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

We describe a combined experimental, theoretical, and simulation study of the structural correlations between cross-linked highly monodisperse and swollen Poly(N-isopropylacrylamide) microgel dispersions in the fluid phase in order to obtain the effective pair-interaction potential between the microgels. The density-dependent experimental pair distribution functions g(r)'s are deduced from real space studies using fluorescent confocal microscopy and compared with integral equation theory and molecular dynamics computer simulations. We use a model of Hertzian spheres that is capable to well reproduce the experimental pair distribution functions throughout the fluid phase, having fixed the particle size and the repulsive strength. Theoretically, a monodisperse system is considered whose properties are calculated within the Rogers-Young closure relation, while in the simulations the role of polydispersity is taken into account. We also discuss the various effects arising from the finite resolution of the microscope and from the noise coming from the fast Brownian motion of the particles at low densities, and compare the information content from data taken in 2D and 3D through a comparison with the corresponding simulations. Finally different potential shapes, recently adopted in studies of microgels, are also taken into account to assess which ones could also be used to describe the structure of the microgel fluid.

/pdf/effective-interactions-between-soft-repulsive-colloids-59voxqpqxg.pdf

Effective interactions between soft-repulsive colloids: Experiments, theory, and simulations

A dramatic increase in the viscosity of reverse micellar solutions of lecithin in a variety of organic solvents of up to a factor of 106 upon the addition of a small amount of water can be observed. The formation of viscoelastic solutions can be explained by a water-induced aggregation of lecithin molecules into flexible cylindrical reverse micelles and the subsequent formation of a transient network of entangled micelles. The viscoelastic properties of these solutions are characterized as a function of water content and temperature for different organic solvents by means of dynamic shear viscosity measurements. The results are interpreted by making analogies to the behavior of semidilute polymer solutions and living polymers.

Viscoelastic properties of polymerlike reverse micelles

We introduce an elegant method that allows the application of diffusing-wave spectroscopy (DWS) to nonergodic, solidlike samples. The method is based on the idea that light transmitted through a sandwich of two turbid cells can be considered ergodic even though only the second cell is ergodic. If absorption and/or leakage of light take place at the interface between the cells, we establish a so-called {open_quotes}multiplication rule,{close_quotes} which relates the intensity autocorrelation function of light transmitted through the double-cell sandwich to the autocorrelation functions of individual cells by a simple multiplication. To test the proposed method, we perform a series of DWS experiments using colloidal gels as model nonergodic media. Our experimental data are consistent with the theoretical predictions, allowing quantitative characterization of nonergodic media and demonstrating the validity of the proposed technique.

https://arxiv.org/pdf/cond-mat/0103097.pdf

Diffusing-wave spectroscopy of nonergodic media.

The Derjaguin−Landau−Verwey−Overbeek (DLVO) theory commonly used to describe interactions of charged surfaces across liquids has traditionally been reported to fail when used for quantitative predictions of deposition and aggregation in aqueous colloidal suspensions. Yet direct force measurements have recently confirmed the theory down to surface separations of a few nanometers. Aggregation studies on latex and hematite colloids now reconcile these contrasting findings. Well-known discrepancies between theory and experiment with respect to the dependence of aggregation rates on pH (or electrolyte concentration) and particle size are shown to disappear when charge densities are reduced.

Aggregation in Charge-Stabilized Colloidal Suspensions Revisited

We report results of a light-scattering (LS) and small-angle neutron-scattering (SANS) investigation of a reverse micellar system in which very large and flexible polymerlike aggregates can be found. We will show that it is possible to find conditions under which we can determine the overall dimension, the flexibility, and the local cylindrical structure of these reverse micelles using LS and SANS. This permits us to directly confirm existing structural models and verify the postulated analogy between the structural properties of polymer chains and lecithin reverse micelles

Peter Schurtenberger

Papers

Effective interactions between soft-repulsive colloids: Experiments, theory, and simulations

Viscoelastic properties of polymerlike reverse micelles

Diffusing-wave spectroscopy of nonergodic media.

Aggregation in Charge-Stabilized Colloidal Suspensions Revisited

Cylindrical structure and flexibility of polymerlike lecithin reverse micelles