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

Structure, dynamics, and optical properties of concentrated milk suspensions: an analogy to hard-sphere liquids.

We have performed a series of small-angle neutron scattering (SANS) and static light scattering (SLS) experiments with dilute and semidilute solutions of polymer-like micelles formed by C 16 E 6 in D 2 O at two different temperatures (T = 26 °C, 35 °C). The local structure has been investigated by applying indirect Fourier transformation and square-root deconvolution techniques. We demonstrate that the micelles maintain their locally cylindrical structure in this temperature regime despite the significant change in the spontaneous curvature of the surfactant. Detailed information on the micellar flexibility has been obtained from the SANS data by applying a nonlinear least-squares fitting procedure based upon a numerical expression for the single-chain scattering function of a worm-like chain with excluded volume effects. Particular attention has been given to the determination of quantitative numbers for the intrinsic' persistence length as well as for the contribution from electrostatic interactions upon the addition of a small fraction of an ionic surfactant. The results have been compared with predictions from theoretical models for polyelectrolytes.

Flexibility of Charged and Uncharged Polymer-like Micelles

Concentrated aqueous solutions of the protein lysozyme undergo a liquid-solid transition upon a temperature quench into the unstable spinodal region below a characteristic arrest temperature of T(f) = 15 °C. We use video microscopy and ultra-small angle light scattering in order to investigate the arrested structures as a function of initial concentration, quench temperature and rate of the temperature quench. We find that the solid-like samples show all the features of a bicontinuous network that is formed through an arrested spinodal decomposition process. We determine the correlation length ξ and demonstrate that ξ exhibits a temperature dependence that closely follows the critical scaling expected for density fluctuations during the early stages of spinodal decomposition. These findings are in agreement with an arrest scenario based on a state diagram where the arrest or gel line extends far into the unstable region below the spinodal line. Arrest then occurs when during the early stage of spinodal decomposition the volume fraction φ(2) of the dense phase intersects the dynamical arrest threshold φ(2,Glass), upon which phase separation gets pinned into a space-spanning gel network with a characteristic length ξ.

/pdf/a-closer-look-at-arrested-spinodal-decomposition-in-protein-235czem5up.pdf

A closer look at arrested spinodal decomposition in protein solutions.

of the metal is bare again and the oxidation process can go on until the whole metal has been destroyed. Once again the oxidative dissolution of metal particles by treatment with NO points out the powerful ability of NO for "desintering" supported metals. The oxidation by O2 is more difficult. For sample reduced at 200 "C a very long time in O2 at 200 "C is needed for recovering the previously ionic state of nickel. But for the sample treated at 500 "C under H2, reoxidation is limited. Even heated at 500 "C the metal cannot be completely converted into ions. This probably occurs because at elevated temperature nickel cannot be prevented from sintering and large particles are formed as shown by magnetic measurements. Moreover it cannot be excluded that oxygen reacts with metal particles forming nonvolatile surface oxide deposited onto the metallic phase. So oxidation would be inhibited.

Static and dynamic light scattering studies of micellar growth and interactions in bile salt solutions

We present a quantitative experimental comparison of fiber-based, single- and few-mode dynamic light scattering with the classical pinhole-detection optics. The recently presented theory of mode-selective dynamic light scattering [Appl. Opt. 32, 2860 (1993)] predicts a collection efficiency and a signal-tobaseline ratio superior to that of a classical pinhole setup. These predictions are confirmed by our experiments. Using single-mode optical fibers with different cutoff wavelengths and commercially available mechanical components, we have constructed a mode-selective detection optics in a simple and compact dynamic light-scattering spectrometer that permits an optimal compromise between signal intensity and dynamical resolution.

/pdf/mode-selective-dynamic-light-scattering-theory-versus-59t7bi6q8b.pdf

Peter Schurtenberger

Papers

Structure, dynamics, and optical properties of concentrated milk suspensions: an analogy to hard-sphere liquids.

Flexibility of Charged and Uncharged Polymer-like Micelles

A closer look at arrested spinodal decomposition in protein solutions.

Static and dynamic light scattering studies of micellar growth and interactions in bile salt solutions

Mode-selective dynamic light scattering: theory versus experimental realization.