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.

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

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

We survey progress over the past 25 years in the development of microscale devices for pumping fluids. We attempt to provide both a reference for micropump researchers and a resource for those outside the field who wish to identify the best micropump for a particular application. Reciprocating displacement micropumps have been the subject of extensive research in both academia and the private sector and have been produced with a wide range of actuators, valve configurations and materials. Aperiodic displacement micropumps based on mechanisms such as localized phase change have been shown to be suitable for specialized applications. Electroosmotic micropumps exhibit favorable scaling and are promising for a variety of applications requiring high flow rates and pressures. Dynamic micropumps based on electrohydrodynamic and magnetohydrodynamic effects have also been developed. Much progress has been made, but with micropumps suitable for important applications still not available, this remains a fertile area for future research.

https://microfluidics.stanford.edu/Publications/Micropumps_Cooling/Laser%20Review%20of%20Micropumps%20in%20JMM.pdf

A review of micropumps

A three-dimensional serpentine microchannel design with a "C shaped" repeating unit is presented in this paper as a means of implementing chaotic advection to passively enhance fluid mixing. The device is fabricated in a silicon wafer using a double-sided KOH wet-etching technique to realize a three-dimensional channel geometry. Experiments using phenolphthalein and sodium hydroxide solutions demonstrate the ability of flow in this channel to mix faster and more uniformly than either pure molecular diffusion or flow in a "square-wave" channel for Reynolds numbers from 6 to 70. The mixing capability of the channel increases with increasing Reynolds number. At least 98% of the maximum intensity of reacted phenolphthalein is observed in the channel after five mixing segments for Reynolds numbers greater than 25. At a Reynolds number of 70, the serpentine channel produces 16 times more reacted phenolphthalein than a straight channel and 1.6 times more than the square-wave channel. Mixing rates in the serpentine channel at the higher Reynolds numbers are consistent with the occurrence of chaotic advection. Visualization of the interface formed in the channel between streams of water and ethyl alcohol indicates that the mixing is due to both diffusion and fluid stirring.

/pdf/passive-mixing-in-a-three-dimensional-serpentine-2csmc8h1zg.pdf

Passive mixing in a three-dimensional serpentine microchannel

A micron-resolution particle image velocimetry (micro-PIV) system has been developed to measure instantaneous and ensemble-averaged flow fields in micron-scale fluidic devices. The system utilizes an epifluorescent microscope, 100–300 nm diameter seed particles, and an intensified CCD camera to record high-resolution particle-image fields. Velocity vector fields can be measured with spatial resolutions down to 6.9×6.9×1.5 μm. The vector fields are analyzed using a double-frame cross-correlation algorithm. In this technique, the spatial resolution and the accuracy of the velocity measurements is limited by the diffraction limit of the recording optics, noise in the particle image field, and the interaction of the fluid with the finite-sized seed particles. The stochastic influence of Brownian motion plays a significant role in the accuracy of instantaneous velocity measurements. The micro-PIV technique is applied to measure velocities in a Hele–Shaw flow around a 30 μm (major diameter) elliptical cylinder, with a bulk velocity of approximately 50 μm s-1.

http://microfluidics.stanford.edu/Publications/Publications/ParticleTracking_Diagnostics/Santiago%20Micro%20PIV%20ExperFluids.pdf

A particle image velocimetry system for microfluidics

A particle image velocimetry (PIV) system has been developed to measure velocity fields with order 1-μm spatial resolution. The technique uses 200 nm diameter flow-tracing particles, a pulsed Nd:YAG laser, an inverted epi-fluorescent microscope, and a cooled interline-transfer CCD camera to record high-resolution particle-image fields. The spatial resolution of the PIV technique is limited primarily by the diffraction-limited resolution of the recording optics. The accuracy of the PIV system was demonstrated by measuring the known flow field in a 30 μm×300 μm (nominal dimension) microchannel. The resulting velocity fields have a spatial resolution, defined by the size of the first window of the interrogation spot and out of plane resolution of 13.6 μm× 0.9 μm×1.8 μm, in the streamwise, wall-normal, and out of plane directions, respectively. By overlapping the interrogation spots by 50% to satisfy the Nyquist sampling criterion, a velocity-vector spacing of 450 nm in the wall-normal direction is achieved. These measurements are accurate to within 2% full-scale resolution, and are the highest spatially resolved PIV measurements published to date.

http://microfluidics.stanford.edu/Publications/ParticleTracking_Diagnostics/Meinhart%20Micro%20PIV%20Measurements%20ExperFluids.pdf

PIV measurements of a microchannel flow

A novel electrokinetic instability (EKI) micromixer and method takes advantage of the EKI to effect active rapid stirring of confluent microstreams of biomolecules without moving parts or complex microfabrication processes. The EKI is induced using an alternating current (A/C) electric field. Within seconds, the randomly fluctuating, three-dimensional velocity field created by the EKI rapidly and effectively stirs an initially heterogeneous solution and generates a homogeneous solution that is useful in a variety of biochemical and bioanalytical systems. Microfabricated on a glass substrate, the inventive EKI micromixer can be easily and advantageously integrated in molecular diagnostics apparatuses and systems, such as a chip-based “Lab-on-a-Chip” microfluidic device.

Juan G. Santiago

Papers

A review of micropumps

Passive mixing in a three-dimensional serpentine microchannel

A particle image velocimetry system for microfluidics

PIV measurements of a microchannel flow

Electrokinetic instability micromixer