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

Comparative studies of five different techniques commonly employed to identify the chaotic strength and mixing efficiency in micro fluidic systems are presented to demonstrate the competitive advantages and shortcomings of each method. The 'chaotic electroosmotic stirrer' of Qian and Bau (2002 Anal. Chem. 74 3616–25) is utilized as the benchmark case due to its well-defined flow kinematics. Lagrangian particle tracking methods are utilized to study particle dispersion in the conceptual device using spectral element and fourth-order Runge–Kutta discretizations in space and time, respectively. Stirring efficiency is predicted using the stirring index based on the box counting method, and Poincare sections are utilized to identify the chaotic and regular regions under various actuation conditions. Finite time Lyapunov exponents are calculated to quantify the chaotic strength, while the probability density function of the stretching field is utilized as an alternative method to demonstrate the statistical analysis of chaotic and partially chaotic cases. Mixing index inverse, based on the standard deviation of scalar species distribution, is utilized as a metric to quantify the mixing efficiency. Series of numerical simulations are performed by varying the Peclet number (Pe) at fixed kinematic conditions. The mixing time (tm) is characterized as a function of the Pe number, and tm ∝ ln(Pe) scaling is demonstrated for fully chaotic cases, while tm ∝ Peα scaling with α ≈ 0.33 and α = 0.5 are observed for partially chaotic and regular cases, respectively. Employing the aforementioned techniques, optimum kinematic conditions and the actuation frequency of the stirrer that result in the highest mixing/stirring efficiency are identified.

http://iopscience.iop.org/article/10.1088/0960-1317/17/11/005/pdf

Quantification of chaotic strength and mixing in a micro fluidic system

A phenomenological continuum model is developed using systematic molecular dynamics (MD) simulations of force-driven liquid argon flows confined in gold nano-channels at a fixed thermodynamic state. Well known density layering near the walls leads to the definition of an effective channel height and a density deficit parameter. While the former defines the slip-plane, the latter parameter relates channel averaged density with the desired thermodynamic state value. Definitions of these new parameters require a single MD simulation performed for a specific liquid-solid pair at the desired thermodynamic state and used for calibration of model parameters. Combined with our observations of constant slip-length and kinematic viscosity, the model accurately predicts the velocity distribution and volumetric and mass flow rates for force-driven liquid flows in different height nano-channels. Model is verified for liquid argon flow at distinct thermodynamic states and using various argon-gold interaction strengths. Further verification is performed for water flow in silica and gold nano-channels, exhibiting slip lengths of 1.2 nm and 15.5 nm, respectively. Excellent agreements between the model and the MD simulations are reported for channel heights as small as 3 nm for various liquid-solid pairs.

A phenomenological continuum model for force-driven nano-channel liquid flows

We report the design and characterization of a disposable light shielded paper–plastic microfluidic device that can detect nanomolar levels of H2O2 using a smartphone camera and a light sealed accessory Chemiluminescence reaction of H2O2 with bis(2,4,6-trichlorophenyl)oxalate in the presence of rubrene and imidazole is confined to a paper reaction site where the individual reagents are delivered via plastic microfluidic channels The net photon emission from the chemiluminescence reactions, detected by using a smartphone, is correlated with H2O2 concentrations With a total reagent volume of 25 μL, the sensor system was able to detect H2O2 concentrations as low as 250 nM The smartphone based chemiluminescence sensing system has great potential as a point of care diagnostic tool for monitoring nanomolar levels of H2O2 in biological samples

Confined chemiluminescence detection of nanomolar levels of H2O2 in a paper–plastic disposable microfluidic device using a smartphone

Deionized water flow through positively charged graphene nano-channels is investigated using molecular dynamics simulations as a function of the surface charge density. Due to the net electric charge, Ewald summation algorithm cannot be used for modeling long-range Coulomb interactions. Instead, the cutoff distance used for Coulomb forces is systematically increased until the density distribution and orientation of water atoms converged to a unified profile. Liquid density near the walls increases with increased surface charge density, and the water molecules reorient their dipoles with oxygen atoms facing the positively charged surfaces. This effect weakens away from the charged surfaces. Force-driven water flows in graphene nano-channels exhibit slip lengths over 60 nm, which result in plug-like velocity profiles in sufficiently small nano-channels. With increased surface charge density, the slip length decreases and the apparent viscosity of water increases, leading to parabolic velocity profiles and decreased flow rates. Results of this study are relevant for water desalination applications, where optimization of the surface charge for ion removal with maximum flow rate is desired.

/pdf/surface-charge-dependent-transport-of-water-in-graphene-nano-4mcwn52xr1.pdf

Surface charge-dependent transport of water in graphene nano-channels

A microfluidic device with planar square electrodes is developed for capturing particles from high conductivity media using negative dielectrophoresis (n-DEP). Specifically, Bacillus subtilis and Clostridium sporogenes spores, and polystyrene particles are tested in NaCl solution (0.05 and 0.225 S/m), apple juice (0.225 S/m), and milk (0.525 S/m). Depending on the conductivity of the medium, the Joule heating produces electrothermal flow (ETF), which continuously circulates and transports the particles to the DEP capture sites. Combination of the ETF and n-DEP results in different particle capture efficiencies as a function of the conductivity. Utilizing 20 μm height DEP chambers, “almost complete” and rapid particle capture from lower conductivity (0.05 S/m) medium is observed. Using DEP chambers above 150 μm in height, the onset of a global fluid motion for high conductivity media is observed. This motion enhances particle capture on the electrodes at the center of the DEP chamber. The n-DEP electrodes ...

/pdf/negative-dielectrophoretic-capture-of-bacterial-spores-in-19lmn1pebe.pdf

Ali Beskok

Papers

Quantification of chaotic strength and mixing in a micro fluidic system

A phenomenological continuum model for force-driven nano-channel liquid flows

Confined chemiluminescence detection of nanomolar levels of H2O2 in a paper–plastic disposable microfluidic device using a smartphone

Surface charge-dependent transport of water in graphene nano-channels

Negative dielectrophoretic capture of bacterial spores in food matrices