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

An introduction to heat transfer

Jets, ie collimated streams of matter, occur from the microscale up to the large-scale structure of the universe Our focus will be mostly on surface tension effects, which result from the cohesive properties of liquids Paradoxically, cohesive forces promote the breakup of jets, widely encountered in nature, technology and basic science, for example in nuclear fission, DNA sampling, medical diagnostics, sprays, agricultural irrigation and jet engine technology Liquid jets thus serve as a paradigm for free-surface motion, hydrodynamic instability and singularity formation leading to drop breakup In addition to their practical usefulness, jets are an ideal probe for liquid properties, such as surface tension, viscosity or non-Newtonian rheology They also arise from the last but one topology change of liquid masses bursting into sprays Jet dynamics are sensitive to the turbulent or thermal excitation of the fluid, as well as to the surrounding gas or fluid medium The aim of this review is to provide a unified description of the fundamental and the technological aspects of these subjects

Physics of liquid jets

This critical review summarizes developments in microfluidic platforms that enable the miniaturization, integration, automation and parallelization of (bio-)chemical assays (see S. Haeberle and R. Zengerle, Lab Chip, 2007, 7, 1094–1110, for an earlier review). In contrast to isolated application-specific solutions, a microfluidic platform provides a set of fluidic unit operations, which are designed for easy combination within a well-defined fabrication technology. This allows the easy, fast, and cost-efficient implementation of different application-specific (bio-)chemical processes. In our review we focus on recent developments from the last decade (2000s). We start with a brief introduction into technical advances, major market segments and promising applications. We continue with a detailed characterization of different microfluidic platforms, comprising a short definition, the functional principle, microfluidic unit operations, application examples as well as strengths and limitations of every platform. The microfluidic platforms in focus are lateral flow tests, linear actuated devices, pressure driven laminar flow, microfluidic large scale integration, segmented flow microfluidics, centrifugal microfluidics, electrokinetics, electrowetting, surface acoustic waves, and dedicated systems for massively parallel analysis. This review concludes with the attempt to provide a selection scheme for microfluidic platforms which is based on their characteristics according to key requirements of different applications and market segments. Applied selection criteria comprise portability, costs of instrument and disposability, sample throughput, number of parameters per sample, reagent consumption, precision, diversity of microfluidic unit operations and the flexibility in programming different liquid handling protocols (295 references).

/pdf/microfluidic-lab-on-a-chip-platforms-requirements-3q5qdadspt.pdf

Microfluidic lab-on-a-chip platforms: requirements, characteristics and applications

We report the use of focused surface acoustic waves (SAWs) generated on 128° rotated Y-cut X-propagating lithium niobate (LiNbO3) for enhancing the actuation of fluids and the manipulation of particle suspensions at microscale dimensions. In particular, we demonstrate increased efficiency and speed in carrying out particle concentration/separation and in generating intense micromixing in microliter drops within which acoustic streaming is induced due to the focused SAW beneath the drop. Concentric circular and elliptical single-phase unidirectional transducers (SPUDTs) were used to focus the SAW. We benchmark our results against a straight SPUDT which does not cause focusing of the SAW. Due to the increased wave intensity and asymmetry of the wave, we found both circular and elliptical SPUDTs concentrate particles in under 1 s, which is one order of magnitude faster than the straight SPUDT and several orders of magnitude faster than conventional microscale devices. The concentric circular SPUDT was found ...

/pdf/particle-concentration-and-mixing-in-microdrops-driven-by-2rlmbke5ff.pdf

Particle concentration and mixing in microdrops driven by focused surface acoustic waves

We exploit large accelerations associated with surface acoustic waves to drive an extraordinary fluid jetting phenomena. Laterally focusing the acoustic energy to a small region beneath a drop placed on the surface causes rapid interfacial destabilization. Above a critical Weber number We, an elongated jet forms for drops with dimensions greater than the fluid sound wavelength. Further increases in We lead to single droplet pinch-off and subsequent axisymmetric breakup to form multiple droplets. A simple equation based on a momentum balance is derived to predict the jet velocity.

/pdf/interfacial-jetting-phenomena-induced-by-focused-surface-1mdq18z2jt.pdf

Interfacial jetting phenomena induced by focused surface vibrations.

