhyay, K. [Department of Materials Engineering, Indian Institute of Science, Bangalore 560012 (India); Chakraborty, S.; Mahapatra, D. R. [Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012 (India)

2014-05-28T23:59:59.000Z

388

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

SciTech Connect (OSTI)

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

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

2014-09-14T23:59:59.000Z

389

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

E-Print Network [OSTI]

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

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

2012-12-20T23:59:59.000Z

390

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

E-Print Network [OSTI]

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

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

2015-01-01T23:59:59.000Z

391

LSUHSC NO Leadership Program Director, Augusto Ochoa, MD  

E-Print Network [OSTI]

D: Project 8 Yan Cui, PhD: COBRE Graduate Mentor Internal Advisory Committee Joseph Moerschbaecher, III: Jonna Ellis Promising Junior Investigators Project 2: Jovanny Zabaleta, PhD Project 3: Paulo Rodriguez, PhD Project 4: Timothy Foster, PhD Project 5: John Schieffelin, MD Tulane University Project 6

392

GRANT AWARDS Justin Annes, MD, PhD  

E-Print Network [OSTI]

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

Bejerano, Gill

393

Joseph P. Vacanti, MD Chief of Pediatric Surgery  

E-Print Network [OSTI]

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

Mootha, Vamsi K.

394

MD6151-8-10 Murdoch Counselling Service  

E-Print Network [OSTI]

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

395

Molecular Dynamics Study  

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

as trends in concentration. The electrode pores are modeled as planar graphite sheets and carbon nanotubes with interstices ranging from one to four nanometers. Ordered layers form...

396

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

E-Print Network [OSTI]

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

Hancock, William O.

397

Asbestos-related diseases in automobile mechanics Jacques Ameille, MD1  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

398

COMMISSION ON HEALTH SCIENCE, EDUCATION, AND P. Roy Vagelos, M.D.  

E-Print Network [OSTI]

Johnson & Johnson Barbara Bell Coleman Chairperson Amelior Foundation Norman H. Edelman, M.D. Vice Princeton University Steven A. Schroeder, M.D. President and CEO The Robert Wood Johnson Foundation Harold and Dentistry of New Jersey Samuel O. Thier, M.D. President and CEO Partners HealthCare System, Inc. #12

Lin, Xiaodong

399

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

SciTech Connect (OSTI)

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

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

2014-04-07T23:59:59.000Z

400

A time-dependent momentum-space density functional theoretical approach for electron transport dynamics in molecular devices  

E-Print Network [OSTI]

We propose a time-dependent density functional theoretical (TDDFT) approach in momentum (\\mathcal{P} ) space for the study of electron transport in molecular devices under arbitrary biases. The basic equation of motion, which is a time...

Chu, Shih-I; Zhou, Zhongyuan

2009-10-27T23:59:59.000Z

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


401

Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer  

E-Print Network [OSTI]

Hsp90 is a molecular chaperone essential for protein folding and activation in normal homeostasis and stress response. ATP binding and hydrolysis facilitate Hsp90 conformational changes required for client activation. Hsp90 plays an important role...

Morra, Giulia; Verkhivker, Gennady M.; Colombo, Giorgio

2009-03-20T23:59:59.000Z

402

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

E-Print Network [OSTI]

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

Wood, Brandon C. (Brandon Christopher)

2007-01-01T23:59:59.000Z

403

A Classical Approach in Simple Nuclear Fusion Reaction 1H2 + 1H3 using Two-Dimension Granular Molecular Dynamics Model  

E-Print Network [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 1H2 and 1H3 is observed. Several products of the fusion reaction have been obtained, even the unreported ones, including temporary 2He4 nucleus.

Sparisoma Viridi; Rizal Kurniadi; Abdul Waris; Yudha Satya Perkasa

2011-09-30T23:59:59.000Z

404

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

405

Research Paper j Using Petri Net Tools to Study Properties and Dynamics of  

E-Print Network [OSTI]

Research Paper j Using Petri Net Tools to Study Properties and Dynamics of Biological Systems MOR PELEG, PHD, DANIEL RUBIN, MD, MSC, RUSS B. ALTMAN, MD, PHD A b s t r a c t Petri Nets (PNs concurrent dynamic systems is Petri Nets (PNs).1 An advantage of PNs is that they can represent system

Rubin, Daniel L.

406

A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions  

SciTech Connect (OSTI)

We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

Markutsya, Sergiy [Ames Laboratory; Lamm, Monica H [Ames Laboratory

2014-11-07T23:59:59.000Z

407

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

E-Print Network [OSTI]

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

Kapko, Vitaliy; Angell, C Austen

2010-01-01T23:59:59.000Z

408

Brain-Computer Interfaces in Medicine Jerry J. Shih, MD; Dean J. Krusienski, PhD; and Jonathan R. Wolpaw, MD  

E-Print Network [OSTI]

Brain-Computer Interfaces in Medicine Jerry J. Shih, MD; Dean J. Krusienski, PhD; and Jonathan R. Wolpaw, MD Abstract Brain-computer interfaces (BCIs) acquire brain signals, analyze them, and translate, electrocorticographic, and other brain signals for increasingly complex control of cursors, robotic arms, prostheses

Nehorai, Arye

409

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

E-Print Network [OSTI]

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

Daggett, Valerie

410

MD/HD Advanced Technology Evaluations | Department of Energy  

Energy Savers [EERE]

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Office of Inspector General Office0-72.pdfGeorgeDoesn't HappenLow-Cost Production ofModelingfor theMACCS2ofMD/HD

411

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

E-Print Network [OSTI]

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

Goddard III, William A.

