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

Fingerprint plots of Hirshfeld surfaces were used to locate and analyze the deficiencies in various methodologies employed in the determination of the relative energies of five polymorphs of 1,8-dihydroxyanthraquinone. Nine crystallographically independent molecules were characterized by X-ray crystallography and Hirshfeld surfaces were derived from the X-ray structures. The space groups and number of independent molecules (Z′) for each of the polymorphs (1−5) is as follows: (1) P41 (or P43),Z′ = 1; (2) Pca21, Z′ = 2; (3) P1, Z′ = 4; (4) P21/n, Z′ = 1; (5) P41212 (or P43212), Z′ = 0.5. Form 1 is the most thermodynamically stable among the reproducible structures, as established by competitive solubility tests, followed by 2 and then 4. The unrestrained structures of the five polymorphs were computed using the CVFF and COMPASS force fields as well as with the density functional code, SIESTA.

Hirshfeld surfaces identify inadequacies in computations of intermolecular interactions in crystals: pentamorphic 1,8-dihydroxyanthraquinone

Crystals of a variety of substances including elements, minerals, simple salts, organic molecular crystals, and high polymers forgo long-range translational order by twisting and bending as they grow. These deviations have been observed in crystals ranging in size from nanometers to centimeters. How and why so many materials choose dramatic non-crystallographic distortions is analyzed, with an emphasis on crystal chemistries that give rise to stresses operating either on surfaces of crystallites or within the bulk.

Growth Actuated Bending and Twisting of Single Crystals

New advances in polarized light microscopy were used to image Congo red-stained cerebral amyloidosis in sharp relief. The rotating-polarizer method was used to separate the optical effects of transmission, linear birefringence, extinction, linear dichroism, and orientation of the electric dipole transition moments and to display them as false-color maps. These effects are typically convolved in an ordinary polarized light microscope. In this way, we show that the amyloid deposits in Alzheimer's disease plaques contain structurally disordered centers, providing clues to mechanisms of crystallization of amyloid in vivo. Comparisons are made with plaques from tissues of subjects having Down's syndrome and a prion disease. In plaques characteristic of each disease, the Congo red molecules are oriented radially. The optical orientation in amyloid deposited in blood vessels from subjects having cerebral amyloid angiopathy was 90° out of phase from that in the plaques, suggesting that the fibrils run tangentially with respect to the circumference of the blood vessels. Our result supports an early model in which Congo red molecules are aligned along the long fiber axis and is in contrast to the most recent binding models that are based on computation. This investigation illustrates that the latest methods for the optical analysis of heterogeneous substances are useful for in situ study of amyloid.

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Imaging linear birefringence and dichroism in cerebral amyloid pathologies

A spectroscopic Mueller matrix polarimeter with four photoelastic modulators (PEMs) and no moving parts is introduced. In the 4-PEM polarimeter, all the elements of the Mueller matrix are simultaneously determined from the analysis of the frequencies of the time-dependent intensity of the light beam.

Mueller matrix polarimetry with four photoelastic modulators: theory and calibration

The growing realization that photoinduced bending of slender photoreactive single crystals is surprisingly common has inspired researchers to control crystal motility for actuation. However, new mechanically responsive crystals are reported at a greater rate than their quantitative photophysical characterization; a quantitative identification of measurable parameters and molecular-scale factors that determine the mechanical response has yet to be established. Herein, a simple mathematical description of the quasi-static and time-dependent photoinduced bending of macroscopic single crystals is provided. This kinetic model goes beyond the approximate treatment of a bending crystal as a simple composite bilayer. It includes alternative pathways for excited-state decay and provides a more accurate description of the bending by accounting for the spatial gradient in the product/reactant ratio. A new crystal form (space group P21/n) of the photoresponsive azo-dye Disperse Red 1 (DR1) is analyzed within the cons...

Bart Kahr

Papers

Hirshfeld surfaces identify inadequacies in computations of intermolecular interactions in crystals: pentamorphic 1,8-dihydroxyanthraquinone

Growth Actuated Bending and Twisting of Single Crystals

Imaging linear birefringence and dichroism in cerebral amyloid pathologies

Mueller matrix polarimetry with four photoelastic modulators: theory and calibration

Model for photoinduced bending of slender molecular crystals.