Sample records for molecular dynamics md

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

    SciTech Connect (OSTI)

    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

    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.

  2. Microscopic dynamical description of proton-induced fission with the Constrained Molecular Dynamics (CoMD) Model

    E-Print Network [OSTI]

    N. Vonta; G. A. Souliotis; M. Veselsky; A. Bonasera

    2015-06-16T23:59:59.000Z

    The microscopic description of nuclear fission still remains a topic of intense basic research. Un- derstanding nuclear fission, apart from a theoretical point of view, is of practical importance for energy production and the transmutation of nuclear waste. In nuclear astrophysics, fission sets the upper limit to the nucleosynthesis of heavy elements via the r-process. In this work we initiated a systematic study of intermediate energy proton-induced fission using the Constrained Molecu- lar Dynamics (CoMD) code. The CoMD code implements an effective interaction with a nuclear matter compressibility of K=200 (soft EOS) with several forms of the density dependence of the nucleon-nucleon symmetry potential. Moreover, a constraint is imposed in the phase-space occu- pation for each nucleon restoring the Pauli principle at each time step of the collision. A proper choice of the surface parameter of the effective interaction has been made to describe fission. In this work, we present results of fission calculations for proton-induced reactions on : a) 232 Th at 27 and 63 MeV, b) 235 U at 10, 30, 60 and 100 MeV, and c) 238 U at 100 and 660 MeV. The calculated observables include fission-fragment mass distributions, total fission energies, neutron multiplicities and fission times. These observables are compared to available experimental data. We show that the microscopic CoMD code is able to describe the complicated many-body dynamics of the fission process at intermediate and high energy and give a reasonable estimate of the fission time scale. Sensitivity of the results to the density dependence of the nucleon symmetry potential (and, thus, the nuclear symmetry energy) is found. Further improvements of the code are necessary to achieve a satisfactory description of low energy fission in which shell effects play a dominant role.

  3. Substructured multibody molecular dynamics.

    SciTech Connect (OSTI)

    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

    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.

  4. FPGA-BASED MULTIGRID COMPUTATION FOR MOLECULAR DYNAMICS SIMULATIONS

    E-Print Network [OSTI]

    Herbordt, Martin

    FPGA-BASED MULTIGRID COMPUTATION FOR MOLECULAR DYNAMICS SIMULATIONS Yongfeng Gu Martin C. Herbordt serial code. 1. INTRODUCTION Molecular Dynamics simulations (MD) are a fundamental tool for gaining Computer Architecture and Automated Design Laboratory Department of Electrical and Computer Engineering

  5. Molecular Dynamics Simulations on High-Performance Reconfigurable

    E-Print Network [OSTI]

    Herbordt, Martin

    23 Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems MATT CHIU. 2010. Molecular dynamics simulations on high performance recon- figurable computing systems. ACM Trans://doi.acm.org/10.1145/1862648.1862653. 1. INTRODUCTION Molecular dynamics simulation (MD) is a

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

    E-Print Network [OSTI]

    Kim, Bo Hung

    2010-07-14T23:59:59.000Z

    Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the wall-fluid interface...

  7. Control-volume representation of molecular dynamics

    E-Print Network [OSTI]

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

    2012-05-24T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Hirunsit, Pussana

    2009-05-15T23:59:59.000Z

    Classical molecular dynamics (MD) simulations are performed to study structural and dynamic properties of water confined within graphite surfaces. The surfaces are separated at distances varying between 7 and 14.5 Å and the water density is held...

  9. Towards Production FPGA-Accelerated Molecular Dynamics: Progress and Challenges

    E-Print Network [OSTI]

    Herbordt, Martin

    dynamics simulation has shown that including on-the-fly neighbor list calculation (particle filtering for this loss. I. INTRODUCTION Molecular dynamics simulation (MD) is a central method in high performance. Herbordt Computer Architecture and Automated Design Laboratory Department of Electrical and Computer

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

    E-Print Network [OSTI]

    Fayer, Michael D.

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

  11. Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

    E-Print Network [OSTI]

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

    2010-01-21T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Tomar, Vikas

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

  13. (Quantum Molecular Dynamics Method) (Classical Molecular Dynamics Method)

    E-Print Network [OSTI]

    Maruyama, Shigeo

    1-1 (Quantum Molecular Dynamics Method) (Classical Molecular Dynamics Method) 2) Verlet(Verlet's leap frog) (17)(18) ( ) i i ii m t t t t t t F vv + -= + 22 (17

  14. Why are MD simulated protein folding times wrong? Dmitry Nerukh

    E-Print Network [OSTI]

    Nerukh, Dmitry

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

  15. FPGA Acceleration of Discrete Molecular Dynamics Simulation

    E-Print Network [OSTI]

    Herbordt, Martin

    ' & $ % FPGA Acceleration of Discrete Molecular Dynamics Simulation Joshua Model Thesis submitted UNIVERSITY COLLEGE OF ENGINEERING Thesis FPGA Acceleration of Discrete Molecular Dynamics Simulation Acceleration of Discrete Molecular Dynamics Simulation Joshua Model ABSTRACT Molecular dynamics simulation

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

    E-Print Network [OSTI]

    Elliott, James

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

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

    E-Print Network [OSTI]

    Southern California, University of

    films that form on aluminum and aluminum alloys in air protect the surface against further oxidationMolecular 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

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

    E-Print Network [OSTI]

    Militzer, Burkhard

    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

  19. EFFICIENT PARTICLE-PAIR FILTERING FOR ACCELERATION OF MOLECULAR DYNAMICS SIMULATION

    E-Print Network [OSTI]

    Herbordt, Martin

    EFFICIENT PARTICLE-PAIR FILTERING FOR ACCELERATION OF MOLECULAR DYNAMICS SIMULATION Matt Chiu ABSTRACT The acceleration of molecular dynamics (MD) simulations using high performance reconfigurable: determining the short-range force between particle pairs. In particular, we present the first FPGA study

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

    E-Print Network [OSTI]

    Han, Kunwoo

    2009-06-02T23:59:59.000Z

    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...

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

    E-Print Network [OSTI]

    Tiezheng Qian; Xiao-Ping Wang

    2004-03-06T23:59:59.000Z

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

  2. Trillion-atom molecular dynamics becomes a reality

    SciTech Connect (OSTI)

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

    2008-01-01T23:59:59.000Z

    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.

  3. Y. Gu, T. VanCourt, M.C. Herbordt / Proc. IEEE Conf. on Field Programmable Logic and Applications (2005) 1 ACCELERATING MOLECULAR DYNAMICS SIMULATIONS

    E-Print Network [OSTI]

    Herbordt, Martin

    2005-01-01T23:59:59.000Z

    (2005) 1 ACCELERATING MOLECULAR DYNAMICS SIMULATIONS WITH CONFIGURABLE CIRCUITS Yongfeng Gu Tom Van-space parameter for MD practitioners. 2. MOLECULAR DYNAMICS OVERVIEW Molecular Dynamics simulations generallyCourt Martin C. Herbordt Department of Electrical and Computer Engineering Boston University, Boston, MA 02215

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

    E-Print Network [OSTI]

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

    2009-01-22T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Brenner, Donald W.

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

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

    E-Print Network [OSTI]

    Kurnikova, Maria

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

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

    SciTech Connect (OSTI)

    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

    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.

  8. Kinetics of Surface Enrichment: A Molecular Dynamics Study

    E-Print Network [OSTI]

    Prabhat K. Jaiswal; Sanjay Puri; Subir K. Das

    2010-11-29T23:59:59.000Z

    We use molecular dynamics (MD) to study the kinetics of surface enrichment (SE) in a stable homogeneous mixture (AB), placed in contact with a surface which preferentially attracts A. The SE profiles show a characteristic double-exponential behavior with two length scales: \\xi_-, which rapidly saturates to its equilibrium value, and \\xi_+, which diverges as a power-law with time (\\xi_+ \\sim t^\\theta). We find that hydrodynamic effects result in a crossover of the growth exponent from \\theta \\simeq 0.5 to \\theta \\simeq 1.0. There is also a corresponding crossover in the growth dynamics of the SE-layer thickness.

  9. Harvesting graphics power for MD simulations

    E-Print Network [OSTI]

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

    2007-09-20T23:59:59.000Z

    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/$.

  10. Adding quantum effects to the semi-classical molecular dynamics simulations

    E-Print Network [OSTI]

    Yang, Siyang

    2011-01-01T23:59:59.000Z

    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 trajecto...

  11. FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS

    E-Print Network [OSTI]

    Herbordt, Martin

    ' & $ % FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS YONGFENG GU Dissertation submitted;BOSTON UNIVERSITY COLLEGE OF ENGINEERING Dissertation FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS DYNAMICS SIMULATIONS (Order No. ) YONGFENG GU Boston University, College of Engineering, 2008 Major

  12. Ab-Initio Molecular Dynamics

    E-Print Network [OSTI]

    Thomas D. Kühne

    2013-03-26T23:59:59.000Z

    Computer simulation methods, such as Monte Carlo or Molecular Dynamics, are very powerful computational techniques that provide detailed and essentially exact information on classical many-body problems. With the advent of ab-initio molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method and the recently devised efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics, which unifies best of both schemes are discussed. The predictive power of this novel second-generation Car-Parrinello approach is demonstrated by a series of applications ranging from liquid metals, to semiconductors and water. This development allows for ab-initio molecular dynamics simulations on much larger length and time scales than previously thought feasible.

  13. Ab-Initio Molecular Dynamics

    E-Print Network [OSTI]

    Kühne, Thomas D

    2012-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2014-01-01T23:59:59.000Z

    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.

  15. Molecular dynamics simulations of gold-catalyzed growth of silicon bulk crystals and nanowires

    E-Print Network [OSTI]

    Cai, Wei

    ARTICLES Molecular dynamics simulations of gold-catalyzed growth of silicon bulk crystals of the orientation, yield, and quality of the NWs. Much of the studies on the VLS growth mechanism have been focused. In this article, we present the first set of MD simu- lations of NW growth using this Au­Si potential model

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

    SciTech Connect (OSTI)

    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

    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.

  17. Towards Microsecond Biological Molecular Dynamics Simulations on Hybrid Processors

    SciTech Connect (OSTI)

    Hampton, Scott S [ORNL; Agarwal, Pratul K [ORNL

    2010-01-01T23:59:59.000Z

    Biomolecular simulations continue to become an increasingly important component of molecular biochemistry and biophysics investigations. Performance improvements in the simulations based on molecular dynamics (MD) codes are widely desired. This is particularly driven by the rapid growth of biological data due to improvements in experimental techniques. Unfortunately, the factors, which allowed past performance improvements of MD simulations, particularly the increase in microprocessor clock frequencies, are no longer improving. Hence, novel software and hardware solutions are being explored for accelerating the performance of popular MD codes. In this paper, we describe our efforts to port and optimize LAMMPS, a popular MD framework, on hybrid processors: graphical processing units (GPUs) accelerated multi-core processors. Our implementation is based on porting the computationally expensive, non-bonded interaction terms on the GPUs, and overlapping the computation on the CPU and GPUs. This functionality is built on top of message passing interface (MPI) that allows multi-level parallelism to be extracted even at the workstation level with the multi-core CPUs as well as extend the implementation on GPU clusters. The results from a number of typically sized biomolecular systems are provided and analysis is performed on 3 generations of GPUs from NVIDIA. Our implementation allows up to 30-40 ns/day throughput on a single workstation as well as significant speedup over Cray XT5, a high-end supercomputing platform. Moreover, detailed analysis of the implementation indicates that further code optimization and improvements in GPUs will allow {approx}100 ns/day throughput on workstations and inexpensive GPU clusters, putting the widely-desired microsecond simulation time-scale within reach to a large user community.

  18. 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...

  19. Radiation in molecular dynamic simulations

    SciTech Connect (OSTI)

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

    2008-10-13T23:59:59.000Z

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

  20. 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...

  1. 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...

  2. 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...

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

    SciTech Connect (OSTI)

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

    2009-10-01T23:59:59.000Z

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

  4. Accelerated molecular dynamics methods: introduction and recent developments

    SciTech Connect (OSTI)

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

    2009-01-01T23:59:59.000Z

    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.

  5. Molecular Dynamic Approach of Enhanced Self-Propelled Nano-Droplet Motion on Wettability Gradient Surfaces

    E-Print Network [OSTI]

    Chakraborty, Monojit; Bhusan, Richa; DasGupta, Sunando

    2015-01-01T23:59:59.000Z

    Droplet motion over a surface with wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics. GROMACS and Visual Molecular Dynamics (VMD) were used for simulation and intermittent visualization of the droplet configuration respectively. The simulations mimic experiments in a comprehensive manner wherein micro-sized droplets are propelled by surface wettability gradient against a number of retarding forces. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature were varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction was observed to be a strong function of temperature at atomistic scales, confirming the experimentally observed inverse functionality between the coefficient of contact line friction and increase in temperatures. These MD simulation results were successfully compared with the results from a model for self-propelled droplet motion on gradient surfaces.

  6. Optimal prediction in molecular dynamics

    E-Print Network [OSTI]

    Benjamin Seibold

    2008-08-22T23:59:59.000Z

    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.

  7. Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen

    SciTech Connect (OSTI)

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

    2008-02-14T23:59:59.000Z

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

  8. Molecular dynamics studies of the primary state of radiation damage

    SciTech Connect (OSTI)

    Diaz de la Rubia, T.; Averback, R.S.; Robertson, I.M.; Benedek, R.

    1988-12-01T23:59:59.000Z

    This paper summarizes recent progress in the understanding of energetic displacement cascades in metals achieved with the molecular-dynamics (MD) simulation technique. Recoil events with primary-knock-on-atom (PKA) energies up to 5 keV were simulated in Cu and Ni. The initial development of displacement cascades was similar in both metals, with replacement collision sequences providing the most efficient mechanism for the separation of interstitials and vacancies. The thermal-spike behavior in these metals, however, is quite different; Cu cascades are characterized by lower defect production and greater atomic disordering than those in Ni. The thermal spike significantly influences various other properties of cascades, such as total defect production and defect clustering. 32 refs., 7 figs., 2 tabs.

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

    SciTech Connect (OSTI)

    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

    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.

  10. 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...

  11. 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...

  12. 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...

  13. An efficient parallelization scheme for molecular dynamics simulations...

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

    efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical An efficient parallelization scheme for molecular dynamics...

  14. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect (OSTI)

    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

    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.

  15. Pasta Nucleosynthesis: Molecular dynamics simulations of nuclear statistical equilibrium

    E-Print Network [OSTI]

    M. E. Caplan; A. S. Schneider; C. J. Horowitz; D. K. Berry

    2014-12-29T23:59:59.000Z

    Background: Exotic non-spherical nuclear pasta shapes are expected in nuclear matter at just below saturation density because of competition between short range nuclear attraction and long range Coulomb repulsion. Purpose: We explore the impact of nuclear pasta on nucleosynthesis, during neutron star mergers, as cold dense nuclear matter is ejected and decompressed. Methods: We perform classical molecular dynamics simulations with 51200 and 409600 nucleons, that are run on GPUs. We expand our simulation region to decompress systems from an initial density of 0.080 fm^{-3} down to 0.00125 fm^{-3}. We study proton fractions of Y_P=0.05, 0.10, 0.20, 0.30, and 0.40 at T =0.5, 0.75, and 1.0 MeV. We calculate the composition of the resulting systems using a cluster algorithm. Results: We find final compositions that are in good agreement with nuclear statistical equilibrium models for temperatures of 0.75 and 1 MeV. However, for proton fractions greater than Y_P=0.2 at a temperature of T = 0.5 MeV, the MD simulations produce non-equilibrium results with large rod-like nuclei. Conclusions: Our MD model is valid at higher densities than simple nuclear statistical equilibrium models and may help determine the initial temperatures and proton fractions of matter ejected in mergers.

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

    E-Print Network [OSTI]

    Wang, Wei

    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

  17. 9/28/98 9:58:58 am, Journal of Non-Crystalline Solids MOLECULAR DYNAMICS SIMULATION OF VITREOUS SILICA STRUCTURES

    E-Print Network [OSTI]

    Goddard III, William A.