412

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

SciTech Connect (OSTI)

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

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

2009-01-01T23:59:59.000Z

413

arXiv:condmat/0607335 Molecular dynamics of shock fronts and their transitions in Lennard-Jonesium and Tin  

E-Print Network [OSTI]

in Lennard-Jonesium and Tin J. M. D. Lane #3; and M. P. Marder y Center for Nonlinear Dynamics, University for shocks in tin which agrees to within 6% with experimental data. We study the strong shock to elastic-plastic shock transition in tin and #12;nd that it is a continuous transition consistent with a transcritical

Texas at Austin. University of

414

Molecular Dynamics Simulations of Solvated Yeast tRNAAsp Pascal Auffinger, Shirley Louise-May, and Eric Westhof  

E-Print Network [OSTI]

of the tRNA molecule. Calculated thermal factors are used to compare the dynamics of the tRNA in solution in the two ends and the "el- bow" of the L-shaped structure, include the 3 -CCA resi- dues of the acceptor

Westhof, Eric

415

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

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

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

416

Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations  

SciTech Connect (OSTI)

The behavior of the UO{sub 2}{sup 2+} uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT +U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 A above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d{sub U-O{sub a{sub d{sub s{sub o{sub r{sub p{sub t{sub i{sub o{sub n}}}}}}}}}}}=2.39 A. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

Sebbari, Karim [EDF-R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Ecuelles, 77818 Moret Sur Loing (France); Institut de Physique Nucleaire d'Orsay, Universite Paris-Sud, CNRS UMR 8608, 15 rue Georges Clemenceau, Batiment 100, 91406 Orsay Cedex (France); Roques, Jerome; Simoni, Eric [Institut de Physique Nucleaire d'Orsay, Universite Paris-Sud, CNRS UMR 8608, 15 rue Georges Clemenceau, Batiment 100, 91406 Orsay Cedex (France); Domain, Christophe [EDF-R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Ecuelles, 77818 Moret Sur Loing (France)

2012-10-28T23:59:59.000Z

417

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

SciTech Connect (OSTI)

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

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

2008-07-01T23:59:59.000Z

418

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

E-Print Network [OSTI]

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

Stanford, Kyle

419

Broadband infrared and Raman probes of excited-state vibrational molecular dynamics; Simulation protocols based on loop diagram  

E-Print Network [OSTI]

Vibrational motions in electronically excited states can be observed by either time and frequency resolved infrared absorption or by off resonant stimulated Raman techniques. Multipoint correlation function expressions are derived for both signals. Three representations for the signal which suggest different simulation protocols are developed. These are based on the forward and the backward propagation of the wavefunction, sum over state expansion using an effective vibration Hamiltonian and a semiclassical treatment of a bath. We show that the effective temporal ($\\Delta t$) and spectral ($\\Delta\\omega$) resolution of the techniques is not controlled solely by experimental knobs but also depends on the system dynamics being probed. The Fourier uncertainty $\\Delta\\omega\\Delta t>1$ is never violated.

Konstantin E. Dorfman; Benjamin P. Fingerhut; Shaul Mukamel

2013-05-23T23:59:59.000Z

420

Spin dynamics simulation of electron spin relaxation in Ni{sup 2+}(aq)  

SciTech Connect (OSTI)

The ability to quantitatively predict and analyze the rate of electron spin relaxation of open-shell systems is important for electron paramagnetic resonance and paramagnetic nuclear magnetic resonance spectroscopies. We present a combined molecular dynamics (MD), quantum chemistry (QC), and spin dynamics simulation method for calculating such spin relaxation rates. The method is based on the sampling of a MD trajectory by QC calculations, to produce instantaneous parameters of the spin Hamiltonian used, in turn, to numerically solve the Liouville-von Neumann equation for the time evolution of the spin density matrix. We demonstrate the approach by simulating the relaxation of electron spin in an aqueous solution of Ni{sup 2+} ion. The spin-lattice (T{sub 1}) and spin-spin (T{sub 2}) relaxation rates are extracted directly from the simulations of the time dependence of the longitudinal and transverse magnetization, respectively. Good agreement with the available, indirectly obtained experimental data is obtained by our method.

Rantaharju, Jyrki, E-mail: jjrantaharju@gmail.com; Mareš, Ji?í, E-mail: jiri.mares@oulu.fi; Vaara, Juha, E-mail: juha.vaara@iki.fi [NMR Research Group, Department of Physics, University of Oulu, P.O. Box 3000, Oulu, FIN-90014 (Finland)

2014-07-07T23:59:59.000Z

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


421

Time-resolved infrared absorption studies of the solvent-dependent vibrational relaxation dynamics of chlorine dioxide  

SciTech Connect (OSTI)

We report a series of time-resolved infrared absorption studies on chlorine dioxide (OClO) dissolved in H{sub 2}O, D{sub 2}O, and acetonitrile. Following the photoexcitation at 401 nm, the evolution in optical density for frequencies corresponding to asymmetric stretch of OClO is measured with a time resolution of 120{+-}50 fs. The experimentally determined optical-density evolution is compared with theoretical models of OClO vibrational relaxation derived from collisional models as well as classical molecular-dynamics (MD) studies. The vibrational relaxation rates in D{sub 2}O are reduced by a factor of 3 relative to H{sub 2}O consistent with the predictions of MD. This difference reflects modification of the frequency-dependent solvent-solute coupling accompanying isotopic substitution of the solvent. Also, the geminate-recombination quantum yield for the primary photofragments resulting in the reformation of ground-state OClO is reduced in D{sub 2}O relative to H{sub 2}O. It is proposed that this reduction reflects enhancement of the dissociation rate accompanying vibrational excitation along the asymmetric-stretch coordinate. In contrast to H{sub 2}O and D{sub 2}O, the vibrational-relaxation dynamics in acetonitrile are not well described by the theoretical models. Reproduction of the optical-density evolution in acetonitrile requires significant modification of the frequency-dependent solvent-solute coupling derived from MD. It is proposed that this modification reflects vibrational-energy transfer from the asymmetric stretch of OClO to the methyl rock of acetonitrile. In total, the results presented here provide a detailed description of the solvent-dependent geminate-recombination and vibrational-relaxation dynamics of OClO in solution.

