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

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

基礎講座 電気泳動(Electrophoresis)

인공고관절의 세라믹 볼 헤드의 기계적 안정성 평가를 위한 3 차원 유한요소 해석

We present a system for the electrocoalescence of microfluidic droplets immersed in an immiscible solvent, where the undeformed droplet diameters are comparable to the channel diameter. The electrodes are not in direct contact with the carrier liquid or the droplets, thereby minimizing the risk of cross-contamination between different coalescence events. Results are presented for the coalescence of buffered aqueous droplets in both quiescent and flowing fluorocarbon streams, and on-flight coalescence is demonstrated. The capillary-based system presented here is readily amenable to further miniaturization to any lab-on-a-chip application where the conductivity of the droplets is much greater than the conductivity of the stream containing them, and should aid in the further application of droplet microreactors to biological analyses.

Droplet fusion by alternating current (AC) field electrocoalescence in microchannels.

Small-angle x-ray scattering experiments conducted with compositionally asymmetric low molar mass poly(isoprene)-b-poly(lactide) diblock copolymers reveal an extraordinary thermal history dependence. The development of distinct periodic crystalline or aperiodic quasicrystalline states depends on how specimens are cooled from the disordered state to temperatures below the order-disorder transition temperature. Whereas direct cooling leads to the formation of documented morphologies, rapidly quenched samples that are then heated from low temperature form the hexagonal C14 and cubic C15 Laves phases commonly found in metal alloys. Self-consistent mean-field theory calculations show that these, and other associated Frank-Kasper phases, have nearly degenerate free energies, suggesting that processing history drives the material into long-lived metastable states defined by self-assembled particles with discrete populations of volumes and polyhedral shapes.

http://science.sciencemag.org/content/sci/356/6337/520.full.pdf

Thermal processing of diblock copolymer melts mimics metallurgy

/pdf/beyond-gel-electrophoresis-microfluidic-separations-3rdn3uy9q5.pdf

Beyond gel electrophoresis: Microfluidic separations, fluorescence burst analysis, and DNA stretching

We present a method for performing polymerase chain reaction (PCR) using isolated droplets flowing in an immiscible fluorinated solvent system. Thanks to an optimized control of interfacial properties, we could achieve in this capillary-based system reproducible amplification factors, without any detectable contamination between neighboring droplets. The system is readily amenable to further miniaturization and automation and serves as the first step toward a clinically viable, high-throughput, quantitative continuous flow PCR apparatus.

Contamination-free continuous flow microfluidic polymerase chain reaction for quantitative and clinical applications

We have used a realistic model for double stranded DNA and Monte Carlo simulations to compute the extension (mean span) of a DNA molecule confined in a nanochannel over the full range of confinement in a high ionic strength buffer. The simulation data for square nanochannels resolve the apparent contradiction between prior simulation studies and the predictions from Flory theory, demonstrating the existence of two transition regimes between weak confinement (the de Gennes regime) and strong confinement (the Odijk regime). The simulation data for rectangular nanochannels support the use of the geometric mean for mapping data obtained in rectangular channels onto models developed for cylinders. The comparison of our results with experimental data illuminates the challenges in applying models for confined, neutral polymers to polyelectrolytes. Using a Flory-type approach, we also provide an improved scaling result for the relaxation time in the transition regime close to that found in experiments.

Kevin D. Dorfman

Papers

Droplet fusion by alternating current (AC) field electrocoalescence in microchannels.

Thermal processing of diblock copolymer melts mimics metallurgy

Beyond gel electrophoresis: Microfluidic separations, fluorescence burst analysis, and DNA stretching

Contamination-free continuous flow microfluidic polymerase chain reaction for quantitative and clinical applications

Simulation of DNA Extension in Nanochannels.