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Isotopic mass-dependence of noble gas diffusion coefficients inwater

Description: Noble gas isotopes are used extensively as tracers inhydrologic and paleoclimatic studies. These applications requireknowledge of the isotopic mass (m) dependence of noble gas diffusioncoefficients in water (D), which has not been measured but is estimatedusing experimental D-values for the major isotopes along with an untestedrelationship from kinetic theory, D prop m-0.5. We applied moleculardynamics methods to determine the mass dependence of D for four noblegases at 298 K, finding that D prop m-beta with beta<0.2, whichrefutes the kinetic theory model underlying all currentapplications.
Date: June 25, 2007
Creator: Bourg, I.C. & Sposito, G.
Partner: UNT Libraries Government Documents Department

Influence of point defects on grain boundary motion.

Description: This work addresses the influence of point defects, in particular vacancies, on the motion of grain boundaries. If there is a non-equilibrium concentration of point defects in the vicinity of an interface, such as due to displacement cascades in a radiation environment, motion of the interface to sweep up the defects will lower the energy and provide a driving force for interface motion. Molecular dynamics simulations are employed to examine the process for the case of excess vacancy concentrations in the vicinity of two grain boundaries. It is observed that the efficacy of the presence of the point defects in inducing boundary motion depends on the balance of the mobility of the defects with the mobility of the interfaces. In addition, the extent to which grain boundaries are ideal sinks for vacancies is evaluated by considering the energy of boundaries before and after vacancy absorption.
Date: September 1, 2010
Creator: Foiles, Stephen Martin
Partner: UNT Libraries Government Documents Department

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

Description: 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.
Date: September 1, 2011
Creator: Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (Oak Ridge National Laboratories, Oak Ridge, TN); Plimpton, Steven James; Zhou, Xiao Wang et al.
Partner: UNT Libraries Government Documents Department

Role of Brownian Motion Hydrodynamics on Nanofluid Thermal Conductivity

Description: We use a simple kinetic theory based analysis of heat flow in fluid suspensions of solid nanoparticles (nanofluids) to demonstrate that the hydrodynamics effects associated with Brownian motion have a minor effect on the thermal conductivity of the nanofluid. Our conjecture is supported by the results of molecular dynamics simulations of heat flow in a model nanofluid with well-dispersed particles. Our findings are consistent with the predictions of the effective medium theory as well as with recent experimental results on well dispersed metal nanoparticle suspensions.
Date: November 14, 2005
Creator: W Evans, J Fish, P Keblinski
Partner: UNT Libraries Government Documents Department

Natural materials for carbon capture.

Description: Naturally occurring clay minerals provide a distinctive material for carbon capture and carbon dioxide sequestration. Swelling clay minerals, such as the smectite variety, possess an aluminosilicate structure that is controlled by low-charge layers that readily expand to accommodate water molecules and, potentially, carbon dioxide. Recent experimental studies have demonstrated the efficacy of intercalating carbon dioxide in the interlayer of layered clays but little is known about the molecular mechanisms of the process and the extent of carbon capture as a function of clay charge and structure. A series of molecular dynamics simulations and vibrational analyses have been completed to assess the molecular interactions associated with incorporation of CO2 in the interlayer of montmorillonite clay and to help validate the models with experimental observation.
Date: November 1, 2010
Creator: Myshakin, Evgeniy M. (National Energy Technology Laboratory, Pittsburgh, PA); Romanov, Vyacheslav N. (National Energy Technology Laboratory, Pittsburgh, PA) & Cygan, Randall Timothy
Partner: UNT Libraries Government Documents Department

Effect of dephasing on DNA sequencing via transverse electronic transport

Description: We study theoretically the effects of dephasing on DNA sequencing in a nanopore via transverse electronic transport. To do this, we couple classical molecular dynamics simulations with transport calculations using scattering theory. Previous studies, which did not include dephasing, have shown that by measuring the transverse current of a particular base multiple times, one can get distributions of currents for each base that are distinguishable. We introduce a dephasing parameter into transport calculations to simulate the effects of the ions and other fluctuations. These effects lower the overall magnitude of the current, but have little effect on the current distributions themselves. The results of this work further implicate that distinguishing DNA bases via transverse electronic transport has potential as a sequencing tool.
Date: January 1, 2009
Creator: Zwolak, Michael; Krems, Matt; Pershin, Yuriy V & Di Ventra, Massimiliano
Partner: UNT Libraries Government Documents Department