    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

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

    SciTech Connect (OSTI)

    Krishna, Rajamani; van Baten, Jasper M

    2011-01-01T23:59:59.000Z

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

  19. Fermionic Molecular Dynamics for nuclear dynamics and thermodynamics

    E-Print Network [OSTI]

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

    2008-12-02T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Chen, Sow-Hsin

    2010-01-01T23:59:59.000Z

    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 ...

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

    SciTech Connect (OSTI)

    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

    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.

  2. Reaction dynamics in polyatomic molecular systems

    SciTech Connect (OSTI)

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

    1993-12-01T23:59:59.000Z

    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.

  3. 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:...

  4. OpenAtom -- Ab initio molecular dynamics package

    SciTech Connect (OSTI)

    Roberto Car

    2008-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2009-10-02T23:59:59.000Z

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

  6. Saturated Sodium Chloride Solution under an External Static Electric Field: a Molecular Dynamics Study

    E-Print Network [OSTI]

    Gan Ren; Yanting Wang

    2015-05-02T23:59:59.000Z

    The behavior of saturated aqueous sodium chloride solutions under a constant external electric field (E) was studied by molecular dynamics (MD) simulation. Our dynamic MD simulations have indicated that the irreversible nucleation process towards crystallization is accelerated by a moderate E, but retarded or even prohibited under a stronger E, which can be understood by the competition between self-diffusion and drift motion. The former increases with E resulting in the acceleration of the nucleation process, and the latter tears oppositely charged ions more apart under a stronger E leading to the deceleration of nucleation. Moreover, our steady-state MD simulations have indicated that a first-order phase transition happens in saturated solutions only when the applied E is below a certain threshold Ec, and the ratio of crystallized ions does not change with the electric field. The magnitude of Ec increases with concentration, because larger clusters are easy to form in a more concentrated solution and require a stronger E to dissociate them.

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

    E-Print Network [OSTI]

    Cai, Wei

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

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

    SciTech Connect (OSTI)

    Kobayashi, Kazuya; Liang, Yunfeng, E-mail: y-liang@earth.kumst.kyoto-u.ac.jp, E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp; Matsuoka, Toshifumi, E-mail: y-liang@earth.kumst.kyoto-u.ac.jp, E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp [Environment and Resource System Engineering, Kyoto University, Kyoto 615-8540 (Japan)] [Environment and Resource System Engineering, Kyoto University, Kyoto 615-8540 (Japan); Sakka, Tetsuo [Department of Energy and Hydrocarbon Chemistry, Kyoto University, Kyoto 615-8510 (Japan)] [Department of Energy and Hydrocarbon Chemistry, Kyoto University, Kyoto 615-8510 (Japan)

    2014-04-14T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    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

    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.

  10. Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics

    E-Print Network [OSTI]

    Zhao, Hongkai

    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

  11. Molecular gas and the dynamics of galaxies

    E-Print Network [OSTI]

    F. Combes

    1999-02-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2014-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Goddard III, William A.

    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

  14. 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...

  15. 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:...

  16. 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....

  17. 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...

  18. 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...

  19. 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...

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

    E-Print Network [OSTI]

    Gopalan, Venkatraman

    .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

  1. 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...

  2. 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...

  3. 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...

  4. Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

    SciTech Connect (OSTI)

    R. James Kirkpatrick; Andrey G. Kalinichev

    2008-11-25T23:59:59.000Z

    Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches to important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for significantly larger systems. These calculations have allowed us, for the first time, to study the effects of metal cations with different charges and charge density on the NOM aggregation in aqueous solutions. Other computational work has looked at the longer-time-scale dynamical behavior of aqueous species at mineral-water interfaces investigated simultaneously by NMR spectroscopy. Our experimental NMR studies have focused on understanding the structure and dynamics of water and dissolved species at mineral-water interfaces and in two-dimensional nano-confinement within clay interlayers. Combined NMR and MD study of H2O, Na+, and Cl- interactions with the surface of quartz has direct implications regarding interpretation of sum frequency vibrational spectroscopic experiments for this phase and will be an important reference for future studies. We also used NMR to examine the behavior of K+ and H2O in the interlayer and at the surfaces of the clay minerals hectorite and illite-rich illite-smectite. This the first time K+ dynamics has been characterized spectroscopically in geochemical systems. Preliminary experiments were also performed to evaluate the potential of 75As NMR as a probe of arsenic geochemical behavior. The 75As NMR study used advanced signal enhancement methods, introduced a new data acquisition approach to minimize the time investment in ultra-wide-line NMR experiments, and provides the first evidence of a strong relationship between the chemical shift and structural parameters for this experimentally challenging nucleus. We have also initiated a series of inelastic and quasi-elastic neutron scattering measurements of water dynamics in the interlayers of clays and layered double hydroxides. The objective of these experiments is to probe the correlations of water molecular motions in confined spaces over the scale of times and distances most directly comparable to our MD simulations and on a time scale different than that probed by NMR. This work is being done in collaboration with Drs. C.-K. Loong, N. de Souza, and A.I. Kolesnikov at the Intense Pulsed

  5. Molecular beam studies of reaction dynamics

    SciTech Connect (OSTI)

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

    1993-12-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Heinz, Stefan

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

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

    SciTech Connect (OSTI)

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

    2014-09-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Cai, Wei

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

  9. Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Quantum-Classical Simulation of Liquid Water

    E-Print Network [OSTI]

    Agarwal, Animesh

    2015-01-01T23:59:59.000Z

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however computationally this technique is very demanding. The abovementioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One possible solution to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this ...

  10. 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...

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

    SciTech Connect (OSTI)

    Kerisit, Sebastien N.; Liu, Chongxuan

    2014-03-03T23:59:59.000Z

    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.

  12. CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS

    SciTech Connect (OSTI)

    Swanson, Jessica

    2011-08-31T23:59:59.000Z

    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.

  13. 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 ?...

  14. atomistic molecular dynamics: Topics by E-print Network

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

    atomistic 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 Simulational...

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

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

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

  16. 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,...

  17. 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

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

    E-Print Network [OSTI]

    Souvatzis, Petros

    2013-01-01T23:59:59.000Z

    We present a first principles molecular dynamics approach that is based on time-reversible ex- tended Lagrangian Born-Oppenheimer molecular dynamics [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) costruction are required in each integration time step. The proposed dy- namics 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 an ideal starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents ...

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

    E-Print Network [OSTI]

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

    2011-01-01T23:59:59.000Z

    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 ...

  20. Molecular dynamics simulation of Li surface erosion and bubble formation

    E-Print Network [OSTI]

    Harilal, S. S.

    .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

  1. Molecular Surgery with Pulsed Electric Fields: Molecular Dynamics Simulations of Nanopore Formation and

    E-Print Network [OSTI]

    Southern California, University of

    Molecular Surgery with Pulsed Electric Fields: Molecular Dynamics Simulations of Nanopore Formation Family Department of Chemical Engineering and Materials Science, §Department of Electrical Engineering of water molecules spanning the membrane, decay within a few nanoseconds when the electric field is removed

  2. Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps

    E-Print Network [OSTI]

    Roie Volkovich; Uri Peskin

    2010-12-01T23:59:59.000Z

    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.

  3. Dynamics of molecular superrotors in external magnetic field

    E-Print Network [OSTI]

    Korobenko, Aleksey

    2015-01-01T23:59:59.000Z

    We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to the qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane in three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

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

    E-Print Network [OSTI]

    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

    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...

  5. Role of dynamics in tuning fidelity of RNA-dependent RNA polymerase elucidated by molecular dynamics simulation

    E-Print Network [OSTI]

    Bjørnstad, Ottar Nordal

    Role of dynamics in tuning fidelity of RNA-dependent RNA polymerase elucidated by molecular dynamics simulation Ibrahim M. Moustafa Department of Biochemistry and Molecular Biology Eberly College fidelity is not clear but suggested to be linked to dynamics of the enzyme [1]. By using molecular dynamics

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

    SciTech Connect (OSTI)

    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

    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.

  7. Dynamical analysis of highly excited molecular spectra

    SciTech Connect (OSTI)

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

    1993-12-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Fayer, Michael D.

    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

  9. Plasticity of metallic nanostructures : molecular dynamics simulations 

    E-Print Network [OSTI]

    Healy, Con

    2014-11-27T23:59:59.000Z

    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 ...

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

    SciTech Connect (OSTI)

    Wang, Jinyang; Zhong, Haimin; Qiu, Wenda; Chen, Liuping, E-mail: cesclp@mail.sysu.edu.cn [KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275 (China)] [KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275 (China); Feng, Huajie [School of Chemistry and Chemical Engineering, Hainan Normal University, Haikou 571158 (China)] [School of Chemistry and Chemical Engineering, Hainan Normal University, Haikou 571158 (China)

    2014-03-14T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    1993-12-01T23:59:59.000Z

    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.

  12. DYNAMICS OF INFRARED MULTIPHOTON DISSOCIATION OF SF6 BY MOLECULAR BEAM METHOD

    E-Print Network [OSTI]

    Grant, E.R.

    2010-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    KuÂ?el, Petr

    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

  14. VUV studies of molecular photofragmentation dynamics

    SciTech Connect (OSTI)

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

    1993-12-01T23:59:59.000Z

    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.

  15. Massively parallel molecular dynamics simulations of

    E-Print Network [OSTI]

    Berne, Bruce J.

    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

  16. 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 DataDepartment of Energy Your Density Isn't Your Destiny: The Future of1 AAccelerated aging of roofing surfaces Hugo Destaillats,Molecular

  17. MD user's manual

    SciTech Connect (OSTI)

    Correll, S.

    1988-04-01T23:59:59.000Z

    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.

  18. accelerated molecular dynamics: Topics by E-print Network

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

    accelerated 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 Accelerating Fermionic...

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

    E-Print Network [OSTI]

    Brenner, Donald W.

    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

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

    E-Print Network [OSTI]

    Schlegel, H. Bernhard

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

  1. Structure and Molecular Dynamics of Multilayered Polycarbonate/Polystyrene Films

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Structure and Molecular Dynamics of Multilayered Polycarbonate/Polystyrene Films M. Walczak,1 W (wileyonlinelibrary.com). ABSTRACT: Multilayered film polycarbonate/polysty- rene (PC/PS) comprising 257 layers Periodi- cals, Inc. J Appl Polym Sci 000: 000­000, 2012 Key words: interface; polystyrene; polycarbonate

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

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

  3. Thermodiffusion in model nanofluids by molecular dynamics simulations

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1 Thermodiffusion in model nanofluids by molecular dynamics simulations G. Galliero1,2,* , S. Volz3-Jones fluids and for model nanofluids (spherical non-metallic nanoparticles + Lennard-Jones fluid) where concentration. Then, in nanofluids in the liquid state, by changing the nature of the nanoparticle (size, mass

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

    E-Print Network [OSTI]

    Rapaport, Dennis C.

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

  5. 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...

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

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

    A Molecular Dynamics Investigation of the Titration of a TrivalentAqueous Ion. A Molecular Dynamics Investigation of the Titration of a TrivalentAqueous Ion. Abstract: We carried...

  7. Spatially Heterogeneous Dynamics and Dynamic Facilitation in a Model of Viscous Silica Michael Vogel* and Sharon C. Glotzer

    E-Print Network [OSTI]

    Weeks, Eric R.

    this behavior. The mode coupling theory [1] describes many aspects of dynamical behavior at high T- stood as a simple activated bondbreaking process. Here, we perform molecular dynamics (MD) simula- tionsSpatially Heterogeneous Dynamics and Dynamic Facilitation in a Model of Viscous Silica Michael

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

    SciTech Connect (OSTI)

    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

    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.

  9. 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

  10. Superadiabatic transition histories in quantum molecular dynamics

    E-Print Network [OSTI]

    Volker Betz; Benjamin D. Goddard; Stefan Teufel

    2009-02-03T23:59:59.000Z

    We study the dynamics of a molecule's nuclear wave-function near an avoided crossing of two electronic energy levels, for one nuclear degree of freedom. We derive the general form of the Schroedinger equation in the n-th superadiabatic representation for all n, and give some partial results about the asymptotics for large n. Using these results, we obtain closed formulas for the time development of the component of the wave function in an initially unoccupied energy subspace, when a wave packet crosses the transition region. In the optimal superadiabatic representation, which we define, this component builds up monontonically. Finally, we give an explicit formula for the transition wave function away from the crossing, which is in excellent agreement with high precision numerical calculations.

  11. Study of the subpicosecond rotational molecular dynamics in liquids

    SciTech Connect (OSTI)

    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

    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)

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

    SciTech Connect (OSTI)

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

    2013-11-15T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2014-05-01T23:59:59.000Z

    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.

  14. Coarse-Grained Molecular Dynamics Simulations of Depletion-Induced Interactions for Soft Matter Systems

    E-Print Network [OSTI]

    Tyler N. Shendruk; Martin Bertrand; James L. Harden; Gary W. Slater; Hendrick W. de Haan

    2014-08-01T23:59:59.000Z

    Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (WCA) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap of the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density.

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

    SciTech Connect (OSTI)

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

    2010-03-14T23:59:59.000Z

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

  16. Collective dynamics of molecular motors pulling on fluid membranes

    E-Print Network [OSTI]

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

    2005-12-08T23:59:59.000Z

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

  17. Molecular dynamics of gas phase hydrogen-bonded complexes

    E-Print Network [OSTI]

    Wofford, Billy Alan

    1987-01-01T23:59:59.000Z

    . These analyses have permitted the calculation of an approximate stretching harmonic force field for the hydrogen-bound heterodimer HCN---HF. In addition, a new technique is developed to determine both the ground state and equilibrium dissociation energies... OF FIGURES. CHAPTER I. INTRODUCTION. CHAPTER II. MOLECULAR DYNAMICS IN HYDROGEN-BONDED INTERACTIONS: A PRELIMINARY EXPERIMENTALLY DETERMINED HARMONIC STRETCHING FORCE FIELD FOR HCN---HF. Introduction. Experimental Calculations. 10 Discussion. 19...

  18. Complete Characterization of Molecular Dynamics in Ultrashort Laser Fields

    SciTech Connect (OSTI)

    Feuerstein, B.; Ergler, Th.; Rudenko, A.; Zrost, K.; Schroeter, C. D.; Moshammer, R.; Ullrich, J.; Niederhausen, T.; Thumm, U. [Max-Planck-Institut fuer Kernphysik, D-69029 Heidelberg (Germany); James R. Macdonald Laboratory, Kansas State University, Manhattan, Kansas 66506-2604 (United States)

    2007-10-12T23:59:59.000Z

    Reaction Microscope-based, complete, and time-resolved Coulomb explosion imaging of vibrating and dissociating D{sub 2}{sup +} molecules with femtosecond time-resolution allowed us to perform an internuclear distance (R-)dependent Fourier analysis of the corresponding wave packets. Calculations demonstrate that the obtained two-dimensional R-dependent frequency spectra enable the complete characterization of the wave packet dynamics and directly visualize the field-modified molecular potential curves in intense, ultrashort laser pulses.

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

    E-Print Network [OSTI]

    Rapaport, D C

    2009-01-01T23:59:59.000Z

    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.

  20. Fast parallel algorithms for short-range molecular dynamics

    SciTech Connect (OSTI)

    Plimpton, S.

    1993-05-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Hall, G.E.

    2011-05-31T23:59:59.000Z

    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.

  2. Enhanced heat transfer through filler-polymer interface by surface-coupling agent in heat-dissipation material: A non-equilibrium molecular dynamics study

    SciTech Connect (OSTI)

    Tanaka, Kouichi [DENSO CORPORATION, Kariya, Aichi 448-8661 (Japan); Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Ogata, Shuji; Kobayashi, Ryo; Tamura, Tomoyuki [Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Kitsunezuka, Masashi; Shinma, Atsushi [DENSO CORPORATION, Kariya, Aichi 448-8661 (Japan)

    2013-11-21T23:59:59.000Z

    Developing a composite material of polymers and micrometer-sized fillers with higher heat conductance is crucial to realize modular packaging of electronic components at higher densities. Enhancement mechanisms of the heat conductance of the polymer-filler interfaces by adding the surface-coupling agent in such a polymer composite material are investigated through the non-equilibrium molecular dynamics (MD) simulation. A simulation system is composed of ?-alumina as the filler, bisphenol-A epoxy molecules as the polymers, and model molecules for the surface-coupling agent. The inter-atomic potential between the ?-alumina and surface-coupling molecule, which is essential in the present MD simulation, is constructed to reproduce the calculated energies with the electronic density-functional theory. Through the non-equilibrium MD simulation runs, we find that the thermal resistance at the interface decreases significantly by increasing either number or lengths of the surface-coupling molecules and that the effective thermal conductivity of the system approaches to the theoretical value corresponding to zero thermal-resistance at the interface. Detailed analyses about the atomic configurations and local temperatures around the interface are performed to identify heat-transfer routes through the interface.