Bolinger, Joshua C.; Bixby, Teresa J.; Reid, Philip J. [Box 351700, Department of Chemistry, University of Washington, Seattle, Washington 98195 (United States)

2005-08-22T23:59:59.000Z

422

Scientist Position In Human Molecular Genetics: Toronto, ON, Canada  

E-Print Network [OSTI]

Scientist Position In Human Molecular Genetics: Toronto, ON, Canada Genetics & Genome Biology) Program at The Hospital for Sick Children (SickKids), Canada's largest paediatric research hospital and research hospitals and Canada's largest university in close proximity. Candidates must have a PhD, or MD Ph

Queitsch, Christine

423

Coupling MD Simulations and X-ray Absorption Spectroscopy to Study Ions in Solution  

SciTech Connect (OSTI)

The structure of ionic solutions is a key-point in understanding physicochemical properties of electrolyte solutions. Among the reduced number of experimental techniques which can supply direct information on the ion environment, X-ray Absorption techniques (XAS) have gained importance during the last decades although they are not free of difficulties associated to the data analysis leading to provide reliable structures. Computer simulations of ions in solution is a theoretical alternative to provide information on the solvation structure. Thus, the use of computational chemistry can increase the understanding of these systems although an accurate description of ionic solvation phenomena represents nowadays a significant challenge to theoretical chemistry. We present: (a) the assignment of features in the XANES spectrum to well defined structural motif in the ion environment, (b) MD-based evaluation of EXAFS parameters used in the fitting procedure to make easier the structural resolution, and (c) the use of the agreement between experimental and simulated XANES spectra to help in the choice of a given intermolecular potential for Computer Simulations. Chemical problems examined are: (a) the identification of the second hydration shell in dilute aqueous solutions of highly-charged cations, such as Cr{sup 3+}, Rh{sup 3+}, Ir{sup 3+}, (b) the invisibility by XAS of certain structures characterized by Computer Simulations but exhibiting high dynamical behavior and (c) the solvation of Br{sup -} in acetonitrile.

Marcos, E. Sanchez; Beret, E. C.; Martinez, J. M.; Pappalardo, R. R. [University of Seville, Dept. of Physical Chemistry (Spain); Ayala, R.; Munoz-Paez, A. [University of Seville, CSIC-ICMSE. Dept. of Inorganic Chemistry (Spain)

2007-11-29T23:59:59.000Z

424

angel savino md: Topics by E-print Network  

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

develop apomorphine therapy in Parkinson's disease. Neurology 2004;62(suppl 4):S12-S17. APO-related Adverse Events Lichtarge, Olivier 169 Report 2004 MDPhD Program "Molecular...

425

Strong Electronic Polarization of the C60 Fullerene by the Imidazolium-Based Ionic Liquids: Accurate Insights from Born-Oppenheimer Molecular Dynamics Simulations  

E-Print Network [OSTI]

Fullerenes are known to be polarizable due to the strained carbon-carbon bonds and high surface curvature. Electronic polarization of fullerenes is of steady practical importance, since it leads to non-additive interactions and, therefore, to unexpected phenomena. For the first time, hybrid density functional theory (HDFT) powered Born-Oppenheimer molecular dynamics (BOMD) simulations have been conducted to observe electronic polarization and charge transfer phenomena in the C60 fullerene at finite temperature (350 K). The non-additive phenomena are fostered by the three selected imidazolium-based room-temperature ionic liquids (RTILs). We conclude that although charge transfer appears nearly negligible in these systems, an electronic polarization is indeed significant leading to a systematically positive effective electrostatic charge on the C60 fullerene: +0.14e in [EMIM][Cl], +0.21e in [EMIM][NO3], +0.17e in [EMIM][PF6]. These results are, to certain extent, unexpected providing an inspiration to consider ...

Chaban, Vitaly V

2015-01-01T23:59:59.000Z

426

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

SciTech Connect (OSTI)

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

Bourg, I.C.; Sposito, G.

2011-04-01T23:59:59.000Z

427

Influence of longitudinal isotope substitution on the thermal conductivity of carbon nanotubes: Results of nonequilibrium molecular dynamics and local density functional calculations  

SciTech Connect (OSTI)

We report reverse nonequilibrium molecular dynamics calculations of the thermal conductivity of isotope substituted (10,10) carbon nanotubes (CNTs) at 300 K. {sup 12}C and {sup 14}C isotopes both at 50% content were arranged either randomly, in bands running parallel to the main axis of the CNTs or in bands perpendicular to this axis. It is found that the systems with randomly distributed isotopes yield significantly reduced thermal conductivity. In contrast, the systems where the isotopes are organized in patterns parallel to the CNTs axis feature no reduction in thermal conductivity when compared with the pure {sup 14}C system. Moreover, a reduction of approximately 30% is observed in the system with the bands of isotopes running perpendicular to the CNT axis. The computation of phonon dispersion curves in the local density approximation and classical densities of vibrational states reveal that the phonon structure of carbon nanotubes is conserved in the isotope substituted systems with the ordered patterns, yielding high thermal conductivities in spite of the mass heterogeneity. In order to complement our conclusions on the {sup 12}C-{sup 14}C mixtures, we computed the thermal conductivity of systems where the {sup 14}C isotope was turned into pseudo-atoms of 20 and 40 atomic mass units.

