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

Bulk nanostructured materials from severe plastic deformation

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Table Of Integrals Series And Products

Mechanical properties of nanocrystalline materials

The understanding of interfaces between unlike solids is recognized as important both from the traditional static perspective (‘What is the work of adhesion?’) and dynamically (e.g. ‘Can one predict friction and wear?’). These questions have also broadened to cover interfacial control, for instance effects on carrier transport and epitaxial relations. We address these issues by atomic-scale modelling, using mainly molecular dynamics combined with self-consistent chemistry. First we shall contrast the systems where chemical bonding is a key component (such as polyimide-metal) with those where the chemistry primarily determines which interface controls adhesion (such as oxide-metal). Second, we shall comment on the other roles of electrons: charge transfer, polarization, and dispersion forces. Third, we shall discuss the interactions which determine friction and wear in atomic force microscopy and indicate how these can be related to macroscopic tribological behaviour.

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How do they stick together? The statics and dynamics of interfaces

The applicability of the structural unit model, developed for tilt boundaries by Sutton and Vitek (1983), to (001) twist boundaries in f.c.c. metals is investigated. The model is found to be useful in discussing the continuity of boundary structure with misorientation and the Burgers vectors of screw grain boundary dislocations. A surprising result is that the structures of low-angle boundaries (with misorientation, less than 22–62°) vary discontinuously with misorientation, in the sense that different boundary units appear in boundaries with slightly (in the limit infinitesimally) different misorientations, in accordance with a simple geometrical rule. At higher misorientations the boundary structure varies smoothly with misorientation and two non-equivalent decompositions into structural units can always be found. One of these decompositions is invariant with respect to the symmetry elements of the overall boundary structure, while the other is not. The continuity of boundary structure and grai...

Atomic structure of (001) twist boundaries in f.c.c metals Structural unit model

Atomically resolved elevated-temperature scanning tunneling microscope (STM) images of (001) cobalt and nickel monoxide surfaces obtained under similar conditions show an order of magnitude difference in the atomic corrugation heights. Surface-electronic structure calculations taking into account the Hubbard U term show that on the CoO (001) surface the lowest unoccupied state has ${d}_{\mathrm{xy}}$ character as compared with the predominantly ${d}_{{3z}^{2}\ensuremath{-}{r}^{2}}$ lowest empty state on NiO (001). The difference in the symmetry of unoccupied d orbitals on CoO (001) and NiO (001) surfaces is responsible for the much lower level of atomic contrast observed in the STM images of cobalt oxide.

Unexpected differences in the surface electronic structure of NiO and CoO observed by STM and explained by first-principles theory

In this article, it is demonstrated that current methods of modelling plasticity as the collective motion of discrete dislocations, such as two-dimensional discrete dislocation plasticity (DDP), ar

https://royalsocietypublishing.org/doi/pdf/10.1098/rspa.2013.0141

Adrian P. Sutton

Papers

How do they stick together? The statics and dynamics of interfaces

Atomic structure of (001) twist boundaries in f.c.c metals Structural unit model

Unexpected differences in the surface electronic structure of NiO and CoO observed by STM and explained by first-principles theory

A dynamic discrete dislocation plasticity method for the simulation of plastic relaxation under shock loading

Irrational tilt grain boundaries as one-dimensional quasicrystals