  3. 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]

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

    2008-01-01T23:59:59.000Z

    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, ...

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

    E-Print Network [OSTI]

    Fayer, Michael D.

    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

  5. The coupling of dynamics and molecular chemistry in galaxies

    E-Print Network [OSTI]

    F. Combes

    2007-09-24T23:59:59.000Z

    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).

  6. 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

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

    E-Print Network [OSTI]

    Pazúriková, Jana

    2014-01-01T23:59:59.000Z

    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...

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

    SciTech Connect (OSTI)

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

    2012-05-29T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Miller, William H.

    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

  10. Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite

    E-Print Network [OSTI]

    A. Ito; H. Nakamura

    2006-04-26T23:59:59.000Z

    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.

  11. Molecular nonlinear dynamics and protein thermal uncertainty quantification

    SciTech Connect (OSTI)

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

    2014-03-15T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Van Vliet, Krystyn J.

    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

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

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    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

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

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

    Plimpton, Steve; Thompson, Aidan; Crozier, Paul

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

  15. Thermodynamic and transport properties of self-assembled monolayers from molecular simulations 

    E-Print Network [OSTI]

    Aydogmus, Turkan

    2006-04-12T23:59:59.000Z

    ........................................................28 3.1 Molecular Modeling..................................................................................28 3.2 Molecular Dynamics (MD) ....................................................................... 31 3.3 Monte Carlo (MC...).....................................................................................32 3.3.1 Canonical Monte Carlo.................................................................34 3.3.2 Coupled-Decoupled Configurational-Bias Monte Carlo (CD- CBMC...

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

    SciTech Connect (OSTI)

    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

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

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

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

    Nikita Tretyakov; Marcus Müller

    2013-02-21T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    1999-10-16T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2014-10-15T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Southern California, University of

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

  2. To appear in Journal of Computational Physics Parallel Discrete Molecular Dynamics Simulation

    E-Print Network [OSTI]

    Herbordt, Martin

    To appear in Journal of Computational Physics Parallel Discrete Molecular Dynamics Simulation and Automated Design Laboratory Department of Electrical and Computer Engineering Boston University; Boston, MA 02215 www.bu.edu/caadlab; email: azkhan@bu.edu, herbordt@bu.edu Abstract: Discrete molecular dynamics

  3. Preliminary Investigation of Advanced Electrostatics in Molecular Dynamics on Reconfigurable Computers

    E-Print Network [OSTI]

    Prasanna, Viktor K.

    that are accelerated in hardware. In this paper, we study molecular dynamics simulation. Specifically, we study the use of the smooth particle mesh Ewald technique in a molecular dynamics simulation program that takes advantage rscrofan@halcyon.usc.edu Viktor K. Prasanna Department of Electrical Engineering-Systems University

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

    E-Print Network [OSTI]

    Ford, Ian

    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

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

    E-Print Network [OSTI]

    de Groot, Bert

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

  6. Molecular Dynamics Study of Stiffness in Polystyrene and Polyethylene

    E-Print Network [OSTI]

    Nazarpourfard, Hamed

    2015-01-01T23:59:59.000Z

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

  7. Molecular Dynamics Study of Stiffness in Polystyrene and Polyethylene

    E-Print Network [OSTI]

    Hamed Nazarpourfard; Mahdi Ahmadi Borji

    2015-04-26T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Tretiak, Sergei

    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

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

    E-Print Network [OSTI]

    Markmann, Andreas

    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

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

    E-Print Network [OSTI]

    Tuscia, Università Degli Studi Della

    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

  11. Constant pressure and temperature discrete-time Langevin molecular dynamics

    E-Print Network [OSTI]

    Niels Grønbech-Jensen; Oded Farago

    2014-11-13T23:59:59.000Z

    We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed stochastic thermostat, which has been shown to provide correct statistical configurational sampling for any time step that yields stable trajectories. Here, we extend the method and develop a set of discrete-time equations of motion for both particle dynamics and system volume in order to seek pressure control that is insensitive to the choice of the numerical time step. The resulting method is simple, practical, and efficient. The method is demonstrated through direct numerical simulations of two characteristic model systems - a one dimensional particle chain for which exact statistical results can be obtained and used as benchmarks, and a three dimensional system of Lennard-Jones interacting particles simulated in both solid and liquid phases. The results, which are compared against the method of Kolb & Dunweg, show that the new method behaves according to the objective, namely that acquired statistical averages and fluctuations of configurational measures are accurate and robust against the chosen time step applied to the simulation.

  12. Molecular Simulation of Reaction and Adsorption in Nanochemical Devices

    E-Print Network [OSTI]

    Lisal, Martin

    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

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

    E-Print Network [OSTI]

    Chu, Shih-I

    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

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

    E-Print Network [OSTI]

    Zhao, Hongkai

    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

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

    SciTech Connect (OSTI)

    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

    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.

  16. 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

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

    SciTech Connect (OSTI)

    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

    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.

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

    SciTech Connect (OSTI)

    Pokorna, Sarka; Jurkiewicz, Piotr; Hof, Martin, 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

    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 ?}.

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

    E-Print Network [OSTI]

    D. C. Rapaport

    2014-11-13T23:59:59.000Z

    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.

  20. Molecular dynamics simulation of self-rotation effects on ultra-precision polishing of single-crystal copper

    SciTech Connect (OSTI)

    Yang, Yihan; Zhao, Hongwei; Zhang, Lin; Shao, Mingkun; Liu, Hongda; Huang, Hu [College of Mechanical Science and Engineering, Jilin University, Renmin Street 5988, Changchun, Jilin 130025 (China)] [College of Mechanical Science and Engineering, Jilin University, Renmin Street 5988, Changchun, Jilin 130025 (China)

    2013-10-15T23:59:59.000Z

    Understanding the behaviors of the material removal mechanism of ultra-precision polishing process has been a critical issue of generating well-formed surface. In order to make clear the abrasive self-rotation effects on material removal at the atomic level, a three-dimensional molecular dynamics (MD) model is conducted to study the mechanics of ultra-precision polishing on single-crystal copper with a diamond abrasive and the effects of abrasive self-rotation velocity and direction. Morse potential energy function and EAM potential energy function are applied to model the copper/diamond and copper/copper interactions, respectively. The simulation results show that the deformation mechanism of single-crystal copper is due to the formation and movement of dislocations in the specimen. In addition, with the increasing of abrasive self-rotation velocity, the deformation mechanism falls from cutting to plowing regimes. The abrasive self-rotation velocity and direction have effects on the morphology and quality of the specimen surface, distribution and evolution of defects under the surface of the specimen. Also, the interatomic force between abrasive and specimen is studied to account for the effects of different polishing conditions.

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

    SciTech Connect (OSTI)

    Bourg, I.C.; Sposito, G.

    2007-05-25T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Wu, Yinghua

    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

  3. MOLECULAR DYNAMICS SIMULATIONS OF DISPLACEMENT CASCADES IN MOLYBDENUM

    SciTech Connect (OSTI)

    Smith, Richard Whiting

    2003-09-08T23:59:59.000Z

    Molecular dynamics calculations have been employed to simulate displacement cascades in neutron irradiated Mo. A total of 90 simulations were conducted for PKA energies between 1 and 40 keV and temperatures from 298 to 923K. The results suggest very little effect of temperature on final defect count and configuration, but do display a temperature effect on peak defect generation prior to cascade collapse. Cascade efficiency, relative to the NRT model, is computed to lie between 1/4 and 1/3 in agreement with simulations performed on previous systems. There is a tendency for both interstitials and vacancies to cluster together following cascade collapse producing vacancy rich regions surrounded by interstitials. Although coming to rest in close proximity, the point defects comprising the clusters generally do not lie within the nearest neighbor positions of one another, except for the formation of dumbbell di-interstitials. Cascades produced at higher PKA energies (20 or 40 keV) exhibit the formation of subcascades.

  4. Dynamical evolution of supernova remnants breaking through molecular clouds

    E-Print Network [OSTI]

    Cho, Wankee; Koo, Bon-Chul

    2015-01-01T23:59:59.000Z

    We carry out three-dimensional hydrodynamic simulations of the supernova remnants (SNRs) produced inside molecular clouds (MCs) near their surface using the HLL code (Harten et al. 1983). We explore the dynamical evolution and the X-ray morphology of SNRs after breaking through the MC surface for ranges of the explosion depths below the surface and the density ratios of the clouds to the intercloud media (ICM). We find that if an SNR breaks out through an MC surface in its Sedov stage, the outermost dense shell of the remnant is divided into several layers. The divided layers are subject to the Rayleigh-Taylor instability and fragmented. On the other hand, if an SNR breaks through an MC after the remnant enters the snowplow phase, the radiative shell is not divided to layers. We also compare the predictions of previous analytic solutions for the expansion of SNRs in stratified media with our onedimensional simulations. Moreover, we produce synthetic X-ray surface brightness in order to research the center-bri...

  5. Novel morphologies for laterally decorated metaparticles: Molecular dynamics simulation

    E-Print Network [OSTI]

    A. Y. Slyusarchuk; J. M. Ilnytskyi

    2015-01-12T23:59:59.000Z

    We consider a mesoscale model for nano-sized metaparticles (MPs) composed of a central sphere decorated by polymer chains with laterally attached spherocylinder. The latter mimics the mesogenic (e.g., cyanobiphenyl) group. Molecular dynamics simulations of $100$ MPs reveal the existence of two novel morphologies: $\\textrm{uCol}_\\mathrm{h}$ (hexagonal columnar arrangement of MPs with strong uniaxial order of mesogens collinear to the columns axis) and $\\mathrm{wCol}_\\mathrm{h}$ [the same arrangement of MPs but with weak or no liquid crystalline (LC) order]. Collinearity of the LC director and the columnar axis in $\\textrm{uCol}_\\mathrm{h}$ morphology indicates its potentially different opto-mechanical response to an external perturbation as compared to the columnar phase for the terminally attached mesogens. Preliminary analysis of the structures of both phases is performed by studying the order parameters and by visualisation of the MPs arrangements. Different mechanisms for the mesogens reorientation are pointed out for the cases of their terminal and lateral attachment.

  6. Molecular Dynamics Simulations of CO2 Formation in Interstellar Ices

    E-Print Network [OSTI]

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

    2013-01-01T23:59:59.000Z

    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...

  7. Dynamics of excess electrons in atomic and molecular clusters

    E-Print Network [OSTI]

    Young, Ryan Michael

    2011-01-01T23:59:59.000Z

    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)

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

    SciTech Connect (OSTI)

    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

    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.

  9. Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity

    E-Print Network [OSTI]

    Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin

    2015-01-01T23:59:59.000Z

    We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.

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

    E-Print Network [OSTI]

    Baty, Austin Alan

    2013-02-06T23:59:59.000Z

    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...

  11. Dynamic First-Principles Molecular-Scale Model for Solid Oxide Fuel Cells V. Hugo Schmidt

    E-Print Network [OSTI]

    Dynamic First-Principles Molecular-Scale Model for Solid Oxide Fuel Cells V. Hugo Schmidt vs. current density i characteristics applies both to the Solid Oxide Fuel Cell (SOFC) and Solid

  12. 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...

  13. 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...

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

    E-Print Network [OSTI]

    Schnadt, Joachim

    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

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

    E-Print Network [OSTI]

    Gaddamanugu, Dhatri

    2010-07-14T23:59:59.000Z

    the velocities of carbon atoms in the nanotube. Results show that the Young's modulus increases with tube diameter in molecular mechanics whereas decreases in molecular dynamics since the inter-atomic potential due to chemical reactions between the atoms is taken...

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

    SciTech Connect (OSTI)

    Krishna, Rajamani; van Baten, Jasper M

    2011-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2014-12-15T23:59:59.000Z

    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 $I(Q,t)$.

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

    E-Print Network [OSTI]

    Mueser, Martin

    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

  19. 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]

    Hammer, David

    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

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

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

    Katsumoto, Shingo

    Coarse-grained Molecular Dynamics Simulation Approach for Polymer Nano-Composites Rubber Katsumi dynamics of entangled long- polymer melts and filled polymer rubber by us- ing coarse-grained model. We of a polymer nano-composite of tire rubber can reproduce almost of feature of the reinforcement effect observed

  2. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics

    SciTech Connect (OSTI)

    Zeidler, Anita [University of Bath; Salmon, Phil [University of Bath; Fischer, Henry E [Institut Laue-Langevin (ILL); Neuefeind, Joerg C [ORNL; Simonson, J Michael {Mike} [ORNL; Markland, Thomas [Columbia University

    2012-01-01T23:59:59.000Z

    The structure of heavy and light water at 300 K was investigated by using a joint approach in which the method of neutron di raction with oxygen isotope substitution was combined with path integral molecular dynamics simulations. The di raction results, which give intra-molecular O-D and O-H bond distances of 0.985(5) and 0.990(5) A, were found to be in best agreement with those obtained by using the exible anharmonic TTM3-F water model. Both techniques show a di erence of '0.5% between the O-D and O-H intra-molecular bond lengths and the results support a competing quantum e ects model for water in which its structural and dynamical properties are governed by an o set between intra-molecular and inter-molecular quantum contributions. Further consideration of the O-O correlations is needed in order to improve agreement with experiment.

  3. Dynamics of micelle-nanoparticle systems undergoing shear: a coarse-grained molecular dynamics approach

    SciTech Connect (OSTI)

    Rolfe, Bryan A.; Chun, Jaehun; Joo, Yong L.

    2013-09-05T23:59:59.000Z

    Recent experimental work has shown that polymeric micelles can template nanoparticles via interstitial sites in shear-ordered micelle solutions. In the current study, we report simulation results based on a coarse-grained molecular dynamics (CGMD) model of a solvent/polymer/nanoparticle system. Our results demonstrate the importance of polymer concentration and the micelle corona length in 2D shear-ordering of neat block copolymer solutions. Although our results do not show strong 3D ordering during shear, we find that cessation of shear allows the system to relax into a 3D configuration of greater order than without shear. It is further shown that this post-shear relaxation is strongly dependent on the length of the micelle corona. For the first time, we demonstrate the presence and importance of a flow disturbance surrounding micelles in simple shear flow at moderate Péclet numbers. This disturbance is similar to what is observed around simulated star polymers and ellipsoids. The extent of the flow disturbance increases as expected with a longer micelle corona length. It is further suggested that without proper consideration of these dynamics, a stable nanoparticle configuration would be difficult to obtain.

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

    E-Print Network [OSTI]

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

    2006-12-20T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    1994-12-01T23:59:59.000Z

    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.

  6. Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture

    SciTech Connect (OSTI)

    Feng, Wei; Xu, Luting [Department of Physics, Beijing Normal University, Beijing 100875 (China); Li, Xin-Qi, E-mail: lixinqi@bnu.edu.cn [Department of Physics, Beijing Normal University, Beijing 100875 (China); Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100875 (China); Fang, Weihai [Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100875 (China); Department of Chemistry, Beijing Normal University, Beijing 100875 (China); Yan, YiJing [Department of Chemistry, Hong Kong University of Science and Technology, Kowloon (Hong Kong)

    2014-07-15T23:59:59.000Z

    Mixed-quantum-classical molecular dynamics simulation implies an effective quantum measurement on the electronic states by the classical motion of atoms. Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods.

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

    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...

  8. Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution

    E-Print Network [OSTI]

    Levitt, Michael

    Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins important in biological macromolecules, where fewer experimental results are available for calibration. Our

  9. Resonant behavior in heat transfer across weak molecular interfaces

    SciTech Connect (OSTI)

    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

    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.

