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

Progress in the supramolecular chemistry of dyeing crystals in the 21st century is reviewed.

Dyeing crystals since 2000

A method is introduced to correlate electromagnetic theory and polarimetric experiments for anisotropic optically active crystals at oblique angles of incidence. It is based on the 4 × 4 algebraic descriptions of light propagation in layered anisotropic media, which can be simplified to 2 × 2 matrices when multiple reflections are disregarded. Spectroscopic Mueller matrix measurements in transmission and at oblique angles of incidence have been made on two uniaxial crystals: α-quartz and silver thiogallate. Their optical activity tensors have been spectroscopically determined using the method presented here.

Reckoning electromagnetic principles with polarimetric measurements of anisotropic optically active crystals

The fullerences C60 and C70 form adducts with toluene, p-xylene and other aromatic compounds when refluxed in these solvents in the presences of FeCl3. Benzene derivatives are produced only when bromine is also present. Mass spectra of the reaction mixtures indicate the presence of derivatives including 1:1 adducts, as well as products of multiple additions of the aromatic molecules and their dehydrogenation products. Tandem mass spectrometry provides evidence for CC bonds formation between the adducts and fullerences.

Aromatic hydrocarbon derivatives of fullerences

The concept of syncrystallization was reinvestigated by focusing on phthalic acid (PA) grown with methyl red (MR). Crystals are alternately red and yellow in adjacent growth sectors. X-ray structures of MR and its cocrystals, revealing MR in the neutral, zwitterionic, and protonated states, as well as measurements of linear birefringence and linear dichroism of mixed crystals, were used to investigate mechanisms of PA coloring. These experiments were complemented by force field calculations of the lowest energy stable surfaces of expressed facets and energies of MR on and in crystals, as well as molecular orbital calculations of MR. Two MR species were detected in PA having distinct energies, polarizations, and face selectivities. Assignments of structures to these MRs, previously thought to be neutral and protonated, required a nuanced analysis of hydrogen bonds. The essential difference between yellow and red species is whether the MR carboxylic acid proton is inter- or intramolecularly hydrogen bound. Inferences about mixed crystal structure drawn from an examination of cocrystals of PA and MR are inconsistent with polarization spectroscopy signaling caution when using stoichiometric compounds as models of dilute solid solutions. Upon heating mixed crystals, linear dichroism diminishes and oriented, elongated pools of MR separate and pass through the bulk in directions perpendicular to the direction of elongation. These bâtonnets subsequently crystallize leaving macroscopic oriented crystals of a MR-rich phase within PA. No evidence was found for the simultaneous crystallization of MR and PA; however, the MR reorientation on heating as well as the separation and recrystallization of a MR-rich phase are distinct processes that could be embraced by the literal meaning of syncrystallization.

Bart Kahr

Papers

Dyeing crystals since 2000

Reckoning electromagnetic principles with polarimetric measurements of anisotropic optically active crystals

Aromatic hydrocarbon derivatives of fullerences

What is syncrystallization? States of the pH indicator methyl red in crystals of phthalic acid

Charge Transfer Interactions in Dyed Crystals of Aromatic Carboxylic Acids and Their Relevance to MALDI Mass Spectrometry