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

Nano-scale fluid transport has vast applications spanning from water desalination to biotechnology [1,2]. It is possible to pump fluids in nano-conduits using pressure gradients [3], thermal methods [4], electric [5,6] and magnetic fields [7], and with manipulations of surface chemistry and electric fields [8-10]. Inspired by the capillary-driven phase change heat transfer devices, we present a phase-change driven nanopump operating almost isothermally. Meticulous computational experiments on different sized nanopumps revealed efficient operation of the pump despite the reduction in system size that extinguishes capillary pumping by annihilating the liquid meniscus structures. Measuring the density distribution of liquid in cross sections near to the evaporating and condensing liquid-vapor interfaces, we discovered that phase change induced molecular scale mass diffusion mechanism replaces the capillary pumping in the absence of meniscus structures. Therefore, proposed pumps can serve as a part of both nanoelectromechanical (NEMS) and microelectromechanical systems (MEMS) with similar working efficiencies, and can be used for continuous gas separation applications.

Molecular Diffusion Replaces Capillary Pumping in Phase-Change Driven Nanopumps.

Inspired by the capillary-driven heat transfer devices, we present a phase-change-driven nanopump operating almost isothermally. Computational experiments on different-sized nanopumps revealed efficient operation of the pump despite the reduction in system size that extinguishes capillary pumping by annihilating the liquid meniscus structures. Measuring the density distribution of liquid near evaporating and condensing liquid/vapor interfaces, we discovered that phase-change-induced molecular-scale mass diffusion mechanism replaces the capillary pumping in the absence of meniscus structures as long as the liquid wets the walls of the capillary conduit. Therefore, proposed pumps can serve as a part of both nanoelectromechanical and microelectromechanical systems with similar working efficiencies.

Molecular diffusion replaces capillary pumping in phase-change-driven nanopumps

We present a microfluidic approach for the continuous capture of Salmonella Newport cells suspended in a phosphate buffer using externally applied electric fields. The effects of flow rate, applied electric field and wall shear stress on cell capture in the device are analyzed using particle tracking via fluorescent microscopy techniques. Analyzing capture across multiple locations on the electrode surface enabled the estimation of average capture over the entire electrode area as a function of time. The device exhibits approximately a constant capture rate over an extended time frame, which is verified independently using the cell culture methods. An increased capture rate with an increased electric field is observed. The capture rate dependence on the flow rate and capture rate at various locations with different wall shear stress magnitudes does not exhibit statistically significant variations. The capture trends presented in this study can be utilized for designing microfluidic systems for biosensors, designed bacterial bio-films and devices for bacterial sample concentration from large volumes.

In situ analysis of bacterial capture in a microfluidic channel

In this study, a separability parameter is introduced to determine the selection of optimum operating parameters for DEP separation of a cell pair. The separability parameter is defined as a function of cells' Clausius-Mossotti (CM) factors. T-cell leukemia Jurkat and mouse melanoma B16 cells are tested to validate the separability parameter. CM factors of cells are measured using a recently developed microfluidic impedance spectroscopy device. Separability maps are generated for varying values of field frequency and buffer conductivity. Cell separation is tested using a planar interdigitated electrode array at different buffer conductivities. Impedance measurements of the DEP device are performed at various buffer conductivities. Electrode polarization effects and energy allocation for dielectrophoretic manipulation of cells are computed from the impedance data utilizing an equivalent circuit model. Cell separation results are explained in the light of the impedance measurements.

A separability parameter for dielectrophoretic cell separation

In this paper, we study rarefied internal gas flows subject to strong adverse pressure gradients and separation in the slip flow regime (Knudsen number Kn < 0.1), with the objective of investigating the validity of continuum-based slip models under separation. Such conditions are encountered in typical components of Micro-Electro-Mechanical Systems (MEMS) and in low pressure/vacuum applications. Solutions of compressible Navier-Stokes equations subject to various velocity slip and temperature jump boundary conditions are compared against predictions of direct simulation Monte Carlo (DSMC) method, employing variable hard sphere (VHS) model. Sudden changes of the flow conditions in backwards-fac ing step geometry result in significant variations of the mean-free path of the gas molecules, with corresponding variations in the wall shear stress affecting the slip velocity directly. Unlike the straight channel flow, significant cross-flow variations are obtained. In addition, the change of characteristi c length scale from the inlet channel height to larger height downstream presents extra difficulties in choosing the proper scaling.

Ali Beskok

Papers

Molecular Diffusion Replaces Capillary Pumping in Phase-Change Driven Nanopumps.

Molecular diffusion replaces capillary pumping in phase-change-driven nanopumps

In situ analysis of bacterial capture in a microfluidic channel

A separability parameter for dielectrophoretic cell separation

Modeling separation in rarefied gas flows