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

Protic Ionic Liquids: Properties and Applications

Annual review of condensed matter physics

1: Magnetic Particles: Preparation, Properties and Applications: M. Ozaki. 2: Maghemite (gamma-Fe2O3): A Versatile Magnetic Colloidal Material C.J. Serna, M.P. Morales. 3: Dynamics of Adsorption and Oxidation of Organic Molecules on Illuminated Titanium Dioxide Particles Immersed in Water M.A. Blesa, R.J. Candal, S.A. Bilmes. 4: Colloidal Aggregation in Two-Dimensions A. Moncho-Jorda, F. Martinez-Lopez, M.A. Cabrerizo-Vilchez, R. Hidalgo Alvarez, M. Quesada-PMerez. 5: Kinetics of Particle and Protein Adsorption Z. Adamczyk.

Surface and Colloid Science

コロイド混合体における有効力 空乏引力から集積斥力へ | 文献情報 | j-global 科学技術総合リンクセンター

http://absimage.aps.org/image/MAR14/MWS_MAR14-2013-000419.pdf

Novel polymer ferroelectric behavior via crystal isomorphism and the nanoconfinement effect

Polymer/inorganic particle nanocomposites (or nanodielectrics) have attracted pronounced attention for electric energy storage applications, based on a hypothesis that polymer nanodielectrics could combine the high permittivity of nanoparticles and the high electrical breakdown strength of the polymer matrix for enhanced dielectric performance. Although higher discharged energy densities have been reported for numerous polymer nanodielectrics, the dielectric loss mechanisms, which are extremely important for ultimate applications, are rarely discussed. In this work, we intend to address the intrinsic dielectric loss mechanisms associated with polymer nanodielectrics using a model system comprised of 70 nm BaTiO3 nanoparticles (BT NPs) in an isotactic polypropylene (PP) matrix. The effect of space charge-induced interfacial polarization on dielectric losses was investigated using bipolar and unipolar electric displacement–electric field (D-E) loop tests. Since the bipolar D-E loops always exhibited greater...

Interfacial Polarization-Induced Loss Mechanisms in Polypropylene/BaTiO3 Nanocomposite Dielectrics

A novel mechanism for counterion-mediated attraction between like-charged spherical macroions is proposed, which originates from a depletion zone of counterions between nearly touching macroions that is induced by Coulomb interactions. Using computer simulations of the primitive model, we show that this depletion effect dominates over the electrostatic contribution in the case of strong Coulomb coupling when all the counterions form a quasi-two-dimensional layer on the spherical macroionic surface. Its range is given by the typical spacing of counterions on the macroion surface.

/pdf/attraction-between-like-charged-macroions-by-coulomb-2251cphduk.pdf

Attraction between Like-Charged Macroions by Coulomb Depletion

Computer simulations and theory are used to systematically investigate how the effective force between two big colloidal spheres in a sea of small spheres depends on the basic ~big-small and small-small! interactions. The latter are modeled as hardcore pair potentials with a Yukawa tail which can be either repulsive or attractive. For a repulsive small-small interaction, the effective force follows the trends as predicted by a mapping onto an effective nonadditive hardcore mixture: both a depletion attraction and an accumulation repulsion caused by small spheres adsorbing onto the big ones can be obtained depending on the sign of the big-small interaction. For repulsive big-small interactions, the effect of adding a small-small attraction also follows the trends predicted by the mapping. But a more subtle ‘‘repulsion through attraction’’ effect arises when both big-small and small-small attractions occur: upon increasing the strength of the small-small interaction, the effective potential becomes more repulsive. We have further tested several theoretical methods against our computer simulations: The superposition approximation works best for an added big-small repulsion, and breaks down for a strong big-small attraction, while density functional theory is very accurate for any big-small interaction when the small particles are pure hard spheres. The theoretical methods perform most

/pdf/effective-forces-in-colloidal-mixtures-from-depletion-1nxpkxae8d.pdf

Elshad Allahyarov

Papers

コロイド混合体における有効力空乏引力から集積斥力へ | 文献情報 | j-global 科学技術総合リンクセンター

Novel polymer ferroelectric behavior via crystal isomorphism and the nanoconfinement effect

Interfacial Polarization-Induced Loss Mechanisms in Polypropylene/BaTiO3 Nanocomposite Dielectrics

Attraction between Like-Charged Macroions by Coulomb Depletion

Effective forces in colloidal mixtures: From depletion attraction to accumulation repulsion

Elshad Allahyarov

Papers

コロイド混合体における有効力 空乏引力から集積斥力へ | 文献情報 | j-global 科学技術総合リンクセンター

Novel polymer ferroelectric behavior via crystal isomorphism and the nanoconfinement effect

Interfacial Polarization-Induced Loss Mechanisms in Polypropylene/BaTiO3 Nanocomposite Dielectrics

Attraction between Like-Charged Macroions by Coulomb Depletion

Effective forces in colloidal mixtures: From depletion attraction to accumulation repulsion

コロイド混合体における有効力空乏引力から集積斥力へ | 文献情報 | j-global 科学技術総合リンクセンター