Direct measurement of the alpha-epsilon transition stress and kinetics for shocked iron

Description: Iron undergoes a polymorphic phase transformation from alpha phase (bcc) to the epsilon phase (hcp) when compressed to stresses exceeding 13 CPa. Bccause the epsilon phase is denser than the alpha phase, a single shock wave is unstable and breaks up into an elastic wave, a plastic wave, and a phase transition wave. Examination of this structured wave coupled with various phase transformation models has been used to indirectly examine the transition kinetics. Recently, multimillion atom simulations (molecular dynamics) have been used to examine the shock-induced transition in single crystal iron illustrating an orientation dependence of the transition stress, mechanisms, and kinetics. The objective of the current work was to perform plate impact experiments to examine the shock-response of polycrystalline and single crystal iron with nanosecond resolution for impact stresses spanning the {alpha} - {epsilon} transition. The current data reveal an orientation dependence of the transition stress coupled with a transition time that is nonlinearly dependent on the impact stress with a duration ranging from picoseconds to hundreds of nanoseconds. The higher transition stress for iron[100] is in agreement with the predictions from MD calculations that describe an orientation dependence of the transition stress. However, MD calculations do not capture the complexity of the continuum states achieved or the transition kinetics. Further results and implications are discussed in this paper.
Date: January 1, 2009
Creator: Jensen, Brian J; Gray, Ill, George T & Hixson, Robert S
Partner: UNT Libraries Government Documents Department

Comparison of binary collision approximation and molecular dynamics for displacement cascades in GaAs.

Description: The predictions of binary collision approximation (BCA) and molecular dynamics (MD) simulations of displacement cascades in GaAs are compared. There are three issues addressed in this work. The first is the optimal choice of the effective displacement threshold to use in the BCA calculations to obtain the best agreement with MD results. Second, the spatial correlations of point defects are compared. This is related to the level of clustering that occurs for different types of radiation. Finally, the size and structure of amorphous zones seen in the MD simulations is summarized. BCA simulations are not able to predict the formation of amorphous material.
Date: October 1, 2011
Creator: Foiles, Stephen Martin
Partner: UNT Libraries Government Documents Department

Computer simulation of boundary effects on bubble growth in metals due to He.

Description: Atomistic simulation methods were used to investigate and identify the relevant physical mechanisms necessary to describe the growth of helium gas bubbles within a metal lattice. Specifically, molecular dynamics simulations were performed to examine the material defects that originate from growing spherical He bubbles in a palladium crystal. These simulations consist of a model system containing bubbles within a metal and near a free surface. The simulation code employed was ParaDyn using the Embedded Atom Method to model the constitutive properties of Pd atoms in a FCC lattice. The results of these simulations are compared with previously run calculations of He bubbles in a bulk lattice [l]. These simulations show the influence of the free surface on defect creation and evolution. Features compared include the formation of inter-bubble dislocations, bubble pressure and swelling as functions of He to metal (He/M) concentration.
Date: March 1, 2003
Creator: Zimmerman, Jonathan A.
Partner: UNT Libraries Government Documents Department

Self-assembly of polymers in confined geometrics.

