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

Recent advances in PCS particle size characterization in turbid suspensions are discussed. We show two complementary routes to overcome the limitations of traditional PCS with respect to multiple scattering of light. The first one, called 3D dynamic light scattering (3DDLS) aims to suppress multiple scattering with a two detector cross correlation scheme. Combined with a parallel processing of experiments at different angles such a setup may significantly improve resolution and stability for the analysis of complex particle size distributions in turbid suspensions. The second technique, diffusing wave spectroscopy (DWS), is shown to be a versatile method to obtain information about the average particle size based on the analysis of diffusely reflected light.

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PCS particle sizing in turbid suspensions: scope and limitations

Sponge phases and balanced microemulsions: What determines their stability?

Microfluidic production of snowman-shaped Janus hydrogel particles

We report an investigation of the microscopic structure and dynamics of biopolymer gels and relate them to the macroscopic viscoelastic properties of such systems. Biopolymer solutions and gels represent one of the most interesting class of gelling systems since they are of major industrial and scientific interest. We performed a systematic study using concentrated solutions of casein micelles which we destabilized and investigated during the process of gelation using diffusing wave spectroscopy (DWS) and rheological measurements. An analysis of the light scattering data shows a significant increase in the characteristic decay time of the correlation functions during the sol—gel transition. For the analysis of the DWS data we developed an algorithm which, based on the so-called microrheology approach, determines the viscoelastic properties G′(ω) and G′'(ω) of the gel. A comparison of the results obtained with DWS and measurements with a rheometer shows excellent agreement of both approaches. We demonstrate that we can clearly link the changes observed in the microscopic dynamics to the formation of a macroscopic gel with drastically modified viscoelastic properties.

Aggregation and gel formation in biopolymer solutions

Lysozyme is known to form equilibrium clusters at pH ≈ 7.8 and at low ionic strength as a result of a mixed potential. While this cluster formation and the related dynamic and static structure factors have been extensively investigated, its consequences on the macroscopic dynamic behavior expressed by the zero shear viscosity η0 remain controversial. Here we present results from a systematic investigation of η0 using two complementary passive microrheology techniques, dynamic light scattering based tracer microrheology, and multiple particle tracking using confocal microscopy. The combination of these techniques with a simple but effective evaporation approach allows for reaching concentrations close to and above the arrest transition in a controlled and gentle way. We find a strong increase of η0 with increasing volume fraction ϕ with an apparent divergence at ϕ ≈ 0.35, and unambiguously demonstrate that this is due to the existence of an arrest transition where a cluster glass forms. These findings demonstrate the power of tracer microrheology to investigate complex fluids, where weak temporary bonds and limited sample volumes make measurements with classical rheology challenging.

Peter Schurtenberger

Papers

PCS particle sizing in turbid suspensions: scope and limitations

Sponge phases and balanced microemulsions: What determines their stability?

Microfluidic production of snowman-shaped Janus hydrogel particles

Aggregation and gel formation in biopolymer solutions

Experimental Evidence for a Cluster Glass Transition in Concentrated Lysozyme Solutions.