Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session V27: Computational Methods:Monte Carlo/Molecular Dynamics II |
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Sponsoring Units: DCOMP Chair: Lee Collins, Los Alamos National Laboratory Room: Baltimore Convention Center 324 |
Thursday, March 16, 2006 11:15AM - 11:27AM |
V27.00001: Parallel kinetic Monte Carlo simulations of island-coarsening in two dimensions F. Shi , Y. Shim, J. G. Amar The evaporation-driven coarsening of 2D islands is studied using a simple bond-counting model along with a recently developed semi-rigorous parallel algorithm for kinetic Monte Carlo (KMC) simulation. Using our parallel algorithm we have been able to simulate both larger system sizes and longer time scales than could be studied using serial KMC simulations. After deposition of less than a half monolayer on a substrate, the flux is stopped and the subsequent time evolution of the average island size and island size distributions were studied for different initial coverages. As expected, the average island size grows as $t^{1/2}$ at intermediate time and approaches the asymptotic $t^ {2/3}$ behavior at very late time. Scaled island-size distributions in both regimes are obtained and compared with the predictions of mean-field theory. The efficiency of our parallel KMC simulations is also discussed. [Preview Abstract] |
Thursday, March 16, 2006 11:27AM - 11:39AM |
V27.00002: Energy optimization of quantum Monte Carlo wave functions C.J. Umrigar, J. Toulouse In recent years many methods have been proposed for energy optimizing quantum Monte Carlo wave functions. Of these, the three highly efficient methods are: 1) The generalized eigenvalue method of Nightingale and Melik-Alaverdian, which was proposed by them for linear parameters only but extended by us to nonlinear parameters. 2) The effective fluctuation potential (EFP) method of Fahy, Filippi and coworkers, and the recent perturbative EFP of Schautz, Scemama and Filippi. We show that the latter can be more simply derived as first-order perturbation theory in a nonorthogonal basis. 3) The modified Newton method of Umrigar and Filippi and of Sorella. We show that the three methods are related to each other and point out that a control parameter can be employed in each of them to make them totally stable. We use these methods to optimize all the parameters in the Jastrow and the determinantal parts of the wave function and point out that different issues arise in optimizing the Jastrow and the determinantal parameters. By systematically increasing the number of determinants we find that seemingly similar systems, such as $C_2$ and $Si_2$ have vastly different fixed-node errors for single-determinant wave functions. [Preview Abstract] |
Thursday, March 16, 2006 11:39AM - 11:51AM |
V27.00003: Monte Carlo Modeling of Luminescent Solar Concentrators Alex Mooney, Paul Fontecchio, Bruce Wittmershaus Luminescent Solar Concentrators (LSCs) offer an inexpensive alternative for solar power generation. A LSC is a flat, translucent plate that absorbs sunlight through embedded, highly fluorescent molecules. The emitted light is concentrated via total internal reflection at the edges of the LSC, where photovoltaic cells covert it into electricity. We've developed a Monte Carlo model that predicts the properties of LSCs by tracing individual light rays. The user controls the plate's geometry and spectral properties, along with the spectral profile of the excitation source. The user can include a specular or diffuse reflective background under the LSC. We've demonstrated the ability to predict the output of a LSC as a function of its optical density. Reabsorption distorts the profile of fluorescence as light propagates through a LSC, and the program can accurately reproduce the effect. The goal is to use the model as a predictive tool for improving the design of LSCs. [Preview Abstract] |
Thursday, March 16, 2006 11:51AM - 12:03PM |
V27.00004: Efficiency of rejection free Monte Carlo methods Hiroshi Watanabe, Yukawa Satoshi, Mark A. Novotny, Nobuyasu Ito We construct asymptotic arguments for the waiting time, the number of trials to achieve one update in Monte Carlo (MC) methods. We find that the waiting time is proportional to $\mbox{e}^\beta$ in the Ising, $\sqrt{\beta}$ in the classical XY, and $\beta$ in the classical Heisenberg spin systems with inverse temperature $\beta$, regardless of the dimension. The behavior in hard particle systems is also obtained, and found to be proportional to $(\rho c -\rho)^{-d}$ with the closest packing density $\rho c$, density $\rho$, and dimension $d$ of the systems. The waiting time determines the efficiency of rejection-free Monte Carlo (RFMC) methods, as well as the inefficiency of the standard MC. Our arguments are general, and applicable to any RFMC implementation of any model studied using kinetic Monte Carlo. [Preview Abstract] |
Thursday, March 16, 2006 12:03PM - 12:15PM |
V27.00005: Improved sampling of computationally expensive potentials Mark Dewing We wish to evaluate statistical properties of systems using potentials that are accurate but computationally expensive, such as those obtained from Density Functional Theory or Quantum Monte Carlo. Using a cheap, approximate potential that is sufficiently close to the potential of interest, sample points can be generated that allow efficient evaluation of properties of the accurate potential. [Preview Abstract] |
Thursday, March 16, 2006 12:15PM - 12:27PM |
V27.00006: Optimally efficient coarse-grained Monte Carlo simulation of rare transition events Babak Sadigh, Tomas Oppelstrup, Wei Cai, Maurice de Koning, Malvin Kalos, Vasily Buolatov We use the idea of coarse graining the multidimensional free energy landscape and present a new Monte Carlo scheme that allows for the exact calculation of the rate of rare transition events within the coarse-grained space defined by a few collective coordinates. This approach is based on a variational algorithm for determining an optimal importance function by which the absolute probability of sampling successful transition events is significantly enhanced, while the relative probabilities of any pair of successful events are preserved. [Preview Abstract] |
Thursday, March 16, 2006 12:27PM - 12:39PM |