Description: Athermal, tethered chains are modeled with Density Functional (DFT) theory for both the explicit solvent and continuum solvent cases. The structure of DFT is shown to reduce to Self-Consistent-Field (SCF) theory in the incompressible limit where there is symmetry between solvent and monomer, and to Single-Chain-Mean-Field (SCMF) theory in the continuum solvent limit. We show that by careful selection of the reference and ideal systems in DFT theory, self-consistent numerical solutions can be obtained, thereby avoiding the single chain Monte Carlo simulation in SCMF theory. On long length scales, excellent agreement is seen between the simplified DFT theory and Molecular Dynamics simulations of both continuum solvents and explicit-molecule solvents. In order to describe the structure of the polymer and solvent near the surface it is necessary to include compressibility effects and the nonlocality of the field.
Date: October 1, 2003
Creator: Curro, John G.; Ye, Yuan (New Mexico Institute of Mining & Technology, Socorro, NM) & McCoy, John Dwane (New Mexico Institute of Mining & Technology, Socorro, NM)
Partner: UNT Libraries Government Documents Department

Higher-order symplectic Born-Oppenheimer molecular dynamics

Description: The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics (TR-BOMD) enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the 6th order have been adapted and optimized to TR-BOMD in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements.
Date: January 1, 2009
Creator: Niklasson, Anders; Bock, Nicolas; Challacombe, Matt; Odell, Anders; Delin, Anna & Johansson, Borje
Partner: UNT Libraries Government Documents Department

Stress-induced phase transformation in nanocrystalline UO2

Description: We report a stress-induced phase transfonnation in stoichiometric UO{sub 2} from fluorite to the {alpha}-PbO{sub 2} structure using molecular dynamics (MD) simulations and density functional theory (DFT) calculations. MD simulations, performed on nanocrystalline microstructure under constant-stress tensile loading conditions, reveal a heterogeneous nucleation of the {alpha}-PbO{sub 2} phase at the grain boundaries followed by the growth of this phase towards the interior of the grain. The DFT calculations confinn the existence of the {alpha}-PbO{sub 2} structure, showing that it is energetically favored under tensile loading conditions.
Date: January 1, 2009
Creator: Uberuaga, Blas Pedro & Desai, Tapan
Partner: UNT Libraries Government Documents Department

Molecular Dynamics Simulation of Polymer Dissolution

Description: In the LIGA process for manufacturing microcomponents, a polymer film is exposed to an x-ray beam passed through a gold pattern. This is followed by the development stage, in which a selective solvent is used to remove the exposed polymer, reproducing the gold pattern in the polymer film. Development is essentially polymer dissolution, a physical process which is not well understood. We have used coarse-grained molecular dynamics simulation to study the early stage of polymer dissolution. In each simulation a film of non-glassy polymer was brought into contact with a layer of solvent. The mutual penetration of the two phases was tracked as a function of time. Several film thicknesses and two different chain lengths were simulated. In all cases, the penetration process conformed to ideal Fickian diffusion. We did not see the formation of a gel layer or other non-ideal effects. Variations in the Fickian diffusivities appeared to be caused primarily by differences in the bulk polymer film density.
Date: February 1, 2003
Creator: THOMPSON, AIDAN P.
Partner: UNT Libraries Government Documents Department

Direct Molecular Simulation of Gradient-Driven Diffusion of Large Molecules using Constant Pressure

Description: Dual control volume grand canonical molecular dynamics (DCV-GCMD) is a boundary-driven non-equilibrium molecular dynamics technique for simulating gradient driven diffusion in multi-component systems. Two control volumes are established at opposite ends of the simulation box. Constant temperature and chemical potential of diffusing species are imposed in the control volumes. This results in stable chemical potential gradients and steady-state diffusion fluxes in the region between the control volumes. We present results and detailed analysis for a new constant-pressure variant of the DCV-GCMD method in which one of the diffusing species for which a steady-state diffusion flux exists does not have to be inserted or deIeted. Constant temperature, pressure and chemical potential of all diffusing species except one are imposed in the control volumes. The constant-pressure method can be applied to situations in which insertion and deletion of large molecules would be prohibitively difficult. As an exampIe, we used the method to shnulate diffusion in a biruuy mixture of spherical particles with a 2:1 size ratio. Steady-state diffusion fluxes of both diffbsi.ng species were established. The constant-pressure diffision coefficients agreed closely with the results of the standard constant-volume calculations. In addition, we show how the concentration, chemical potential and flux profiles can be used to calculate kwd binary and Maxwell-Stefim diffusion coefficients. In the case of the 2:1 size ratio mixture, we found that the binary dlffision coefficients were asymmetric and composition dependent, whereas the Maxwell-Stefan diffision coefficients changed very little with composition and were symmetric. This last result verified that the Gibbs-Duhem relation was satisfied locally, thus validating the assumption of local equilibrium.
Date: December 23, 1998
Creator: Heffelfinger, G.S. & Thompson, A.P.
Partner: UNT Libraries Government Documents Department

