2,665 research outputs found

    Plasma simulation using the massively parallel processor

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    Two dimensional electrostatic simulation codes using the particle-in-cell model are developed on the Massively Parallel Processor (MPP). The conventional plasma simulation procedure that computes electric fields at particle positions by means of a gridded system is found inefficient on the MPP. The MPP simulation code is thus based on the gridless system in which particles are assigned to processing elements and electric fields are computed directly via Discrete Fourier Transform. Currently, the gridless model on the MPP in two dimensions is about nine times slower that the gridded system on the CRAY X-MP without considering I/O time. However, the gridless system on the MPP can be improved by incorporating a faster I/O between the staging memory and Array Unit and a more efficient procedure for taking floating point sums over processing elements. The initial results suggest that the parallel processors have the potential for performing large scale plasma simulations

    Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

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    The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J. Chem. Phys. 123{\bf 123}, 084108 (2005)]. As an application, we perform the binding affinity calculations of six theophylline-related ligands with RNA aptamer. Basically, our method is applicable when using many compute nodes to accelerate simulations, thus a parallel computing system is also developed. To further reduce the computational cost, the adequate non-uniform intervals of coupling constant λ\lambda, connecting two equilibrium states, namely bound and unbound, are determined. The absolute binding energies ΔG\Delta G thus obtained have effective linear relation between the computed and experimental values. If the results of two other different methods are compared, thermodynamic integration (TI) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) by the paper of Gouda etalet al [H. Gouda, I. D. Kuntz, D. A. Case, and P. A. Kollman, Biopolymers 68{\bf 68}, 16 (2003)], the predictive accuracy of the relative values ΔΔG\Delta\Delta G is almost comparable to that of TI: the correlation coefficients (R) obtained are 0.99 (this work), 0.97 (TI), and 0.78 (MM-PBSA). On absolute binding energies meanwhile, a constant energy shift of \sim -7 kcal/mol against the experimental values is evident. To solve this problem, several presumable reasons are investigated.Comment: 23 pages including 6 figure

    An Application Perspective on High-Performance Computing and Communications

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    We review possible and probable industrial applications of HPCC focusing on the software and hardware issues. Thirty-three separate categories are illustrated by detailed descriptions of five areas -- computational chemistry; Monte Carlo methods from physics to economics; manufacturing; and computational fluid dynamics; command and control; or crisis management; and multimedia services to client computers and settop boxes. The hardware varies from tightly-coupled parallel supercomputers to heterogeneous distributed systems. The software models span HPF and data parallelism, to distributed information systems and object/data flow parallelism on the Web. We find that in each case, it is reasonably clear that HPCC works in principle, and postulate that this knowledge can be used in a new generation of software infrastructure based on the WebWindows approach, and discussed in an accompanying paper

    Investigating Interactions of Biomembranes and Alcohols: A Multiscale Approach

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    We study the interaction of lipid bilayers with short chain alcohols using molecular dynamics on different length scales. We use detailed atomistic modeling and modeling on the length scale where an alcohol is just an amphiphilic dimer. Our strategy is to calibrate a coarse--grained model against the detailed model at selected state points at low alcohol concentration and then perform a wider range of simulations using the coarse--grained model. We get semiquantitative agreement with experiment for the major observables such as order parameter and area per molecule. We find a linear increase of area per molecule with alcohol concentration. The alcohol molecules in both system descriptions are in close contact with the glycerol backbone. Butanol molecules can enter the bilayer to some extent in contrast to the behavior of shorter alcohols. At very high alcohol concentrations we find clearly increased interdigitation between leaflets.Comment: 14 pages, 6 figure
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