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

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.

This is a review of Collected Works of John Tate. Parts I, II, edited by Barry Mazur and Jean-Pierre Serre. American Mathematical Society, Providence, Rhode Island, 2016. For several decades it has been clear to the friends and colleagues of John Tate that a “Collected Works” was merited. The award of the Abel Prize to Tate in 2010 added impetus, and finally, in Tate’s ninety-second year we have these two magnificent volumes, edited by Barry Mazur and Jean-Pierre Serre. Beyond Tate’s published articles, they include five unpublished articles and a selection of his letters, most accompanied by Tate’s comments, and a collection of photographs of Tate. For an overview of Tate’s work, the editors refer the reader to [4]. Before discussing the volumes, I describe some of Tate’s work. 1. Hecke L-series and Tate’s thesis Like many budding number theorists, Tate’s favorite theorem when young was Gauss’s law of quadratic reciprocity. When he arrived at Princeton as a graduate student in 1946, he was fortunate to find there the person, Emil Artin, who had discovered the most general reciprocity law, so solving Hilbert’s ninth problem. By 1920, the German school of algebraic number theorists (Hilbert, Weber, . . .) together with its brilliant student Takagi had succeeded in classifying the abelian extensions of a number field K: to each group I of ideal classes in K, there is attached an extension L of K (the class field of I); the group I determines the arithmetic of the extension L/K, and the Galois group of L/K is isomorphic to I. Artin’s contribution was to prove (in 1927) that there is a natural isomorphism from I to the Galois group of L/K. When the base field contains an appropriate root of 1, Artin’s isomorphism gives a reciprocity law, and all possible reciprocity laws arise this way. In the 1930s, Chevalley reworked abelian class field theory. In particular, he replaced “ideals” with his “idèles” which greatly clarified the relation between the local and global aspects of the theory. For his thesis, Artin suggested that Tate do the same for Hecke L-series. When Hecke proved that the abelian L-functions of number fields (generalizations of Dirichlet’s L-functions) have an analytic continuation throughout the plane with a functional equation of the expected type, he saw that his methods applied even to a new kind of L-function, now named after him. Once Tate had developed his harmonic analysis of local fields and of the idèle group, he was able prove analytic continuation and functional equations for all the relevant L-series without Hecke’s complicated theta-formulas. Received by the editors September 5, 2016. 2010 Mathematics Subject Classification. Primary 01A75, 11-06, 14-06. c ©2017 American Mathematical Society

The collected works

Intermolecular And Surface Forces

Crystallisation is at the heart of various scientific disciplines, but still the understanding of the molecular mechanisms underlying phase separation and the formation of the first solid particles in aqueous solution is rather limited. In this review, classical nucleation theory, as well as established concepts of spinodal decomposition and liquid–liquid demixing, is introduced together with a description of the recently proposed pre-nucleation cluster pathway. The features of pre-nucleation clusters are presented and discussed in relation to recent modifications of the classical and established models for phase separation, together with a review of experimental work and computer simulations on the characteristics of pre-nucleation clusters of calcium phosphate, calcium carbonate, iron(oxy)(hydr)oxide, silica, and also amino acids as an example of small organic molecules. The role of pre-nucleation clusters as solute precursors in the emergence of a new phase is summarized, and the link between the chemical speciation of homogeneous solutions and the process of phase separation via pre-nucleation clusters is highlighted.

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Pre-nucleation clusters as solute precursors in crystallisation

In biomineralization, living organisms carefully control the crystallization of calcium carbonate to create functional materials and thereby often take advantage of polymorphism by stabilizing a specific phase that is most suitable for a given demand. In particular, the lifetime of usually transient amorphous calcium carbonate (ACC) seems to be thoroughly regulated by the organic matrix, so as to use it either as an intermediate storage depot or directly as a structural element in a permanently stable state. In the present study, we show that the temporal stability of ACC can be influenced in a deliberate manner also in much simpler purely abiotic systems. To illustrate this, we have monitored the progress of calcium carbonate precipitation at high pH from solutions containing different amounts of sodium silicate. It was found that growing ACC particles provoke spontaneous polymerization of silica in their vicinity, which is proposed to result from a local decrease of pH nearby the surface. This leads to ...

Stabilization of amorphous calcium carbonate in inorganic silica-rich environments.

Calcium carbonate precipitation proceeds via a complex multistage scenario involving neutral ion clusters as precursors and amorphous phases as intermediates, which fi nally transform to crystals. Although the existence of stable clusters in solution prior to nucleation has been demonstrated, the molecular mechanisms by which they precipitate are still obscure. Here, direct insight into the processes that drive the transformation of individual clusters into amorphous nanoparticles is provided by progressive colloidal stabilization of different transient states in silica-containing environments. Nucleation of calcium carbonate in the presence of silica can only take place via cluster aggregation at low pH values. At higher pH, prenucleation clusters become colloidally stabilized and cannot aggregate. Nucleation through structural reorganization within the clusters is not observed under these conditions, indicating that this pathway is blocked by kinetic and/or thermodynamic means. The degree of stabilization against nucleation is found to be suffi cient to allow for a dramatic enrichment of solutions with prenucleation clusters and enable their isolation into the dry state. This approach renders direct analyses of the clusters by conventional techniques possible and is thus likely to facilitate deeper insight into the chemistry and structure of these elusive species in the future.

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Matthias Kellermeier

Papers

Pre-nucleation clusters as solute precursors in crystallisation

Stabilization of amorphous calcium carbonate in inorganic silica-rich environments.

Colloidal Stabilization of Calcium Carbonate Prenucleation Clusters with Silica

New Perspectives on Mineral Nucleation and Growth : From Solution Precursors to Solid Materials

Calcium sulfate precipitation pathways in natural and engineered environments