The ability to detect microbes, pollens and other microparticles is a critically important ability given the increasing risk of bioterrorism and emergence of antibiotic-resistant bacteria. The efficient collection of microparticles via a liquid water droplet moved by a surface acoustic wave (SAW) device is demonstrated in this study. A fluidic track patterned on the SAW device directs the water droplet's motion, and fluid streaming induced inside the droplet as it moves along is a key advantage over other particle collection approaches, because it enhances microparticle collection and concentration. Test particles consisted of 2, 10, 12 and 45 μm diameter monodisperse polystyrene and melamine microparticles; pollen from the Populus deltoides, Kochia scoparia, Secale cerale, and Broussonetia papyrifera (Paper Mulberry) species; and Escherichia coli bacteria. The collection efficiency for the synthetic particles ranged from 16 to 55%, depending on the particle size and surface tension of the collection fluid. The method was more effective in collecting pollen and the bacteria with an efficiency of 45–68% and 61.0–69.8%, respectively. Pollen collection was strongly influenced by its diameter, size, and surface geometry in a manner contrary to initial expectations. Reasons for the consistent yet unexpected collection results include leaky SAW pressure boundary segregation and shear-induced concentration of larger particles, and the subtle effects of wetting interactions. These results demonstrate a new method for collecting microparticles requiring only about one second per run, and illustrate the inadequacy of using synthetic microparticles as a substitute for their biological counterparts in experiments studying particle collection and behavior.

https://users.monash.edu/~lyeo/Dr_Leslie_Yeo/Publications_files/Tan_etal_LabChip_7_618_2007.pdf

Microparticle collection and concentration via a miniature surface acoustic wave device

A surface acoustic wave-based sample delivery and ionization method that requires minimal to no sample pretreatment and that can operate under ambient conditions is described. This miniaturized technology enables real-time, rapid, and high-throughput analysis of trace compounds in complex mixtures, especially high ionic strength and viscous samples that can be challenging for conventional ionization techniques such as electrospray ionization. This technique takes advantage of high order surface acoustic wave (SAW) vibrations that both manipulate small volumes of liquid mixtures containing trace analyte compounds and seamlessly transfers analytes from the liquid sample into gas phase ions for mass spectrometry (MS) analysis. Drugs in human whole blood and plasma and heavy metals in tap water have been successfully detected at nanomolar concentrations by coupling a SAW atomization and ionization device with an inexpensive, paper-based sample delivery system and mass spectrometer. The miniaturized SAW ionization unit requires only a modest operating power of 3 to 4 W and, therefore, provides a viable and efficient ionization platform for the real-time analysis of a wide range of compounds.

/pdf/paper-based-microfluidic-surface-acoustic-wave-sample-1buhde129k.pdf

Paper-based microfluidic surface acoustic wave sample delivery and ionization source for rapid and sensitive ambient mass spectrometry.

Very-high-frequency surface acoustic waves, generated and transmitted along single-crystal lithium niobate, are used to drive homogeneous aqueous suspensions of polystyrene nanoparticles along microchannels At a few hundred milliwatts, uniform and mixing flows with speeds of up to 10 mm/s were obtained in centimetres-long rectangular channels with cross-sectional dimensions of tens to a few hundreds of microns A transition from uniform to mixing flow occurs as the channel width grows beyond the wavelength of sound in the fluid at the chosen excitation frequency At far lower input powers, the suspension agglomerates into equally spaced, serpentine lines coincident with nodal lines in the acoustic pressure field We expose the physics underlying these disparate phenomena with experimental results aided by numerical models

https://iopscience.iop.org/article/10.1209/0295-5075/87/47003/pdf

Ming K. Tan

Papers

Particle concentration and mixing in microdrops driven by focused surface acoustic waves

Interfacial jetting phenomena induced by focused surface vibrations.

Microparticle collection and concentration via a miniature surface acoustic wave device

Paper-based microfluidic surface acoustic wave sample delivery and ionization source for rapid and sensitive ambient mass spectrometry.

Rapid fluid flow and mixing induced in microchannels using surface acoustic waves