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 consider the free energies of the single-period (SP) and double-period (DP) core reconstructions of the straight 90° partial dislocation in silicon. The vibrational contributions are calculated with a harmonic model. It is found that it leads to a diminishing difference between the free energies of the two core reconstructions with increasing temperature. The question of the relative populations of SP and DP reconstructions in a single straight 90° partial dislocation is solved by mapping the problem onto a one-dimensional Ising model in a magnetic field. The model contains only two parameters and is solved analytically. It leads to the conclusion that for the majority of the published energy differences between the SP and DP reconstructions the equilibrium core structure is dominated by the DP reconstruction at all temperatures up to the melting point. We review whether it is possible to distinguish between the SP and DP reconstructions experimentally, both in principle and in practice. We conclude that aberration corrected transmission electron microscopy should be able to distinguish between these two core reconstructions, but published high resolution micrographs do not allow the distinction to be made.

The equilibrium structures of the 90° partial dislocation in silicon

We employ constant temperature molecular dynamics simulations to study, at the atomistic level, the interactions of an Ir tip with a Pb substrate. We have considered the complete cycle of approach.contact, indentation and retraction of the tip from the substrate. We have observed the wetting of the tip by the substrate atoms, and the formation of atomic necking between the tip and the substrate. We have carried out further simulations to study the interactions of an Ir tip with an Ir substrate covered with an adsorbate monolayer of Pb film. We show that the introduction of the adsorbate considerably reduces the work of adhesion and the extent of plastic flow, in agreement with experimental results. Three-dimensional geometries have been generated on computer and used for the animation of the simulation runs.

Influence of Adsorbate Monolayer on the Nano-Mechanics of TIP-Substrate Interactions

Using first principles methods, we calculated the entire -surface of the first-order pyramidal planes in -titanium. Slip on these planes involving dislocations with -type Burgers vectors is one means by which -titanium polycrystals may supplement slip on prism planes with -type Burgers vectors to maintain ductility. We find one low energy and one high energy stacking fault with energies of 163 and 681 , respectively. Contrary to previous suggestions, we do not find a stable stable stacking fault at .

Stacking faults and the -surface on first-order pyramidal planes in -titanium

Mechanical properties of crystalline materials are almost always dominated by the defects within them. The ability to shape metals into pipes, girders and furniture stems from the generation, motion and interaction of these defects. Defects are also the agents of chemical changes within crystals, enabling mass transport by atomic diffusion and changes of phase. Defects distort the crystal and these distortions enable defects to interact over large distances. The theory of elasticity is used to describe these interactions. Assuming no familiarity with the theory, this book introduces the reader to linear elasticity and its application to point defects, dislocations and cracks. A unique feature of the book is the attention given to the atomic structure of defects and its influence on their properties and their elastic fields. Where it is available brief biographical information is provided about prominent contributors to the field. This textbook is written for postgraduate students in physics, engineering and materials science. It is very likely that even those students with some knowledge of elasticity and defects will find much that is new to them in this book.There are exercises to help the student check their understanding as they work through each chapter. The student is guided through more advanced problems at the end of each chapter. Worked solutions to all exercises and problems are available to course instructors from the OUP website. The last chapter describes four technologically important areas requiring fundamental research, with suggestions for possible PhD projects.

Physics of Elasticity and Crystal Defects

We present in detail a thermodynamic equilibrium model for the growth of nanostructures on semiconductor substrates in heteroepitaxy and its application to germanium deposition on silicon. Some results of this model have been published previously, but the details of the formulation of the model are given here for the first time. The model allows the computation of the shape and size distributions of the surface nanostructures, as well as other properties of the system. We discuss the results of the model, and their incorporation into a nanostructure diagram that summarizes the relative stability of domes and pyramids in the bimodal size distributions.

/pdf/equilibrium-distributions-and-the-nanostructure-diagram-for-46nrxlyn7d.pdf

Adrian P. Sutton

Papers

The equilibrium structures of the 90° partial dislocation in silicon

Influence of Adsorbate Monolayer on the Nano-Mechanics of TIP-Substrate Interactions

Stacking faults and the -surface on first-order pyramidal planes in -titanium

Physics of Elasticity and Crystal Defects

Equilibrium Distributions and the Nanostructure Diagram for Epitaxial Quantum Dots