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

The zeta potentials of E. coli, GFP (green fluorescence protein)-labeled E. coli, Salmonella Newport, and Pseudomonas sp. in different states (nutrient-starved and dead) and grown in rich and minimal media were measured. Capillary electrophoresis experiments were conducted to measure the zeta potential of the different cells suspended in a drinking water sample. Salmonella Newport strain showed a lower zeta potential compared to E. coli, GFP-labeled E. coli, and Pseudomonas sp. Starved E. coli cells had a lower zeta potential compared to E. coli cells grown under rich media conditions. Salmonella Newport cells grown in minimal media also had a lower zeta potential compared to rich, starved, and dead cells. The different bacterial cell types exhibited differences in size as well. These results suggest that when bacterial cells are present in drinking water they can exhibit significant heterogeneity in the size and zeta potential, depending on their physiological state.

Zeta Potential of Selected Bacteria in Drinking Water When Dead, Starved, or Exposed to Minimal and Rich Culture Media

A spectral element algorithm is developed to analyze mixed electroosmotic/pressure driven flows in complex two-dimensional geometries. The new algorithm exhibits spectral accuracy in resolving thin electric double layers. Mixed electroosmotic/pressure driven flows are simulated in straight channels. Electrokinetic pumping and the means of producing large pressure gradients in microchannels are explored. Finally, electroosmotic flow in a T-junction geometry is analyzed under various external electric field strengths. Flowrate in the T-junction is shown to vary linearly with the electroosmotic body forces in the Stokes flow regime.

http://www.mstf.wsu.edu/articles/pros_NHT1.pdf

Numerical simulation of mixed electroosmotic/pressure driven microflows

Numerical simulation results for pure electroosmotic and combined electroosmotic/pressure driven Stokes flows are presented in the cross-flow and Y-split junctions. The numerical algorithm is based on a mixed structured/unstructured spectral element formulation, which results in high-order accurate resolution of thin electric double layers with discretization flexibility for complex engineering geometries. The results for pure electroosmotic flows in cross-flow junctions under multiple electric fields show similarities between the electric and velocity fields. The combined electroosmotic/pressure driven flows are also simulated by regulating the flowrate in different branches of the cross-flow junctions. Flow control in the Stokes flow regime is shown to have linear dependence on the magnitude of the externally applied electric field, both for pure electroosmotic and combined flows. This linear behavior enables utilization of electroosmotic forces as nonmechanical means of flow control for microfluidic applications.

http://www.mstf.wsu.edu/articles/pros_MEMS.pdf

Electroosmotic flow control in complex microgeometries

/pdf/probing-nanoparticle-interactions-in-cell-culture-media-unt77gosiz.pdf

Probing nanoparticle interactions in cell culture media

Molecular dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model interactions and thermal exchange at the wall–fluid interface. We present a new interactive thermal wall model that can properly simulate the flow and heat transfer in nano-scale channels. The new model utilizes fluid molecules freely interacting with the thermally oscillating wall molecules, which are connected to the lattice positions with “bonds”. Thermostats are applied separately to each layer of the walls to keep the wall temperature constant, while temperature of the fluid is sustained without the application of a thermostat. Two-dimensional MD simulation results for shear driven nano-channel flow shows parabolic temperature distribution within the domain, induced by viscous heating due to a constant shear rate. As a result of the Kapitza resistance, temperature profiles exhibit jumps at the fluid–wall interface. Time dependent simulation results for freezing of liquid argon in a nano-channel are also presented.

/pdf/thermal-interactions-in-nanoscale-fluid-flow-molecular-2rqqm5k65f.pdf

Ali Beskok

Papers

Zeta Potential of Selected Bacteria in Drinking Water When Dead, Starved, or Exposed to Minimal and Rich Culture Media

Numerical simulation of mixed electroosmotic/pressure driven microflows

Electroosmotic flow control in complex microgeometries

Probing nanoparticle interactions in cell culture media

Thermal interactions in nanoscale fluid flow : molecular dynamics simulations with solid-liquid interfaces