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

We report the measurement of the thermal conductivity of a suspended single-layer graphene. The room temperature values of the thermal conductivity in the range ∼(4.84 ± 0.44) × 103 to (5.30 ± 0.48) × 103 W/mK were extracted for a single-layer graphene from the dependence of the Raman G peak frequency on the excitation laser power and independently measured G peak temperature coefficient. The extremely high value of the thermal conductivity suggests that graphene can outperform carbon nanotubes in heat conduction. The superb thermal conduction property of graphene is beneficial for the proposed electronic applications and establishes graphene as an excellent material for thermal management.

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Superior Thermal Conductivity of Single-Layer Graphene

There is intense interest in graphene in fields such as physics, chemistry, and materials science, among others. Interest in graphene's exceptional physical properties, chemical tunability, and potential for applications has generated thousands of publications and an accelerating pace of research, making review of such research timely. Here is an overview of the synthesis, properties, and applications of graphene and related materials (primarily, graphite oxide and its colloidal suspensions and materials made from them), from a materials science perspective.

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Graphene and Graphene Oxide: Synthesis, Properties, and Applications

Recent years have seen a rapid growth of interest by the scientific and engineering communities in the thermal properties of materials. Heat removal has become a crucial issue for continuing progress in the electronic industry, and thermal conduction in low-dimensional structures has revealed truly intriguing features. Carbon allotropes and their derivatives occupy a unique place in terms of their ability to conduct heat. The room-temperature thermal conductivity of carbon materials span an extraordinary large range--of over five orders of magnitude--from the lowest in amorphous carbons to the highest in graphene and carbon nanotubes. Here, I review the thermal properties of carbon materials focusing on recent results for graphene, carbon nanotubes and nanostructured carbon materials with different degrees of disorder. Special attention is given to the unusual size dependence of heat conduction in two-dimensional crystals and, specifically, in graphene. I also describe the prospects of applications of graphene and carbon materials for thermal management of electronics.

Thermal properties of graphene and nanostructured carbon materials

In this paper, the effect of crystal cut error on ion-implanted impurity profiles in silicon is examined. Accurate measurements of crystal cut errors have been performed using the X-ray diffraction method, and a method of calculating the effect of crystal cut error on the implant tilt/rotation angle is provided. The subsequent effect of crystal cut error on ion-implanted profiles is simulated, and the results are compared with SIMS experimental data. The comparison shows the validity of the crystal cut error calculation outlined in this paper, and the importance of taking crystal cut error into account in the comparison of measured and simulated impurity profiles, and in evaluating, calibrating, and comparing ion implant tools.

The impact of crystal cut error on the measured impurity profiles resulting from ion implantation

The structure theorem of three-way concept lattice

Biomechanics of cell reorientation in a three-dimensional matrix under compression.

Hyperautomation for Air Quality Evaluations: A Perspective of Evidential Three-way Decision-making

Decision implication is an important form of knowledge representation and acquisition in Formal Concept Analysis. Decision implication reduces the redundancy of knowledge extracted from data. However, decision implication cannot extract negative information from data, so there is information loss in decision implication. This paper introduces negative attributes to decision implication and proposes mixed decision implication, enabling decision implication to extract negative knowledge from data and to represent richer decision knowledge. This paper studies the logical systems of mixed decision implications. The semantical system of mixed decision implications is constructed to represent and deduce sound mixed decision implications and avoid contradictory mixed decision implications. In the syntactical system, Mixed Augmentation and Mixed Combination are introduced and the soundness, completeness and non-redundancy of these two inference rules are proved. 

Deyu Li

Papers

The impact of crystal cut error on the measured impurity profiles resulting from ion implantation

The structure theorem of three-way concept lattice

Biomechanics of cell reorientation in a three-dimensional matrix under compression.

Hyperautomation for Air Quality Evaluations: A Perspective of Evidential Three-way Decision-making

Research on Mixed Decision Implications Based on Formal Concept Analysis