V27.00007: Optimized parallel tempering simulations of proteins Simon Trebst, Matthias Troyer, Ulrich Hansmann We introduce an adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an optimal set of temperatures/replicas which are found to concentrate at the bottlenecks of the simulations. A measure of convergence for the equilibration of the parallel tempering algorithm is discussed. We test our algorithm by simulating the 36-residue villin headpiece sub-domain HP-36 where we find a lowest-energy configuration with a root-mean-square-deviation of less than $4$ \AA\ to the experimentally determined structure. [Preview Abstract] |
Thursday, March 16, 2006 12:39PM - 12:51PM |
V27.00008: Hybrid DFT/Thomas-Fermi simulations and applications to biological systems Miroslav Hodak, Wenchang Lu, Jerry Bernholc We have developped a hybrid simulation method suitable for performing calculations on biological systems. Within this method, Density Functional Theory (DFT) is used for the chemically active region and some solvent molecules, while the rest of the solvent molecules are treated with a variant of Thomas-Fermi (TF) theory, which uses the generalized gradient approximation (GGA) kinetic energy functional. These TF solvent molecules are assumed to be rigid and have frozen electron densities, which allows for their efficient treatment. Both Kleinman-Bylander and ultrasoft types of pseudopotentials are implemented within our method. We find it efficient to first equilibriate bio-molecules in solvent environment using classical molecular dynamics. After the initial equilibriation we use the hybrid method to study chemical reactions involving the bio-molecule. Initial applications to transition metal ions-protein complexes in solution will be discussed. [Preview Abstract] |
Thursday, March 16, 2006 12:51PM - 1:03PM |
V27.00009: Environment Dependent Dynamic Charge Interatomic Potential for Silica Lex Kemper, Krishna Muralidharan, Yingxia Wan, Hai-Ping Cheng We present a new interatomic potential to model the various silica polymorphs. Our formulation is loosely based on the embedded atom method (EAM), and accounts for explicit charge variations of atoms as a function of the local chemical environment of atoms. The parameters for the potential are derived from density functional (DFT) calculations. Some preliminary results will be discussed. Work supported by NSF ITR award DMR-0325553. [Preview Abstract] |
Thursday, March 16, 2006 1:03PM - 1:15PM |
V27.00010: Universal Dynamic Exponent at the Liquid-Gas Transition from Molecular Dynamics Subhranil De, An Chen, Eldred Chimowitz, Yonathan Shapir The liquid-gas system is expected to exhibit distinct dynamic behavior in the fluid's critical region (Model H). In this work we present molecular dynamics simulations of a Lennard-Jones fluid model starting from specially designed, near-equilibrium, initial conditions. By following the fluid's relaxation towards equilibrium, we calculate the requisite transport coefficients in the fluid's critical region. The results yield the scaling behavior of the thermal diffusion coefficient $D_T \sim \xi^{-1.023\pm0.018}$ ($\xi$ is the correlation length) and a non-conventional divergent heat conductivity, all of which are in accord with mode-coupling and renormalization group predictions, as well as some experimental data. [Preview Abstract] |
Thursday, March 16, 2006 1:15PM - 1:27PM |
V27.00011: Global and local properties used as analyses tools for molecular-dynamics simulations Martina E. Bachlechner, Jonas T. Anderson, Deng Cao, Robert H. Leonard, Eli T. Owens, Jarrod E. Schiffbauer, Melissa R. Burky, Samuel C. Ducatman, Eric J. Guffey, Fernando Serrano Ramos2 Molecular dynamics simulations have been used to study mechanical failure in realistic interface materials. Averaging over the individual atoms' contributions yields local and global information including displacements, bond angles, strains, stress tensor components, and pair distribution functions. A combined analysis of global and local properties facilitates detailed insight in the mechanisms of failure, which will eventually guide on how to prevent failure of interfaces. [Preview Abstract] |
Thursday, March 16, 2006 1:27PM - 1:39PM |
V27.00012: Molecular Dynamics Simulations of Nanoscratching of 3C-SiC Alice Noreyan, J.G. Amar We have carried out molecular dynamics simulations of nanoindentation followed by nanoscratching on the Si terminated (001) surface of 3C-SiC. In particular, we have investigated the dependence of the friction coefficient, scratch hardness and wear on indentation-scratching depth, scratching velocity, scratching direction, indenter size and indenter shape. In general, the scratch hardness decreases with increasing scratching speed, while it increases with increasing indentation depth. In addition, the scratch hardness and the nanoscale chip formation mechanisms depend on the scratching direction. We also find that scratching leads to amorphization of the material along the scratching trajectory. The size of the amorphization region increases with an increase in scratching velocity, which causes the decrease in scratch hardness and friction coefficient for higher scratching velocities. [Preview Abstract] |
Thursday, March 16, 2006 1:39PM - 1:51PM |
V27.00013: Charge density wave and phonon softening in the Holstein model: A Quantum Monte Carlo study Prabuddha Chakraborty, Alexandru Macridin, Richard Scalettar, Warren Pickett, Rajiv Singh We present a Quantum Monte Carlo study of electron-phonon dynamics in the two dimensional Holstein model on a square lattice. We concentrate here on the softening of the phonon modes as the coupling between the electrons and the phonons is varied. Information about the instability of the electronic system toward the formation of a charge-density wave is also extracted from the phonon correlation functions. We also extract information about the phonon spectral densities using the Maximum Entropy method. Results are presented for various values of the wave-vectors in the two dimensional lattice. An intriguing softening of the phonon frequency at vanishing wave-vector is presented. We also present the effect of anharmonicity on the dynamics of the Holstein model. [Preview Abstract] |
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