  10. Temperature-dependent mechanisms for the dynamics of protein-hydration waters: a molecular dynamics simulation study

    E-Print Network [OSTI]

    Michael Vogel

    2009-02-20T23:59:59.000Z

    Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon cooling, the mechanisms for water dynamics continuously change from small-step diffusive motion to large-step jump motion, the temperature dependence of water dynamics shows a weak crossover from fragile behavior to strong behavior, and the order of the hydrogen-bond network increases. The temperature of the weak crossover from fragile to strong behavior is found to coincide with the temperature at which maximum possible order of the hydrogen-bond network is reached so that the structure becomes temperature independent. In the strong regime, the temperature dependence of water translation and rotational dynamics is characterized by an activation energy of ca. E_a=0.43 eV, consistent with results from previous dielectric spectroscopy and nuclear magnetic resonance studies on protein hydration waters. At these temperatures, a distorted pi-flip motion about the twofold molecular symmetry axes, i.e., a water-specific beta process is an important aspect of water dynamics, at least at the water-peptide interfaces. In addition, it is shown that the hydration waters exhibit pronounced dynamical heterogeneities, which can be traced back to a strong slowdown of water motion in the immediate vicinity of peptide molecules due to formation of water-peptide hydrogen bonds.

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

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

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

    2014-06-13T23:59:59.000Z

    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.

  13. The Dynamical Structure and Evolution of Giant Molecular Clouds

    E-Print Network [OSTI]

    Christopher F. McKee

    1999-01-26T23:59:59.000Z

    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.

  14. Theoretical aspects of gas-phase molecular dynamics

    SciTech Connect (OSTI)

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

    1993-12-01T23:59:59.000Z

    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.

  15. Steve Nelson, MD Backes, PhD

    E-Print Network [OSTI]

    Dean Steve Nelson, MD Associate Dean for Research Wayne Backes, PhD Associate Dean for Fiscal Gregory, PhD Assistant Dean of VA Affairs Paul Rosenfeld, MD Basic Science Department Heads (6) Clinical, MD Director of Basic Sciences Curriculum Michael Levitzky, PhD Assistant Dean at Children's Hospital

  16. OPTIMAL CONTROL OF ATOMIC, MOLECULAR AND ELECTRON DYNAMICS

    E-Print Network [OSTI]

    Kassel, Universität

    , the dream was realized to actively exert control over quantum systems. Active control over the dynamics of quantum mechanical systems is a fascinating perspective in modern physics. Cleavage and creation? The theoretical and experimental development of suitable control schemes is a fascinating prospect of modern

  17. Electric field induced switching of poly,,ethylene glycol... terminated self-assembled monolayers: A parallel molecular dynamics simulation

    E-Print Network [OSTI]

    Southern California, University of

    : A parallel molecular dynamics simulation Satyavani Vemparala, Rajiv K. Kalia, Aiichiro Nakano, and Priya on the atomistic structure of PEG terminated SAMs using molecular dynamics simulations on parallel computersElectric field induced switching of poly,,ethylene glycol... terminated self-assembled monolayers

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

    E-Print Network [OSTI]

    Soljaèiæ, Marin

    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

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

    E-Print Network [OSTI]

    Drabold, David

    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

  20. Electron Transfer Dynamics in Efficient Molecular Solar Cells

    SciTech Connect (OSTI)

    Meyer, Gerald John

    2014-10-01T23:59:59.000Z

    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.

  1. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOnItemResearch > The EnergyCenterDioxide Capture inFacility AMFInnovationMolecular

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

    E-Print Network [OSTI]

    Sorin, Eric J.

    , 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

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

    E-Print Network [OSTI]

    Boyer, Edmond

    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

  4. Molecular Dynamics Simulation of Damage Cascade Formation in Ion Bombarded Solids

    E-Print Network [OSTI]

    Chen, Di

    2012-10-19T23:59:59.000Z

    .......................................................................................................... 10 CHAPTER III MOLECULAR DYNAMICS SIMULATION OF DEFECT……………... CREATION DUE TO INTERACTIONS OF DAMAGE CASCADE IN SELF ION…… IRRADIATED SI………….…….………........................................................................12 3... ....................................................................................... 14 CHAPTER IV USING CLUSTER ION BOMBARDMENT TO DETERMINE………… AMORPHIZATION MODE..…………………………………………...........................26 4.1 Introduction of Irradiated Amorphization ........................................................... 26 4...

  5. Molecular dynamics simulation of the plastic to triclinic phase transition in clusters of SF6

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    41 Molecular dynamics simulation of the plastic to triclinic phase transition in clusters of SF6 A agrégats n'a pas été entreprise. Abstract. 2014 Clusters of 512 SF6 molecules in their condensed phases of finite systems such as clusters [2]. Liquid sulphur hexafluoride, SF6, forms on cooling what is known

  6. 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

  7. 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...

  8. all-atom molecular dynamics: Topics by E-print Network

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

    all-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 Ab Initio Folding of...

  9. 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

  10. Understanding graphene production by ionic surfactant exfoliation: A molecular dynamics simulation study

    E-Print Network [OSTI]

    Simons, Jack

    Understanding graphene production by ionic surfactant exfoliation: A molecular dynamics simulation simulated sodium dodecyl sulfate (SDS) surfactant/water þ bilayer graphene mixture system to investigate two mechanisms of graphene exfoliation: changing the interlayer distance and sliding away the relative distance

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

    E-Print Network [OSTI]

    H. Feldmeier; J. Schnack

    1997-03-17T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Hammes-Schiffer, Sharon

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

  13. Molecular Dynamics of Methylamine, Methanol, and Methyl Fluoride Cations in Intense 7 Micron Laser Fields

    E-Print Network [OSTI]

    Schlegel, H. Bernhard

    Molecular Dynamics of Methylamine, Methanol, and Methyl Fluoride Cations in Intense 7 Micron Laser of methylamine (CH3NH2 + ), methanol (CH3OH+ ), and methyl fluoride (CH3F+ ) cations by short, intense laser 7 m laser pulses. This work is motivated by recent studies of methanol cations by Yamanouchi and co

  14. Particle--Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations

    E-Print Network [OSTI]

    Plimpton, Steve

    ` (` \\Gamma ` 0 ) 2 + X dihedrals K OE p [1 + d p cos(n p OE)] \\Lambda MS 1111, Sandia National Laboratories Roy Pollock y Mark Stevens z Abstract The parallel implementation of a molecular dynamics code for the system of N atoms that is typically of the form E = X bonds K b (r \\Gamma r 0 ) 2 + X angles K

  15. Change of the unbinding mechanism upon a mutation: A molecular dynamics study

    E-Print Network [OSTI]

    Caflisch, Amedeo

    by Honegger et al. reports the X-ray structure of FITC-E2 with a derivative of fluorescein, which was usedChange of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody April 11, 2005) Abstract We study forced unbinding of fluorescein from the wild type (WT) and a mutant

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

    E-Print Network [OSTI]

    Franchetti, Franz

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

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

    E-Print Network [OSTI]

    Herbert, John

    in order to accelerate convergence of the electronic structure calculations, can suffer from systematic­Oppenheimer molecular dynamics calculations, especially those that exploit information retained from previous time steps, on a potential energy surface obtained by ``on-the-fly'' solution of the quantum-mechanical electronic structure

  18. Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a waterNa

    E-Print Network [OSTI]

    Nerukh, Dmitry

    Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water complexity. One of the advantages of this approach is that it is based on informatic-theoretical analysis; accepted 9 September 2002 The computational mechanics approach has been applied to the orientational

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

    E-Print Network [OSTI]

    Southern California, University of

    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

  20. Proton-coupled electron transfer reactions in solution: Molecular dynamics with quantum transitions for model systems

    E-Print Network [OSTI]

    Hammes-Schiffer, Sharon

    Proton-coupled electron transfer reactions in solution: Molecular dynamics with quantum transitions A general minimal model for proton-coupled electron transfer PCET reactions in solution is presented. This model consists of three coupled degrees of freedom that represent an electron, a proton, and a solvent

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

    E-Print Network [OSTI]

    Meirovitch, Hagai

    Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids for calculating the absolute entropy, S, and free energy, F, by analyzing Boltzmann samples obtained by Monte energy evaluation is a central issue in atomistic modeling.1­5 When the free energy is known, equilibrium

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

    E-Print Network [OSTI]

    Chen, Liao Y.

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

  3. Investigating a Back Door Mechanism of Actin Phosphate Release by Steered Molecular Dynamics

    E-Print Network [OSTI]

    Wriggers, Willy

    Investigating a Back Door Mechanism of Actin Phosphate Release by Steered Molecular Dynamics Willy from actin. Arg177 remains attached to Pi along the putative back door pathway, suggesting a shuttle the subject of intense research (reviewed in Carlier6), but the basic structural mechanism of the chemi- cal

  4. Energy Conservation in Adaptive Hybrid Atomistic/ Coarse-Grain Molecular Dynamics

    E-Print Network [OSTI]

    Nielsen, Steven O.

    Energy Conservation in Adaptive Hybrid Atomistic/ Coarse-Grain Molecular Dynamics Bernd Ensing and space. We supplement the potential and kinetic energy expressions with auxiliary terms in order to recover the total energy as a conserved quantity, even when the total number of degrees of freedom changes

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

    E-Print Network [OSTI]

    Schumaker, Mark

    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

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

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Non-Fourier heat conduction in a single-walled carbon nanotube: Classical molecular dynamics of the simulations exhibit non-Fourier heat conduction where the distinct amount of heat is transported in a wavelike called non-Fourier heat conduction equations in order to investigate the applicability

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

    E-Print Network [OSTI]

    Stanley, H. Eugene

    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

  8. 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

  9. Large-scale molecular dynamics simulation of magnetic properties of amorphous iron under pressure

    E-Print Network [OSTI]

    ) Enhanced refrigerant capacity and magnetic entropy flattening using a two-amorphous FeZrB(Cu) compositeLarge-scale molecular dynamics simulation of magnetic properties of amorphous iron under pressure Appl. Phys. Lett. 99, 232501 (2011) Nonlinear motion of magnetic vortex under alternating

  10. The effects of stress concentrators on strength of materials at nanoscale: A molecular dynamics study

    E-Print Network [OSTI]

    Deymier, Pierre

    materials. There is evidence that when at least one spatial dimension is below a critical one the effects, suggests that such critical dimensions are in the nanometer range and, of course, depend on the materialThe effects of stress concentrators on strength of materials at nanoscale: A molecular dynamics

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

    E-Print Network [OSTI]

    Nielsen, Steven O.

    reproduces the isotope effect. The heat capacity in the liquid D2O has been calculated to be 10% higher than important in the liquid phase. In fact, in many systems, the heat capacity has an isotope effect, whichCalculation of heat capacities of light and heavy water by path-integral molecular dynamics

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

    E-Print Network [OSTI]

    Saiz, Leonor

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

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

    E-Print Network [OSTI]

    Rahmani, Amir M; Jupiterwala, Mehlam; Colosqui, Carlos E

    2015-01-01T23:59:59.000Z

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

  14. Graphics processing units accelerated semiclassical initial value representation molecular dynamics

    SciTech Connect (OSTI)

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

    2014-05-07T23:59:59.000Z

    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.

  15. A quantum simulator for molecules: Imaging molecular orbitals and electronic dynamics with ultracold atoms

    E-Print Network [OSTI]

    Lühmann, Dirk-Sören; Sengstock, Klaus

    2015-01-01T23:59:59.000Z

    In the recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly-correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully-adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated pi electron system with special regard to localization and spin order. The dynamical timescale of ultracold atom simulators are on the order milliseconds which allow for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated pi system of the artificial benzene molecule.

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

    SciTech Connect (OSTI)

    Miller III, Thomas F.

    2008-08-04T23:59:59.000Z

    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}.

  17. Collective Molecular Dynamics of a Floating Water Bridge

    E-Print Network [OSTI]

    Emilio Del Giudice; Elmar C. Fuchs; Giuseppe Vitiello

    2010-04-06T23:59:59.000Z

    When a high voltage is applied to pure water filling two beakers kept close to each other, a connection forms spontaneously, giving the impression of a floating water bridge. This phenomenon is of special interest, since it comprises a number of phenomena currently tackled in modern water science. The formation and the main properties of this floating water bridge are analyzed in the conceptual framework of quantum electrodynamics. The necessary conditions for the formation are investigated as well as the time evolution of the dynamics. The predictions are found in agreement with the observations.

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

    E-Print Network [OSTI]

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

    2015-01-03T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2015-01-30T23:59:59.000Z

    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.

  20. 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]

    Mootha, Vamsi K.

    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

  1. Molecular-dynamics calculation of the vacancy heat of transport

    SciTech Connect (OSTI)

    Schelling, Patrick K.; Ernotte, Jacques; Shokeen, Lalit; Tucker, William C. [Advanced Material Processing and Analysis Center and Department of Physics, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816 (United States); Woods Halley, J. [Department of Physics, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota 555455 (United States)

    2014-07-14T23:59:59.000Z

    We apply the recently developed constrained-dynamics method to elucidate the thermodiffusion of vacancies in a single-component material. The derivation and assumptions used in the method are clearly explained. Next, the method is applied to compute the reduced heat of transport Q{sub v}{sup *}?h{sub fv} for vacancies in a single-component material. Results from simulations using three different Morse potentials, with one providing an approximate description of Au, and an embedded-atom model potential for Ni are presented. It is found that the reduced heat of transport Q{sub v}{sup *}?h{sub fv} may take either positive or negative values depending on the potential parameters and exhibits some dependence on temperature. It is also found that Q{sub v}{sup *}?h{sub fv} may be correlated with the activation entropy. The results are discussed in comparison with experimental and previous simulation results.

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

    SciTech Connect (OSTI)

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

    2009-06-15T23:59:59.000Z

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

  3. 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]

    V. A. Levashov

    2014-06-23T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    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

    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.

  5. Quantum molecular dynamics simulation of shock-wave experiments in aluminum

    SciTech Connect (OSTI)

    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

    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.

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

    SciTech Connect (OSTI)

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (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

    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.

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

    E-Print Network [OSTI]

    Richters, Dorothee; Kühne, Thomas D

    2012-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    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

    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.

  9. From gyroscopic to thermal motion: a crossover in the dynamics of molecular superrotors

    E-Print Network [OSTI]

    Milner, A A; Rezaiezadeh, K; Milner, V

    2015-01-01T23:59:59.000Z

    Localized heating of a gas by intense laser pulses leads to interesting acoustic, hydrodynamic and optical effects with numerous applications in science and technology, including controlled wave guiding and remote atmosphere sensing. Rotational excitation of molecules can serve as the energy source for raising the gas temperature. Here, we study the dynamics of energy transfer from the molecular rotation to heat. By optically imaging a cloud of molecular superrotors, created with an optical centrifuge, we experimentally identify two separate and qualitatively different stages of its evolution. The first non-equilibrium "gyroscopic" stage is characterized by the modified optical properties of the centrifuged gas - its refractive index and optical birefringence, owing to the ultrafast directional molecular rotation, which survives tens of collisions. The loss of rotational directionality is found to overlap with the release of rotational energy to heat, which triggers the second stage of thermal expansion. The ...

  10. Molecular imaging and dynamics at the LCLS John C H Spence*

    E-Print Network [OSTI]

    Crowther, Paul

    Molecular imaging and dynamics at the LCLS John C H Spence* ASU Physics/LBNL/NSF BioXFEL STC%summary%of%achievements%since% 12/2009%% %%%%%%%%The% LCLS near Stanford was the world s first hard X-ray laser. It produces 9 kV X ! No goniometer ! Our Liquid jet uses gas focusing to make a micron jet from bigger nozzle.. LCLS Rep Rate ~100 Hz

  11. Semiclassical analysis of quantum dynamics

    E-Print Network [OSTI]

    Siyang Yang

    2011-11-15T23:59:59.000Z

    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.

  12. Study of slow dynamics in supercooled water by molecular dynamics and quasi-elastic neutron scattering

    E-Print Network [OSTI]

    Liu, Li, Ph. D. Massachusetts Institute of Technology

    2005-01-01T23:59:59.000Z

    The slow dynamics of supercooled water is studied by modelling the spectrum of test particle fluctuations: intermediate scattering function (ISF). The theoretical models are compared with experimental measurements by ...

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

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

    Levis, Robert J.

