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.

/pdf/reticular-synthesis-and-the-design-of-new-materials-lazbx7tdux.pdf

Reticular synthesis and the design of new materials

In this article, the authors - three scientists and a diplomat, working across multiple continents - intend to impart some of the broad perspective and deep experience they’ve gained over the years as professionals The diplomat among us, stationed in the Middle East, has played a role in fostering peace in a region long beset by conflict Drawing from accumulated lessons, we intend to discuss how others can be encouraged to contribute to global science, regardless of their background or national origin In taking on this challenge, we will share insights from our various tenures as operators of bilateral aid programs, members of international science organizations, and participants in government negotiations and other events featuring the development of global science

/pdf/global-engagement-in-science-the-university-s-fourth-mission-17gamvvhph.pdf

Global Engagement in Science: The University’s Fourth Mission?

The disclosure provides for zirconium terephthalate-based metal organic frameworks with open metal sites, and uses thereof.

Zirconium terephthalate-based metal organic framework with open metal sites

Provided herein are atmospheric moisture harvester systems, as well as methods using such systems, for capturing water from surrounding air. The systems and methods use adsorbents to adsorb water from the air. For example, the adsorbents may be metal-organic frameworks. The systems and methods desorb this water in the form of water vapor, and the water vapor is condensed into liquid water and collected. The liquid water is suitable for use as drinking water.

Atmospheric moisture harvester

The disclosure provides for metal organic frameworks (MOFs) which comprise a plurality of repeating magnesium-based SBUs that are linked together by BTB-based linking ligands. The disclosure further provides for the use of these MOFs in variety of applications, including for gas separation, gas storage, catalysis, and water storage.

Very low density metal organic frameworks with large pore volumes

The square grid structure of MOF-2, constructed from 
paddle-wheel units of Zn(II) and 1,4-benzenedicarboxylate (BDC) 
links, persists for 2-amino-1,4-benzenedicarboxylate (ABDC) links but not 
for the sterically demanding 2,3,5,6-tetramethyl-1,4-benzenedicarboxylate 
(TBDC); the dihedral angle between planes of the benzene and carboxylate 
groups play a determining role in the formation of the paddle-wheel 
motif.

Omar M. Yaghi

Papers

Global Engagement in Science: The University’s Fourth Mission?

Zirconium terephthalate-based metal organic framework with open metal sites

Atmospheric moisture harvester

Very low density metal organic frameworks with large pore volumes

1,4-Benzenedicarboxylate Derivatives as Links in the Design of Paddle-Wheel Units and Metal—Organic Frameworks.