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

Design of MOFs with Absolute Structures: A Case Study

The structures of all 1127 three-periodic extended metal−organic frameworks (MOFs) reported in the Cambridge Structure Database have been analyzed, and their underlying topology has been determined. It is remarkable that among the almost infinite number of net topologies that are available for MOFs to adopt, only a handful of nets are actually observed. The discovery of this inversion between expected and observed nets led us to deduce a system of classification “taxonomy” for interpreting and rationalizing known MOF structures, as well as those that will be made in future. The origin of this inversion is attributed to the different modes with which MOF synthesis has been approached. Specifically, three levels of complexity are defined that embody rules “grammar” for the design of MOFs and other extended structures. This system accounts for the present proliferation of MOF structures of high symmetry nets, but more importantly, it provides the basis for designing a building block that “codes” for a specif...

/pdf/reticular-chemistry-occurrence-and-taxonomy-of-nets-and-3acjuheotc.pdf

Reticular Chemistry: Occurrence and Taxonomy of Nets and Grammar for the Design of Frameworks

The present invention provides a metal-organic framework ('MOF”) comprising a plurality of metal clusters and a plurality of multidentate, linking ligands. Each metal of the plurality of metal clusters comprises one or more metal ions. Each ligand of the plurality of multidentate linking ligands connects adjacent metal clusters. The present invention also provides a method of forming the metalorganic framework. The method of the invention comprises combining a solution comprising one or metal ions with a multidentate linking ligand having a sufficient number of accessible sites for atomic or molecular adsorption that the surface area of the resulting metal-organic framework is greater than 2,900 M2/g.

MOFs with a high surface area and methods for producing them

A porous aluminum-based metal-organic framework (MOF) comprises inorganic aluminum chains linked via carboxylate groups of 1H-pyrazole-3,5-dicarboxylate (HPDC) linkers, and of formula: [A1(OH)(C5H2O4N2)(H2O)]

Porous aluminum pyrazoledicarboxylate frameworks

A linker extension strategy for generating metal–organic frameworks (MOFs) with superior moisture-capturing properties is presented. Applying this design approach involving experiment and computation results in MOF-LA2-1 {[Al(OH)(PZVDC)], where PZVDC2– is (E)-5-(2-carboxylatovinyl)-1H-pyrazole-3-carboxylate}, which exhibits an approximately 50% water capacity increase compared to the state-of-the-art water-harvesting material MOF-303. The power of this approach is the increase in pore volume while retaining the ability of the MOF to harvest water in arid environments under long-term uptake and release cycling, as well as affording a reduction in regeneration heat and temperature. Density functional theory calculations and Monte Carlo simulations give detailed insight pertaining to framework structure, water interactions within its pores, and the resulting water sorption isotherm.

https://doi.org/10.1021/acscentsci.3c00018

Omar M. Yaghi

Papers

Design of MOFs with Absolute Structures: A Case Study

Reticular Chemistry: Occurrence and Taxonomy of Nets and Grammar for the Design of Frameworks

MOFs with a high surface area and methods for producing them

Porous aluminum pyrazoledicarboxylate frameworks

MOF Linker Extension Strategy for Enhanced Atmospheric Water Harvesting