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

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

Wetting phenomena are ubiquitous in nature and technology. A solid substrate exposed to the environment is almost invariably covered by a layer of fluid material. In this review, the surface forces that lead to wetting are considered, and the equilibrium surface coverage of a substrate in contact with a drop of liquid. Depending on the nature of the surface forces involved, different scenarios for wetting phase transitions are possible; recent progress allows us to relate the critical exponents directly to the nature of the surface forces which lead to the different wetting scenarios. Thermal fluctuation effects, which can be greatly enhanced for wetting of geometrically or chemically structured substrates, and are much stronger in colloidal suspensions, modify the adsorption singularities. Macroscopic descriptions and microscopic theories have been developed to understand and predict wetting behavior relevant to microfluidics and nanofluidics applications. Then the dynamics of wetting is examined. A drop, placed on a substrate which it wets, spreads out to form a film. Conversely, a nonwetted substrate previously covered by a film dewets upon an appropriate change of system parameters. The hydrodynamics of both wetting and dewetting is influenced by the presence of the three-phase contact line separating "wet" regions from those that are either dry or covered by a microscopic film only. Recent theoretical, experimental, and numerical progress in the description of moving contact line dynamics are reviewed, and its relation to the thermodynamics of wetting is explored. In addition, recent progress on rough surfaces is surveyed. The anchoring of contact lines and contact angle hysteresis are explored resulting from surface inhomogeneities. Further, new ways to mold wetting characteristics according to technological constraints are discussed, for example, the use of patterned surfaces, surfactants, or complex fluids.

/pdf/wetting-and-spreading-56ditqbfmj.pdf

Wetting and Spreading

DLS and zeta potential - What they are and what they are not?

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

Biological Compatibility of Electromanipulation Media

Fluid film damping in laterally oscillating microstructures is investigated in the entire Knudsen regime and a wide Stokes number range using analytical and numerical results from Park et al. [“Rarefaction effects on shear driven oscillatory gas flows: A direct simulation Monte Carlo study in the entire Knudsen regime,” Phys. Fluids 16, 317 (2004)] and Hadjiconstantinou [“Oscillatory shear driven gas flows in the transition and free-molecular-flow regimes,” Phys. Fluids 17, 100611 (2005)]. An energy dissipation parameter per oscillation cycle that allows a consistent interpretation of the quality factor utilized in the design of microelectromechanical system devices is presented.

Quantification of energy dissipation for laterally oscillating microstructures

the erous S The micro heat spreader ~MHS! is a micro-fluidic device designed fo thermal management of microelectronic components. It connects two ervoirs by a set of micro-channels ~Fig. 1!. The bottom surfaces of the reservoirs are membranes that are driven with a phase difference p, either by electrostatic or piezoelectric actuation. The idea is to minim the chip surface temperature by oscillatory flow forced convection and mixing. Numerical simulations are performed for an MHS device w channel to reservoir expansion ratio H/h525. The boundary conditions and the MHS geometry are shown in Fig. 2. Both the flow and tempera fields are time-periodic, and Womersley and Prandtl numbers

Shear layer instability and mixing in micro heat spreaders

We analyze steady one-dimensional plane Couette flows in the entire Knudsen regime with the objective of modelling shear-driven rarefied gas flows encountered in various micro electromechanical system (MEMS) applications. In particular, we develop a unified empirical model, which includes analytical expressions for the velocity distribution and shear stress. The new model is validated by comparisons with the linearized Boltzmann solutions available in the literature, as well as hard-sphere direct simulation Monte Carlo (DSMC) results. Overall, the new model predicts the velocity distribution and shear stress with good accuracy for a wide range of Knudsen numbers (0 < Kn ≤ 12), and it is valid for incompressible or low subsonic compressible flows (Ma ≤ 0.3).© 2002 ASME

A Unified Model for Shear Driven Gas Micro Flows

Alternating current (AC) electrokinetic motion of colloidal particles suspended in an aqueous medium and subjected to a spatially nonuniform AC electric field are examined using a simple theoretical model that considers the relative magnitudes of dielectrophoresis, electrophoresis, AC-electroosmosis, and Brownian motion Dominant electrokinetic forces are explained as a function of the electric field frequency, amplitude, and conductivity of the suspending medium for given material properties and geometry Parametric experimental validations of the model are conducted utilizing interdigitated microelectrodes with polystyrene and gold particles The theoretical model provides quantitative descriptions of AC electro?kinetic transport for the given target species in a wide spectrum of electric field amplitude and frequency, and medium conductivity The presented model, previously published in Ref [1], can be used as an effective frame-work for design and optimization of AC electrokinetic devices

Ali Beskok

Papers

Biological Compatibility of Electromanipulation Media

Quantification of energy dissipation for laterally oscillating microstructures

Shear layer instability and mixing in micro heat spreaders

A Unified Model for Shear Driven Gas Micro Flows

AC Electrokinetic Flows