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

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Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Methods in Enzymology.

介绍了Kirk—Othmer Encyclopedia of Chemical Technology（化工技术百科全书）（第五版）电子图书网络版数据库，并对该数据库使用方法和检索途径作出了说明，且结合实例简单地介绍了该数据库的检索方法。

Kirk-Othmer Encyclopedia of Chemical Technology数据库介绍及实例

We report the use of atomically thin layers of graphene as a protective coating that inhibits corrosion of underlying metals. Here, we employ electrochemical methods to study the corrosion inhibition of copper and nickel by either growing graphene on these metals, or by mechanically transferring multilayer graphene onto them. Cyclic voltammetry measurements reveal that the graphene coating effectively suppresses metal oxidation and oxygen reduction. Electrochemical impedance spectroscopy measurements suggest that while graphene itself is not damaged, the metal under it is corroded at cracks in the graphene film. Finally, we use Tafel analysis to quantify the corrosion rates of samples with and without graphene coatings. These results indicate that copper films coated with graphene grown via chemical vapor deposition are corroded 7 times slower in an aerated Na2SO4 solution as compared to the corrosion rate of bare copper. Tafel analysis reveals that nickel with a multilayer graphene film grown on it corro...

Graphene: Corrosion-Inhibiting Coating

Self-assembled monolayers (SAMs) formed by the adsorption of n-alkanethiols [CH3(CH2)n-1SH; n = 8, 12, 16, 18, 20, 22, and 29] onto copper provide a flexible method for producing coatings that can protect the underlying metal against corrosion The ability to tailor the thickness of the coatings at the angstrom-level by choice of adsorbate allows examination of the effect of angstrom-level variations in film thickness on the performance of the SAM as a barrier layer A combination of infrared (IR) spectroscopy and electrochemical impedance spectroscopy (EIS) was used to correlate the structure of the SAM with its barrier properties during extended exposures to 1 atm of O2 at 100% relative humidity (RH) EIS results reveal that the coating resistances provided by SAMs with chain lengths of 16 carbons or more (ie n ≥ 16) exhibit a linear increase with chain length and are orders of magnitude greater than those provided by SAMs with n ≤ 12 due to the more crystalline nature of the thicker films Upon expos

Effect of Chain Length on the Protection of Copper by n-Alkanethiols

The kinetics and mechanism for the solution-phase adsorption of n-alkanethiols onto gold to form self-assembled monolayers (SAMs) have been monitored in situ using atomic force microscopy (AFM). Time-dependent AFM images reveal detailed structural information about the adsorbed layer during its growth. In 2-butanol, CH3(CH2)17SH molecules initially adsorb on gold with the molecular axis of their hydrocarbon chains oriented parallel to the surface. As the surface coverage increases to near saturation, a two-dimensional phase transition occurs and produces islands composed of molecules with their hydrocarbon axis oriented ∼30° from the surface normal. Continued exposure to the thiol solution results in a greater number of these islands and the growth of these nuclei until a SAM is formed with a commensurate (∛×∛)R30° structure. The growth of the lying-down phase follows a first-order Langmuir adsorption isotherm, while the phase transition is best described by a second-order reaction. The kinetics of the se...

In situ studies of thiol self-assembly on gold from solution using atomic force microscopy

Plants and some types of bacteria demonstrate an elegant means to capitalize on the superabundance of solar energy that reaches our planet with their energy conversion process called photosynthesis. Seeking to harness Nature’s optimization of this process, we have devised a biomimetic photonic energy conversion system that makes use of the photoactive protein complex Photosystem I, immobilized on the surface of nanoporous gold leaf (NPGL) electrodes, to drive a photoinduced electric current through an electrochemical cell. The intent of this study is to further the understanding of how the useful functionality of these naturally mass-produced, biological light-harvesting complexes can be integrated with nonbiological materials. Here, we show that the protein complexes retain their photonic energy conversion functionality after attachment to the nanoporous electrode surface and, further, that the additional PSI/electrode interfacial area provided by the NPGL allows for an increase in PSI-mediated electron ...

G. Kane Jennings

Papers

Graphene: Corrosion-Inhibiting Coating

Effect of Chain Length on the Protection of Copper by n-Alkanethiols

In situ studies of thiol self-assembly on gold from solution using atomic force microscopy

Functionalized nanoporous gold leaf electrode films for the immobilization of photosystem I.

Self-assembled monolayers of alkanethiols on copper provide corrosion resistance in aqueous environments