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

We demonstrate how by taking better account of electron correlations in the $3d$ shell of metal ions in nickel oxide it is possible to improve the description of both electron energy loss spectra and parameters characterizing the structural stability of the material compared with local spin density functional theory.

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Electron-energy-loss spectra and the structural stability of nickel oxide: An LSDA+U study

The geometry of interfaces Dislocation for interfaces Models of interatomic forces at interfaces Models and experimental observations of structure Thermodynamics of interfaces Interface phases and phase transitions Segregation of solute atoms to interfaces Diffusion at interfaces Conservative motion of interfaces Non-conservative motion of interfaces: interfaces as sources/sinks for diffusional fluxes of atoms Electronic properties of interfaces Mechanical properties of interfaces.

Interfaces in Crystalline Materials

Finnis–Sinclair potentials are developed for computer simulations in which van der Waals type interactions between well separated atomic clusters are as important as the description of metallic bonding at short range. The potentials always favour f.c.c. and h.c.p. structures over the b.c.c. structure. They display convenient scaling properties for both length and energy, and a number of properties of the perfect crystal may be derived analytically.

Long-range Finnis–Sinclair potentials

The results of the study of symmetrical tilt boundaries, reported in the preceding part I, are generalized to asymmetrical tilt boundaries. A classification of tilt boundaries in cubic crystals is developed that reveals which boundaries to choose in order to study equilibrium faceting or intrinsic grain boundary dislocations (g.b.ds) accommodating a misorientation. Two series of atomistic studies of asymmetrical tilt boundary structures are presented based on this classification. The first is a study of long-period (27 ^ 97) [110] asymmetrical tilt boundaries in aluminium. The aims of this study are to investigate whether these boundaries are composed of fundamental structural elements, in the same way as was found in part I for symmetrical tilt boundaries, and to see if localized, distinct stress fields of edge g.b.ds exist throughout the misorientation range. With use of the results of this study, and the principle of continuity of boundary structure enunciated in part I, the boundary unit representation of a 27 — 1193 asymmetrical tilt boundary is derived as an example. It is generally found that the Burgers vectors of intrinsic secondary g.b.ds in tilt boundaries, based on favoured boundary reference structures, are non-primitive d.s.c. vectors. The reason for this is given and a simple formula is presented to derive the Burgers vectors of such dislocations for any favoured tilt boundary reference structure. It is pointed out that, in general, very low angle {0

On the Structure of Tilt Grain Boundaries in Cubic Metals I. Symmetrical Tilt Boundaries

The semi-empirical Tight Binding model1,2 is the simplest scheme for describing the energetics of semi-conductors and transition metals within a quantum mechanical framework.

https://iopscience.iop.org/article/10.1088/0022-3719/21/1/007/pdf

Adrian P. Sutton

Papers

Electron-energy-loss spectra and the structural stability of nickel oxide: An LSDA+U study

Interfaces in Crystalline Materials

Long-range Finnis–Sinclair potentials

On the Structure of Tilt Grain Boundaries in Cubic Metals I. Symmetrical Tilt Boundaries

The tight-binding bond model