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

Crystalline metal-organic frameworks (MOFs) are formed by reticular synthesis, which creates strong bonds between inorganic and organic units. Careful selection of MOF constituents can yield crystals of ultrahigh porosity and high thermal and chemical stability. These characteristics allow the interior of MOFs to be chemically altered for use in gas separation, gas storage, and catalysis, among other applications. The precision commonly exercised in their chemical modification and the ability to expand their metrics without changing the underlying topology have not been achieved with other solids. MOFs whose chemical composition and shape of building units can be multiply varied within a particular structure already exist and may lead to materials that offer a synergistic combination of properties.

The Chemistry and Applications of Metal-Organic Frameworks

The chemistry of graphene oxide is discussed in this critical review Particular emphasis is directed toward the synthesis of graphene oxide, as well as its structure Graphene oxide as a substrate for a variety of chemical transformations, including its reduction to graphene-like materials, is also discussed This review will be of value to synthetic chemists interested in this emerging field of materials science, as well as those investigating applications of graphene who would find a more thorough treatment of the chemistry of graphene oxide useful in understanding the scope and limitations of current approaches which utilize this material (91 references)

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The chemistry of graphene oxide

The long-standing challenge of designing and constructing new crystalline solid-state materials from molecular building blocks is just beginning to be addressed with success. A conceptual approach that requires the use of secondary building units to direct the assembly of ordered frameworks epitomizes this process: we call this approach reticular synthesis. This chemistry has yielded materials designed to have predetermined structures, compositions and properties. In particular, highly porous frameworks held together by strong metal-oxygen-carbon bonds and with exceptionally large surface area and capacity for gas storage have been prepared and their pore metrics systematically varied and functionalized.

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Reticular synthesis and the design of new materials

Studies on the assembly of metal -organic frameworks (MOFs) have uncovered methods to build extended structures from molecular building blocks. 1-3 The synthesis of a new type of porous material using strategies based on the expansion and decoration of vertexes in basic nets has demonstrated the wide scope of this chemistry. 4 In particular, crystalline MOFs that maintain their open structure in the absence of guests can perform highly selective separations. 5

Tertiary building units: synthesis, structure, and porosity of a metal-organic dendrimer framework (MODF-1).

Retikuläre Chemie metall‐organischer Polyeder

/pdf/multivariate-metal-organic-frameworks-14ilsy493z.pdf

Multivariate metal-organic frameworks

We report a strategy to uniformly wrap Morella thermoacetica bacteria with a metal-organic framework (MOF) monolayer of nanometer thickness for cytoprotection in artificial photosynthesis. The catalytic activity of the MOF enclosure toward decomposition of reactive oxygen species (ROS) reduces the death of strictly anaerobic bacteria by fivefold in the presence of 21% O2, and enables the cytoprotected bacteria to continuously produce acetate from CO2 fixation under oxidative stress. The high definition of the MOF-bacteria interface involving direct bonding between phosphate units on the cell surface and zirconium clusters on MOF monolayer, provides for enhancement of life throughout reproduction. The dynamic nature of the MOF wrapping allows for cell elongation and separation, including spontaneous covering of the newly grown cell surface. The open-metal sites on the zirconium clusters lead to 600 times more efficient ROS decomposition compared with zirconia nanoparticles.

/pdf/cytoprotective-metal-organic-frameworks-for-anaerobic-37pb2tqwan.pdf

Omar M. Yaghi

Papers

Tertiary building units: synthesis, structure, and porosity of a metal-organic dendrimer framework (MODF-1).

Retikuläre Chemie metall‐organischer Polyeder

Multivariate metal-organic frameworks

Cytoprotective metal-organic frameworks for anaerobic bacteria.

Potassium Octadecatungstodiphosphates(V) and Related Lacunary Compounds