Atomic scale modeling of boron transient diffusion in silicon

Description: We presents results from a predictive atomic level simulation of Boron diffusion in Silicon under a wide variety of implant and annealing conditions. The parameters for this simulation have been extracted from first principle approximation models and molecular dynamics simulations. The results are compared with experiments showing good agreement in all cases. The parameters and reactions used have been implemented into a continuum-level model simulator.
Date: June 17, 1998
Creator: Caturla, M. J.; Diaz de la Rubia, T.; Foad, M.; Giles, M.; Johnson, M. D.; Law, M. et al.
Partner: UNT Libraries Government Documents Department

Shock compression science: Dynamic material properties and computation

Description: Constitutive models used in computational prediction of high-rate deformation related to SBSS are determined by validation experiments that can be interpreted with some degree of uniqueness and without ambiguity. Here we include not only material strength and fracture, but also equation-of-state information, and, in the case of reactive solids, initiation concepts related to material strength and fracture. By equation of state we mean material information derived from equilibrium thermodynamics. For fluids this is normally the p, V, E, T information necessary for high-pressure shock-wave applications. For elastic solids it can also be second- and third-order adiabatic elastic moduli for crystals of arbitrary symmetry. Material strength and fracture are generally related to the defect state of the material, and are thus distinct from equilibrium thermodynamics. Likewise, initiation of solid explosives is related to hot spots arising from defects such as porosity and cracking. Finally, by the term {open_quotes}validation{close_quotes} we mean the repeated comparison of a computational model with a set of interpretable experiments, each exercising a particular aspect of the model under well-controlled loading conditions. To be explicitly clear on the thrust of this section, emphasis is on the experimentation necessary to define and elucidate models. Here the role of computation is in the analysis of experiments. Of course, once the validity of a model is established with some confidence, large-scale computation can be used as a predictive tool.
Date: October 1, 1996
Creator: Johnson, J.N.
Partner: UNT Libraries Government Documents Department

Accelerating the dynamics of infrequent events: Combining hyperdynamics and parallel replica dynamics to treat epitaxial layer growth

Description: During the growth of a surface, morphology-controlling diffusion events occur over time scales that far exceed those accessible to molecular dynamics (MD) simulation. Kinetic Monte Carlo offers a way to reach much longer times, but suffers from the fact that the dynamics are correct only if all possible diffusion events are specified in advance. This is difficult due to the concerted nature of many of the recently discovered surface diffusion mechanisms and the complex configurations that arise during real growth. Here the authors describe two new approaches for this type of problem. The first, hyperdynamics, is an accelerated MD method, in which the trajectory is run on a modified potential energy surface and time is accumulated as a statistical property. Relative to regular MD, hyperdynamics can give computational gains of more than 10{sup 2}. The second method offers a way to parallelize the dynamics efficiently for systems too small for conventional parallel MD algorithms. Both methods exploit the infrequent-event nature of the diffusion process. After an introductory description of these methods, the authors present preliminary results from simulations combining the two approaches to reach near-millisecond time scales on systems relevant to epitaxial metal growth.
Date: Spring 1998
Creator: Voter, A. F. & Germann, T. C.
Partner: UNT Libraries Government Documents Department

Molecular dynamics simulations and thermochemistry of reactive ion etching of silicon by chlorine, chlorine dimer, bromine, and bromine dimer cations

