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

Peptides or proteins convert under some conditions from their soluble forms into highly ordered fibrillar aggregates. Such transitions can give rise to pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. In this review, we identify the diseases known to be associated with formation of fibrillar aggregates and the specific peptides and proteins involved in each case. We describe, in addition, that living organisms can take advantage of the inherent ability of proteins to form such structures to generate novel and diverse biological functions. We review recent advances toward the elucidation of the structures of amyloid fibrils and the mechanisms of their formation at a molecular level. Finally, we discuss the relative importance of the common main-chain and side-chain interactions in determining the propensities of proteins to aggregate and describe some of the evidence that the oligomeric fibril precursors are the primary origins of pathological behavior.

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Protein Misfolding, Functional Amyloid, and Human Disease

비만아 부모의 돌봄 경험: q 방법론

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

The recently discovered glass-crystal (GC) growth mode in some glass-forming liquids is characterized by strong and abrupt growth rate enhancement just in the vicinity of the glass transition temperature. GC growth previously has been observed in only 10 compounds. The data on testosterone propionate presented here indicate the fastest GC growth acceleration observed to date. Moreover, testosterone propionate is the first compound to show a helically twisted morphology concomitant with GC growth. It has been previously stated that an aryl ring is a prerequisite of GC growth, but testosterone propionate obviates that claim.

Glass-crystal growth mode for testosterone propionate

Trimorphic paracetamol, one of the most commonly used analgesic and antipyretic drugs, has been a model system for studying transformations among phases of molecular crystalline materials. During c...

Melt Crystallization for Paracetamol Polymorphism

Ferdinand Bernauer proposed in his monograph, "Gedrillte" Kristalle (1929), that a great number of simple, crystalline substances grow from solution or from the melt as polycrystalline spherulites with helically twisting radii that give rise to distinct bull's-eye patterns of concentric optical bands between crossed polarizers. The idea that many common molecular crystals can be induced to grow as mesoscale helices is a remarkable proposition poorly grounded in theories of polycrystalline pattern formation. Recent reinvestigation of one of the systems Bernauer described revealed that rhythmic precipitation in the absence of helical twisting accounted for modulated optical properties [Gunn, E. et al. J. Am. Chem. Soc. 2006, 128, 14234-14235]. Herein, the Bernauer hypothesis is re-examined in detail for three substances described in "Gedrillte" Kristalle, potassium dichromate, hippuric acid, and tetraphenyl lead, using contemporary methods of analysis not available to Bernauer, including micro-focus X-ray diffraction, electron microscopy, and Mueller matrix imaging polarimetry. Potassium dichromate is shown to fall in the class of rhythmic precipitates of undistorted crystallites, while hippuric acid spherulites are well described as helical fibrils. Tetraphenyl lead spherulites grow by twisting and rhythmic precipitation. The behavior of tetraphenyl lead is likely typical of many substances in "Gedrillte" Kristalle. Rhythmic precipitation and helical twisting often coexist, complicating optical analyses and presenting Bernauer with difficulties in the characterization and classification of the objects of his interest.

Bernauer's bands

The optical symmetry of many crystals is lower than would be expected from their external form and X-ray diffraction data. Recently such optical anomalies have been attributed to nonequilibrium structures resulting from kinetically controlled crystal growth. Impurities are incorporated to different extents at various surface sites that would otherwise have become symmetry-related within the bulk crystal. After their discovery by Brewster in 1815, optically anomalous crystals were the subject of lively debate throughout the 19th century among some of the most distinguished contributors to the development of crystallography including Biot, Berzelius, Herschel, Mitscherlich, Frankenheim, Pasteur, Mallard, Klein, Groth, Wyrouboff, Barlow, Brauns, Rinne, Pockels, and Friedel. From a sea of wild speculation two conflicting postulates emerged: that the symmetric form resulted from accidental twinning of segments with lower symmetry, or that the optical peculiarities resulted from stress due to impurities or external perturbations. Neither postulate expresses the present view. Interest in this research waned at the turn of the century, and after 1917 no one pursued Tammann's alternative correct insight. The problem of anomalous double refraction attracted no attention for more than half a century until its recent solution. This review discusses both mineral and organic systems with particular emphasis on the phyllosilicate apophyllite and on 1,5-dichloro-2,3-dinitrobenzene. These nonequilibrium structures relate to questions of crystal order, crystal growth, molecular recognition, and the design of new materials. The review provides a reminder of the enduring value of the polarizing microscope as a research tool in chemistry.

Optically Anomalous Crystals

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P21 with lattice parameters a = 11.479(4) A, b = 11.030(1) A, c = 10.840(6) A, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit (R05-1 and R05-2) are 44.9° and -34.0°. These values are between those previously determined for the red and orange forms of ROY. The crystal packing and intermolecular interactions in R05 are explained herein through Hirshfeld surface analysis and an updated energy stability ranking is determined using computational methods. Although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT van der Waals (vdW)-inclusive models substantially differ from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.

Bart Kahr

Papers

Glass-crystal growth mode for testosterone propionate

Melt Crystallization for Paracetamol Polymorphism

Bernauer's bands

Optically Anomalous Crystals

ROY revisited, again: the eighth solved structure