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

J. Appl. Cryst.の発刊に際して

Graphene-Like Two-Dimensional Materials

Since the discovery of mechanically exfoliated graphene in 2004, research on ultrathin two-dimensional (2D) nanomaterials has grown exponentially in the fields of condensed matter physics, material science, chemistry, and nanotechnology. Highlighting their compelling physical, chemical, electronic, and optical properties, as well as their various potential applications, in this Review, we summarize the state-of-art progress on the ultrathin 2D nanomaterials with a particular emphasis on their recent advances. First, we introduce the unique advances on ultrathin 2D nanomaterials, followed by the description of their composition and crystal structures. The assortments of their synthetic methods are then summarized, including insights on their advantages and limitations, alongside some recommendations on suitable characterization techniques. We also discuss in detail the utilization of these ultrathin 2D nanomaterials for wide ranges of potential applications among the electronics/optoelectronics, electrocat...

Recent Advances in Ultrathin Two-Dimensional Nanomaterials

A newly identified severe acute respiratory syndrome coronavirus (SARS-CoV), is the etiological agent responsible for the outbreak of SARS. The SARS-CoV main protease, which is a 33.8-kDa protease (also called the 3C-like protease), plays a pivotal role in mediating viral replication and transcription functions through extensive proteolytic processing of two replicase polyproteins, pp1a (486 kDa) and pp1ab (790 kDa). Here, we report the crystal structures of the SARS-CoV main protease at different pH values and in complex with a specific inhibitor. The protease structure has a fold that can be described as an augmented serine-protease, but with a Cys-His at the active site. This series of crystal structures, which is the first, to our knowledge, of any protein from the SARS virus, reveal substantial pH-dependent conformational changes, and an unexpected mode of inhibitor binding, providing a structural basis for rational drug design.

https://www.pnas.org/content/pnas/100/23/13190.full.pdf

The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor

Nanoporous Gold Leaf: “Ancient Technology”/Advanced Material

Supported Au nanoclusters are well-known for their unusual properties in catalysis. We describe here that nanostructured porous Au made via dealloying represents a new class of unsupported catalysts with extraordinary activities in important reactions such as CO oxidation. Although nanoporous Au may contain some oxides on the surface, our results demonstrate that it is metallic Au that plays the main role in this catalytic reaction. Furthermore, this material has good low-temperature catalytic stability and is extremely CO tolerant.

Low Temperature CO Oxidation over Unsupported Nanoporous Gold

Mg(OH)2 nanocrystallines with rod-, tube-, needle-, or lamella-like morphologies have been synthesized by a hydrothermal reaction using different magnesium precursors and solvents as the reactants. The products appeared to have narrow size distributions with a monodisperse nature. Subsequent thermal decomposition at 450 °C gave nanosized MgO, which preserved well the morphological features of the Mg(OH)2 samples. The specific surface areas of the MgO samples were determined by the BET technique, which gave a feature of high surface area generally larger than 100 m2/g. The channels formed in the thermal dehydroxylation process may account for this feature of the MgO nanocrystallines.

Nanoscale Magnesium Hydroxide and Magnesium Oxide Powders: Control over Size, Shape, and Structure via Hydrothermal Synthesis

A simple two-step dealloying strategy is described to make free-standing metal membranes with hierarchical porous architecture. This structure has a bimodal pore size distribution composed of large porosity channels and small porosity channel walls, where each pore size can be tailored independently of the others. A new gas-phase electroless plating technique was also developed here that could be used to uniformly fill porous structures with pore size as small as 10 nm.

Yi Ding

Papers

The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor

Nanoporous Gold Leaf: “Ancient Technology”/Advanced Material

Low Temperature CO Oxidation over Unsupported Nanoporous Gold

Nanoscale Magnesium Hydroxide and Magnesium Oxide Powders: Control over Size, Shape, and Structure via Hydrothermal Synthesis

Nanoporous metals with controlled multimodal pore size distribution.