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

Herein we present our results on the investigation of the influence of external magnetic fields on the anisotropic collective dynamics of core/shell colloidal cubes having a hematite core and silica shell. Owing to the hematite cores, these micrometer-sized particles possess permanent dipole moments, which are at an angle with respect to the long diagonal of the cubes. As a result, they self-assemble into chains, which subsequently sediment to form higher-order structures. Using multispeckle ultrasmall-angle x-ray photon correlation spectroscopy, the anisotropic dynamics within these structures at the nearest-neighbor length scale was probed. The relaxation of the intermediate scattering function follows a compressed exponential behavior along all the different directions with respect to the external field---parallel, perpendicular, and at an angle $\ensuremath{\approx}{45}^{\ensuremath{\circ}}$---indicating hyperdiffusive behavior. We believe that the inhomogeneous distribution of stress points originating from the interplay of external field-induced (both gravitational and magnetic) alignment of the chains are responsible for the anomalous dynamics. The effective diffusion coefficients along and at $\ensuremath{\approx}{45}^{\ensuremath{\circ}}$ angle exhibit mild de Gennes narrowing, which is not very common for hyperdiffusive dynamics. We rationalize our observations by considering a superposition of diffusive and stress-induced ballistic processes and argue that depending on the azimuthal direction the relative contribution from these two processes changes.

https://link.aps.org/pdf/10.1103/PhysRevMaterials.5.035603

Anisotropic dynamics of magnetic colloidal cubes studied by x-ray photon correlation spectroscopy

Diffusion of proteins on length scales of their size is crucial for understanding the machinery of living cells. X-ray photon correlation spectroscopy (XPCS) is currently the only way to access long-time collective diffusion on these length scales, but radiation damage so far limits the use in biological systems. We apply a new approach to use XPCS to measure cage relaxation in crowded α-crystallin solutions. This allows us to correct for radiation effects, obtain missing information on long time diffusion, and support the fundamental analogy between protein and colloid dynamical arrest.

/pdf/probing-cage-relaxation-in-concentrated-protein-solutions-by-2qlszwhq.pdf

Probing Cage Relaxation in Concentrated Protein Solutions by X-Ray Photon Correlation Spectroscopy.

The non-linear rheology of colloidal gels, glasses, and pastes is rather complex. For instance, colloidal glasses and pastes yield at a certain strain, followed by shear thinning. A detailed understanding of the yielding point, and what causes it, is lacking. Here, we perform constant shear rate rheology on a pre-sheared material, smooth peanut butter, which is a glassy colloidal paste. Controlling the ageing appears to control the yield stress value, whose associated stress scales with the applied pre-shear with a power law of 1/2. This corresponds to the governing formula for the work hardening mechanism in metals, from which an analogy is drawn.

Peter Schurtenberger

Papers

Anisotropic dynamics of magnetic colloidal cubes studied by x-ray photon correlation spectroscopy

Probing Cage Relaxation in Concentrated Protein Solutions by X-Ray Photon Correlation Spectroscopy.

Work hardening of soft glassy materials, or a metallurgist’s view of peanut butter

Two-Cell Echo DWS

Scattering from Wormlike Micelles