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

J. Appl. Cryst.の発刊に際して

1. Introduction 20642. Synthesis of Magnetic Nanoparticles 20662.1. Classical Synthesis by Coprecipitation 20662.2. Reactions in Constrained Environments 20682.3. Hydrothermal and High-TemperatureReactions20692.4. Sol-Gel Reactions 20702.5. Polyol Methods 20712.6. Flow Injection Syntheses 20712.7. Electrochemical Methods 20712.8. Aerosol/Vapor Methods 20712.9. Sonolysis 20723. Stabilization of Magnetic Particles 20723.1. Monomeric Stabilizers 20723.1.1. Carboxylates 20733.1.2. Phosphates 20733.2. Inorganic Materials 20733.2.1. Silica 20733.2.2. Gold 20743.3. Polymer Stabilizers 20743.3.1. Dextran 20743.3.2. Polyethylene Glycol (PEG) 20753.3.3. Polyvinyl Alcohol (PVA) 20753.3.4. Alginate 20753.3.5. Chitosan 20753.3.6. Other Polymers 20753.4. Other Strategies for Stabilization 20764. Methods of Vectorization of the Particles 20765. Structural and Physicochemical Characterization 20785.1. Size, Polydispersity, Shape, and SurfaceCharacterization20795.2. Structure of Ferro- or FerrimagneticNanoparticles20805.2.1. Ferro- and Ferrimagnetic Nanoparticles 20805.3. Use of Nanoparticles as Contrast Agents forMRI20825.3.1. High Anisotropy Model 20845.3.2. Small Crystal and Low Anisotropy EnergyLimit20855.3.3. Practical Interests of Magnetic NuclearRelaxation for the Characterization ofSuperparamagnetic Colloid20855.3.4. Relaxation of Agglomerated Systems 20856. Applications 20866.1. MRI: Cellular Labeling, Molecular Imaging(Inﬂammation, Apoptose, etc.)20866.2.

Magnetic Iron Oxide Nanoparticles: Synthesis, Stabilization, Vectorization, Physicochemical Characterizations, and Biological Applications

Low Molecular Mass Gelators of Organic Liquids and the Properties of Their Gels

Controlling interparticle interactions, aggregation and cluster formation is of central importance in a number of areas, ranging from cluster formation in various disease processes to protein crystallography and the production of photonic crystals. Recent developments in the description of the interaction of colloidal particles with short-range attractive potentials have led to interesting findings including metastable liquid-liquid phase separation and the formation of dynamically arrested states (such as the existence of attractive and repulsive glasses, and transient gels). The emerging glass paradigm has been successfully applied to complex soft-matter systems, such as colloid-polymer systems and concentrated protein solutions. However, intriguing problems like the frequent occurrence of cluster phases remain. Here we report small-angle scattering and confocal microscopy investigations of two model systems: protein solutions and colloid-polymer mixtures. We demonstrate that in both systems, a combination of short-range attraction and long-range repulsion results in the formation of small equilibrium clusters. We discuss the relevance of this finding for nucleation processes during protein crystallization, protein or DNA self-assembly and the previously observed formation of cluster and gel phases in colloidal suspensions.

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Equilibrium cluster formation in concentrated protein solutions and colloids

Foods make up some of the most complex examples of soft condensed matter (SCM) with which we interact daily. Their complexity arises from several factors: the intricacy of components, the different aggregation states in which foods are encountered, and the multitude of relevant characteristic time and length scales. Because foodstuffs are governed by the rules of SCM physics but with all the complications related to real systems, the experimental and theoretical approaches of SCM physics have deepened our comprehension of their nature and behaviour, but many questions remain. In this review we discuss the current understanding of food science, by considering established SCM methods as well as emerging techniques and theoretical approaches. With their complexity, heterogeneity and multitude of states, foods provide SCM physics with a challenge of remarkable importance.

Understanding foods as soft materials

Off-lattice Monte Carlo simulations on semiflexible polymer chains with and without excluded volume interactions have been performed. The model used in the simulations is a discrete representation of the worm-like chain model of Kratky and Porod applied in the pseudocontinuous limit. The ratio between the cross-section radius R of the chain and the statistical segment length b was chosen to be R/b = 0.1 which corresponds to the value found for polymer-like micelles. The ratio R/b is equivalent to a reduced binary cluster integral of B = 0.30, which is in accordance with the value for polystyrene in a good solvent. The scattering functions of the semiflexible chains have been determined with a precision of 1−2% for L/b = 0.3−640, where L is the contour length of the chain. Numerical approximations to these functions have been determined which interpolate between the simulated functions, and these can be used in the analysis of experimental scattering data. The approximations have been used in least-squares...

Scattering Functions of Semiflexible Polymers with and without Excluded Volume Effects

In this work we study the kinetics of coagulation of monodisperse spherical colloids in aqueous suspension at the early stage of coagulation. We have performed the measurements on a multiangle static and dynamic light scattering instrument using a fiber-optics-based detection system which permits simultaneous time-resolved measurements at different angles. The absolute coagulation rate constants are determined from the change of the scattering light intensity as well as from the increase of the hydrodynamic radius at different angles. The combined evaluation of static and dynamic light scattering results permits the determination of coagulation rate constants without the explicit use of light scattering form factors for the aggregates. For different electrolytes fast coagulation rate constants were estimated. Stability curves were measured as a function of ionic strength using different particle concentrations.

Peter Schurtenberger

Papers

Equilibrium cluster formation in concentrated protein solutions and colloids

Understanding foods as soft materials

Scattering Functions of Semiflexible Polymers with and without Excluded Volume Effects

Coagulation Rate Measurements of Colloidal Particles by Simultaneous Static and Dynamic Light Scattering

Micelle to vesicle transition in aqueous solutions of bile salt and lecithin