Leroy, Frédéric, E-mail: f.leroy@theo.chemie.tu-darmstadt.de; Böhm, Michael C., E-mail: boehm@theo.chemie.tu-darmstadt.de [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt (Germany); Schulte, Joachim [Bruker Biospin GmbH, Silberstreifen, D-76287 Rheinstetten (Germany)] [Bruker Biospin GmbH, Silberstreifen, D-76287 Rheinstetten (Germany); Balasubramanian, Ganesh [Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011 (United States)] [Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011 (United States)

2014-04-14T23:59:59.000Z

428

Electron localization following attosecond molecular photoionization  

E-Print Network [OSTI]

- second pump­probe strategies as a powerful tool for investigating the complex molecular dynamics , their use in studying atomic photo- excitation and photoionization6,7 and electron dynamics in solids8 has and biomolecular complexes11,12 . Extremely fast molecular dynamics involving electron correlation can also

Kling, Matthias

429

Molecular dynamics simulation comparison of atomic scale intermixing at the amorphous Al2O3/semiconductor interface for a-Al2O3/Ge, a-Al2O3/InGaAs,  

E-Print Network [OSTI]

Molecular dynamics simulation comparison of atomic scale intermixing at the amorphous Al2O3/semiconductor interface for a-Al2O3/Ge, a-Al2O3/InGaAs, and a-Al2O3/InAlAs/InGaAs Evgueni A. Chagarov *, Andrew oxides Ge InGaAs InAlAs Oxide­semiconductor stack High-K oxide a b s t r a c t The structural properties

Kummel, Andrew C.

430

Andrea E. Reid, M.D., M.P.H. INFORMATION  

E-Print Network [OSTI]

to practice State: District of Columbia License No: MD038392 Initial Date: 01/01/2011 Renewal/Expiration Date Providence, RI 02912 9/1980-6/1984 ScB with Honors, Psychology Medical Education: Harvard Medical School 25

Goodrich, Lisa V.

431

Intelligent Mobile Health Monitoring System (IMHMS) Rifat Shahriyar, Md. Faizul Bari, Gourab Kundu, Sheikh Iqbal Ahamed,  

E-Print Network [OSTI]

, Sheikh Iqbal Ahamed, Md. Mostofa Akbar Department of Computer Science and Engineering, Bangladesh.com, sheikh.ahamed@mu.edu, mostofa@cse.buet.ac.bd Abstract. Health monitoring is repeatedly mentioned as one

Boutaba, Raouf

432

Vehicle Technologies Office Merit Review 2014: Cummins MD & HD Accessory Hybridization CRADA  

Broader source: Energy.gov [DOE]

Presentation given by Oak Ridge National Laboratory at 2014 DOE Hydrogen and Fuel Cells Program and Vehicle Technologies Office Annual Merit Review and Peer Evaluation Meeting about Cummins MD &...

433

E-Print Network 3.0 - amory codman md Sample Search Results  

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

proud. During... , Emergency Surgery, and Surgical Critical Care (TESSCC), led by George P. Velmahos, MD, PhD, MSEd. George... is a skilled and committed teacher who has recruited...

434

Benzene Dimer: Dynamic Structure and Thermodynamics Derived from...  

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

Benzene Dimer: Dynamic Structure and Thermodynamics Derived from On-the-Fly ab initio DFT-D Molecular Dynamic Simulations. Benzene Dimer: Dynamic Structure and Thermodynamics...

435

Studies of structure and dynamics of biological macro-molecular assemblies by low angle neutron diffraction and inelastic X-ray scattering  

E-Print Network [OSTI]

This thesis is organized into two parts which focus on the studies of the dynamic structure factor and static inter-particle structure factor respectively. In the first part, we have measured and analyzed the dynamic ...

Liu, Yun, 1973-

2005-01-01T23:59:59.000Z

436

Assessment of Molecular Modeling & Simulation  

SciTech Connect (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

437

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

SciTech Connect (OSTI)

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

Agieienko, Vira N.; Kolesnik, Yaroslav V.; Kalugin, Oleg N., E-mail: onkalugin@gmail.com [Department of Inorganic Chemistry, V. N. Karazin Kharkiv National University, Kharkiv 61022 (Ukraine)

2014-05-21T23:59:59.000Z

438

Intramolecular and nonlinear dynamics  

SciTech Connect (OSTI)

Research in this program focuses on three interconnected areas. The first involves the study of intramolecular dynamics, particularly of highly excited systems. The second area involves the use of nonlinear dynamics as a tool for the study of molecular dynamics and complex kinetics. The third area is the study of the classical/quantum correspondence for highly excited systems, particularly systems exhibiting classical chaos.

Davis, M.J. [Argonne National Laboratory, IL (United States)

1993-12-01T23:59:59.000Z

439

Interfacial Ionic Liquids: Connecting Static and Dynamic Structures  

E-Print Network [OSTI]

It is well-known that room temperature ionic liquids (RTILs) often adopt a charge-separated layered structure, i.e., with alternating cation- and anion-rich layers, at electrified interfaces. However, the dynamic response of the layered structure to temporal variations in applied potential is not well understood. We used in situ, real-time X-ray reflectivity (XR) to study the potential-dependent electric double layer (EDL) structure of an imidazolium-based RTIL on charged epitaxial graphene during potential cycling as a function of temperature. The results suggest that the graphene-RTIL interfacial structure is bistable in which the EDL structure at any intermediate potential can be described by the combination of two extreme-potential structures whose proportions vary depending on the polarity and magnitude of the applied potential. This picture is supported by the EDL structures obtained by fully atomistic molecular dynamics (MD) simulations at various static potentials. The potential-driven transition between the two structures is characterized by an increasing width but with an approximately fixed hysteresis magnitude as a function of temperature. The results are consistent with the coexistence of distinct anion and cation adsorbed structures separated by an energy barrier (~0.15 eV).

Ahmet Uysal; Hua Zhou; Guang Feng; Sang Soo Lee; Song Li; Peter T. Cummings; Pasquale F. Fulvio; Sheng Dai; John K. McDonough; Yury Gogotsi; Paul Fenter

2014-12-06T23:59:59.000Z

440

HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations  

E-Print Network [OSTI]

HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD translocation, were provided by wide-angle X-ray scattering (WAXS) and neutron scattering. CD spectroscopy for Neutron Research, 100 Bureau Drive, Stop 6102, Gaithersburg, MD 20899, United States d CHESS, Cornell

Nagle, John F.

