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

The manipulation of fluids in channels with dimensions of tens of micrometres--microfluidics--has emerged as a distinct new field. Microfluidics has the potential to influence subject areas from chemical synthesis and biological analysis to optics and information technology. But the field is still at an early stage of development. Even as the basic science and technological demonstrations develop, other problems must be addressed: choosing and focusing on initial applications, and developing strategies to complete the cycle of development, including commercialization. The solutions to these problems will require imagination and ingenuity.

The origins and the future of microfluidics

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.

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Microfluidics: Fluid physics at the nanoliter scale

Microfluidic devices for manipulating fluids are widespread and finding uses in many scientific and industrial contexts. Their design often requires unusual geometries and the interplay of multiple physical effects such as pressure gradients, electrokinetics, and capillarity. These circumstances lead to interesting variants of well-studied fluid dynamical problems and some new fluid responses. We provide an overview of flows in microdevices with focus on electrokinetics, mixing and dispersion, and multiphase flows. We highlight topics important for the description of the fluid dynamics: driving forces, geometry, and the chemical characteristics of surfaces.

Engineering flows in small devices

The past decade has seen researchers develop and apply novel technologies for biomolecular detection, at times approaching hard limits imposed by physics and chemistry. In nearly all sensors, the transport of target molecules to the sensor can play as critical a role as the chemical reaction itself in governing binding kinetics, and ultimately performance. Yet rarely does an analysis of the interplay between diffusion, convection and reaction motivate experimental design or interpretation. Here we develop a physically intuitive and practical understanding of analyte transport for researchers who develop and employ biosensors based on surface capture. We explore the qualitatively distinct behaviors that result, develop rules of thumb to quickly determine how a given system will behave, and derive order-of-magnitude estimates for fundamental quantities of interest, such as fluxes, collection rates and equilibration times. We pay particular attention to collection limits for micro- and nanoscale sensors, and highlight unexplained discrepancies between reported values and theoretical limits.

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Making it stick: convection, reaction and diffusion in surface-based biosensors.

We give a general, physical description of "induced-charge electro-osmosis" (ICEO), the nonlinear electrokinetic slip at a polarizable surface, in the context of some new techniques for microfluidic pumping and mixing. ICEO generalizes "ac electro-osmosis" at microelectrode arrays to various di-electric and conducting structures in weak dc or ac electric fields. The basic effect produces microvortices to enhance mixing in microfluidic devices, while various broken symmetries--controlled potential, irregular shape, nonuniform surface properties, and field gradients--can be exploited to produce streaming flows. Although we emphasize the qualitative picture of ICEO, we also briefly describe the mathematical theory (for thin double layers and weak fields) and apply it to a metal cylinder with a dielectric coating in a suddenly applied dc field.

/pdf/induced-charge-electrokinetic-phenomena-theory-and-57jai3zera.pdf

Induced-Charge Electrokinetic Phenomena: Theory and Microfluidic Applications

We describe the general phenomenon of ‘induced-charge electro-osmosis’ (ICEO) – the nonlinear electro-osmotic slip that occurs when an applied field acts on the ionic charge it induces around a polarizable surface. Motivated by a simple physical picture, we calculate ICEO flows around conducting cylinders in steady (DC), oscillatory (AC), and suddenly applied electric fields. This picture, and these systems, represent perhaps the clearest example of nonlinear electrokinetic phenomena. We complement and verify this physically motivated approach using a matched asymptotic expansion to the electrokinetic equations in the thin-double-layer and low-potential limits. ICEO slip velocities vary as $u_s \,{\propto}\,E_0^2 L$, where $E_0$ is the field strength and $L$ is a geometric length scale, and are set up on a time scale $\tau_c \,{=}\,\lambda_D L/D$, where $\lambda_D$ is the screening length and $D$ is the ionic diffusion constant. We propose and analyse ICEO microfluidic pumps and mixers that operate without moving parts under low applied potentials. Similar flows around metallic colloids with fixed total charge have been described in the Russian literature (largely unnoticed in the West). ICEO flows around conductors with fixed potential, on the other hand, have no colloidal analogue and offer further possibilities for microfluidic applications.

/pdf/induced-charge-electro-osmosis-54fisklonh.pdf

Induced-charge electro-osmosis

In microrheology, the local and bulk mechanical properties of a complex fluid are extracted from the motion of probe particles embedded within it. In passive microrheology, particles are forced by thermal fluctuations and probe linear viscoelasticity, whereas active microrheology involves forcing probes externally and can be extended out of equilibrium to the nonlinear regime. Here we review the development, present state, and future directions of this field. We organize our review around the generalized Stokes-Einstein relation (GSER), which plays a central role in the interpretation of microrheology. By discussing the Stokes and Einstein components of the GSER individually, we identify the key assumptions that underpin each, and the consequences that occur when they are violated. We conclude with a discussion of two techniques—multiple particle-tracking and nonlinear microrheology— that have arisen to handle systems in which the GSER breaks down.

Todd M. Squires

Papers

Microfluidics: Fluid physics at the nanoliter scale

Making it stick: convection, reaction and diffusion in surface-based biosensors.

Induced-Charge Electrokinetic Phenomena: Theory and Microfluidic Applications

Induced-charge electro-osmosis

Fluid Mechanics of Microrheology