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

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

This thesis explores transport phenomena in nanochannels on a chip. Fundamental nanofluidic ionic studies form the basis for novel separation and preconcentration applications for proteomic purposes. The measurements were performed with 50-nm-high 1D nanochannels, which are easily accessible from both sides by two microchannels. Nanometer characteristic apertures were manufactured in the bonded structure of Pyrex-amorphous silicon – Pyrex, in which the thickness of the amorphous silicon layer serves as a spacer to define the height of the nanochannels. The geometry of the nanometer-sized apertures is well defined, which simplifies the modeling of the transport across them. Compared to biological pores, the present nanochannels in Pyrex offer increased stability. Fundamental characteristics of nanometer-sized apertures were obtained by impedance spectroscopy measurements of the nanochannel at different ionic strengths and pH values. A conductance plateau (on a log-log scale) was modeled and measured, establishing due to the dominance of the surface charge density in the nanochannels, which induces an excess of mobile counterions to maintain electroneutrality. The nanochannel conductance can be regulated at low ionic strengths by pH adjustment, and by an external voltage applied on the chip to change the zeta potential. This field-effect allows the regulation of ionic flow which can be exploited for the fabrication of nanofluidic devices. Fluorescence measurements confirm that 50-nm-high nanochannels show an exclusion of co-ions and an enrichment of counterions at low ionic strengths. This permselectivity is related to the increasing thickness of the electrical double layer (EDL) with decreasing salt concentrations, which results in an EDL overlap in an aperture if the height of the nanochannel and the thickness of the EDL are comparable in size. The diffusive transport of charged species and therefore the exclusion-enrichment effect was described with a simple model based on the Poisson-Boltzmann equation. The negatively charged Pyrex surface of the nanometer characteristic apertures can be inversed with chemical surface pretreatments, resulting in an exclusion of cations and an enrichment of anions. When a pressure gradient is applied across the nanochannels, charged molecules are electrostatically rejected at the entrance of the nanometer-sized apertures, which can be used for separation processes. Proteomic applications are presented such as the separation and preconcentration of proteins. The diffusion of Lectin proteins with different isoelectric points and very similar compositions were controlled by regulating the pH value of the buffer. When the proteins are neutral at their pI value, the diffusion coefficient is maximal because the biomolecules does not interact electrostatically with the charged surfaces of the nanochannel. This led to a fast separation of three Lectin proteins across the nanochannel. The pI values measured in this experiment are slightly shifted compared to the values obtained with isoelectric focusing because of reversible adsorption of proteins on the walls which affects the pH value in the nanochannel. An important application in the proteomic field is the preconcentration of biomolecules. By applying an electric field across the nanochannel, anionic and cationic analytes were preconcentrated on the cathodic side of the nanometer-sized aperture whereas on the anodic side depletion of ions was observed. This is due to concentration polarization, a complex of effects related to the formation of ionic concentration gradients in the electrolyte solution adjacent to an ion-selective interface. It was measured that the preconcentration factor increased with the net charge of the molecule, leading to a preconcentration factor of > 600 for rGFP proteins in 9 minutes. Such preconcentrations are important in micro total analysis systems to achieve increased detection signals of analytes contained in dilute solutions. Compared to cylindrical pores, our fabrication process allows the realization of nanochannels on a chip in which the exclusion-enrichment effect and a big flux across the nanometer-sized aperture can be achieved, showing the interest for possible micro total analysis system applications. The described exclusion-enrichment effect as well as concentration polarization play an important role in transport phenomena in nanofluidics. The appendix includes preliminary investigations in DNA molecule separation and fluorescence correlation spectroscopy measurements, which allows investigating the behavior of molecules in the nanochannel itself.

