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.

Switchable Catenanes and Molecular Shuttles

Industrial-scale thermal separation processes have contributed greatly to the rise in carbon dioxide emissions. Porous materials, such as metal-organic frameworks (MOFs), can potentially reduce these emissions by achieving nonthermal chemical separations through the physical adsorption of targeted species with high selectivity. Here, we report the synthesis of the channel-based MOFs NU-2000 and NU-2001, which are constructed from three-dimensional (3D) linkers, to separate the industrially relevant xylene isomers under ambient conditions by leveraging sub-Ångstrom differences in the sizes of each isomer. While the rotation of two-dimensional (2D) linkers in MOFs often affords changes in pore apertures and pore sizes that are substantial enough to hinder separation efficiency, increasing the linker dimensionality from 2D to three-dimensional (3D) enables precise control of the MOF pore size and aperture regardless of the linker orientation, establishing this design principle as a broadly applicable strategy.

Separation of Aromatic Hydrocarbons in Porous Materials.

Five potential molecular shuttles based on degenerate [2]rotaxanes - wherein the ring component is a bis-1,4-phenylene[34]crown-10 and the dumbbell components are terminated by tetraarylmethane (slippage) stoppers and contain two identical bipyridinium recognition sites and a central 1,3-phenylene unit carrying a CH 2 OR (R = Me, Et, Ph, i-Pr, and t -Bu) substituent on its C-5 position - have been prepared by acylating the parent hydroxymethyl derivative with the appropriate reagents. Dynamic 1 H NMR spectroscopy, carried out on these five potential molecular shuttles in CD 3 CN solutions, has revealed average Gibbs energy barriers to shuttling of 11.5, 12.0, 14.6, and 14.8 kcal mol -1 for the [2]rotaxanes where R = Me, Et, i-Pr, and Ph, respectively. For the [2]rotaxane where R = t -Bu, the Gibbs energy barrier to shuttling must exceed 17.2 kcal mol -1 .

J. Fraser Stoddart

Papers

Switchable Catenanes and Molecular Shuttles

Separation of Aromatic Hydrocarbons in Porous Materials.

Speed-Controlled Molecular Shuttles

Ein polymolekularer Donor-Acceptor-Stapel†

Kinetically controlled self-assembly of pseudorotaxanes on crystallization.