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

There is a special reason for reviewing this book at this time: it is the 50th edition of a compendium that is known and used frequently in most chemical and physical laboratories in many parts of the world. Surely, a publication that has been published for 56 years, withstanding the vagaries of science in this century, must have had something to offer. There is another reason: while the book is a standard fixture in most chemical and physical laboratories, including those in medical centers, it is not as frequently seen in the laboratories of physician's offices (those either in solo or group practice). I believe that the Handbook can be useful in those laboratories. One of the reasons, among others, is that the various basic items of information it offers may be helpful in new tests, either physical or chemical, which are continuously being published. The basic information may relate

Handbook of Chemistry and Physics

Water molecules confined to nonpolar pores and cavities of nanoscopic dimensions exhibit highly unusual properties. Water filling is strongly cooperative, with the possible coexistence of filled and empty states and sensitivity to small perturbations of the pore polarity and solvent conditions. Confined water molecules form tightly hydrogen-bonded wires or clusters. The weak attractions to the confining wall, combined with strong interactions between water molecules, permit exceptionally rapid water flow, exceeding expectations from macroscopic hydrodynamics by several orders of magnitude. The proton mobility along 1D water wires also substantially exceeds that in the bulk. Proteins appear to exploit these unusual properties of confined water in their biological function (e.g., to ensure rapid water flow in aquaporins or to gate proton flow in proton pumps and enzymes). The unusual properties of water in nonpolar confinement are also relevant to the design of novel nanofluidic and molecular separation devices or fuel cells.

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Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond *

Surface nanobubbles are nanoscopic gaseous domains on immersed substrates which can survive for days. They were first speculated to exist about 20 years ago, based on stepwise features in force curves between two hydrophobic surfaces, eventually leading to the first atomic force microscopy (AFM) image in 2000. While in the early years it was suspected that they may be an artifact caused by AFM, meanwhile their existence has been confirmed with various other methods, including through direct optical observation. Their existence seems to be paradoxical, as a simple classical estimate suggests that they should dissolve in microseconds, due to the large Laplace pressure inside these nanoscopic spherical-cap-shaped objects. Moreover, their contact angle (on the gas side) is much smaller than one would expect from macroscopic counterparts. This review will not only give an overview on surface nanobubbles, but also on surface nanodroplets, which are nanoscopic droplets (e.g., of oil) on (hydrophobic) substrates immersed in water, as they show similar properties and can easily be confused with surface nanobubbles and as they are produced in a similar way, namely, by a solvent exchange process, leading to local oversaturation of the water with gas or oil, respectively, and thus to nucleation. The review starts with how surface nanobubbles and nanodroplets can be made, how they can be observed (both individually and collectively), and what their properties are. Molecular dynamic simulations and theories to account for the long lifetime of the surface nanobubbles are then reported on. The crucial element contributing to the long lifetime of surface nanobubbles and nanodroplets is pinning of the three-phase contact line at chemical or geometric surface heterogeneities. The dynamical evolution of the surface nanobubbles then follows from the diffusion equation, Laplace’s equation, and Henry’s law. In particular, one obtains stable surface nanobubbles when the gas influx from the gas-oversaturated water and the outflux due to Laplace pressure balance. This is only possible for small enough surface bubbles. It is therefore the gas or oil oversaturation ζ that determines the contact angle of the surface nanobubble or nanodroplet and not the Young equation. The review also covers the potential technological relevance of surface nanobubbles and nanodroplets, namely, in flotation, in (photo)catalysis and electrolysis, in nanomaterial engineering, for transport in and out of nanofluidic devices, and for plasmonic bubbles, vapor nanobubbles, and energy conversion. Also given is a discussion on surface nanobubbles and nanodroplets in a nutshell, including theoretical predictions resulting from it and future directions. Studying the nucleation, growth, and dissolution dynamics of surface nanobubbles and nanodroplets will shed new light on the problems of contact line pinning and contact angle hysteresis on the submicron scale.

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Surface nanobubbles and nanodroplets

Electrospray ionization (ESI) generates intact gas-phase ions from analytes in solution for mass spectrometric investigations. ESI can proceed via different mechanisms. Low molecular weight analyte...

http://pubs.acs.org/doi/pdf/10.1021/ac302789c

Unraveling the Mechanism of Electrospray Ionization

We manifest a significant influence of field direction and polarity on surface wetting, when the latter is tuned by application of an external electric field. Thermodynamics of field-induced filling of hydrocarbon-like nanopores with water is studied by open ensemble molecular simulation. Increased field strength consistently results in water-filling and electrostriction in hydrophobic nanopores. A threshold field commensurate with surface charge density of about one elementary charge per 10 nm2 suffices to render prototypical paraffin surfaces hydrophilic. When a field is applied in the direction perpendicular to the confining walls, the competition between orientational polarization and angle preferences of interfacial water molecules relative to the walls results in an asymmetric wettability of opposing surfaces (Janus interface). Reduction of surface free energy observed upon alignment of confinement walls with field direction suggests a novel mechanism whereby the applied electric field can operate s...

