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

Although gold is the subject of one of the most ancient themes of investigation in science, its renaissance now leads to an exponentially increasing number of publications, especially in the context of emerging nanoscience and nanotechnology with nanoparticles and self-assembled monolayers (SAMs). We will limit the present review to gold nanoparticles (AuNPs), also called gold colloids. AuNPs are the most stable metal nanoparticles, and they present fascinating aspects such as their assembly of multiple types involving materials science, the behavior of the individual particles, size-related electronic, magnetic and optical properties (quantum size effect), and their applications to catalysis and biology. Their promises are in these fields as well as in the bottom-up approach of nanotechnology, and they will be key materials and building block in the 21st century. Whereas the extraction of gold started in the 5th millennium B.C. near Varna (Bulgaria) and reached 10 tons per year in Egypt around 1200-1300 B.C. when the marvelous statue of Touthankamon was constructed, it is probable that “soluble” gold appeared around the 5th or 4th century B.C. in Egypt and China. In antiquity, materials were used in an ecological sense for both aesthetic and curative purposes. Colloidal gold was used to make ruby glass 293 Chem. Rev. 2004, 104, 293−346

Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology.

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

A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes.

From supramolecular complexes to interlocked molecular compounds

The [3.3.3]cryptand (3), prepared stereospecifically from 2,3-O-isopropylidene-D-glycerol D-(1) and 2,3-di-O-benzyl-L-glycerol L-(2), has been separated chromatographically at –5 °C into slowly interconverting in-in ii-(3) and out-out oo-(3) conformational diastereoisomers [ΔGii→oo‡=ca. 24 kcal mol–1(1 kcal = 4.184 kj) in CD3COCD3 at +38 °C]; an X-ray structure analysis has shown (3) to from a crystalline 1 : 1 complex with Ba(SCN)2 in which the Ba2+ ion is encapsulated by oo-(3) and the two SCN– ion in an 11-co-ordinate manner.

Sterospecific syntheses of marcrobicyclic polyethers with carbon bridgeheads from chiral glycerol derivatives

Second Sphere Coordination of Tetraammineplatinum(II) by a Macropolycyclic Crown Ether Bisamide Receptor

Amphidynamic crystals have close links to molecular machines, which have considerable potential for developing smart materials. A recently published article in Matter ( Colin-Molina et al .) reports an amphidynamic supramolecular rotor that displays a remarkable thermosalient effect when undergoing a phase transition, concomitant with a substantial structural reconfiguration resulting in crystal motility.

Amphidynamic Crystals Key to Artificial Molecular Machines

The self-assembly of CdSe quantum dots (QDs) onto a patterned silica surface generated from surface microcontact click printing is presented. The mechanically robust self-assembly process produces patterns of QDs which remain steadfast, even as subsequent reactions are performed on the substrate, demonstrating the utility and ease of this self-assembly process.

J. Fraser Stoddart

Papers

From supramolecular complexes to interlocked molecular compounds

Sterospecific syntheses of marcrobicyclic polyethers with carbon bridgeheads from chiral glycerol derivatives

Second Sphere Coordination of Tetraammineplatinum(II) by a Macropolycyclic Crown Ether Bisamide Receptor

Amphidynamic Crystals Key to Artificial Molecular Machines

Patterned assembly of quantum dots onto surfaces modified with click microcontact printing.