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

A key challenge in the field of electrochemical carbon dioxide reduction is the design of catalytic materials featuring high product selectivity, stability, and a composition of earth-abundant elements. In this work, we introduce thin films of nanosized metal-organic frameworks (MOFs) as atomically defined and nanoscopic materials that function as catalysts for the efficient and selective reduction of carbon dioxide to carbon monoxide in aqueous electrolytes. Detailed examination of a cobalt-porphyrin MOF, Al2(OH)2TCPP-Co (TCPP-H2 = 4,4',4″,4‴-(porphyrin-5,10,15,20-tetrayl)tetrabenzoate) revealed a selectivity for CO production in excess of 76% and stability over 7 h with a per-site turnover number (TON) of 1400. In situ spectroelectrochemical measurements provided insights into the cobalt oxidation state during the course of reaction and showed that the majority of catalytic centers in this MOF are redox-accessible where Co(II) is reduced to Co(I) during catalysis.

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Metal−Organic Frameworks for Electrocatalytic Reduction of Carbon Dioxide

The disclosure provides for multivariant zeolitic imidazolate frameworks (ZIFs), methods of making thereof, and methods of use therefrom.

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Zeolitic imidazolate frameworks

Frameworks for Extended Solids: Geometrical Design Principles

Metal-organic polyhedra (MOPs), are discrete metal-organic molecular assemblies. They are useful as host molecules that can provide tailorable internal volume in terms of metrics, functionality, and active metal sites. As a result, these materials are potentially useful for a variety of applications, such as highly selective guest inclusion and gas storage, and as nanoscale reaction vessels. This review identifies the nine most important polyhedra, and describes the design principles for the five polyhedra most likely to result from the assembly of secondary building units, and provides examples of these shapes that are known as metal-organic crystals.

Reticular chemistry of metal-organic polyhedra.

The combination of terbium nitrate and 1,4-benzenedicarboxylic acid (H2BDC) in the presence of triethylamine yields the compound Tb2(BDC)3·(H2O)4, which has an extended nonporous structure constructed from copolymerized BDC and Tb(III) units. The multidentate functionality of BDC and the tendency of Tb to have a high coordination number has allowed water to act as a terminal ligand to Tb in the structure. Upon thermally liberating the water ligands, a microporous material, Tb2(BDC)3, is achieved, which has extended 1-D channels and the same framework structure as that of the as-synthesized solid as evidenced by XRPD. Water sorption isotherm data proves that Tb2(BDC)3 has permanent microporosity, and points to the presence of accessible metal sites within the pores, which also allows the sorption of ammonia to give Tb2(BDC)3·(NH3)4. Luminescence lifetime measurements confirm that resorbed water and sorbed ammonia are bound to Tb and that they give distinctly different decay constants.

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Omar M. Yaghi

Papers

Metal−Organic Frameworks for Electrocatalytic Reduction of Carbon Dioxide

Zeolitic imidazolate frameworks

Frameworks for Extended Solids: Geometrical Design Principles

Reticular chemistry of metal-organic polyhedra.

From Condensed Lanthanide Coordination Solids to Microporous Frameworks Having Accessible Metal Sites