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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: Large scale molecular dynamics simulations of Lennard-Jones fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface.
Abstract: Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature $T/T_c$, where $T_c$ is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.

12 citations

Journal ArticleDOI
TL;DR: The distributions of heterogeneous cellular responses that the statistical ensemble formulation generates reveal the effect of different cellular conditions, e.g., effects due to wild type versus mutant cells or between different dosages of external stimulants.
Abstract: Gene expression profiles and protein dynamics in single cells have a large cell-to-cell variability due to intracellular noise. Intracellular fluctuations originate from two sources: intrinsic noise due to the probabilistic nature of biochemical reactions and extrinsic noise due to randomized interactions of the cell with other cellular systems or its environment. Presently, there is no systematic parameterization and modeling scheme to simulate cellular response at the single cell level in the presence of extrinsic noise. In this paper, we propose a novel statistical ensemble method to simulate the distribution of heterogeneous cellular responses in single cells. We capture the effects of extrinsic noise by randomizing values of the model parameters. In this context, a statistical ensemble is a large number of system replicates, each with randomly sampled model parameters from biologically feasible intervals. We apply this statistical ensemble approach to the well-studied NF-κB signaling system. We predict several characteristic dynamic features of NF-κB response distributions; one of them is the dosage-dependent distribution of the first translocation time of NF-κB. The distributions of heterogeneous cellular responses that our statistical ensemble formulation generates reveal the effect of different cellular conditions, e.g., effects due to wild type versus mutant cells or between different dosages of external stimulants. Distributions generated in the presence of extrinsic noise yield valuable insight into underlying regulatory mechanisms, which are sometimes otherwise hidden.

12 citations

Proceedings ArticleDOI
15 Apr 2002
TL;DR: Preliminary benchmarks indicate reasonable scalability of the algorithm for performing multipoint linkage analysis of genetic marker data on large family pedigrees, with parallel efficiencies of 75% or more on up to a few dozen processors.
Abstract: We present a parallel algorithm for performing multipoint linkage analysis of genetic marker data on large family pedigrees. The algorithm effectively distributes both the computation and memory requirements of the analysis. We discuss an implementation of the algorithm in the Genehunter linkage analysis package (version 2.1), enabling Genehunter to be run on distributed memory platforms for the first time. Our preliminary benchmarks indicate reasonable scalability of the algorithm for even small fixed-size problems, with parallel efficiencies of 75% or more on up to a few dozen processors.

10 citations

Journal ArticleDOI
TL;DR: Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost of 2-4× that of standard MD.
Abstract: Hyperdynamics (HD) is a method for accelerating the timescale of standard molecular dynamics (MD). It can be used for simulations of systems with an energy potential landscape that is a collection of basins, separated by barriers, where transitions between basins are infrequent. HD enables the system to escape from a basin more quickly while enabling a statistically accurate renormalization of the simulation time, thus effectively boosting the timescale of the simulation. In the work of Kim et al. [J. Chem. Phys. 139, 144110 (2013)], a local version of HD was formulated, which exploits the intrinsic locality characteristic typical of most systems to mitigate the poor scaling properties of standard HD as the system size is increased. Here, we discuss how both HD and local HD can be formulated to run efficiently in parallel. We have implemented these ideas in the LAMMPS MD code, which means HD can be used with any interatomic potential LAMMPS supports. Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost of 2-4× that of standard MD. As examples, we performed two simulations of a million-atom system to model the diffusion and clustering of Pt adatoms on a large patch of the Pt(100) surface for 80 μs and 160 µs.

10 citations

Journal ArticleDOI
TL;DR: The LAMMPS and GULP packages for molecular dynamics and lattice dynamics were developed as part of a community effort as mentioned in this paper, and the authors highlight lessons they have learned about how to create such codes and the pros and cons of being part of such efforts.
Abstract: For this article, we call scientific software a community code if it is freely available, written by a team of developers who welcome user input, and has attracted users beyond the developers. There are obviously many such materials modeling codes. The authors have been part of such efforts for many years in the field of atomistic simulation, specifically for two community codes, the LAMMPS and GULP packages for molecular dynamics and lattice dynamics respectively. Here we highlight lessons we have learned about how to create such codes and the pros and cons of being part of a community effort. Many of our experiences are similar, but we also have some differences of opinion (like modeling vs modelling). Our hope is that readers will find these lessons useful as they design, implement, and distribute their own materials modelling software for others to use.

10 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