    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

  15. 2.13 HEAT TRANSFER & FLUID FLOW IN MICROCHANNELS 2.13.7-1 Molecular dynamics methods in

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

  16. PHYSICAL REVIEW E 84, 021907 (2011) Effectiveness of beads for tracking small-scale molecular motor dynamics

    E-Print Network [OSTI]

    2011-01-01T23:59:59.000Z

    PHYSICAL REVIEW E 84, 021907 (2011) Effectiveness of beads for tracking small-scale molecular motor into molecular motor dynamics are increasingly focused on small-scale features of the motor's motion. We define to the motor. We find that the best parameter choice depends on the objective of the experiments, and give

  17. Water dynamics: Relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity

    E-Print Network [OSTI]

    John Tatini Titantah; Mikko Karttunen

    2013-03-29T23:59:59.000Z

    Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. Here we employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was approx 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond stretch oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

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

    E-Print Network [OSTI]

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

    2015-04-13T23:59:59.000Z

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

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

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

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

    2015-03-20T23:59:59.000Z

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

  20. Should Thermostatted Ring Polymer Molecular Dynamics be used to calculate reaction rates?

    E-Print Network [OSTI]

    Hele, Timothy J H

    2015-01-01T23:59:59.000Z

    We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to rigorous Quantum Transition-State Theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H+H$_2$, D+MuH and F+H$_2$, and the prototypical polyatomic reaction H+CH$_4$. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is less accurate than Ring Polymer Molecular Dynamics (RPMD) for symmetric reactions, and in certain asymmetric systems closer to the q...

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

    E-Print Network [OSTI]

    Alford, Simon

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

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

    E-Print Network [OSTI]

    Y. Kanada-En'yo; H. Horiuchi

    2002-04-15T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2014-01-01T23:59:59.000Z

    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.

  4. Experimental and Numerical Study of Molecular Mixing Dynamics in Rayleigh- Taylor Unstable Flows

    E-Print Network [OSTI]

    Mueschke, Nicholas J.

    2010-01-16T23:59:59.000Z

    of Department, Dennis O?Neal May 2008 Major Subject: Mechanical Engineering iii ABSTRACT Experimental and Numerical Study of Molecular Mixing Dynamics in Rayleigh?Taylor Unstable Flows. (May 2008) Nicholas J. Mueschke, B.S., University of Louisiana... at Lafayette; M.S., Texas A&M University Chair of Advisory Committee: Dr. Malcolm J. Andrews Experiments and simulations were performed to examine the complex processes that occur in Rayleigh?Taylor driven mixing. A water channel facility was used to examine a...

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

    SciTech Connect (OSTI)

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

    2013-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    M. Kimura

    2011-05-17T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    1999-05-21T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Yoshiko Kanada-En'yo; Hisashi Horiuchi

    2003-04-28T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Y. Kanada-En'yo

    2002-04-15T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Akinori Isshiki; Kenichi Naito; Akira Ohnishi

    2005-07-13T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Rydzewski, Jakub; Nowak, Wieslaw

    2015-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Carla Goldman; Elisa T. Sena

    2008-10-07T23:59:59.000Z

    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.

  14. Dynamical consequences of a constraint on the Langevin thermostat in molecular cluster simulation

    SciTech Connect (OSTI)

    Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

    2014-11-17T23:59:59.000Z

    We investigate some unusual behaviour observed while performing molecular dynamics simulations with the DL_POLY_4.03 code. Under the standard Langevin thermostat, atoms appear to be thermalised to different temperatures, depending on their mass and on the total number of particles in the system. We find that an imposed constraint whereby no thermal noise acts on the centre of mass of the system is the cause of the unexpected behaviour. This is demonstrated by solving the stochastic dynamics for the constrained thermostat and comparing the results with simulation data. The effect of the constraint can be considerable for small systems with disparate masses. By removing the constraint the Langevin thermostat may be restored to its intended behaviour and this has been implemented as an option in DL_POLY_4.05. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

  15. Wavelet analysis of molecular dynamics: Efficient extraction of time-frequency information in ultrafast optical processes

    SciTech Connect (OSTI)

    Prior, Javier; Castro, Enrique [Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202 (Spain)] [Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202 (Spain); Chin, Alex W. [Theory of Condensed Matter Group, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom)] [Theory of Condensed Matter Group, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Almeida, Javier; Huelga, Susana F.; Plenio, Martin B. [Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm (Germany)] [Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm (Germany)

    2013-12-14T23:59:59.000Z

    New experimental techniques based on nonlinear ultrafast spectroscopies have been developed over the last few years, and have been demonstrated to provide powerful probes of quantum dynamics in different types of molecular aggregates, including both natural and artificial light harvesting complexes. Fourier transform-based spectroscopies have been particularly successful, yet “complete” spectral information normally necessitates the loss of all information on the temporal sequence of events in a signal. This information though is particularly important in transient or multi-stage processes, in which the spectral decomposition of the data evolves in time. By going through several examples of ultrafast quantum dynamics, we demonstrate that the use of wavelets provide an efficient and accurate way to simultaneously acquire both temporal and frequency information about a signal, and argue that this greatly aids the elucidation and interpretation of physical process responsible for non-stationary spectroscopic features, such as those encountered in coherent excitonic energy transport.

  16. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    E-Print Network [OSTI]

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01T23:59:59.000Z

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  17. 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

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

    SciTech Connect (OSTI)

    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

    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}.

  19. High-explosive properties from classical molecular dynamics simulations and quantum-chemical computations

    SciTech Connect (OSTI)

    Sewell, T. D. (Thomas D.); Gan, C. K. (Chee Kwan); Jaramillo, E. (Eugenio); Strachan, A. H. (Alejandro H.)

    2004-01-01T23:59:59.000Z

    We are using classical molecular dynamics and condensed phase electronic-structure methods to predict some of the thermophysical and mechanical properties that are needed as input to realistic mesoscale models for plastic-bonded explosives. The main materials studied to date are HMX, PETN, Estane copolymer, and bi(2,2-dinitropropyl) formal/acetal (BDNPF/A). Emphasis is placed on non-reactive properties and thermodynamic states relevant to cookoff and shock initiation phenomena. Both crystal and liquid-state properties are of interest. Typical simulation sizes and times are {approx}10{sup 2} molecules and 2-10 ns, respectively. The overarching goal is to develop internally consistent model thermodynamic and elastic mechanical descriptions for the materials. Prioritization among the set of properties amenable to atomistic simulation is made based on ongoing interactions with mesoscale modelers at Los Alamos and elsewhere. Recent work will be summarized and our view of profitable directions for future research will be discussed, including preliminary results for large-scale molecular dynamics simulations of shock response of crystalline HMX.

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

    E-Print Network [OSTI]

    Shugo Yasuda; Ryoichi Yamamoto

    2014-07-16T23:59:59.000Z

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

  1. Laser Control of Dissipative Two-Exciton Dynamics in Molecular Aggregates

    E-Print Network [OSTI]

    Yun-an Yan; Oliver Kühn

    2012-07-09T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    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

    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.

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

    SciTech Connect (OSTI)

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

    2014-09-07T23:59:59.000Z

    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.

  4. Dynamical simulation of heavy-ion collisions in the energy range from a few tens MeV/A to a few hundreds MeV/A

    E-Print Network [OSTI]

    M. V. Garzelli

    2008-10-13T23:59:59.000Z

    The overlapping stage of heavy-ion reactions can be simulated by dynamical microscopical models, such as those built on the basis of the Molecular Dynamics (MD) approaches, allowing to study the fragment formation process. The present performances of the Quantum MD (QMD) code developed at the University of Milano are discussed, showing results concerning fragment and particle production at bombarding energies up to $\\lsim$ 700 MeV/A, as well as a preliminary analysis on the isoscaling behaviour of isotopic yield ratios for reactions with isospin composition N/Z in the (1 - 1.2) range, at a 45 MeV/A bombarding energy.

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

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

    Hirunsit, Pussana

    2009-05-15T23:59:59.000Z

    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...

  7. Materials Science and Engineering A 447 (2007) 5157 Molecular dynamics study of the stressstrain behavior of

    E-Print Network [OSTI]

    Pan, Ernie

    2007-01-01T23:59:59.000Z

    In recent years, nanoparticle reinforced polymer composites have led to intensive research in the field properties of polymers. Besides the improved electrical conductivity [3­6] and thermal conductivity [7 is an important tool to understand the proper- ties of polymer­CNT composites. In several earlier works, MD

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

    E-Print Network [OSTI]

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

    2007-03-22T23:59:59.000Z

    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.

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

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

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

    2015-03-04T23:59:59.000Z

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

  10. Symplectic algorithm for constant-pressure molecular dynamics using a Nosé–Poincaré thermostat

    E-Print Network [OSTI]

    Sturgeon, Jess B.; Laird, Brian Bostian

    2000-01-01T23:59:59.000Z

    adjoint guarantees a time-reversible method.# This method is a simple example of a class of symplectic integrators for nonseparable Hamiltonians.14–17 Applying the GLA to the NPA equations of motion gives pi ,n11/25pi ,n2 h 2 snVn 1/3 „ iU~V1/3qn!, ~10a...! pv ,n11/25pv ,n1 h sn@P~qn ,pn11/2 ,Vn ,sn!2Pext# , 3475plectic algorithm for constant-pressure molecular dynamics2 ~10b! ject to the terms at: http://scitation.aip.org/termsconditions. Downloaded to IP: 16 Sep 2014 16:37:32 This aps ,n11/25ps ,n1...

  11. Molecular dynamic simulations of electric microfield distributions in a nonideal electron-positron plasma

    SciTech Connect (OSTI)

    Sadykova, S. P.; Ebeling, W.; Sokolov, I. M. [Humboldt-Universitaet zu Berlin (Germany); Valuev, I. A. [Russian Academy of Sciences, Joint Institute for High Temperatures (Russian Federation)

    2010-12-15T23:59:59.000Z

    A symmetric model of a two-component plasma is considered and the distributions of electric microfields acting on charged and neutral particles are calculated using the method of molecular dynamics at a fixed temperature of T = 30000 K and different values of the coupling parameter 0.2 {<=} {Gamma} {<=} 1.2. Changes in these distributions with varying {Gamma} are discussed. Special attention is paid to the behavior of the distribution tails. The behavior of these tails at a neutral point is shown to agree with the tails of the Holtsmark distribution, whereas the tails of the distribution at a charge are considerably heavier and are characterized by the exponent that varies within the range from -2.2 up to -1.8 as {Gamma} increases.

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

    E-Print Network [OSTI]

    Yasuda, Shugo

    2015-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2013-02-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2007-09-05T23:59:59.000Z

    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.

  15. Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions

    E-Print Network [OSTI]

    Priezjev, Nikolai V

    2012-01-01T23:59:59.000Z

    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.

  16. Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions

    E-Print Network [OSTI]

    Nikolai V. Priezjev

    2012-08-27T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2015-04-21T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2008-06-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2008-08-01T23:59:59.000Z

    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.

  20. Ab initio molecular dynamics study of manganese porphine hydration and interaction with nitric oxide

    E-Print Network [OSTI]

    Kevin Leung; Craig J. Medforth

    2007-01-23T23:59:59.000Z

    The authors use ab initio molecular dynamics and the density functional theory+U (DFT+U) method to compute the hydration environment of the manganese ion in manganese (II) and manganese (III) porphines (MnP) dispersed in liquid water. These are intended as simple models for more complex water soluble porphyrins, which have important physiological and electrochemical applications. The manganese ion in Mn(II)P exhibits significant out-of-porphine plane displacement and binds strongly to a single H2O molecule in liquid water. The Mn in Mn(III)P is on average coplanar with the porphine plane and forms a stable complex with two H2O molecules. The residence times of these water molecules exceed 15 ps. The DFT+U method correctly predicts that water displaces NO from Mn(III)P-NO, but yields an ambiguous spin state for the MnP(II)-NO complex.

  1. Molecular Dynamics Simulation of Semiflexible Polyampholyte Brushes - The Effect of Charged Monomers Sequence

    E-Print Network [OSTI]

    M. Baratlo; H. Fazli

    2009-03-15T23:59:59.000Z

    Planar brushes formed by end-grafted semiflexible polyampholyte chains, each chain containing equal number of positively and negatively charged monomers is studied using molecular dynamics simulations. Keeping the length of the chains fixed, dependence of the average brush thickness and equilibrium statistics of the brush conformations on the grafting density and the salt concentration are obtained with various sequences of charged monomers. When similarly charged monomers of the chains are arranged in longer blocks, the average brush thickness is smaller and dependence of brush properties on the grafting density and the salt concentration is stronger. With such long blocks of similarly charged monomers, the anchored chains bond to each other in the vicinity of the grafting surface at low grafting densities and buckle toward the grafting surface at high grafting densities.

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

    E-Print Network [OSTI]

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

    2014-12-09T23:59:59.000Z

    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.

  3. Brushes of flexible, semiflexible and rodlike diblock polyampholytes: Molecular dynamics simulation and scaling analysis

    E-Print Network [OSTI]

    M. Baratlo; H. Fazli

    2009-12-11T23:59:59.000Z

    Planar brushes of flexible, semiflexible and rodlike diblock polyampholytes are studied using molecular dynamics simulations and scaling analysis in a wide range of the grafting density. Simulations show linear dependence of the average thickness on the grafting density for all the brushes regardless of their different equilibrium conformations and different flexibility of anchored chains. Slopes of fitted lines to the average thickness of the brushes of semiflexible and rodlike polyampholytes versus the grafting density are approximately the same and differ considerably from that of the brush of flexible chains. The average thickness of the brush of diblock polyampholytes is also obtained as a function of the grafting density using a simple scaling analysis which is in good agreement with the results of our simulations.

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

    SciTech Connect (OSTI)

    Trueba, Alondra Torres [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6 (Canada); Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, Separation Technology Group, Den Dolech 2, 5612 AZ Eindhoven (Netherlands); Kroon, Maaike C. [Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, Separation Technology Group, Den Dolech 2, 5612 AZ Eindhoven (Netherlands); Peters, Cor J. [Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, Separation Technology Group, Den Dolech 2, 5612 AZ Eindhoven (Netherlands); The Petroleum Institute, Chemical Engineering Department, P. O. Box 2533, Abu Dhabi (United Arab Emirates); Moudrakovski, Igor L.; Ratcliffe, Christopher I.; Ripmeester, John A., E-mail: John.Ripmeester@nrc-cnrc.gc.ca [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6 (Canada); Alavi, Saman [Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6 (Canada); Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5 (Canada)

    2014-06-07T23:59:59.000Z

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

  5. Babar K. Rao, M.D., Clinical Associate Professor and Acting Chair Donald J. Baker, M.D., Clinical Assistant Professor (Camden)

    E-Print Network [OSTI]

    Garfunkel, Eric

    Hametz, M.D., Clinical Assistant Professor Stanley N. Katz, M.D., Clinical Assistant Professor Steven. Lathrop, M.D., Clinical Associate Professor Lawrence S. Meyers, M.D., Clinical Associate Professor Sandy S

  6. Lyapunov instability of rigid diatomic molecules via diatomic potential molecular dynamics Agency for Defense Development, P. O. Box 35, Yuseong, Taejon, Korea

    E-Print Network [OSTI]

    Lee, EokKyun

    Lyapunov instability of rigid diatomic molecules via diatomic potential molecular dynamics Oyeon Received 15 July 1998 We develop a molecular dynamic method to evaluate the full Lyapunov spectrum for two-dimensonal fluids composed of rigid diatomic molecules. The Lyapunov spectra are obtained for 18 rigid diatomic

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

    E-Print Network [OSTI]

    Y. Kanada-En'yo; M. Kimura

    2005-10-15T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    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

    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.

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

    SciTech Connect (OSTI)

    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

    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.

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

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

    Southern California, University of

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

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

    E-Print Network [OSTI]

    Goddard III, William A.

    Friction anisotropy at Ni,,100...Õ,,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

  13. Molecular Dynamics of a 1,4-Polybutadiene Melt. Comparison of Experiment and Simulation. G. D. Smith*

    E-Print Network [OSTI]

    Utah, University of

    recently, we have studied n-C100H202 melts using a combination of molecular dynamics and neutron scattering were studied on time scales up to 22 ns via neutron- spin echo (NSE) spectroscopy with momentum with neutron spin-echo (NSE) measurements yielded good agreement over the entire momentum transfer and time

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

    E-Print Network [OSTI]

    Brown, Michael F.

