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

Rarefied gas flows in channels, pipes, and ducts with smooth surfaces are studied in a wide range of Knudsen number (Kn) at low Mach number (M) with the objective of developing simple, physics-based models. Such flows are encountered in microelectromechanical systems (MEMS), in nanotechnology applications, and in low-pressure environments. A new general boundary condition that accounts for the reduced momentum and heat exchange with wall surfaces is proposed and its validity is investigated. It is shown that it is applicable in the entire Knudsen range and is second-order accurate in Kn in the slip flow regime. Based on this boundary condition, a universal scaling for the velocity profile is obtained, which is used to develop a unified model predicting mass flow rate and pressure distribution with reasonable accuracy for channel, pipe, and duct flows in the regime (0 Kn). A rarefaction coefficient is introduced into this two-parameter model to account for the increasingly reduced intermolecular collisions...

Report: a model for flows in channels, pipes, and ducts at micro and nano scales

Basic Concepts and Technologies * Governing Equations and Slip Models * Shear-Driven and Separated Micro Flows * Pressure-Driven Micro Flows: Slip Flow Regime * Pressure-Driven Flows: Transition and Free- Molecular Regimes * Thermal Effects in Micro Scales * Prototype Applications of Gas Micro Flows * Electrokinetically-Driven Liquid Micro Flows * Numerical Methods for Continuous Simulation * Numerical Methods for Atomistic Simulation

Micro Flows: Fundamentals and Simulation

Gas microflows are encountered in many applications of Micro-Electro-Mechanical Systems (MEMS). Computational modeling and simulation can provide an effective predictive capability for heat and momentum transfer in microscales as well as means of evaluating the performance of a new microdevice before hardware fabrication. In this article, we present models and a computational methodology for simulating gas microflows in the slip-flow regime for which the Knudsen number is less than 0.3. The formulation is based on the classical Maxwell/Smoluchowski boundary conditions that allow partial slip at the wall. We first modify a high-order slip boundary condition we developed in previous work so that it can be easily implemented to provide enhanced numerical stability. We also extend a previous formulation for incompressible flows to include compressibility effects which are primarily responsible for the nonlinear pressure distribution in microchannel flows. The focus of the paper is on the competing effects of compressibility and rarefaction in internal flows in long channels.

Rarefaction and Compressibility Effects in Gas Microflows

Microflows and nanoflows

Analytical results for the velocity distribution, mass flow rate, pressure gradient, wall shear stress, and vorticity in mixed electroosmotic/pressure driven flows are presented for two-dimensional straight channel geometry. We particularly analyze the electric double-layer (EDL) region near the walls and define three new concepts based on the electroosmotic potential distribution. These are the effective EDL thickness, the EDL displacement thickness, and the EDL vorticity thickness. We show that imposing Helmholtz-Smoluchowski velocity at the edge of the EDL as the velocity matching condition between the EDL and the bulk flow region is incomplete under spatial bulk flow variations across the finite EDL. However, the Helmholtz-Smoluchowski velocity can be used as the appropriate slip velocity on the wall. We discuss the limitations of this approach in satisfying the global conservation laws.

Ali Beskok

Papers

Report: a model for flows in channels, pipes, and ducts at micro and nano scales

Micro Flows: Fundamentals and Simulation

Rarefaction and Compressibility Effects in Gas Microflows

Microflows and nanoflows

Analytical solution of combined electroosmotic/pressure driven flows in two-dimensional straight channels: finite Debye layer effects.