/pdf/transport-phenomena-in-nanofluidics-1di3nwdyom.pdf

Transport phenomena in nanofluidics

Capillarity and Wetting Phenomena: Drops, Bubbles, Pearls, Waves

Robust validation of the space–time structure of remotely sensed precipitation estimates is critical to improving their quality and confident application in water cycle–related research. In this work, the performance of the Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks-Cloud Classification System (PERSIANN-CCS) precipitation product is evaluated against warm season precipitation observations from the North American Monsoon Experiment (NAME) Event Rain Gauge Network (NERN) in the complex terrain region of northwestern Mexico. Analyses of hourly and daily precipitation estimates show that the PERSIANN-CCS captures well active and break periods in the early and mature phases of the monsoon season. While the PERSIANN-CCS generally captures the spatial distribution and timing of diurnal convective rainfall, elevation-dependent biases exist, which are characterized by an underestimate in the occurrence of light precipitation at high elevations and an overestimate in the occurrence of precipitation at low elevations. The elevation-dependent biases contribute to a 1–2-h phase shift of the diurnal cycle of precipitation at various elevation bands. For reasons yet to be determined, the PERSIANN-CCS significantly underestimated a few active periods of precipitation during the late or “senescent” phase of the monsoon. Despite these shortcomings, the continuous domain and relatively high spatial resolution of PERSIANN-CCS quantitative precipitation estimates (QPEs) provide useful characterization of precipitation space–time structures in the North American monsoon region of northwestern Mexico, which should prove useful for hydrological applications.

/pdf/evaluation-of-persiann-ccs-rainfall-measurement-using-the-4vtfqngh76.pdf

Evaluation of PERSIANN-CCS rainfall measurement using the NAME event rain gauge network

We describe studies of the pressure driven flow of several classical fluids through lithographically produced channels in which one dimension, the channel height h, is in the micron or nanometer size range. The measured flow rates are compared with theoretical predictions assuming no-slip boundary conditions at the walls of the channel. The results for water agree well with this prediction for h as small as 40 nm (our smallest channels). However, for hexane, decane, hexadecane, and silicone oil we find deviations from this theory when h is reduced below about 100 nm. The observed flow rates for small h are larger than theoretical expectations, implying significant slip at the walls, and values of the slip length are estimated. The results are compared with previous experimental and theoretical work.

/pdf/fluid-flow-through-nanometer-scale-channels-159pvadmms.pdf

Fluid flow through nanometer-scale channels.

We investigated water vapor condensation on a two-tier superhydrophobic surface in an environmental scanning electron microscope (ESEM) and in a customer-designed vapor chamber. We have observed continuous dropwise condensation (DWC) on the textured surface in ESEM. However, a film layer of condensate was formed on the multiscale texture in the vapor chamber. Due to the filmwise condensation, the condensation heat transfer coefficient of the superhydrophobic surface is lower than that of a flat hydrophobic surface especially under high heat flux situations. Our studies indicate that adaptive and prompt condensate droplet purging is the dominant factor for sustaining long-term DWC.

Condensation heat transfer on two-tier superhydrophobic surfaces

[1] Using transparent microfluidic cells to study the two-phase properties of a synthetic porous medium, we establish that the interfacial area per volume between nonwetting and wetting fluids lifts the ambiguity associated with the hysteretic relationship between capillary pressure and saturation in porous media. The interface between the nonwetting and wetting phases is composed of two subsets: one with a unique curvature determined by the capillary pressure, and the other with a distribution of curvatures dominated by disjoining pressure. This work provides experimental support for recent theoretical predictions that the capillary-dominated subset plays a role analogous to a state variable. Any comprehensive description of multiphase flow properties must include this interfacial area with the traditional variables of pressure and fluid saturation.

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2003GL019282

Linking Pressure and Saturation through Interfacial Areas in Porous Media

We report an electrowetting-controlled optofluidic system for adaptive beam tracking and agile steering. With two immiscible fluids in a transparent cell, we can actively control the contact angle along the fluid-fluid-solid tri-junction line and hence the orientation of the fluid-fluid interface via electrowetting. The naturally formed meniscus between the two liquids can function as an optical prism. We have fabricated a liquid prism module with an aperture size of 10 mm × 10mm. With 1 wt. % KCl and 1 wt. % Sodium Dodecyl Sulfate added into deionized water, the orientation of the water-silicone oil interface has been modulated between −26° and 26° that can deflect and steer beam within the incidence angle of 0°–15°. The wide-range beam tracking and steering enables the liquid prism work as an electrowetting solar cell.

Jiangtao Cheng

Papers

Evaluation of PERSIANN-CCS rainfall measurement using the NAME event rain gauge network

Fluid flow through nanometer-scale channels.

Condensation heat transfer on two-tier superhydrophobic surfaces

Linking Pressure and Saturation through Interfacial Areas in Porous Media

Adaptive beam tracking and steering via electrowetting-controlled liquid prism