    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

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

    E-Print Network [OSTI]

    Boyer, Edmond

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    de Gispert, Adrià

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

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

    E-Print Network [OSTI]

    Maruyama, Shigeo

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

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

    E-Print Network [OSTI]

    Gong, Xingao

    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

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

    SciTech Connect (OSTI)

    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

    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.

  20. Properties of gravitationally equilibrated Yukawa systems—A molecular dynamics study

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

    Akira Koyama; Takashi Odagaki; Koji Fukao

    2008-03-25T23:59:59.000Z

    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}

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

    SciTech Connect (OSTI)

    Stoller, Roger E [ORNL] [ORNL

    2013-01-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2010-01-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    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

    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.

  5. Practical Attacks on Digital Signatures Using MD5 Message Digest

    E-Print Network [OSTI]

    schemes based on MD5 message digest on an example using GPG. Keywords: collision, hash function, MD5 1 on digital signatures on an example using GPG (section 5) and finally an exam- ple of real-world attack

  6. Poster Presentations Marcella Alsan, MD, MPH, PhD

    E-Print Network [OSTI]

    Kay, Mark A.

    15 Poster Presentations Marcella Alsan, MD, MPH, PhD The direct and indirect effects of mass vaccination: Evidence from the 1985 Turkish campaign Michele Barry, MD; Stephen Luby, MD; Nancy Federspiel, PhD Global Health Fellows and Scholars Consortium Cynthia M. Castro, PhD; Abby C. King, PhD; Marcia Stefanick

  7. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab-Initio Molecular Dynamics Simulations

    E-Print Network [OSTI]

    Kessler, Jan; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

    2015-01-01T23:59:59.000Z

    The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab-initio molecular dynamics simulations in conjunction with an instantaneous surface definition [A. P. Willard and D. Chandler, J. Phys. Chem. B 114, 1954 (2010)]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

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

    SciTech Connect (OSTI)

    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

    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.

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

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Shugo Yasuda; Ryoichi Yamamoto

    2015-03-25T23:59:59.000Z

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

  11. Thermal Degradation of Adsorbed Bottle-Brush Macromolecules: Molecular Dynamics Simulation

    E-Print Network [OSTI]

    Andrey Milchev; Jaroslaw Paturej; Vakhtang G. Rostiashvili; Thomas A. Vilgis

    2011-03-03T23:59:59.000Z

    The scission kinetics of bottle-brush molecules in solution and on an adhesive substrate is modeled by means of Molecular Dynamics simulation with Langevin thermostat. Our macromolecules comprise a long flexible polymer backbone with $L$ segments, consisting of breakable bonds, along with two side chains of length $N$, tethered to each segment of the backbone. In agreement with recent experiments and theoretical predictions, we find that bond cleavage is significantly enhanced on a strongly attractive substrate even though the chemical nature of the bonds remains thereby unchanged. We find that the mean bond life time $$ decreases upon adsorption by more than an order of magnitude even for brush molecules with comparatively short side chains $N=1 \\div 4$. The distribution of scission probability along the bonds of the backbone is found to be rather sensitive regarding the interplay between length and grafting density of side chains. The life time $$ declines with growing contour length $L$ as $\\propto L^{-0.17}$, and with side chain length as $\\propto N^{-0.53}$. The probability distribution of fragment lengths at different times agrees well with experimental observations. The variation of the mean length $L(t)$ of the fragments with elapsed time confirms the notion of the thermal degradation process as a first order reaction.

  12. Molecular dynamics simulations of intergranular fracture in UO2 with nine empirical interatomic potentials

    SciTech Connect (OSTI)

    Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner

    2014-09-01T23:59:59.000Z

    The intergranular fracture behavior of UO2 was studied using molecular dynamics simulations with a bicrystal model. The anisotropic fracture behavior due to the different grain boundary characters was investigated with the View the MathML source symmetrical tilt S5 and the View the MathML source symmetrical tilt S3 ({1 1 1} twin) grain boundaries. Nine interatomic potentials, seven rigid-ion plus two core–shell ones, were utilized to elucidate possible potential dependence. Initiating from a notch, crack propagation along grain boundaries was observed for most potentials. The S3 boundary was found to be more prone to fracture than the S5 one, indicated by a lower energy release rate associated with the former. However, some potential dependence was identified on the existence of transient plastic deformation at crack tips, and the results were discussed regarding the relevant material properties including the excess energies of metastable phases and the critical energy release rate for intergranular fracture. In general, local plasticity at crack tips was observed in fracture simulations with potentials that predict low excess energies for metastable phases and high critical energy release rates for intergranular fracture.

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

    E-Print Network [OSTI]

    M. Ebrahim Foulaadvand; Neda Ojaghlou

    2014-09-27T23:59:59.000Z

    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. .

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

    E-Print Network [OSTI]

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

    2014-02-19T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Guido Tiana; Carlo Camilloni

    2012-07-05T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Hua Y. Geng

    2014-12-19T23:59:59.000Z

    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 $r_{s}=0.912$.

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

    E-Print Network [OSTI]

    Igor Rychkov; Kenichi Yoshikawa

    2003-10-06T23:59:59.000Z

    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.

  18. Evaluation of healing in asphalt binders using dynamic shear rheometer and molecular modeling techniques

    E-Print Network [OSTI]

    Bommavaram, Ramamohan Reddy

    2009-05-15T23:59:59.000Z

    the parameters of characteristic healing function of asphalt binders. In the second part of this study, Molecular Modeling (MM) techniques were used to determine the interrelationship between molecular structure, surface free energy, self diffusivity, and other...

  19. Free Energy Calculation in MD Simulation

    E-Print Network [OSTI]

    Nielsen, Steven O.

    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

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

    E-Print Network [OSTI]

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

    2001-04-07T23:59:59.000Z

    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.

  1. Effects of sub-Tg annealing on Cu64.5Zr35.5 glasses: A molecular dynamics study

    SciTech Connect (OSTI)

    Zhang, Feng [Ames Laboratory; Mendelev, Mikhail I. [Ames Laboratory; Zhang, Yue [Ames Laboratory; Wang, Cai-Zhuang [Ames Laboratory; Kramer, Matthew J. [Ames Laboratory; Ho, Kai-Ming [Ames Laboratory

    2014-02-11T23:59:59.000Z

    Creating metallic glasses by cooling liquid melts in molecular dynamics simulations faces a well-known challenge that the cooling rate is too fast compared with experiments. Taking the prototypical Cu 64.5Zr35.5 glasses as an example, we propose an efficient cooling strategy in which most of the computer time is spent on a prolonged isothermal process slightly below the glass-transition temperature, Tg . The glassy sample prepared in this way demonstrates significant energetic stability, slow dynamics, and well-developed short-range icosahedral order. By conventional uniform cooling, similar properties can only be obtained using a cooling rate more than 15 times slower.

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

    SciTech Connect (OSTI)

    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

    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.

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

    SciTech Connect (OSTI)

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

    2014-07-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Silva Hernandez, Carlos Ardenis A.

    2011-08-08T23:59:59.000Z

    MOLECULAR DYNAMIC SIMULATION OF THERMO-MECHANICAL PROPERTIES OF ULTRA-THIN POLY(METHYL METHACRYLATE) FILMS A Dissertation by CARLOS ARDENIS SILVA HERNANDEZ Submitted to the Office of Graduate Studies of Texas A&M University... A Dissertation by CARLOS ARDENIS SILVA HERNANDEZ Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Co-Chairs of Committee...

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

    E-Print Network [OSTI]

    Ball, Katherine Aurelia

    2013-01-01T23:59:59.000Z

    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

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

    SciTech Connect (OSTI)

    Furuhama, Ayako; Dupuis, Michel; Hirao, Kimihiko

    2008-05-29T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

    Diddo Diddens; Andreas Heuer

    2013-02-20T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Rich, Sarah Celeste

    2008-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Stuart, Steven J.

    2014-02-25T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Zhigilei, Leonid V.

    Time-resolved diffraction profiles and atomic dynamics in short-pulse laser-induced structural Short pico- and femtosecond pulse laser irradiation has the ability to bring material into a highly dynamics simulations of a 20 nm Au film irradiated with 200 fs laser pulses of different intensity

  12. Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis

    E-Print Network [OSTI]

    2011-01-01T23:59:59.000Z

    are consistent with RipA tetramer formation and suggest aMD) simulation shows that the tetramer is stable over theform a doughnut-like tetramer where the buried surface area

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

    SciTech Connect (OSTI)

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

    2007-09-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    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

    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.

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

    SciTech Connect (OSTI)

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

    2011-11-08T23:59:59.000Z

    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.

  16. Molecular Gas in Candidate Double Barred Galaxies I. The Diverse Morphology and Dynamics of NGC 2273 and NGC 5728

    E-Print Network [OSTI]

    Glen Petitpas; Christine Wilson

    2002-04-24T23:59:59.000Z

    Double bars have been proposed as a means of transporting molecular gas past inner Lindblad resonances into the nuclear regions, where it can fuel active or starburst nuclei. Thus far, the existence of double bars has been determined predominantly through analysis of near infrared images, which can tell us little about the dynamics and inflow rates of these systems. We have observed two double bar galaxy candidates (NGC 2273 and NGC 5728) in CO J=1-0 with the Owens Valley Radio Observatory Millimeter Array. Despite the similarity in the near infrared images of these galaxies, we see rather different nuclear morphologies in the CO maps. NGC 2273 shows evidence of a nuclear gas bar, aligned with the nuclear stellar bar seen in the near infrared images. Both the nuclear gaseous and stellar bars are misaligned from the large scale bar by approximately 90 degrees, which also allows the possibility that both are the result of stars and gas populating the $x_2$ orbits of the primary bar. Estimates using dynamical friction arguments and star formation rates suggest significant gas inflow rates along the nuclear bar of NGC 2273. Conversely, NGC 5728 does not show any evidence for a nuclear molecular bar, but shows an arc of CO clumps that peaks just to the south-west of the dynamical center and curves to the south-east where it follows the dust lane to the south. Models of double-barred galaxies suggest that these galaxies should contain large amounts of molecular gas in their nuclei. Our calculations suggest that both galaxies contain sufficient amounts of gas in their nuclei, but only NGC 2273 shows evidence for a nuclear gas bar. This may be the result of past episodes of star formation exhausting and dispersing the nuclear gas of NGC 5728, but is more likely evidence that NGC 5728 has undergone a minor merger event.

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

    SciTech Connect (OSTI)

    Wang, Tianjiao

    2008-12-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Maruyama, Shigeo

    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

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

    SciTech Connect (OSTI)

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

    2014-09-30T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2014-07-11T23:59:59.000Z

    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.

  1. 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...

  2. Quantum Wavepacket Ab Initio Molecular Dynamics: An Approach for Computing Dynamically Averaged Vibrational Spectra Including Critical Nuclear Quantum Effects

    E-Print Network [OSTI]

    Iyengar, Srinivasan S.

    the precise vibrational signatures that contribute to dynamics in soft-mode hydrogen-bonded systems ReceiVed: June 12, 2007; In Final Form: August 11, 2007 We have introduced a computational methodology of hydrogen-bonded systems and hydrogen transfer extends beyond fundamental chemistry and well into the areas

  3. Net Zero Residential Test Facility Gaithersburg, MD Solar Photovoltaic Panels

    E-Print Network [OSTI]

    Oak Ridge National Laboratory

    1 Net Zero Residential Test Facility Gaithersburg, MD Solar Photovoltaic Panels Solar Thermal;NZERTF Gaithersburg, MD 3 Objectives Demonstrate Net-Zero Energy for a home similar in nature: · Demonstrate Net-Zero Energy Usage · Measure All Building Loads (Sensible and Latent) · Operate Dedicated

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

    E-Print Network [OSTI]

    Iyengar, Srinivasan S.

    electronic structure calculations (at the level of density functional theory, Hartree-Fock, post- Hartree approach to treat the simultaneous dynamics of electrons and nuclei. The method is based on a synergy-H-Cl]- and [CH3-H-Cl]- along with simultaneous dynamical treatment of the electrons and classical nuclei, through

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

    E-Print Network [OSTI]

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

    2007-01-12T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2014-10-23T23:59:59.000Z

    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 $S$.

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

    E-Print Network [OSTI]

    Guidoni, Leonardo

    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

  8. 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

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

    E-Print Network [OSTI]

    Ferreira, Márcia M. C.

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

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

    E-Print Network [OSTI]

    Perera, Lalith

    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

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

    E-Print Network [OSTI]

    Nordlund, Kai

    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

  12. Tuning thermal conductivity of nanoporous crystalline silicon by surface passivation: A molecular dynamics study

    E-Print Network [OSTI]

    Pilon, Laurent

    ) Electron-dependent thermoelectric properties in Si/Si1-xGex heterostructures and Si1-xGex alloys from first dynamics study Jin Fang and Laurent Pilona) Mechanical and Aerospace Engineering Department, Henry Samueli

  13. 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

  14. Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO{sub 2}–H{sub 2}O systems

    SciTech Connect (OSTI)

    Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang, E-mail: byx@sdu.edu.cn [School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100 (China)] [School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100 (China)

    2014-01-28T23:59:59.000Z

    In view of the important implications of excess electrons (EEs) interacting with CO{sub 2}–H{sub 2}O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO{sub 2}–H{sub 2}O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO{sub 2} molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO{sub 2}, an EE can stably reside in the empty, low-lying ?{sup *} orbital of a CO{sub 2} molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ?OCO angle of the core CO{sub 2}{sup ?} oscillates in the range of 127°?142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO{sub 2}-bound solvated EE in [CO{sub 2}(H{sub 2}O){sub n}]{sup ?} systems. Interestingly, hydration occurs not only on the O atoms of the core CO{sub 2}{sup ?} through formation of O?H–O H–bond(s), but also on the C atom, through formation of a C?H–O H–bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C?H distance in the C?H–O H–bonds, and vice versa. The number of water molecules associated with the CO{sub 2}{sup ?} anion in the first hydration shell is about 4?7. No dimer-core (C{sub 2}O{sub 4}{sup ?}) and core-switching were observed in the double CO{sub 2} aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO{sub 2}–H{sub 2}O media.

  15. Electronic and Vibrational Properties of Low-Dimensional Heterogeneous Systems: Materials and Device Perspectives

    E-Print Network [OSTI]

    Neupane, Mahesh Raj

    2015-01-01T23:59:59.000Z

    electronic structure calculation package QUANTUM ESPRESSO [311]. MD Calculation Molecular dynamics (

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

    SciTech Connect (OSTI)

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

    2014-01-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    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

    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.

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

    SciTech Connect (OSTI)

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

    2014-05-19T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2014-07-14T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    B. Joo; UKQCD Collaboration

    2001-10-11T23:59:59.000Z

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

  1. Molecular Dynamics in Shape Space and Femtosecond Vibrational Spectroscopy of Metal Constantine Yannouleas and Uzi Landman*

    E-Print Network [OSTI]

    Yannouleas, Constantine

    , with the potential energy surfaces (PES's), which underlie the dynamics, determined via electronic structure. The shell correction method is used to calculate the electronic potential energy surface underlying calculated electronic PES's [e.g., through local density functional (LDF) theory], have been introduced

  2. Molecular Dynamics in Strong Laser Fields: A New Algorithm for ab Initio Classical Trajectories

    E-Print Network [OSTI]

    Schlegel, H. Bernhard

    dynamics (AIMD) calculations13-15 in the time-varying field. In AIMD calculations, an electronic structure of electronic structure computations, but without sacrificing accuracy of the trajectory calculation. Methods the electronic structure calculations.17 However, the step size must be relatively small in order to maintain

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

    E-Print Network [OSTI]

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

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

  4. Mode-dependent phonon transport analysis of silicon crystal by molecular dynamics method Takuma HORI*4

    E-Print Network [OSTI]

    Maruyama, Shigeo

    Mode Projection(NMP)(17,18,20,21) Spectral Energy Density (SED)(22) LDeMDu u'MDu' 1 Fig. 1 Flow chart[(8)] 22 0 )( 1 )( f (8) k(22) Fig. 3 Flow chart of the lattice dynamics method. 1 2 3 4 5 6 7 8 9 methods using normal mode projection and spectral energy density. By performing the calculations

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

    SciTech Connect (OSTI)

    Smith, P. E.