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


441

An NMR (nuclear magnetic resonance) investigation of the chemical association and molecular dynamics in asphalt ridge tar sand ore and bitumen  

SciTech Connect (OSTI)

Preliminary studies on tar sand bitumen given in this report have shown that the reassociation of tar sand bitumen to its original molecular configuration after thermal stressing is a first-order process requiring nearly a week to establish equilibrium. Studies were also conducted on the dissolution of tar sand bitumen in solvents of varying polarity. At a high-weight fraction of solute to solvent the apparent molecular weight of the bitumen molecules was greater than that of the original bitumen when dissolved in chloroform-d/sub 1/ and benzene-d/sub 6/. This increase in the apparent molecular weight may be due to micellar formation or a weak solute-solvent molecular complex. Upon further dilution with any of the solvents studied, the apparent molecular weight of the tar sand bitumen decreased because of reduced van der Waals forces of interaction and/or hydrogen bonding. To define the exact nature of the interactions, it will be necessary to have viscosity measurements of the solutions. 30 refs., 3 figs., 3 tabs.

Netzel, D.A.; Coover, P.T.

1987-09-01T23:59:59.000Z

442

Magnetismo Molecular (Molecular Magentism)  

SciTech Connect (OSTI)

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

443

says Michel Torbey, MD, medical director of OSU Medical Center's Neurovascular Stroke Center.  

E-Print Network [OSTI]

stroke says Michel Torbey, MD, medical director of OSU Medical Center's Neurovascular Stroke Center. "That means calling 911 as soon as you recognize signs in yourself or in someone nearby." When a stroke is brain,'" Dr. Torbey explains. `aMeriCa's best' stroke Care When a stroke patient arrives at The Ohio

444

CityBizList US Green Building Council -MD Celebrating Move to  

E-Print Network [OSTI]

CityBizList US Green Building Council - MD Celebrating Move to Hunt Valley Share Email this Article Baltimore County Executive Jim Smith will join the U.S. Green Building Council Maryland to celebrate Horst, Senior Vice President, U.S. Green Building Council. Horst has served as chair of USGBC's LEED

445

Vendor Location PHS Assurance# A&G Pharmaceutical, Inc. MD A4404-01  

E-Print Network [OSTI]

BioScience Labs MD A3467-01 Alpha Genesis, Inc. SC A3645-01 Antibody Research Corporation MO A4489. On the BPA Program website open the current 'BPA Commodity List' and use the 'animal services', 'biological materials' or 'blood/blood products' tabs to search for these vendors. If a vendor is listed, the purchaser

Bandettini, Peter A.

446

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 September 2003 Published online: 24 October 2003 Abstract We propose a new computational methodology methods for determination of solvation free energies. We employ the RISM formulation of solvation free

Truong, Thanh N.

447

DEWS: A Decentralized Engine for Web Search Reaz Ahmed, Rakibul Haque, Md. Faizul Bari, Raouf Boutaba  

E-Print Network [OSTI]

. Centrally controlled, company owned search engines, like Google, Yahoo and Bing, may not be sufficientDEWS: A Decentralized Engine for Web Search Reaz Ahmed, Rakibul Haque, Md. Faizul Bari, Raouf search engines, which is not healthy for our freedom in the Internet. A better solution is to enable

Waterloo, University of

448

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

E-Print Network [OSTI]

Ira 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 of studies have shown that a limited, regional nuclear war between India and Pakistan would cause significant

Robock, Alan

449

The National Institutes of Health Announces the 2014 NIH Regional Seminar in Baltimore, MD  

E-Print Network [OSTI]

The National Institutes of Health Announces the 2014 NIH Regional Seminar in Baltimore, MD · GRANT REGULATIONS AND POLICIES · AND MORE! Except for a visit to NIH, there is not another opportunity like the NIH, while spending 2 days learning the latest NIH grants policy and process information first-hand. Who

Baker, Chris I.

450

Hot Water DJ: Saving Energy by Pre-mixing Hot Water Md Anindya Prodhan  

E-Print Network [OSTI]

Hot Water DJ: Saving Energy by Pre-mixing Hot Water Md Anindya Prodhan Department of Computer University of Virginia whitehouse@virginia.edu Abstract After space heating and cooling, water heating consumption. Current water heating systems waste up to 20% of their energy due to poor insulation in pipes

Whitehouse, Kamin

451

EMC/FDTD/MD FOR MULTIPHYSICS CHARACTERIZATION OF SEMICONDUCTORS AT THZ FREQUENCIES  

E-Print Network [OSTI]

EMC/FDTD/MD FOR MULTIPHYSICS CHARACTERIZATION OF SEMICONDUCTORS AT THZ FREQUENCIES by Keely Willis.1 Ensemble Monte Carlo (EMC) . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 2.2 Finite difference) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 3 EMC/FDTD for 2D analysis of materials with low carrier density . . . . . . . . . 22 3.1 EMC

Knezevic, Irena

452

Photon Echo Studies on Coherence Dynamics in the Photosynthetic Bacterial Reaction Center  

E-Print Network [OSTI]

molecular understanding of electronic and vibrational couplings governing the dynamics of excitation

Ryu, Seungwan

2013-01-01T23:59:59.000Z

453

Molecular eigenstate spectroscopy: Application to the intramolecular dynamics of some polyatomic molecules in the 3000 to 7000 cm{sup {minus}1} region  

SciTech Connect (OSTI)

Intramolecular vibrational redistribution (IVR) appears to be a universal property of polyatomic molecules in energy regions where the vibrational density of states is greater than about 5 to 30 states per cm{sup {minus}1}. Interest in IVR stems from its central importance to the spectroscopy, photochemistry, and reaction kinetics of these molecules. A bright state, {var_phi}{sub s}, which may be a C-H stretching vibration, carries the oscillator strength from the ground state. This bright state may mix with bath rotational-vibrational levels to form a clump of molecular eigenstates, each of which carries a portion of the oscillator strength from the ground state. In this work the authors explicitly resolve transitions to each of these molecular eigenstates. Detailed information about the nature of IVR is contained in the frequencies and intensities of the observed discrete transitions. The primary goal of this research is to probe the coupling mechanisms by which IVR takes place. The most fundamental distinction to be made is between anharmonic coupling which is independent of molecular rotation and rotationally-mediated coupling. The authors are also interested in the rate at which IVR takes place. Measurements are strictly in the frequency domain but information is obtained about the decay of the zero order state, {var_phi}{sub s}, which could be prepared in a hypothetical experiment as a coherent excitation of the clump of molecular eigenstates. As the coherent superposition dephases, the energy would flow from the initially prepared mode into nearby overtones and combinations of lower frequency vibrational modes. The decay of the initially prepared mode is related to a pure sequence infrared absorption spectrum by a Fourier transform.

