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

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

J. Appl. Cryst.の発刊に際して

Silver nanoparticles as antimicrobial agent: a case study on E. coli as a model for Gram-negative bacteria

Copolymerization of Ethylene and Propylene with Functionalized Vinyl Monomers by Palladium(II) Catalysts

Mechanistic aspects of palladium-catalyzed insertion copolymerizations of ethylene and α-olefins with methyl acrylate to give high molar mass polymers are described. Complexes [(N∧N)Pd(CH2)3C(O)OMe]BAr‘4 (2) or [(N∧N)Pd(CH3)(L)]BAr‘4 (1:  L = OEt2; 3:  L ⋮ NCMe; 4:  L ⋮ NCAr‘) (N∧N ≡ ArNC(R)−C(R)NAr, e.g., Ar ⋮ 2,6-C6H3(i-Pr)2, R ⋮ H (a), Me (b); Ar‘ ⋮ 3,5-C6H3(CF3)2) with bulky substituted α-diimine ligands were used as catalyst precursors. The copolymers are highly branched, the acrylate comonomer being incorporated predominantly at the ends of branches as −CH2CH2C(O)OMe groups. The effects of reaction conditions and catalyst structure on the copolymerization reaction are rationalized. Low-temperature NMR studies show that migratory insertion in the η2-methyl acrylate (MA) complex [(N∧N)PdMe{H2CCHC(O)OMe}]+ (5) occurs to give initially the 2,1-insertion product [(N∧N)PdCH(CH2CH3)C(O)OMe]+ (6), which rearranges stepwise to yield 2 as the final product upon warming to −20 °C. Activation parameters (ΔH⧧ = ...

/pdf/mechanistic-studies-of-the-palladium-catalyzed-3lx8cv51qj.pdf

Mechanistic Studies of the Palladium-Catalyzed Copolymerization of Ethylene and α-Olefins with Methyl Acrylate

/pdf/nanoparticles-of-conjugated-polymers-1nls9f7jbi.pdf

Nanoparticles of conjugated polymers.

Naturally occurring polymers have been utilized for a long time as materials, however, their application as plastics has been restricted because of their limited thermoplastic processability. Recently, the microbial synthesis of polyesters directly from carbohydrate sources has attracted considerable attention. The industrial-scale production of poly(lactic acid) from lactic acid generated by fermentation now provides a renewable resources-based polyester as a commodity plastic for the first time. The biodegradability of a given material is independent of its origin, and biodegradable plastics can equally well be prepared from fossil fuel feedstocks. A consideration of the overall carbon dioxide emissions and consumption of non-renewable resources over the entire life-cycle of a product is not necessarily favorable for plastics based on renewable resources with current technology-in addition to the feedstocks for the synthesis of the polymer materials, the feedstock for generation of the overall energy required for production and processing is decisive.

/pdf/nature-or-petrochemistry-biologically-degradable-materials-1414gyw2ib.pdf

Nature or Petrochemistry?—Biologically Degradable Materials

Ligands, Lewis bases that coordinate to the metal center in a complex, can completely change the catalytic behavior of the metal center. In this Account, we summarize new reactions enabled by a single class of ligands, phosphine–sulfonates (ortho-phosphinobenzenesulfonates). Using their palladium complexes, we have developed four unusual reactions, and three of these have produced novel types of polymers.In one case, we have produced linear high-molecular weight polyethylene, a type of polymer that group 10 metal catalysts do not typically produce. Secondly, complexes using these ligands catalyzed the formation of linear poly(ethylene-co-polar vinyl monomers). Before the use of phosphine–sulfonate catalysts, researchers could only produce ethylene/polar monomer copolymers that have different branched structures rather than linear ones, depending on whether the polymers were produced by a radical polymerization or a group 10 metal catalyzed coordination polymerization. Thirdly, these phosphine–sulfonate ca...

Stefan Mecking

Papers

Copolymerization of Ethylene and Propylene with Functionalized Vinyl Monomers by Palladium(II) Catalysts

Mechanistic Studies of the Palladium-Catalyzed Copolymerization of Ethylene and α-Olefins with Methyl Acrylate

Nanoparticles of conjugated polymers.

Nature or Petrochemistry?—Biologically Degradable Materials

Ortho-phosphinobenzenesulfonate: a superb ligand for palladium-catalyzed coordination-insertion copolymerization of polar vinyl monomers.