    2003-07-16T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    1997-05-02T23:59:59.000Z

    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.

  7. Molecular Dynamics Simulation of Water between Metal Walls under Electric Field: Dielectric Response and Dynamics after Field Reversal

    E-Print Network [OSTI]

    Kyohei Takae; Akira Onuki

    2015-03-08T23:59:59.000Z

    We study water between parallel metal walls under applied electric field accounting for the image effect at $T=298$ K. The electric field due to the surface charges serves to attract and orient nearby water molecules, while it tends to a constant determined by the mean surface charge density away from the walls. We find Stern boundary layers with thickness about $5$ $\\rm \\AA$ and a homogeneously polarized bulk region. The molecules in the layers more sensitively respond to the applied field than in the bulk. As a result, the potential drop in the layers is larger than that in the bulk unless the cell length exceeds 10 nm. We also examine the hydrogen bonds, which tend to make small angles with respect to the walls in the layers even without applied field. The average local field considerably deviates from the classical Lorentz field and the local field fluctuations are very large in the bulk. If we suppose a nanometer-size sphere around each molecule, the local field contribution from its exterior is nearly equal to that from the continuum electrostatics and that from its interior yields the deviation from the classical Lorentz field. As a nonequilibrium problem, we investigate the dynamics after a reversal of applied field, where the relaxation is mostly caused by large-angle rotational jumps after 1 ps due to the presence of the hydrogen bond network. The molecules undergoing these jumps themselves form hydrogen-bonded clusters heterogeneously distributed in space.

  8. The Centre for Blood Research Jos Lpez, MD

    E-Print Network [OSTI]

    Strynadka, Natalie

    The Centre for Blood Research José López, MD Executive Vice-President of Research Puget Sound Blood for Blood Research Von Willebrand factor (VWF) is the largest protein in the blood and involved in both

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

    E-Print Network [OSTI]

    Walter, Nils G.

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

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

    E-Print Network [OSTI]

    Richmond, Geraldine L.

    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

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

    E-Print Network [OSTI]

    Maruyama, Shigeo

    The 1st International Symposium on Micro & Nano Technology, 14-17 March, 2004, Honolulu, Hawaii, 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

  12. Ab initio molecular dynamics study of CaSiO3 perovskite at P-T conditions of Earth's lower mantle

    E-Print Network [OSTI]

    Oganov, Artem R.

    manuscript received 16 February 2006; published 4 May 2006 First-principles molecular dynamics calculations,15 found the cubic Pm3m structure stable at 0 K, whereas more recent LDA pseudopotential calculations16 and all-electron projector-augmented wave PAW generalized gradient approximation GGA calculations17 find

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

    SciTech Connect (OSTI)

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

    2009-11-15T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2014-03-18T23:59:59.000Z

    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.

  15. Circularly Polarized X Rays: Another Probe of Ultrafast Molecular Decay Dynamics

    SciTech Connect (OSTI)

    Travnikova, Oksana; Lindblad, Andreas; Nicolas, Christophe; Soederstroem, Johan; Kimberg, Victor; Miron, Catalin [Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, B.P. 48, F-91192 Gif-sur-Yvette Cedex (France); Liu Jicai; Gel'mukhanov, Faris [Department of Theoretical Chemistry, Roslagstullsbacken 15, Royal Institute of Technology, S-106 91 Stockholm (Sweden)

    2010-12-03T23:59:59.000Z

    Dissociative nuclear motion in core-excited molecular states leads to a splitting of the fragment Auger lines: the Auger-Doppler effect. We present here for the first time experimental evidence for an Auger-Doppler effect following F1s{yields}a{sub 1g}* inner-shell excitation by circularly polarized x rays in SF{sub 6}. In spite of a uniform distribution of the dissociating S-F bonds near the polarization plane of the light, the intersection between the subpopulation of molecules selected by the core excitation with the cone of dissociation induces a strong anisotropy in the distribution of the S-F bonds that contributes to the scattering profile measured in the polarization plane.

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

    E-Print Network [OSTI]

    Takashi Hosokawa; Shu-ichiro Inutsuka

    2007-04-05T23:59:59.000Z

    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)

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

    E-Print Network [OSTI]

    Christoph Theis; Rolf Schilling

    1998-08-07T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard, E-mail: elliot1@uakron.edu [Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325 (United States)

    2013-12-21T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2005-10-06T23:59:59.000Z

    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.

  20. THE BLAST SURVEY OF THE VELA MOLECULAR CLOUD: DYNAMICAL PROPERTIES OF THE DENSE CORES IN VELA-D

    SciTech Connect (OSTI)

    Olmi, Luca [Physics Department, University of Puerto Rico, Rio Piedras Campus, Box 23343, UPR station, San Juan (Puerto Rico); Angles-Alcazar, Daniel [Department of Physics, University of Arizona, 1118 E. Fourth Street, P.O. Box 210081, Tucson, AZ 85721 (United States); De Luca, Massimo [LERMA-LRA, UMR 8112 du CNRS, Observatoire de Paris, Ecole Normale Superieure, UPMC and UCP, 24 rue Lhomond, 75231 Paris Cedex 05 (France); Elia, Davide [Istituto di Fisica dello Spazio Interplanetario-INAF, via Fosso del Cavaliere 100, I-00133 Roma (Italy); Giannini, Teresa; Lorenzetti, Dario [Osservatorio Astronomico di Roma-INAF, Via Frascati 33, I-00040 Monteporzio Catone, Roma (Italy); Massi, Fabrizio [Osservatorio Astrofisico di Arcetri-INAF, Largo E. Fermi 5, I-50125, Firenze (Italy); Martin, Peter G. [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Strafella, Francesco, E-mail: olmi.luca@gmail.co, E-mail: olmi@arcetri.astro.i [Dipartimento di Fisica, Universita del Salento, CP 193, I-73100 Lecce (Italy)

    2010-11-10T23:59:59.000Z

    The Vela-D region, according to the nomenclature given by Murphy and May, of the star-forming complex known as the Vela molecular ridge (VMR), has recently been analyzed in detail by Olmi, who studied the physical properties of 141 pre- and proto-stellar cold dust cores, detected by the Balloon-borne Large-Aperture Submillimeter Telescope (BLAST) during a much larger (55 deg{sup 2}) Galactic plane survey encompassing the whole VMR. This survey's primary goal was to identify the coldest dense dust cores possibly associated with the earliest phases of star formation. In this work, the dynamical state of the Vela-D cores is analyzed. Comparison to dynamical masses of a sub-sample of the Vela-D cores estimated from the {sup 13}CO survey of Elia is complicated by the fact that the {sup 13}CO linewidths are likely to trace the lower density intercore material, in addition to the dense gas associated with the compact cores observed by BLAST. In fact, the total internal pressure of these cores, if estimated using the {sup 13}CO linewidths, appears to be higher than the cloud ambient pressure. If this were the case, then self-gravity and surface pressure would be insufficient to bind these cores and an additional source of external confinement (e.g., magnetic field pressure) would be required. However, if one attempts to scale down the {sup 13}CO linewidths, according to the observations of high-density tracers in a small sample of sources, then most proto-stellar cores would be effectively gravitationally bound.

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

    E-Print Network [OSTI]

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

    2005-12-23T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Herman, Agnieszka

    2011-01-01T23:59:59.000Z

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

  3. Principal Component Analysis of Molecular Clouds: Can CO reveal the dynamics?

    E-Print Network [OSTI]

    Bertram, Erik; Glover, Simon C O; Klessen, Ralf S; Roman-Duval, Julia; Federrath, Christoph

    2014-01-01T23:59:59.000Z

    We use Principal Component Analysis (PCA) to study the gas dynamics in numerical simulations of typical MCs. Our simulations account for the non-isothermal nature of the gas and include a simplified treatment of the time-dependent gas chemistry. We model the CO line emission in a post-processing step using a 3D radiative transfer code. We consider mean number densities n_0 = 30, 100, 300 cm^{-3} that span the range of values typical for MCs in the solar neighbourhood and investigate the slope \\alpha_{PCA} of the pseudo structure function computed by PCA for several components: the total density, H2 density, 12CO density, 12CO J = 1 -> 0 intensity and 13CO J = 1 -> 0 intensity. We estimate power-law indices \\alpha_{PCA} for different chemical species that range from 0.5 to 0.9, in good agreement with observations, and demonstrate that optical depth effects can influence the PCA. We show that when the PCA succeeds, the combination of chemical inhomogeneity and radiative transfer effects can influence the observ...

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

    SciTech Connect (OSTI)

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

    2014-09-14T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2013-11-27T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    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

    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.

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

    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...

  8. Efficient "on-the-fly" calculation of Raman spectra from \\textit{ab-initio} molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water

    E-Print Network [OSTI]

    Partovi-Azar, Pouya

    2015-01-01T23:59:59.000Z

    We present a computational method to accurately calculate Raman spectra from first principles with an at least one order of magnitude higher efficiency. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of \\textit{ab-initio} molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra.

  9. First-principles molecular-dynamics simulations for neutral p-chloranil and its radical anion Groupe Matie`re Condensee et Materiaux, Universite Rennes I, Campus de Beaulieu, F-35042 Rennes Cedex, France

    E-Print Network [OSTI]

    Boyer, Edmond

    First-principles molecular-dynamics simulations for neutral p-chloranil and its radical anion C compounds as they can ex- hibit a high electrical conductivity.1­3 But more recently, the discovery

  10. Einstein M.D. Program 20132014 applicant guide

    E-Print Network [OSTI]

    Emmons, Scott

    Einstein M.D. Program 2013­2014 applicant guide O F Y E S H I V A U N I V E R S I T Y Albert Einstein College of Medicine #12;2 Welcome Explore how Einstein can give you the skills to develop, learning opportunities and experiences that create the unique educational environment at Einstein

  11. Einstein M.D. Program 20112012 applicant guide

    E-Print Network [OSTI]

    Jenny, Andreas

    Einstein M.D. Program 2011­2012 applicant guide O F Y E S H I V A U N I V E R S I T Y Albert Einstein College of Medicine #12;2 Welcome Explore how Einstein can give you the skills to develop, learning opportunities and experiences that create the unique educational environment at Einstein

  12. 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

  13. Diabetes A Growing Epidemic Michael McKee, MD, MPH

    E-Print Network [OSTI]

    Goldman, Steven A.

    Diabetes ­ A Growing Epidemic Michael McKee, MD, MPH March 28, 2013 #12;Goals Diabetes Introduction Types of Diabetes Testing Prevention Treatments #12;In Memory of Benno Houver Bernd "Benno" Houver (1973-2013) #12;Diabetes Info 25.8 million people in the USA (8.3%) have diabetes ~25% of people with diabetes do

  14. Conformational and Structural Relaxations of Poly(ethylene oxide) and Poly(propylene oxide) Melts: Molecular Dynamics Study of Spatial Heterogeneity, Cooperativity, and Correlated Forward-Backward Motion

    E-Print Network [OSTI]

    Michael Vogel

    2007-10-30T23:59:59.000Z

    Performing molecular dynamics simulations for all-atom models, we characterize the conformational and structural relaxations of poly(ethylene oxide) and poly(propylene oxide) melts. The temperature dependence of these relaxation processes deviates from an Arrhenius law for both polymers. We demonstrate that mode-coupling theory captures some aspects of the glassy slowdown, but it does not enable a complete explanation of the dynamical behavior. When the temperature is decreased, spatially heterogeneous and cooperative translational dynamics are found to become more important for the structural relaxation. Moreover, the transitions between the conformational states cease to obey Poisson statistics. In particular, we show that, at sufficiently low temperatures, correlated forward-backward motion is an important aspect of the conformational relaxation, leading to strongly nonexponential distributions for the waiting times of the dihedrals in the various conformational states

  15. End-to-End Rate-Distortion Optimized MD Mode Selection for Multiple Description Video Coding

    E-Print Network [OSTI]

    Apostolopoulos, John G.

    Multiple description (MD) video coding can be used to reduce the detrimental effects caused by transmission over lossy packet networks. A number of approaches have been proposed for MD coding, where each provides a different ...

  16. COMMISSION ON HEALTH SCIENCE, EDUCATION, AND P. Roy Vagelos, M.D.

    E-Print Network [OSTI]

    Lin, Xiaodong

    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

  17. Asbestos-related diseases in automobile mechanics Jacques Ameille, MD1

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    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

  18. Molecular Dynamics Study

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

    low viscosity of the brine. 16 The primary disadvantage of an aqueous electrolyte supercapacitor is the limitation of the electric potential to 1 V. 17 Atomic scale...

  19. Einstein M.D. Program 20142015 APPLICANT GUIDE

    E-Print Network [OSTI]

    Emmons, Scott

    Einstein M.D. Program 2014­2015 APPLICANT GUIDE O F Y E S H I V A U N I V E R S I T Y Albert Einstein College of Medicine #12;2 Welcome Explore how Einstein can give you the skills to develop at Einstein. There are 183 students in the first- year class. 8,193 applicants applied for entrance and 1

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

    E-Print Network [OSTI]

    Chu, Shih-I; Zhou, Zhongyuan

    2009-10-27T23:59:59.000Z

    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...

  1. Exploring kinetics and thermodynamics in fast-ion conductors and hydrogen-storage materials using ab-initio molecular dynamics

    E-Print Network [OSTI]

    Wood, Brandon C. (Brandon Christopher)

    2007-01-01T23:59:59.000Z

    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 ...

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

    E-Print Network [OSTI]

    Leung, Kevin; 10.1039/B925853A

    2010-01-01T23:59:59.000Z

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

  3. A Classical Approach in Simple Nuclear Fusion Reaction 1H2 + 1H3 using Two-Dimension Granular Molecular Dynamics Model

    E-Print Network [OSTI]

    Sparisoma Viridi; Rizal Kurniadi; Abdul Waris; Yudha Satya Perkasa

    2011-09-30T23:59:59.000Z

    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.

  4. Research Paper j Using Petri Net Tools to Study Properties and Dynamics of

    E-Print Network [OSTI]

    Rubin, Daniel L.

    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

  5. Brain-Computer Interfaces in Medicine Jerry J. Shih, MD; Dean J. Krusienski, PhD; and Jonathan R. Wolpaw, MD

    E-Print Network [OSTI]

    Nehorai, Arye

    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

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

    SciTech Connect (OSTI)

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

    2011-02-28T23:59:59.000Z

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

  7. UC Davis-LLNL Scientific Advisory Committee Timothy Albertson, MD, PhD, Vice Chair, Internal Medicine

    E-Print Network [OSTI]

    Carmichael, Owen

    UC Davis-LLNL Scientific Advisory Committee Timothy Albertson, MD, PhD, Vice Chair, Internal Berglund, MD, PhD, CTSC Program Director Stuart Cohen, MD, Head of Infection Control, UCDMC Jeffrey Elias, PhD, Manager, Grant Coordination **Captain** Hernando Garzon, MD, Emergency Medicine, Kaiser Jeffrey

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

    E-Print Network [OSTI]

    Ulm, Universität

    adsorption poisoned by a co- adsorbate [19, 26­29]. According to electronic structure calculations based of the electronic structure of Pd(100). Dynamical studies performed on a potential energy surface (PES) based calculations, poisoning, adsorption dynamics, subsurface penetration I. INTRODUCTION Under realistic ambient

  9. High-dynamic-range extinction mapping of infrared dark clouds: Dependence of density variance with sonic Mach number in molecular clouds

    E-Print Network [OSTI]

    Kainulainen, Jouni

    2012-01-01T23:59:59.000Z

    Measuring the mass distribution of infrared dark clouds (IRDCs) over the wide dynamic range of their column densities is a fundamental obstacle in determining the initial conditions of high-mass star formation and star cluster formation. We present a new technique to derive high-dynamic-range, arcsecond-scale resolution column density data for IRDCs and demonstrate the potential of such data in measuring the density variance - sonic Mach number relation in molecular clouds. We combine near-infrared data from the UKIDSS/Galactic Plane Survey with mid-infrared data from the Spitzer/GLIMPSE survey to derive dust extinction maps for a sample of ten IRDCs. We then examine the linewidths of the IRDCs using 13CO line emission data from the FCRAO/Galactic Ring Survey and derive a column density - sonic Mach number relation for them. For comparison, we also examine the relation in a sample of nearby molecular clouds. The presented column density mapping technique provides a very capable, temperature independent tool f...