Perry, D.S. [Univ. of Akron, OH (United States)

1993-12-01T23:59:59.000Z

454

arXiv:cond-mat/0607335v113Jul2006 Molecular dynamics of shock fronts and their transitions in Lennard-Jonesium and Tin  

E-Print Network [OSTI]

in Lennard-Jonesium and Tin J. M. D. Lane and M. P. Marder Center for Nonlinear Dynamics, University of Texas for shocks in tin which agrees to within 6% with experimental data. We study the strong shock to elastic-plastic shock transition in tin and find that it is a continuous transition consistent with a transcritical

Texas at Austin. University of

455

Quantum dynamics of molecular multiphoton excitation in intense laser and static electric fields: Floquet theory, quasienergy spectra, and application to the HF molecule  

E-Print Network [OSTI]

of the HF molecule as functions of field strengths and frequency. Nonlinear effects such as power broadening, dynamic Stark shift, Autler–Townes multiplet splitting, hole burning, and S?hump behaviors, etc., are observed and discussed in terms of quasienergy...

Chu, Shih-I; Tietz, James V.; Datta, Krishna K.

1982-01-01T23:59:59.000Z

456

Geometry and Nanolength Scales versus Interface Interactions: Water Dynamics in AOT Lamellar Structures and  

E-Print Network [OSTI]

occur in the water structure and dynamics. At the same time, MD simulations have shown that the mostGeometry and Nanolength Scales versus Interface Interactions: Water Dynamics in AOT Lamellar Structures and Reverse Micelles David E. Moilanen, Emily E. Fenn, Daryl Wong, and M. D. Fayer* Department

Fayer, Michael D.

457

Heart Rate Dynamics Before Spontaneous Onset of Ventricular  

E-Print Network [OSTI]

Heart Rate Dynamics Before Spontaneous Onset of Ventricular Fibrillation in Patients With Healed V. Huikuri, MD The traditional methods of analyzing heart rate (HR) variability have failed myocardial infarction has been shown to be in- creased in patients with reduced heart rate (HR) vari- ability

458

A Linear Algorithm for Compact Box-Drawings of Trees Masud Hasan , Md. Saidur Rahman y , and Takao Nishizeki z  

E-Print Network [OSTI]

A Linear Algorithm for Compact Box-Drawings of Trees Masud Hasan #3; , Md. Saidur Rahman y, Bangladesh. Email: m2hasan@hopper.math.uwaterloo.ca y Graduate School of Information Sciences, Tohoku Univer

Wismath, Stephen

459

Molecular Simulations of Electrolytes and Electrolyte/Electrode...  

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

"Mega" Merit Review 2008 on February 25, 2008 in Bethesda, Maryland. merit08smith.pdf More Documents & Publications Molecular dynamics simulation and ab intio studies...

460

Material dynamics under extreme conditions of pressure and strain rate  

SciTech Connect (OSTI)

Solid state experiments at extreme pressures (10-100 GPa) and strain rates ({approx}10{sup 6}-10{sup 8}s{sup -1}) are being developed on high-energy laser facilities, and offer the possibility for exploring new regimes of materials science. These extreme solid-state conditions can be accessed with either shock loading or with a quasi-isentropic ramped pressure drive. Velocity interferometer measurements establish the high pressure conditions. Constitutive models for solid-state strength under these conditions are tested by comparing 2D continuum simulations with experiments measuring perturbation growth due to the Rayleigh-Taylor instability in solid-state samples. Lattice compression, phase, and temperature are deduced from extended x-ray absorption fine structure (EXAFS) measurements, from which the shock-induced {alpha}-{omega} phase transition in Ti and the {alpha}-{var_epsilon} phase transition in Fe are inferred to occur on sub-nanosec time scales. Time resolved lattice response and phase can also be measured with dynamic x-ray diffraction measurements, where the elastic-plastic (1D-3D) lattice relaxation in shocked Cu is shown to occur promptly (< 1 ns). Subsequent large-scale molecular dynamics (MD) simulations elucidate the microscopic dynamics that underlie the 3D lattice relaxation. Deformation mechanisms are identified by examining the residual microstructure in recovered samples. The slip-twinning threshold in single-crystal Cu shocked along the [001] direction is shown to occur at shock strengths of {approx}20 GPa, whereas the corresponding transition for Cu shocked along the [134] direction occurs at higher shock strengths. This slip-twinning threshold also depends on the stacking fault energy (SFE), being lower for low SFE materials. Designs have been developed for achieving much higher pressures, P > 1000 GPa, in the solid state on the National Ignition Facility (NIF) laser.

Remington, B A; Allen, P; Bringa, E; Hawreliak, J; Ho, D; Lorenz, K T; Lorenzana, H; Meyers, M A; Pollaine, S W; Rosolankova, K; Sadik, B; Schneider, M S; Swift, D; Wark, J; Yaakobi, B

2005-09-06T23:59:59.000Z

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


461

Computer, MD  

E-Print Network [OSTI]

Clinical decision support is an emerging type of healthcare information technology that aims to actively guide doctors' decision-making processes. In its various forms, it can help physicians design treatment regimens, ...

