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.

Fast parallel algorithms for short-range molecular dynamics

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。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. (C) 1997 John Wiley & Sons, Inc.

LINCS : A linear constraint solver for molecular simulations

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

Classical Dynamics of Nonequilibrium Processes in Fluids

Department of Chemical Engineering, Colorado School of Mines, Golden CO 80401 Departments of Chemical Engineering, Chemistry and Computer Science, University of Tennessee, Knoxville TN 37996 Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge TN George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta GA 30332 Department of Chemical Engineering and Materials Science, Wayne State University, Detroit MI 48202

Characterizing the high pressure behaviour of lubricant basestocks

We review our molecular-based study of infinitely dilute supercritical aqueous electrolyte (isolated Na+ and Cl- as well as the ion pair Na+/Cl-) and non-electrolyte (Ar, Xe, methanol, benzene, toluene, benzonitrile) solutions, and report new simulation· results on the potential of mean-force for Na+/Cl- at two thermodynamic states: one at the critical density and at 5% above the critical temperature, the other at 50% above the critical density and along the critical isotherm. The main thrust of this work is the determination of the solute-induced effect on the system's structure and thermodynamics aimed at developing a molecular understanding of the solubility of nonpolar noble gases, ionic fluids and organics in supercritical water. Such an understanding can provide important insight into fundamental thermodynamic and kinetics aspects of supercritical water oxidation of organic wastes.

Molecular simulation of supercritical aqueous solutions

Modification of the structure and morphology of MXene electrodes and the formulation of the electrolytes used in their supercapacitor configurations are significant factors affecting the performance of electrochemical devices. In this study, we investigated the electrochemical performance and ion dynamics of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [EmimTFSI], ionic liquid in the presence of acetonitrile (ACN) at different concentrations in Ti3C2T x MXene supercapacitor. We found an optimum concentration of ACN, at which more cations from the ionic liquid attach to the MXene electrode surface, providing higher electrochemical performance. This higher capacitance is also associated with increased microscopic dynamics of the cation away from the pore wall. These findings give a guideline to optimize the performance of MXene-based supercapacitors using organic solvents-ionic liquid-based electrolyte systems.

Peter T. Cummings

Papers

Classical Dynamics of Nonequilibrium Processes in Fluids

Characterizing the high pressure behaviour of lubricant basestocks

Molecular simulation of supercritical aqueous solutions

Maximizing ion dynamics and electrochemical performance of ionic liquid-acetonitrile electrolyte in Ti3C2T x MXene

Phase behavior of a simple model of ferrocolloidal fluid