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

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

Wetting phenomena are ubiquitous in nature and technology. A solid substrate exposed to the environment is almost invariably covered by a layer of fluid material. In this review, the surface forces that lead to wetting are considered, and the equilibrium surface coverage of a substrate in contact with a drop of liquid. Depending on the nature of the surface forces involved, different scenarios for wetting phase transitions are possible; recent progress allows us to relate the critical exponents directly to the nature of the surface forces which lead to the different wetting scenarios. Thermal fluctuation effects, which can be greatly enhanced for wetting of geometrically or chemically structured substrates, and are much stronger in colloidal suspensions, modify the adsorption singularities. Macroscopic descriptions and microscopic theories have been developed to understand and predict wetting behavior relevant to microfluidics and nanofluidics applications. Then the dynamics of wetting is examined. A drop, placed on a substrate which it wets, spreads out to form a film. Conversely, a nonwetted substrate previously covered by a film dewets upon an appropriate change of system parameters. The hydrodynamics of both wetting and dewetting is influenced by the presence of the three-phase contact line separating "wet" regions from those that are either dry or covered by a microscopic film only. Recent theoretical, experimental, and numerical progress in the description of moving contact line dynamics are reviewed, and its relation to the thermodynamics of wetting is explored. In addition, recent progress on rough surfaces is surveyed. The anchoring of contact lines and contact angle hysteresis are explored resulting from surface inhomogeneities. Further, new ways to mold wetting characteristics according to technological constraints are discussed, for example, the use of patterned surfaces, surfactants, or complex fluids.

/pdf/wetting-and-spreading-56ditqbfmj.pdf

Wetting and Spreading

When a capillary is inserted into a liquid, the liquid will rapidly flow into it. This phenomenon, well studied and understood on the macroscale, is investigated by molecular dynamics simulations for coarse-grained models of nanotubes. Both a simple Lennard-Jones fluid and a model for a polymer melt are considered. In both cases after a transient period (of a few nanoseconds) the meniscus rises according to a (time)1/2 law. For the polymer melt, however, we find that the capillary flow exhibits a slip length delta, comparable in size with the nanotube radius R. We show that a consistent description of the imbibition process in nanotubes is only possible upon modification of the Lucas-Washburn law which takes explicitly into account the slip length delta. We also demonstrate that the velocity field of the rising fluid close to the interface is not a simple diffusive spreading.

Capillary rise in nanopores: molecular dynamics evidence for the Lucas-Washburn equation.

A simple theoretical model describing the influence of disorder on transport properties (viscosity, diffusion coefficients, etc.) in undercooled melts and crystals is suggested. The basic assumption is that structural disarray results in a random probability distribution of energy barriers for diffusion characterized by dispersion σ around some mean value 〈E〉. It is shown that the effect of σ on the mean jump frequency 〈v(E)〉 may lead to corrections of many order of magnitude as compared to the hopping frequency calculated traditionally in terms of the average activation energy 〈E〉 only. The temperature course of 〈v(E)〉 is then examined making use of the relation between σ and the entropy of the system S. Thus an analytical formula is obtained which properly describes molecular transport in both the crystalline and the amorphous state. Even in a simplified form, η=η0 exp(β/Tα), it reproduces well the existing data on temperature variation of viscosity η (or self-diffusion) in glassforming melts. In another aspect - in terms of the percolation theory - the model describes the diffusion of a foreign particle in a rigid host structure and yields also a qualitative estimate of the variation of the percolation threshold Ep with the degree of amorphisation σ.

Effect of disorder on diffusion and viscosity in condensed systems

Theoretical descriptions of static properties of polymer brushes are reviewed, with an emphasis on monodisperse macromolecules grafted to planar, cylindrical, or spherical substrates. Blob concepts and resulting scaling relations are outlined, and various versions of the self-consistent field theory are summarized: the classical approximation and the strong stretching limit, as well as the lattice formulation. The physical justification of various inherent assumptions is discussed, and computer simulation results addressing the test of the validity of these approximations are reviewed. Also, alternative theories, such as the single chain mean field theory and the density functional theory, are briefly mentioned, and the main facts about the models used in the computer simulations are summarized. Both molecular dynamics and Monte Carlo simulations are described, the latter including lattice models and bead-spring models in the continuum. Also extensions such as brush–brush interactions or nanoparticles inside of brushes as well as the solubility of free chains in brushes are briefly mentioned. Pertinent experimental results, though still somewhat scarce, are mentioned throughout and their consequences on the status of the theoretical understanding of polymer brushes is emphasized. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012

Polymer brushes on flat and curved surfaces: How computer simulations can help to test theories and to interpret experiments

The adsorption of flexible polymers from dilute solution in good solvents at attractive walls is studied by Monte Carlo simulation of a coarse-grained off-lattice model, varying chain length N and ...

Andrey Milchev

Papers

Capillary rise in nanopores: molecular dynamics evidence for the Lucas-Washburn equation.

Effect of disorder on diffusion and viscosity in condensed systems

Polymer brushes on flat and curved surfaces: How computer simulations can help to test theories and to interpret experiments

Static and Dynamic Properties of Adsorbed Chains at Surfaces: Monte Carlo Simulation of a Bead-Spring Model

Atomistic theory of electrolytic nucleation: I