https://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf

Fast parallel algorithms for short-range molecular dynamics

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.

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

/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

http://kth.diva-portal.org/smash/get/diva2:1303357/FULLTEXT01

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

We model indentation of a metal surface by combining an atomistic metal with a hard-sphere indenter. This work provides atomistic imaging of dislocation nucleation during displacement controlled indentation on a passivated surface. Dislocations and defects are located and imaged by local deviations from centrosymmetry. For a Au(111) surface, nucleation of partial dislocation loops occurs below the surface inside the indenter contact area. We compare and contrast these observations with empirical criteria for dislocation nucleation and corresponding continuum elasticity solutions.

Dislocation nucleation and defect structure during surface indentation

We have performed a systematic, large-scale simulation study of granular media in two and three dimensions, investigating the rheology of cohesionless granular particles in inclined plane geometries, i.e., chute flows. We find that over a wide range of parameter space of interaction coefficients and inclination angles, a steady-state flow regime exists in which the energy input from gravity balances that dissipated from friction and inelastic collisions. In this regime, the bulk packing fraction (away from the top free surface and the bottom plate boundary) remains constant as a function of depth z, of the pile. The velocity profile in the direction of flow vx(z) scales with height of the pile H, according to vx(z) proportional to H(alpha), with alpha=1.52+/-0.05. However, the behavior of the normal stresses indicates that existing simple theories of granular flow do not capture all of the features evidenced in the simulations.

/pdf/granular-flow-down-an-inclined-plane-bagnold-scaling-and-4056jr0hsg.pdf

Steven J. Plimpton

Papers

Fast parallel algorithms for short-range molecular dynamics

Fast parallel algorithms for short-range molecular dynamics

LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Dislocation nucleation and defect structure during surface indentation

Granular flow down an inclined plane: Bagnold scaling and rheology