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Steven J. Plimpton

Bio: Steven J. Plimpton is an academic researcher from Sandia National Laboratories. The author has contributed to research in topics: Parallel algorithm & Direct simulation Monte Carlo. The author has an hindex of 44, co-authored 128 publications receiving 62532 citations.


Papers
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Journal ArticleDOI
TL;DR: In this article, the self part of the van Hove correlation function was used to identify mobile particles in supercooled Lennard-Jones liquid, and these particles formed clusters whose sizes grow with decreasing temperature.
Abstract: We present the results of a molecular dynamics computer simulation study in which we investigate whether a supercooled Lennard-Jones liquid exhibits dynamical heterogeneities. We evaluate the non-Gaussian parameter for the self part of the van Hove correlation function and use it to identify {open_quotes}mobile{close_quotes} particles. We find that these particles form clusters whose sizes grow with decreasing temperature. We also find that the relaxation time of the mobile particles is significantly shorter than that of the average particle, and that this difference increases with decreasing temperature. {copyright} {ital 1997} {ital The American Physical Society}

829 citations

Journal ArticleDOI
TL;DR: In this paper, extensive molecular dynamics simulations are performed on a glass-forming Lennard-Jones mixture to determine the nature of the cooperative motions occurring in this model fragile liquid, and they observe stringlike cooperative molecular motion (''strings'') at temperatures well above the glass transition.
Abstract: Extensive molecular dynamics simulations are performed on a glass-forming Lennard-Jones mixture to determine the nature of the cooperative motions occurring in this model fragile liquid. We observe stringlike cooperative molecular motion (``strings'') at temperatures well above the glass transition. The mean length of the strings increases upon cooling, and the string length distribution is found to be nearly exponential.

807 citations

Journal ArticleDOI
TL;DR: Three distinct forms are derived for the force virial contribution to the pressure and stress tensor of a collection of atoms interacting under periodic boundary conditions, and are valid for arbitrary many-body interatomic potentials.
Abstract: Three distinct forms are derived for the force virial contribution to the pressure and stress tensor of a collection of atoms interacting under periodic boundary conditions. All three forms are written in terms of forces acting on atoms, and so are valid for arbitrary many-body interatomic potentials. All three forms are mathematically equivalent. In the special case of atoms interacting with pair potentials, they reduce to previously published forms. (i) The atom-cell form is similar to the standard expression for the virial for a finite nonperiodic system, but with an explicit correction for interactions with periodic images. (ii) The atom form is particularly suited to implementation in modern molecular dynamics simulation codes using spatial decomposition parallel algorithms. (iii) The group form of the virial allows the contributions to the virial to be assigned to individual atoms.

737 citations

Journal ArticleDOI
TL;DR: Algorithm for efficient short range force calculation on hybrid high-performance machines, an approach for dynamic load balancing of work between CPU and accelerator cores, and the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators are described.

557 citations

Journal ArticleDOI
TL;DR: In this article, a semi-implicit time-advance approach was used to simulate the growth rate of resistive tearing modes in 3D nonlinear non-ideal magnetohydrodynamics.

517 citations


Cited by
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Journal ArticleDOI
TL;DR: In this article, three parallel algorithms for classical molecular dynamics are presented, which can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors.

32,670 citations

01 May 1993
TL;DR: 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.
Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed 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 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. 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 a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

29,323 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.

12,985 citations