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

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)

/pdf/the-chemistry-of-graphene-oxide-507zcedhhu.pdf

The chemistry of graphene oxide

An improved method for the preparation of graphene oxide (GO) is described. Currently, Hummers’ method (KMnO4, NaNO3, H2SO4) is the most common method used for preparing graphene oxide. We have found that excluding the NaNO3, increasing the amount of KMnO4, and performing the reaction in a 9:1 mixture of H2SO4/H3PO4 improves the efficiency of the oxidation process. This improved method provides a greater amount of hydrophilic oxidized graphene material as compared to Hummers’ method or Hummers’ method with additional KMnO4. Moreover, even though the GO produced by our method is more oxidized than that prepared by Hummers’ method, when both are reduced in the same chamber with hydrazine, chemically converted graphene (CCG) produced from this new method is equivalent in its electrical conductivity. In contrast to Hummers’ method, the new method does not generate toxic gas and the temperature is easily controlled. This improved synthesis of GO may be important for large-scale production of GO as well as the ...

https://www.researchgate.net/file.PostFileLoader.html?id=54ca19b4cf57d79a768b4618&assetKey=AS%3A273691751976961%401442264606356

Improved Synthesis of Graphene Oxide

There is intense interest in graphene in fields such as physics, chemistry, and materials science, among others. Interest in graphene's exceptional physical properties, chemical tunability, and potential for applications has generated thousands of publications and an accelerating pace of research, making review of such research timely. Here is an overview of the synthesis, properties, and applications of graphene and related materials (primarily, graphite oxide and its colloidal suspensions and materials made from them), from a materials science perspective.

/pdf/graphene-and-graphene-oxide-synthesis-properties-and-2q80uaujok.pdf

Graphene and Graphene Oxide: Synthesis, Properties, and Applications

http://staff.ulsu.ru/moliver/ref/polymers/pott11.pdf

Graphene-based polymer nanocomposites

Living ring-opening metathesis polymerization

Herein we propose a new structure for poly(dopamine), a synthetic eumelanin that has found broad utility as an antifouling agent. Commercially available 3-hydroxytyramine hydrochloride (dopamine HCl) was polymerized under aerobic, aqueous conditions using tris(hydroxymethyl)aminomethane (TRIS) as a basic polymerization initiator, affording a darkly colored powder product upon isolation. The polymer was analyzed using a variety of solid state spectroscopic and crystallographic techniques. Collectively, the data showed that in contrast to previously proposed models, poly(dopamine) is not a covalent polymer but instead a supramolecular aggregate of monomers (consisting primarily of 5,6-dihydroxyindoline and its dione derivative) that are held together through a combination of charge transfer, π-stacking, and hydrogen bonding interactions.

Elucidating the Structure of Poly(dopamine)

There has been an intense surge in interest in graphene during recent years. However, graphene-like materials derived from graphite oxide were reported in 1962, and related chemical modifications of graphite were described as early as 1840. In this detailed account of the fascinating development of the synthesis and characterization of graphene, we hope to demonstrate that the rich history of graphene chemistry laid the foundation for the exciting research that continues to this day. Important challenges remain, however; many with great technological relevance.

Christopher W. Bielawski

Papers

The chemistry of graphene oxide

Graphene-based polymer nanocomposites

Living ring-opening metathesis polymerization

Elucidating the Structure of Poly(dopamine)

From Conception to Realization: An Historial Account of Graphene and Some Perspectives for Its Future