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

The disclosure relates generally to materials that comprise organic frameworks. The disclosure also relates to materials that are useful to store and separate biological agents that are environmentally friendly and biocompatible.

Edible and biocompatible metal-organic frameworks

It is a general and common practice to carry out single-crystal X-ray diffraction experiments at cryogenic temperatures in order to obtain high-resolution data. In this report, we show that this practice is not always applicable to metal–organic frameworks (MOFs), especially when these structures are highly porous. Specifically, two new MOFs are reported here, MOF-1004 and MOF-1005, for which the collection of the diffraction data at lower temperature (100 K) did not give data of sufficient quality to allow structure solution. However, collection of data at higher temperature (290 K) gave atomic-resolution data for MOF-1004 and MOF-1005, allowing for structure solution. We find that this inverse behavior, contrary to normal practice, is also true for some well-established MOFs (MOF-177 and UiO-67). Close examination of the X-ray diffraction data obtained for all four of these MOFs at various temperatures led us to conclude that disordered guest–framework interactions play a profound role in introducing di...

Impact of Disordered Guest–Framework Interactions on the Crystallography of Metal–Organic Frameworks

The disclosure provides metal organic frameworks useful for sensing, gas sorption, microelectronics and switches.

Chemical framework compositions and methods of use

Ein mikroporöses Gerüst aus Lanthanoid‐Ionen und organischen Bausteinen

Three new post-synthetic modification reactions, namely amidation, esterification, and thioesterification, were demonstrated on a novel highly crystalline two-dimensional covalent organic framework (COF), COF-616, bearing pre-installed carboxyl groups. The strategy can be used to introduce a large variety of functional groups into COFs and the modifications can be carried out under mild reaction conditions, with high yields, and an easy work-up protocol. As a proof of concept, various chelating functionalities were successfully incorporated into COF-616 to yield a family of adsorbents for efficient removal of several contaminants in the water.

Omar M. Yaghi

Papers

Edible and biocompatible metal-organic frameworks

Impact of Disordered Guest–Framework Interactions on the Crystallography of Metal–Organic Frameworks

Chemical framework compositions and methods of use

Ein mikroporöses Gerüst aus Lanthanoid‐Ionen und organischen Bausteinen

Amidation, Esterification, and Thioesterification of a Carboxyl-Functionalized Covalent Organic Framework.