Feblowitz, Joshua

2010-01-01T23:59:59.000Z

462

MD 715  

National Nuclear Security Administration (NNSA)

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May Jun Jul(Summary) "ofEarlyEnergyDepartmentNational NuclearhasAdministration77NuclearSecurityAdministrator |Life0239. S .

463

VA-MD-DC Hydrogen Education for Decision Makers | Department of Energy  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankCombustion |Energy Usage »of EnergyTheTwoVulnerabilities | Department of Energy 5:VA4-BVA-MD-DC

464

adhesive system self-etching: Topics by E-print Network  

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

the adhesive contact between elastic solids with randomly rough, self affine fractal surfaces. We present molecular dynamics (MD) simulation results for the interfacial stress...

465

Effects of Oxygen-Containing Functional Groups on Supercapacitor...  

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

Oxygen-Containing Functional Groups on Supercapacitor Performance. Effects of Oxygen-Containing Functional Groups on Supercapacitor Performance. Abstract: Molecular dynamics (MD)...

466

Nano-crystallization and magnetic mechanisms of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy by ab initio molecular dynamics simulation  

SciTech Connect (OSTI)

Iron-based amorphous and nano-crystalline alloys have attracted a growing interest due to their potential in the application of magnetic coil production. However, fundamental understanding of the nano-crystallization mechanisms and magnetic features in the amorphous structure are still lack of knowledge. In the present work, we performed ab initio molecular dynamics simulation to clarify the ionic and electronic structure in atomic scale, and to derive the origin of the good magnetic property of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy. The simulation gave a direct evidence of the Cu-P bonding preference in the amorphous alloy, which may promote nucleation in nano-crystallization process. On the other hand, the electron transfer and the band/orbital features in the amorphous alloy suggests that alloying elements with large electronegativity and the potential to expand Fe disordered matrix are preferred for enhancing the magnetization.

Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro [Institute for Material Research, Tohoku University, Sendai 980-8577 (Japan); Liang, Yunye [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kawazoe, Yoshiyuki [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kutateladze Institute of Thermophysics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk (Russian Federation)

2014-05-07T23:59:59.000Z

467

Molecular Science Research Center 1992 annual report  

SciTech Connect (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

468

A study of QM/Langevin-MD simulation for oxygen-evolving center of photosystem II  

SciTech Connect (OSTI)

We have performed three QM/Langevin-MD simulations for oxygen-evolving complex (OEC) and surrounding residues, which are different configurations of the oxidation numbers on Mn atoms in the Mn{sub 4}O{sub 5}Ca cluster. By analyzing these trajectories, we have observed sensitivity of the change to the configuration of Mn oxidation state on O atoms of carboxyl on three amino acids, Glu354, Ala344, and Glu333. The distances from Mn to O atoms in residues contacting with the Mn{sub 4}O{sub 5}Ca cluster were analyzed for the three trajectories. We found the good correlation of the distances among the simulations. However, the distances with Glu354, Ala344, and Glu333 have not shown the correlation. These residues can be sensitive index of the changes of Mn oxidation numbers.

Uchida, Waka; Kimura, Yoshiro; Wakabayashi, Masamitsu [Department of Biomolecular Engineering, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8503 (Japan); Hatakeyama, Makoto; Ogata, Koji; Nakamura, Shinichiro [RIKEN Research Cluster for Innovation, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Yokojima, Satoshi [Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan and RIKEN Research Cluster for Innovation, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

2013-12-10T23:59:59.000Z

469

Atomistic simulation of structure and dynamics of columnar phases of hexabenzocoronene derivatives  

E-Print Network [OSTI]

Using atomistic molecular dynamics simulations we study solid and liquid crystalline columnar discotic phases formed by alkyl-substituted hexabenzocoronene mesogens. Correlations between the molecular structure, packing, and dynamical properties of these materials are established.

Denis Andrienko; Valentina Marcon; Kurt Kremer

2006-07-27T23:59:59.000Z

470

Surface Tensions in NaCl-Water-Air Systems from MD Simulations Ranjit Bahadur, Lynn M. Russell,*, and Saman Alavi  

E-Print Network [OSTI]

Surface Tensions in NaCl-Water-Air Systems from MD Simulations Ranjit Bahadur, Lynn M. Russell, Ottawa, Ontario K1A 0R6, Canada ReceiVed: July 9, 2007; In Final Form: July 30, 2007 Surface tensions to the surface tension, while the energy-integral and test area methods provide direct estimates. At 1 atm

Russell, Lynn

471

Survival in Academy AwardWinning Actors and Actresses Donald A. Redelmeier, MD, and Sheldon M. Singh, BSc  

E-Print Network [OSTI]

Survival in Academy Award­Winning Actors and Actresses Donald A. Redelmeier, MD, and Sheldon M in status from winning an academy award is associated with long-term mortality among actors and actresses. Design: Retrospective cohort analysis. Setting: Academy of Motion Picture Arts and Sciences. Participants

Reid, Nancy

472

Second Order Co-occurrence PMI for Determining the Semantic Similarity of Md. Aminul Islam and Diana Inkpen  

E-Print Network [OSTI]

Second Order Co-occurrence PMI for Determining the Semantic Similarity of Words Md. Aminul Islam for calculating the semantic similarity of two target words. Our method, called Second Order Co-occurrence PMI (SOC-PMI), uses Pointwise Mutual Information to sort lists of important neighbor words of the two

Inkpen, Diana

473

FRAppE: Detecting Malicious Facebook Applications Md Sazzadur Rahman, Ting-Kai Huang, Harsha V. Madhyastha, and Michalis Faloutsos  

E-Print Network [OSTI]

FRAppE: Detecting Malicious Facebook Applications Md Sazzadur Rahman, Ting-Kai Huang, Harsha V for the popularity and addictiveness of Facebook. Unfortu- nately, hackers have realized the potential of using apps and campaigns. In this paper, we ask the question: given a Facebook application, can we determine

Madhyastha, Harsha V.

