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

National Institute of Standards and Technology における超伝導研究及び生活

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

A positive temperature coefficient is the term which has been used to indicate that an increase in solubility occurs as the temperature is raised, whereas a negative coefficient indicates a decrease in solubility with rise in temperature.

Effect of Temperature

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

The aim of this paper is to quantitatively characterize the appearance, stability, density, and shape of surface nanobubbles on hydrophobic surfaces under varying conditions such as temperature and temperature variation, gas type and concentration, surfactants, and surface treatment. The method we adopt is atomic force microscopy (AFM) operated in the tapping mode. In particular, we show (i) that nanobubbles can slide along grooves under the influence of the AFM tip, (ii) that nanobubbles can spontaneously form by substrate heating, allowing for a comparison of the surface topology with and without the nanobubble, (iii) that a water temperature increase leads to a drastic increase in the nanobubble density, (iv) that pressurizing the water with CO2 also leads to a larger nanobubble density, but typically to smaller nanobubbles, (v) that alcohol-cleaning of the surface is crucial for the formation of surface nanobubbles, (vi) that adding 2-butanol as surfactant leads to considerably smaller surface nanobubbles, and (vii) that flushing water over alcohol-covered surfaces strongly enhances the formation of surface nanobubbles.

Characterization of Nanobubbles on Hydrophobic Surfaces in Water

Individual surface nanobubbles are visualized with nonintrusive optical interference-enhanced reflection microscopy, demonstrating that their formation is not a consequence of the hitherto used intrusive atomic force microscopy technique. We then use this new and fast technique to demonstrate that surface nanobubbles form in less than a few seconds after ethanol-water exchange, which is the standard procedure for their preparation, and examine how they react to temperature variations.

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Nonintrusive optical visualization of surface nanobubbles

The motion of droplets under the influence of lithographically created anisotropic chemically defined patterns is described and discussed. The patterns employed in our experiments consist of stripes of alternating wettability: hydrophobic stripes are created via fluorinated self-assembled monolayers, and for hydrophilic stripes, the SiO2 substrate is used. The energy gradient required to induce the motion of the droplets is created by varying the relative widths of the stripes in such a way that the fraction of the hydrophilic area increases. The anisotropic patterns create a preferential direction for liquid spreading parallel to the stripes and confine motion to the perpendicular direction, giving rise to markedly higher velocities as compared to nonstructured surface energy gradients. Consequently, the influence of the distinct pattern features on the overall motion as well as suggestions for design improvements from an application point of view are discussed.

Smart Design of Stripe-Patterned Gradient Surfaces to Control Droplet Motion

Electrolysis of water is employed to produce surface nanobubbles on highly orientated pyrolytic graphite (HOPG) surfaces Hydrogen (oxygen) nanobubbles are formed when the HOPG surface acts as a negative (positive) electrode The coverage and volume of the nanobubbles increase with increasing voltage The yield of hydrogen nanobubbles is much larger than the yield of oxygen nanobubbles The growth of the individual nanobubbles during the electrolysis process is recorded in time with the help of AFM measurements and correlated with the total current Both the size of the individual nanobubbles and the total current saturate typically after 1 min; then the nanobubbles are in a dynamic equilibrium, meaning that they do not further grow, in spite of ongoing gas production and nonzero current The surface area of nanobubbles shows a good correlation with the nanobubble volume growth rate, suggesting that either the electrolytic gas emerges directly at the nanobubbles’ surface or it emerges at the electrode’s surface and then diffuses through the nanobubbles’ surface Moreover, the experiments reveal that the time constants of the current and the aspect ratio of nanobubbles are the same under all conditions Replacement of pure water by water containing a small amount of sodium chloride (001 M) allows for larger currents, but qualitatively gives the same results

Electrolytically Generated Nanobubbles on Highly Orientated Pyrolytic Graphite Surfaces

Pt atoms adsorbed onto Ge(001) surface form extremely well-ordered nanowire arrays by self-organization after high-temperature annealing. Using scanning tunneling spectroscopy/microscopy, it is shown that they are metallic and defect free. They are only 0.4 nm thick with a spacing of 1.6 nm in between, and have aspect ratios up to 1000. Their formation can be discussed in terms of a relativistic property possessed by heaviest 5d elements, and the pathway to their formation can be explained by dimer breakup on Ge(001) surface at elevated temperatures followed by a surface polymerization reaction

Harold J.W. Zandvliet

Papers

Characterization of Nanobubbles on Hydrophobic Surfaces in Water

Nonintrusive optical visualization of surface nanobubbles

Smart Design of Stripe-Patterned Gradient Surfaces to Control Droplet Motion

Electrolytically Generated Nanobubbles on Highly Orientated Pyrolytic Graphite Surfaces

Self-organized, one-dimensional Pt nanowires on Ge(001)