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

    Office of Legacy Management (LM)

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOn AprilA group currentBradleyTable ofArizonaBuffaloJohns Hopkins University - MD 02 FUSRAP

  11. First-principles molecular-dynamics study of glassy As2Se3 Jun Li and D. A. Drabold

    E-Print Network [OSTI]

    Drabold, David

    static structure factor in the range 2­6 Å 1 . The preferred structural unit is pyramidal AsSe3 loosely on the cluster model8 consisting mostly of pyramidal AsSe3 molecules,9 and the other is the layer structure using a molecular model and several vibrational frequencies were assigned to pyramidal AsSe3

  12. Molecular dynamics simulation study of valyl-tRNA synthetase with its pre-and post-transfer editing substrates

    E-Print Network [OSTI]

    Lee, Keun Woo

    of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 660-701, Republic of Korea a b s t r a c ta r t i c l e i n f o Article history: Received 25

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

    E-Print Network [OSTI]

    Goddard III, William A.

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

  14. Molecular Dynamics Simulations of Solvated Yeast tRNAAsp Pascal Auffinger, Shirley Louise-May, and Eric Westhof

    E-Print Network [OSTI]

    Westhof, Eric

    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

  15. 7498 Biochemistry 1991, 30, 7498-7506 Effects of Melittin on Molecular Dynamics and Ca-ATPase Activity in

    E-Print Network [OSTI]

    Thomas, David D.

    Birmachu, Deborah M. Hussey, and David D. Thomas* Department of Biochemistry, University of Minnesota association (Birmachu & Thomas, 1990). In addition, ST-EPR studies of Ca-ATPase rotational dynamics show that enzyme activity correlates with protein rotational mobility (Squier & Thomas, 1988; Squier et al., 1988a

  16. arXiv:condmat/0607335 Molecular dynamics of shock fronts and their transitions in Lennard-Jonesium and Tin

    E-Print Network [OSTI]

    Texas at Austin. University of

    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

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

    SciTech Connect (OSTI)

    Ghobadi, Ahmadreza F.; Elliott, J. Richard, E-mail: elliot1@uakron.edu [Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325 (United States)

    2014-07-14T23:59:59.000Z

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

  18. Free Energy & Kinetics from Molecular Dynamics Objective: To give a presentation of about 60 minutes at the end of the week covering the key aspects of how to get kinetic

    E-Print Network [OSTI]

    Goldschmidt, Christina

    Free Energy & Kinetics from Molecular Dynamics 14.6.10 Objective: To give a presentation of about of determining macroscopic parameters by simulations. One of the most important examples would be free energy and rate constants. The above illustration is the standard description of free energy and rates of going

  19. Chitosan Molecular Structure as a Function of N-Acetylation....

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

    Chitosan Molecular Structure as a Function of N-Acetylation. Abstract: Molecular dynamics simulations have been carried out to characterize the structure and solubility of...

  20. Scientist Position In Human Molecular Genetics: Toronto, ON, Canada

    E-Print Network [OSTI]

    Queitsch, Christine

    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

  1. DFT-MD approach to TiO2/liquid interface systems for photocatalysis and dye-sensitised solar cell

    E-Print Network [OSTI]

    Katsumoto, Shingo

    DFT-MD approach to TiO2/liquid interface systems for photocatalysis and dye-sensitised solar cell- namics (MD) analysis of TiO2/solution in- terfaces related to photocatalysis and dye- sensitized solar

  2. amory codman 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 73 Report 2004 MDPhD Program "Molecular...

  3. 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...

  4. Dynamic

    Office of Legacy Management (LM)

    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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625 1,006 492 742EnergyOn AprilA group currentBradleyTableSelling7111AWell: Gas productionDynamic , and Static ,

  5. Name Role Contact Thomas G Keens, M.D., C.I.P. Chair, Committee on Clinical Investigations tkeens@chla.usc.edu

    E-Print Network [OSTI]

    Valero-Cuevas, Francisco

    @chla.usc.edu (323) 3612265 Alan B. Lewis, M.D. Vice Chair, Committee on Clinical Investigations alewis Deirdre Anglin, MD ViceChair, IRB Email: anglin@usc.edu Phone: (323) 2232340 Robert Larsen, MD Vice

  6. Spin dynamics simulation of electron spin relaxation in Ni{sup 2+}(aq)

    SciTech Connect (OSTI)

    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

    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.

  7. Coupling MD Simulations and X-ray Absorption Spectroscopy to Study Ions in Solution

    SciTech Connect (OSTI)

    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

    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.

  8. Time-resolved infrared absorption studies of the solvent-dependent vibrational relaxation dynamics of chlorine dioxide

    SciTech Connect (OSTI)

    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

    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.

  9. Broadband infrared and Raman probes of excited-state vibrational molecular dynamics; Simulation protocols based on loop diagram

    E-Print Network [OSTI]

    Konstantin E. Dorfman; Benjamin P. Fingerhut; Shaul Mukamel

    2013-05-23T23:59:59.000Z

    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.

  10. Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations

    SciTech Connect (OSTI)

    Nguyen, Trung D [ORNL] [ORNL; Carrillo, Jan-Michael Y [ORNL] [ORNL; Brown, W Michael [ORNL] [ORNL; Matheson, Michael A [ORNL] [ORNL

    2014-01-01T23:59:59.000Z

    The ability of liquid crystal (LC) molecules to respond to changes in their environment makes them an interesting candidate for thin film applications, particularly in bio-sensing, bio-mimicking devices, and optics. Yet the understanding of the (in)stability of this family of thin films has been limited by the inherent challenges encountered by experiment and continuum models. Using unprecedented largescale molecular dynamics (MD) simulations, we address the rupture origin of LC thin films wetting a solid substrate at length scales similar to those in experiment. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation, and importantly, for the first time, evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. We further demonstrate that the primary driving force for rupture is closely related to the tendency of the LC mesogens to recover their local environment in the bulk state. Our study not only provides new insights into the rupture mechanism of liquid crystal films, but also sets the stage for future investigations of thin film systems using peta-scale molecular dynamics simulations.

  11. Electron localization following attosecond molecular photoionization

    E-Print Network [OSTI]

    Kling, Matthias

    - 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

  12. 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)

    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

    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.

  13. animal studies molecular: Topics by E-print Network

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

    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 Supplementary Animations Chemistry Websites Summary: Molecular dynamics of B...

  14. Vehicle Technologies Office Merit Review 2015: Cummins MD & HD Accessory Hybridization CRADA

    Broader source: Energy.gov [DOE]

    Presentation given by Oak Ridge National Laboratory at 2015 DOE Hydrogen and Fuel Cells Program and Vehicle Technologies Office Annual Merit Review and Peer Evaluation Meeting about Cummins MD &...

  15. 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 &...

  16. Andrea E. Reid, M.D., M.P.H. INFORMATION

    E-Print Network [OSTI]

    Goodrich, Lisa V.

    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

  17. Intelligent Mobile Health Monitoring System (IMHMS) Rifat Shahriyar, Md. Faizul Bari, Gourab Kundu, Sheikh Iqbal Ahamed,

    E-Print Network [OSTI]

    Boutaba, Raouf

    , 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

  18. Catharine Whiteside, MD PhD Vice Provost, Relations with Health Care Institutions

    E-Print Network [OSTI]

    Zandstra, Peter W.

    Catharine Whiteside, MD PhD Dean Vice Provost, Relations with Health Care Institutions Office. Professor Andrews received her PhD from the University of Toronto and completed further training

  19. 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...

  20. BOSTON UNIVERSITY COLLEGE OF ENGINEERING

    E-Print Network [OSTI]

    Herbordt, Martin

    D, Associate Professor of Electrical and Computer Engineering ABSTRACT While Molecular Dynamics Simulation (MDBOSTON UNIVERSITY COLLEGE OF ENGINEERING Dissertation SCALABLE MOLECULAR DYNAMICS SIMULATION USING #12;SCALABLE MOLECULAR DYNAMICS SIMULATION USING FPGAS AND MULTICORE PROCESSORS (Order No. ) MD

  1. Annu. Rev. Biophys. Biomol. Struct. 2001. 30:21143 Copyright c 2001 by Annual Reviews. All rights reserved

    E-Print Network [OSTI]

    Wang, Wei

    -mail: odonini@kintekpharm.com Key Words molecular dynamics, molecular recognition, electronic structural calculations s Abstract Computer modeling has been developed and widely applied in studying molecules) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE

  2. Dynamics of dendritic polymers in the bulk and under confinement

    SciTech Connect (OSTI)

    Chrissopoulou, K. [Foundation for Research and Technology-Hellas, Institute of Electronic Structure and Laser, P.O. Box 1527, 711 10, Heraklion Crete (Greece); Fotiadou, S. [Foundation for Research and Technology-Hellas, Institute of Electronic Structure and Laser, P.O. Box 1527, 711 10, Heraklion Crete, Greece and Aristotle University of Thessaloniki, Department of Chemical Engineering, Thessaloniki (Greece); Androulaki, K.; Anastasiadis, S. H. [Foundation for Research and Technology-Hellas, Institute of Electronic Structure and Laser, P.O. Box 1527, 711 10, Heraklion Crete, Greece and University of Crete, Department of Chemistry, Heraklion Crete (Greece); Tanis, I.; Karatasos, K. [Aristotle University of Thessaloniki, Department of Chemical Engineering, Thessaloniki (Greece); Prevosto, D.; Labardi, M. [CNR-IPCF, Department of Physics, University of Pisa, Pisa (Italy); Frick, B. [ILL-Institut Laue-Langevin, Grenoble (France)

    2014-05-15T23:59:59.000Z

    The structure and dynamics of a hyperbranched polyesteramide (Hybrane® S 1200) polymer and its nanocomposites with natural montmorillonite (Na{sup +}-MMT) are investigated by XRD, DSC, QENS, DS and Molecular Dynamics (MD) simulation. In bulk, the energy-resolved elastically scattered intensity from the polymer exhibits two relaxation steps, one attributed to sub-T{sub g} motions and one observed at temperatures above the glass transition, T{sub g}. The QENS spectra measured over the complete temperature range are consistent with the elastic measurements and can be correlated to the results emerging from the detailed description afforded by the atomistic simulations, which predict the existence of three relaxation processes. Moreover, dielectric spectroscopy shows the sub- T{sub g} beta process as well as the segmental relaxation. For the nanocomposites, XRD reveals an intercalated structure for all hybrids with distinct interlayer distances due to polymer chains residing within the galleries of the Na{sup +}-MMT. The polymer chains confined within the galleries show similarities in the behavior with that of the polymer in the bulk for temperatures below the bulk polymer T{sub g}, whereas they exhibit frozen dynamics under confinement at temperatures higher than that.

  3. Assessment of Molecular Modeling & Simulation

    SciTech Connect (OSTI)

    None

    2002-01-03T23:59:59.000Z

    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.

  4. Molecular simulations studies of gas adsorption in metal–organic frameworks 

    E-Print Network [OSTI]

    Chen, Linjiang

    2014-06-30T23:59:59.000Z

    Using computational tools ranging from molecular simulations – including both Monte Carlo and molecular dynamics methods – to quantum mechanical (QM) calculations (primarily at density functional theory (DFT) level), ...

  5. Encoding Molecular Motions in Voxel Maps Juan Cortes, Sophie Barbe, Monique Erard and Thierry Simeon

    E-Print Network [OSTI]

    Cortés, Juan

    1 Encoding Molecular Motions in Voxel Maps Juan Cort´es, Sophie Barbe, Monique Erard and Thierry] have been devel- oped to overcome the limitations of MD. Such methods present however a major drawback, France sbarbe@insa-toulouse.fr M. Erard is with the IPBS, F-31077 Toulouse, France monique

  6. Encoding Molecular Motions in Voxel Maps Juan Cortes, Sophie Barbe, Monique Erard and Thierry Simeon

    E-Print Network [OSTI]

    Cortés, Juan

    Encoding Molecular Motions in Voxel Maps Juan Cort´es, Sophie Barbe, Monique Erard and Thierry Sim] have been developed to overcome the limitations of MD. Such methods present however a major drawback, France sbarbe@insa-toulouse.fr M. Erard is with the IPBS, F-31077 Toulouse, France monique

  7. Magnetismo Molecular (Molecular Magentism)

    SciTech Connect (OSTI)

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

    2010-07-01T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Agieienko, Vira N.; Kolesnik, Yaroslav V.; Kalugin, Oleg N., E-mail: onkalugin@gmail.com [Department of Inorganic Chemistry, V. N. Karazin Kharkiv National University, Kharkiv 61022 (Ukraine)

    2014-05-21T23:59:59.000Z

    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.

  9. HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations

    E-Print Network [OSTI]

    Nagle, John F.

    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

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

    E-Print Network [OSTI]

    California at Davis, University of

    States, Inc. Thomas Williams, Dr.P.H., M.B.A. President and Chief Executive Officer Integrated Healthcare. Scott, M.D., M.P.H., Ex officio Chief Medical Information Officer California Department of Health CareCalifornia Health eQuality Advisory Committee Kenneth W. Kizer, M.D., M.P.H. - Chair Distinguished

  11. MARYLAND BIOTECHNOLOGY CENTER JOINS HOPKINS, UNIVERSITY OF MD IN AWARDING 2013 BIOMARYLAND LIFE PRIZE

    E-Print Network [OSTI]

    Weber, David J.

    PRIZE $50,000 grants help further research, bring new discoveries to commercial market BALTIMORE, MD will use the funding to develop technology that will aid in the safer delivery of radiation therapy to continue his research on a safer way to deliver radiation therapy." "This is a fantastic opportunity

  12. HOPKINS, UNIVERSITY OF MD, BALTIMORE FACULTY RESEARCHERS WIN 2014 BIOMARYLAND LIFE PRIZES

    E-Print Network [OSTI]

    Weber, David J.

    ,000 grants help further research, bring new discoveries to commercial market BALTIMORE, MD (February 19, 2014 for her development of a blood test for the early detection of pancreatic cancer. #12;The LIFE prize the funding to develop technology that will aid in the safer delivery of radiation therapy. Previous winners

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

    E-Print Network [OSTI]

    Robock, Alan

    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

  14. Hot Water DJ: Saving Energy by Pre-mixing Hot Water Md Anindya Prodhan

    E-Print Network [OSTI]

    Whitehouse, Kamin

    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

  15. Corbicula Active (ABM) Biomonitoring and Passive (POM) Chlordane Monitoring in the Anacostia River Watershed (MD).

    E-Print Network [OSTI]

    District of Columbia, University of the

    in the Anacostia River Watershed (MD). Final Report to the DC Water Resources Research Center Dr. Harriette L hydrocarbons (PAHs), 28 polychlorinated biphenyl congeners (PCBs), 6 Aroclors, 21 pesticides, and five metals (Cd, Cr, Cu, Fe, Pb) plus technical chlordane, percent water and percent lipid. This ABM study

  16. 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

  17. Vendor Location PHS Assurance# A&G Pharmaceutical, Inc. MD A4404-01

    E-Print Network [OSTI]

    Bandettini, Peter A.

    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

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

    E-Print Network [OSTI]

    Truong, Thanh N.

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

  19. Limbic System Page 1 of 10 Srdjan D. Antic, M.D. Limbic system Emotional Experience

    E-Print Network [OSTI]

    Oliver, Douglas L.

    function. NMDA-dependent long-term potentiation is a cellular mechanism responsible for fear conditioning.M. is the most studied patient with Urbach-Wiethe disease. After a battery of tests, which included spiders Srdjan D. Antic, M.D. 3 as well as an appetitive (positive) conditioning. Individuals with larger

  20. The Centre for Blood Research Athan Kuliopulos, MD, PhD

    E-Print Network [OSTI]

    Strynadka, Natalie

    The Centre for Blood Research Athan Kuliopulos, MD, PhD Director, Hemostasis & Thrombosis coating blood vessel walls rupture and expose collagen, platelets spring into action to form a blood clot, according to the researchers. Compared to other diseases, blood clotting has been very well understood