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 β-scission growth mechanism at the diamond (100) (2×1) surface is studied by a combination of nanoscale ab-initio LDA/GGA and semiempirical tight-binding techniques to provide the necessary input into the mesoscale variable time step Kinetic Monte-Carlo (KMC) simulations of CVD diamond growth. The reaction path of the beta-scission reaction is critically examined and the activation barrier of the reverse etching of the methylene adsorbate is deduced. Our quantum mechanical calculations support a previous semiempirical PM3 study confirming that the molecular mechanics values for the entalphy of the reaction are a factor of 2 wrong. This conclusion provides strong support for the preferential etching mechanism introduced into KMC to predict experimentally measured growth rates.

Surface Chemistry of CVD Diamond: Linking the Nanoscale and Mesoscale Modelling Hierarchies

Methods of calculating the electronic and atomic structures of interfaces are described. An introduction to pseudopotentials and LCAO methods is given. Methods of calculating the electronic structure of an interface with a given atomic structure are considered. The feasibility of total energy calculations, in which the atomic and electronic structures are calculated simultaneously, is discussed.

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Methods of calculating the electronic and atomic structures of interfaces

Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Vacancy diffusion is modeled by comparing the energies of trial states, where the system is partially relaxed for each trial state. Only a limited precision is required for the energy of each trial state, determined by the value of k{sub B}T. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r{sup 3}, it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centered on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice. However on a flexible lattice vacancy trapping by Mg atoms in the ternary Al-Cu-Mg system makes clustering slower than the corresponding rigid lattice calculation.

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Including Long-range Interactions in Atomistic Modelling of Diffusional Phase Changes

Recently Mendelev, Underwood, and Ackland1 (MUA) published three interatomic potentials (IPs) Ti1, Ti2, and Ti3 for pure Ti. These IPs were developed to model atomistically defects, plasticity, and phase changes in Ti. In this comment we compare quantitatively the γsurfaces predicted by these IPs on the basal and {11̄01} first order pyramidal or pyramidal I planes of hexagonal close-packed Ti with those we computed recently by density functional theory (DFT)2. We also compare with the γ-surfaces computed with the IP developed by Ackland3, which we call Ti0. Local minima in the γ-surface4 correspond to stable stacking faults, which indicate the possibility, depending on the energy of the local minimum, of dissociation of lattice dislocations into partial dislocations separated by the stacking fault. In addition, the slope of the γ-surface determines the force per unit area tending to constrict the core of dislocations in the slip plane5. The accuracy of a γ-surface is therefore of some importance for modelling plasticity on that slip plane.

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Comment on "Development of an interatomic potential for the simulation of defects, plasticity, and phase transformations in titanium" [J. Chem. Phys. 145, 154102 (2016)].

A range of molecular dynamics simulations (reviewed in [1]) has been carried out to study adhesion, sintering, friction and fracture between a metallic nanoscale tip and a flat metallic substrate. Long-range N-body interatomic potentials [2–3] of the Finnis-Sinclair type have been used, in addition to pair potential descriptions.

Adrian P. Sutton

Papers

Surface Chemistry of CVD Diamond: Linking the Nanoscale and Mesoscale Modelling Hierarchies

Methods of calculating the electronic and atomic structures of interfaces

Including Long-range Interactions in Atomistic Modelling of Diffusional Phase Changes

Comment on "Development of an interatomic potential for the simulation of defects, plasticity, and phase transformations in titanium" [J. Chem. Phys. 145, 154102 (2016)].

Mechanical and Electrical Properties of Metallic Contacts