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

http://www.zhugroup.gatech.edu/paper/PMS10.pdf

Ultra-strength materials

Review on superior strength and enhanced ductility of metallic nanomaterials

Combining the benefits of nanocrystals with those of amorphous metallic glasses leads to a dual-phase material—comprising sub-10-nanometre-sized nanocrystalline grains embedded in amorphous glassy shells—that exhibits a strength approaching the ideal theoretical limit. Nanostructuring of crystalline metal alloys can yield high-strength materials, but these tend to soften as the strain is increased. Ge Wu et al. describe a strategy that combines the benefits of nanocrystallinity with those of single-phase amorphous metallic glasses to yield a dual-phase material—nanocrystalline grains each enclosed in an amorphous glassy shell—that exhibits strength approaching the ideal theoretical limit. They demonstrate this approach with a magnesium alloy and prepare the strongest thin films yet achieved for any magnesium alloy. The authors suggest that this material could be a promising coating for wear-resistant surfaces. It is not easy to fabricate materials that exhibit their theoretical ‘ideal’ strength. Most methods of producing stronger materials are based on controlling defects to impede the motion of dislocations, but such methods have their limitations. For example, industrial single-phase nanocrystalline alloys1,2 and single-phase metallic glasses3 can be very strong, but they typically soften at relatively low strains (less than two per cent) because of, respectively, the reverse Hall–Petch effect4 and shear-band formation. Here we describe an approach that combines the strengthening benefits of nanocrystallinity with those of amorphization to produce a dual-phase material that exhibits near-ideal strength at room temperature and without sample size effects. Our magnesium-alloy system consists of nanocrystalline cores embedded in amorphous glassy shells, and the strength of the resulting dual-phase material is a near-ideal 3.3 gigapascals—making this the strongest magnesium-alloy thin film yet achieved. We propose a mechanism, supported by constitutive modelling, in which the crystalline phase (consisting of almost-dislocation-free grains of around six nanometres in diameter) blocks the propagation of localized shear bands when under strain; moreover, within any shear bands that do appear, embedded crystalline grains divide and rotate, contributing to hardening and countering the softening effect of the shear band.

Dual-phase nanostructuring as a route to high-strength magnesium alloys

Shear-coupled grain boundary (GB) migration is of general significance in the deformation of nanocrystalline and polycrystalline materials, but comprehensive understanding of the migration mechanism at the atomic scale remains largely lacking. Here, we systematically investigate the atomistic migration of Σ11(113) coherent GBs in gold bicrystals using a state-of-art in situ shear testing technique combined with molecular dynamic simulations. We show that shear-coupled GB migration can be realised by the lateral motion of layer-by-layer nucleated GB disconnections, where both single-layer and double-layer disconnections have important contributions to the GB migration through their frequent composition and decomposition. We further demonstrate that the disconnection-mediated GB migration is fully reversible in shear loading cycles. Such disconnection-mediated GB migration should represent a general deformation phenomenon in GBs with different structures in polycrystalline and nanocrystalline materials, where the triple junctions can act as effective nucleation sites of GB disconnections. Shear-induced grain boundary migration at the atomic level is still not well understood. Here the authors combine in situ shear testing experiments and molecular dynamic simulations to reveal the atomistic mechanism of disconnection-mediated GB migration in different gold nanostructures.

/pdf/in-situ-atomistic-observation-of-disconnection-mediated-4thake9298.pdf

In situ atomistic observation of disconnection-mediated grain boundary migration.

Fundamental differences in the plasticity of periodically twinned nanowires in Au, Ag, Al, Cu, Pb and Ni

The ideal strength of crystalline solids refers to the stress at elastic instability of a hypothetical defect-freecrystalwithinfinitedimensionssubjectedtoanincreasingload.Experimentallyobservedmetallicwires of a few tens of nanometers in diameter usually yield far before the ideal strength, because different types of surface or structural defects, such as surface inhomogeneities or grain boundaries, act to decrease the stress required for dislocation nucleation and irreversible deformation. In this study, however, we report on atomistic simulations of near-ideal strength in pure Au nanowires with complex faceted structures related to realistic nanowires. The microstructure dependence of tensile strength in face-centered cubic Au nanowires with either cylindrical or faceted surface morphologies was studied by classical molecular dynamics simulations. We demonstrate that maximum strength and steep size effects from the twin boundary spacing are best achieved in zigzagAunanowiresmadeofaparallelarrangementofcoherenttwinboundariesalongtheaxis,and{111 ¯ }surface facets. Surface faceting in Au NWs gives rise to a novel yielding mechanism associated with the nucleation and propagation of full dislocations along {001}110slip systems, instead of the common {111 ¯ }112partial slip observed in face-centered cubic metals. Furthermore, a shift from surface dislocation nucleation to homogeneous dislocationnucleationarisesasthetwinboundaryspacingisdecreasedbelowacriticallimitinfacetednanowires. It is thus discovered that special defects can be utilized to approach the ideal strength of gold in nanowires by microstructural design.

/pdf/near-ideal-strength-in-gold-nanowires-achieved-through-1afgh71wuy.pdf

Near-Ideal Strength in Gold Nanowires Achieved through Microstructural Design

By using molecular dynamics simulations, we show that significant strain hardening and ultrahigh flow stresses are enabled in gold nanowires containing coherent (111) growth twins when balancing nanowire diameter and twin boundary spacing at the nanoscale. A fundamental transition in mechanical behavior occurs when the ratio of diameter to twin boundary spacing is larger than 2.14. A model based on site-specific dislocation nucleation and cross-slip mechanisms is proposed to explain the size dependence of flow behavior in twinned nanowires under tensile loading.

/pdf/enabling-ultrahigh-plastic-flow-and-work-hardening-in-2tm7iai0tc.pdf

Enabling ultrahigh plastic flow and work hardening in twinned gold nanowires.

Large-scale molecular dynamics simulations were performed to demonstrate the synergistic effects of twin boundaries and free surfaces on dislocation emission in gold nanowires under tensile loading It is revealed that the addition of nanoscale twins to crystalline nanowires can act to either increase or decrease their resistance to slip in tension, depending on both sample diameter and number of twins per unit length Site-specific surface dislocation emission and image forces due to twin boundaries are used to explain the size-dependence of yield stress in twinned gold nanowires

Chuang Deng

Papers

In situ atomistic observation of disconnection-mediated grain boundary migration.

Fundamental differences in the plasticity of periodically twinned nanowires in Au, Ag, Al, Cu, Pb and Ni

Near-Ideal Strength in Gold Nanowires Achieved through Microstructural Design

Enabling ultrahigh plastic flow and work hardening in twinned gold nanowires.

Size-dependent yield stress in twinned gold nanowires mediated by site-specific surface dislocation emission