/pdf/effect-of-field-direction-on-electrowetting-in-a-nanopore-1wm8tqhhdt.pdf

Effect of field direction on electrowetting in a nanopore

Using molecular simulations of nanosized aqueous droplets on a model graphite surface, we demonstrate remarkable sensitivity of water contact angles to the applied electric field polarity and direction relative to the liquid/solid interface. The effect is explained by analyzing the influence of the field on interfacial hydrogen bonding in the nanodrop, which in turn affects the interfacial tensions. The observed anisotropy in droplet wetting is a new nanoscale phenomenon that has so far been elusive as, in current experimental setups, surface molecules represent a very low fraction of the total number affected by the field. Our findings may have important implications for the design of electrowetting techniques in fabrication and property tuning of nanomaterials.

Electrowetting at the Nanoscale

We examine the effect of nanoscale roughness on spreading and surface mobility of water nanodroplets. Using molecular dynamics, we consider model surfaces with sub-nanoscale asperities at varied surface coverage and with different distribution patterns. We test materials that are hydrophobic, and those that are hydrophilic in the absence of surface corrugations. Interestingly, on both types of surfaces, the introduction of surface asperities gives rise to a sharp increase in the apparent contact angle. The Cassie–Baxter equation is obeyed approximately on hydrophobic substrates, however, the increase in the contact angle on a hydrophilic surface differs qualitatively from the behavior on macroscopically rough surfaces described by the Wenzel equation. On the hydrophobic substrate, the superhydrophobic state with the maximal contact angle of 180 degrees is reached when the asperity coverage falls below 25%, suggesting that superhydrophobicity can also be achieved by the nanoscale roughness of a macroscopically smooth material. We further examine the effect of surface roughness on droplet mobility on the substrate. The apparent diffusion constant shows a dramatic slow down of the nanodroplet translation even for asperity coverage in the range of 1% for a hydrophilic surface, while droplets on corrugated hydrophobic surfaces retain the ability to flow around the asperities. In contrast, for smooth surfaces we find that the drop mobility on the hydrophilic surface exceeds that on the hydrophobic one.

The influence of molecular-scale roughness on the surface spreading of an aqueous nanodrop

Aqueous nanoscale systems feature a distinct electrowetting behavior, sensitive to not only the strength but also the direction and polarity of the applied electric field. These effects have so far not been tested in solutions of ions, although electrolytes are commonly present in electrowetting experiments. We describe atomistic simulations of sessile salty nanodrops on an apolar substrate under electric fields in a miniature mimic of the experimental setup of a drop inside a capacitor. In the absence of field, the contact angle rises with salt concentration. The effect is weaker when the surface is more hydrophobic. The electric field lowers the contact angle, but the polarity dependence, observed in neat water and related to directional hydrogen bond effects, is diminished in the presence of screening ions. This is important for nanofluidics, as the addition of salt can improve electrowetting inside a nanopore where uneven wettabilities of opposing walls are found in pure water. The different hydration...

Electric Control of Wetting by Salty Nanodrops: Molecular Dynamics Simulations

Interfacial polar molecules feature a strongly anisotropic response to applied electric field, favoring dipole orientations parallel to the interface. In water, in particular, this effect combines with generic orientational preferences induced by spatial asymmetry of water hydrogen bonding under confined geometry, which may give rise to a Janus interface. The two effects manifest themselves in considerable dependence of water polarization on both the field direction relative to the interface and the polarity (sign) of the field. Using molecular simulations, we demonstrate strong field-induced orientational forces acting on apolar surfaces through water mediation. At a field strength comparable to electric fields around a DNA polyion, the torques we predict to act on an adjacent nanoparticle are sufficient to overcome thermal fluctuations. These torques can align a particle with surface as small as 1 nm2. The mechanism can support electrically controlled ordering of suspended nanoparticles as a means of tuning their properties and can find application in electro-nanomechanical devices.

Christopher D. Daub

Papers

Effect of field direction on electrowetting in a nanopore

Electrowetting at the Nanoscale

The influence of molecular-scale roughness on the surface spreading of an aqueous nanodrop

Electric Control of Wetting by Salty Nanodrops: Molecular Dynamics Simulations

Water-mediated ordering of nanoparticles in an electric field