Description: Simulations of Cl plasma etch of Si surfaces with MD techniques agree reasonably well with the available experimental information on yields and surface morphologies. This information has been supplied to a Monte Carlo etch profile resulting in substantial agreement with comparable inputs provided through controlled experiments. To the extent that more recent measurements of etch rates are more reliable than older ones, preliminary MD simulations using bond-order corrections to the atomic interactions between neighboring Si atoms on the surface improves agreement with experiment through an increase in etch rate and improved agreement with XPS measurements of surface stoichiometry. Thermochemical and geometric analysis of small Si-Br molecules is consistent with the current notions of the effects of including brominated species in etchant gases.
Date: May 8, 1998
Creator: Valone, S.M.; Hanson, D.E. & Kress, J.D.
Partner: UNT Libraries Government Documents Department

Electrical conductivity of compressed argon

Description: The authors report calculations of the electrical conductivity of solid argon as a function of compression within the density functional local density approximation formulation for a norm-conserving pseudopotential using both electron-phonon coupling and molecular dynamics techniques.
Date: October 1, 1997
Creator: Bauer, R.; Windl, W.; Collins, L.; Kress, J. & Kwon, I.
Partner: UNT Libraries Government Documents Department

Simple Simulations of DNA Condensation

Description: Molecular dynamics simulations of a simple, bead-spring model of semiflexible polyelectrolytes such as DNA are performed. All charges are explicitly treated. Starting from extended, noncondensed conformations, condensed structures form in the simulations with tetravalent or trivalent counterions. No condensates form or are stable for divalent counterions. The mechanism by which condensates form is described. Briefly, condensation occurs because electrostatic interactions dominate entropy, and the favored Coulombic structure is a charge ordered state. Condensation is a generic phenomena and occurs for a variety of polyelectrolyte parameters. Toroids and rods are the condensate structures. Toroids form preferentially when the molecular stiffness is sufficiently strong.
Date: July 12, 2000
Creator: STEVENS,MARK J.
Partner: UNT Libraries Government Documents Department

Defect Dependent Elasticity: Nanoindentation as a Probe of Stress-State

Description: Nanoindentation studies reveal that the measured elastic properties of materials can be strongly dependent upon their stress-state and defect structure. Using an interfacial force microscope (IFM), the measured elastic response of 100 nm thick Au films was found to be strongly correlated with the films' stress state and thermal history. Indentation elasticity was also found to vary in close proximity to grain boundaries in thin films and near surface steps on single crystal surfaces. Molecular dynamics simulations suggest that these results cannot be explained by elasticity due only to bond stretching. Instead, the measured elastic properties appear to be a combination of bond and defect compliance representing a composite modulus. We propose that stress concentration arising from the structure of grains, voids and grain boundaries is the source of an additional compliance which is sensitive to the stress state and thermal history of a material. The elastic properties of thin metallic films appear to reflect the collective elastic response of the grains, voids and grain boundaries. These results demonstrate that nanoindentation can be useful as a highly localized probe of stress-state and defect structures.
Date: January 18, 2000
Creator: JARAUSCH,K.F.; KIELY,J.D.; HOUSTON,JACK E. & RUSSELL,P.E.
Partner: UNT Libraries Government Documents Department

Molecular dynamics simulation of impurities in nanocrystalline diamond grain boundaries

Description: Nanocrystalline diamond films grown on Si substrates at 800 C from hydrogen-poor plasmas have a number of highly desirable mechanical and electronic properties. Impurities were found by SIMS measurements to be uniformly distributed throughout the thickness of the films at a level of 10{sup 17}--10{sup 18} cm{sup {minus}3}. It is likely that the impurities are located at the grain boundaries, which play a crucial role in controlling important characteristics of the films, such as electrical conductivity and electron emission. Density-functional based tight-binding (DFTB) molecular dynamics simulations were performed for diamond light-energy high-angle (100) twist grain boundaries with impurities such as N, Si and H.
Date: January 12, 2000
Creator: Sternberg, M.; Zapol, P.; Frauenheim, T.; Gruen, D. M. & Curtiss, L. A.
Partner: UNT Libraries Government Documents Department