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

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Table Of Integrals Series And Products

Microfabricated integrated circuits revolutionized computation by vastly reducing the space, labor, and time required for calculations. Microfluidic systems hold similar promise for the large-scale automation of chemistry and biology, suggesting the possibility of numerous experiments performed rapidly and in parallel, while consuming little reagent. While it is too early to tell whether such a vision will be realized, significant progress has been achieved, and various applications of significant scientific and practical interest have been developed. Here a review of the physics of small volumes (nanoliters) of fluids is presented, as parametrized by a series of dimensionless numbers expressing the relative importance of various physical phenomena. Specifically, this review explores the Reynolds number Re, addressing inertial effects; the Peclet number Pe, which concerns convective and diffusive transport; the capillary number Ca expressing the importance of interfacial tension; the Deborah, Weissenberg, and elasticity numbers De, Wi, and El, describing elastic effects due to deformable microstructural elements like polymers; the Grashof and Rayleigh numbers Gr and Ra, describing density-driven flows; and the Knudsen number, describing the importance of noncontinuum molecular effects. Furthermore, the long-range nature of viscous flows and the small device dimensions inherent in microfluidics mean that the influence of boundaries is typically significant. A variety of strategies have been developed to manipulate fluids by exploiting boundary effects; among these are electrokinetic effects, acoustic streaming, and fluid-structure interactions. The goal is to describe the physics behind the rich variety of fluid phenomena occurring on the nanoliter scale using simple scaling arguments, with the hopes of developing an intuitive sense for this occasionally counterintuitive world.

/pdf/microfluidics-fluid-physics-at-the-nanoliter-scale-4bpahtd8qa.pdf

Microfluidics: Fluid physics at the nanoliter scale

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

Wang et al. [Proc. Natl. Acad. Sci. U.S.A. 106, 15160 (2009)] have found that in several systems the linear time dependence of the mean-square displacement (MSD) of diffusing colloidal particles, typical of normal diffusion, is accompanied by a non-Gaussian displacement distribution $G(x,t)$, with roughly exponential tails at short times, a situation they termed ``anomalous yet Brownian'' diffusion. The diversity of systems in which this is observed calls for a generic model. We present such a model where there is diffusivity memory but no direction memory in the particle trajectory, and we show that it leads to both a linear MSD and a non-Gaussian $G(x,t)$ at short times. In our model, the diffusivity is undergoing a (perhaps biased) random walk, hence the expression ``diffusing diffusivity''. $G(x,t)$ is predicted to be exactly exponential at short times if the distribution of diffusivities is itself exponential, but an exponential remains a good fit for a variety of diffusivity distributions. Moreover, our generic model can be modified to produce subdiffusion.

Diffusing diffusivity: a model for anomalous, yet Brownian, diffusion.

The free-draining properties of DNA normally make it impossible to separate nucleic acids by free-flow electrophoresis. However, little is known, either theoretically or experimentally, about the diffusion coefficient of DNA molecules during free-flow electrophoresis. In fact, many authors simply assume that the Nernst-Einstein relation between the mobility and the diffusion coefficient still holds under such conditions. In this paper, we present an experimental study of the diffusion coefficient of both ssDNA and dsDNA molecules during free-flow electrophoresis. Our results unequivocally show that a simplistic use of Nernst-Einstein's relation fails, and that the electric field actually has no effect on the thermal diffusion process. Finally, we compare the dependence of the diffusion coefficient upon DNA molecular size to results obtained previously by other groups and to Zimm's theory.

Diffusion coefficient of DNA molecules during free solution electrophoresis

We introduce a new biased reptation theory that allows a qualitative and semiquantitative study of DNA gel electrophoresis. We prove that stretching of the end-to-end vector of a very long charged reptating chain in an electric field occurs in a short period of time during a typical electrophoresis experiment, and that this leads to a field-dependent mobility only weaky dependent upon the size of the chain, in agreement with experiments on DNA. We also propose a practical technique to avoid chain stretching. Finally, many scaling laws are predicted, most of them being verifiable by experiment.

On the reptation theory of gel electrophoresis

Debate over the nature of temporary agency work has intensified in recent times, spurred on by a proposed European directive and by speculation about links with the much heralded ‘knowledge’ economy. This paper examines the debate, focusing on the current character of agency work in Britain. Using data from the Labour Force Survey (LFS), we assess some of the claims commonly made about agency work, relating to the personal and employment characteristics of those engaged in such work, the motives of agency workers and the prospects for those who take up agency jobs. In considering the arguments surrounding regulatory change, we find there is a strong case for regulation, but that this rests on the continued disadvantage associated with agency work, with little evidence of an impact from the purported ‘knowledge’ economy.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1467-8543.2005.00354.x

Agency Working in Britain: Character, Consequences and Regulation

An extensive series of experiments has been performed to study the mobility of DNA fragments ranging in size from 2.0 to 48.5 kilobose pairs. By varying the agarose concentration in the gels and the electric field strength, three DNA electrophoresis regimes were clearly identified: the Ogston regime (small DNA fragments in large pores of agarose), the reptation regime without DNA chain stretching (small pores of agarose and weak electric fields), and the reptation regime with DNA chain stretching (small pores of agarose, strong electric fields, and large DNA fragments). Here we report on the experimental identification of these regimes and on the conditions governing the transition between each of them. The onset of reptation and of stretching of DNA chains in gel electrophoresis are described quantitatively for the first time, and a phase diagram for the dynamics of DNA during electrophoresis is presented.

Gary W. Slater

Papers

Diffusing diffusivity: a model for anomalous, yet Brownian, diffusion.

Diffusion coefficient of DNA molecules during free solution electrophoresis

On the reptation theory of gel electrophoresis

Agency Working in Britain: Character, Consequences and Regulation

Quantitative analysis of the three regimes of DNA electrophoresis in agarose gels.