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

Vesicles consisting of a bilayer membrane of amphiphilic lipid molecules are remarkably flexible surfaces that show an amazing variety of shapes of different symmetry and topology. Owing to the fluidity of the membrane, shape transitions such as budding can be induced by temperature changes or the action of optical tweezers. Thermally excited shape fluctuations are both strong and slow enough to be visible by video microscopy. Depending on the physical conditions, vesicles adhere to and unbind from each other or a substrate. This article describes the systematic physical theory developed to understand the static and dynamic aspects of membrane and vesicle configurations. The preferred shapes arise from a competition between curvature energy, which derives from the bending elasticity of the membrane, geometrical constraints such as fixed surface area and fixed enclosed volume, and a signature of the bilayer aspect. These shapes of lowest energy are arranged into phase diagrams, which separate regi...

Configurations of fluid membranes and vesicles

Janus particles: synthesis, self-assembly, physical properties, and applications.

Supramolecular nanotube architectures based on amphiphilic molecules.

https://www.comp.tmu.ac.jp/shigekomura/paper/YIMKO07.pdf

Growth Dynamics of Domains in Ternary Fluid Vesicles

Surface-active powders have recently attracted much attention in the field of colloid and surface science, particularly in emulsion science.1 When certain wettability conditions are satisfied, solid particles exhibit surface activity.1-4 Hydrophobic silica, iron oxide, clay mineral, carbon black, and polymer latex are some examples of the particles. The adsorbed surface-active powders align at liquid-liquid interfaces and form self-assembled structures.2,3 The so-called “Janus beads” (J-beads) having two surface regions of different wettability are unique particles which can be compared with ordinary surfactant molecules.5 As a result of their amphiphilic nature, the J-beads exhibit stronger surface activity than the homogeneous surface-active powders. It was shown that spherical J-beads are anchored along the boundary line of two surface regions. A mechanism for the adsorption of homogeneous surface-active powders has been described by Levine et al. based on the adsorption energy argument.6 When a spherical particle is adsorbed at a planar liquid-liquid interface, the adsorption energy is governed by the various interfacial tensions between the particle and the liquids as well as the particle radius. The particle is adsorbed at the interface when the interfacial tensions among the three phases are balanced according to the Young’s equation. For the J-beads, on the other hand, Clint and Binks obtained the corresponding adsorption energy to see the effect of the particle amphiphilicity.7 They showed that the amphiphilic J-beads have a typically larger adsorption energy (hence, stronger adsorption) than the homogeneous particles. For traditional surfactant molecules, effects of the molecular shape on the interfacial properties have been extensively studied by using the models proposed by Israelachvili or Helfrich.8,9 However, there is little precedent literature as to the shape of the surface-active particle. In our previous experimental studies, we showed that the shape of the particles indeed affects their selfassembled structures.2,3 Rossmy also reported that the morphology of the emulsions stabilized by J-beads depends onthegeometricalpropertyof thebeads.10 Recently,Brown et al. have shown that amphiphilic curved disks distort an air-water interface, giving rise to anisotoropic forces between the disks.11 These observations imply that the self-assembled structures of the surface-active particles are governed not only by the wettabilities but also by the shapes of the particle. In the present work, we obtain the adsorption energy of the disk-shaped J-beads as illustrated in Figure 1a. In contrast to the spherical J-beads, the adsorption energy changes discontinuously for the disk-shaped J-beads. We also show the effect of the adsorption on the geometry of the liquid-liquid interface. We discuss the adsorption of a disk-shaped J-bead at a liquid-liquid interface. As shown in Figure 1a, a diskshaped J-bead consists of part P1 with thickness l1 and part P2 with thickness l2. Let F be the adsorption energy per bead when it is adsorbed at the interface between the liquid A and the liquid B (see Figure 1b). When the whole bead is immersed either in liquid A or in liquid B, F is given by eq 1 or 2:

Adsorption of disk-shaped janus beads at liquid-liquid interfaces.

In an effort to understand "rafts" in biological membranes, we propose phenomenological models for saturated and unsaturated lipid mixtures, and lipid-cholesterol mixtures. We consider simple couplings between the local composition and internal membrane structure, and their influence on transitions between liquid and gel membrane phases. Assuming that the gel transition temperature of the saturated lipid is shifted by the presence of the unsaturated lipid, and that cholesterol acts as an external field on the chain melting transition, a variety of phase diagrams are obtained. The phase diagrams for binary mixtures of saturated/unsaturated lipids and lipid/cholesterol are in semi-quantitative agreement with the experiments. Our results also apply to regions in the ternary phase diagram of lipid/lipid/cholesterol systems.

/pdf/lateral-phase-separation-in-mixtures-of-lipids-and-240ma5wswc.pdf

Lateral phase separation in mixtures of lipids and cholesterol

Neutron spin–echo investigations of membrane undulations in complex fluids involving amphiphiles

Dynamics of microphase separation of an oil-water-surfactant system is investigated by means of cell dynamical system approach on the basis of the proposed two-order-parameter time dependent Ginzburg-Landau model. For equal volumes of oil and water, the time evolution of characteristic length scale of domains is investigated by changing the average surfactant concentration. The more the amount of surfactant, the slower the dynamics. The results are analyzed by using the crossover scaling assumption.

/pdf/two-order-parameter-model-for-an-oil-water-surfactant-system-1zk81ouftm.pdf

Shigeyuki Komura

Papers

Growth Dynamics of Domains in Ternary Fluid Vesicles

Adsorption of disk-shaped janus beads at liquid-liquid interfaces.

Lateral phase separation in mixtures of lipids and cholesterol

Neutron spin–echo investigations of membrane undulations in complex fluids involving amphiphiles

Two-order-parameter model for an oil-water-surfactant system