474

The evaluation within the development and deployment of IMS LD-based didactic materials: The MD2 + runtime adaptation approach  

E-Print Network [OSTI]

The evaluation within the development and deployment of IMS LD-based didactic materials: The MD2 in the didactic materials creation since it allows developers to check if the features of created material satisfy]. They have been applied to asses IMS LD based didactic material in conjunction with the experience provided

Paris-Sud XI, Université de

475

Transient Analysis of a Preemptive Resume M/D/1/2/2 through Petri Nets \\Lambda  

E-Print Network [OSTI]

Transient Analysis of a Preemptive Resume M/D/1/2/2 through Petri Nets \\Lambda Andrea Bobbio a semantical generalization of the DSPNs by including preemptive mechanisms of resume type. This generalization different preemptive resume policies. Key words: Markov regenerative processes, Stochastic Petri Nets

Telek, Miklós

476

Determination of the Dynamic Characteristics in the CO Transient Process in a PEM Fuel Cell Woo-kum Lee and J. W. Van Zee  

E-Print Network [OSTI]

Determination of the Dynamic Characteristics in the CO Transient Process in a PEM Fuel Cell Woo Road, Elkton, MD 21922-1488 Key words: PEM Fuel Cell, CO transient, Time constant Prepared publications #12;1 Determination of the Dynamic Characteristics in the CO Transient Process in a PEM Fuel Cell

Van Zee, John W.

477

Sandia National Laboratories: molecular dynamics simulations  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1developmentturbine bladelifetime ismobile test system Solar

478

Molecular Dynamics Simulation Studies of Electrolytes and  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankCombustion | Department ofT ib l L d F S i DOE TribaltheMyMinutes fromBased|SEI5: Fuel

479

Molecular dynamics simulation studies of electrolytes and  

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

AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious RankCombustion | Department ofT ib l L d F S i DOE TribaltheMyMinutes fromBased|SEI5:

480

Applied Statistical Physics Molecular Engineering Conference Puerto Vallarta, Mexico, 24-29 August 2003  

E-Print Network [OSTI]

of the sessions: Complex Fluids: Equilibrium and Dynamics, Nano-biotechnology, Nanoscience, Quantum EngineeringFOREWORD Applied Statistical Physics Molecular Engineering Conference Puerto Vallarta, Mexico, 24, RS, Brazil The Second International Conference on `Applied Statistical Physics: Molecular Engineering

Barbosa, Marcia C. B.

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


481

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

E-Print Network [OSTI]

Molecular Science and Technology (MST) Program The Taiwan International Graduate Program (TIGP Science and Technology (MST) graduate program: (1) Chemical dynamics and molecular spectroscopy, and transient species, and covers mechanisms involved in photodissociation, reactive scattering, energy transfer

482

Ref. ESO doc number File name Document title Author MD03 E-PLA-MET-503-0003 e-pla-met-503-0003-future_man_dev_plan.pdf Future Development and Management Plan F. Molster  

E-Print Network [OSTI]

Ref. ESO doc number File name Document title Author MD03 E-PLA-MET-503-0003 e-pla-met-503 S. Hippler MD16 E-PLA-MET-503-0016 e-pla-met-503-0016-ait_plan.pdf AIT Plan F. Molster MD17 E

Siebenmorgen, Ralf

483

Molecular Gas in Galaxies  

E-Print Network [OSTI]

Knowledge of the molecular component of the ISM is fundamental to understand star formation. The H2 component appears to dominate the gas mass in the inner parts of galaxies, while the HI component dominates in the outer parts. Observation of the CO and other lines in normal and starburst galaxies have questioned the CO-to-H2 conversion factor, and detection of CO in dwarfs have shown how sensitive the conversion f actor is to metallicity. Our knowledge has made great progress in recent years, because of sensitivity and spatial resolution improvements. Large-scale CO maps of nearby galaxies are now available, which extend our knowledge on global properties, radial gradients, and spiral structure of the molecular ISM. Millimetric interferometers reveal high velocity gradients in galaxy nuclei, and formation of embedded structures, like bars within bars. Galaxy interactions are very effective to enhance gas concentrations and trigger starbursts. Nuclear disks or rings are frequently observed, that concentrate the star formation activity. Since the density of starbursting galaxies is strongly increasing with redshift, the CO lines and the mm dust emission are a privileged tool to follow evolution of galaxies and observe the ISM dynamics at high redshift: they could give an answer about the debated question of the star-formation history, since many massive remote starbursts could be dust-enshrouded.

F. Combes

2000-07-21T23:59:59.000Z

484

Accurate static and dynamic properties of liquid electrolytes...  

Office of Scientific and Technical Information (OSTI)

electrolytes. However, to date, almost all molecular-dynamics simulations of these fluids rely on classical force fields, while a complete description of the functionality of...

485

Exciton Dynamics and Structural Investigations of Singlet Fission...  

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

Exciton Dynamics and Structural Investigations of Singlet Fission in Molecular Solids October 11, 2012 at 3pm36-428 Michael R. Wasielewski Director, Argonne-Northwestern Solar...

486

E-Print Network 3.0 - ag-thiocrownethers molecular stability...  

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

92710 102910 Summary: to protein stability, the thermodynamics and kinetics of protein folding, and molecular dynamics simulations... Department of Biochemistry Module II: 9...

487

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

SciTech Connect (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

488

Stochastic heating of a molecular nanomagnet  

E-Print Network [OSTI]

We study the excitation dynamics of a single molecular nanomagnet by static and pulsed magnetic fields. Based on a stability analysis of the classical magnetization dynamics we identify analytically the fields parameters for which the energy is stochastically pumped into the system in which case the magnetization undergoes diffusively and irreversibly a large angle deflection. An approximate analytical expression for the diffusion constant in terms of the fields parameters is given and assessed by full numerical calculations.

L. Chotorlishvili; P. Schwab; Z. Toklikishvili; J. Berakdar

2010-07-02T23:59:59.000Z