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

Confinement of matter on the nanometre scale can induce phase transitions not seen in bulk systems1. In the case of water, so-called drying transitions occur on this scale2,3,4,5 as a result of strong hydrogen-bonding between water molecules, which can cause the liquid to recede from nonpolar surfaces to form a vapour layer separating the bulk phase from the surface6. Here we report molecular dynamics simulations showing spontaneous and continuous filling of a nonpolar carbon nanotube with a one-dimensionally ordered chain of water molecules. Although the molecules forming the chain are in chemical and thermal equilibrium with the surrounding bath, we observe pulse-like transmission of water through the nanotube. These transmission bursts result from the tight hydrogen-bonding network inside the tube, which ensures that density fluctuations in the surrounding bath lead to concerted and rapid motion along the tube axis7,8,9. We also find that a minute reduction in the attraction between the tube wall and water dramatically affects pore hydration, leading to sharp, two-state transitions between empty and filled states on a nanosecond timescale. These observations suggest that carbon nanotubes, with their rigid nonpolar structures10,11, might be exploited as unique molecular channels for water and protons, with the channel occupancy and conductivity tunable by changes in the local channel polarity and solvent conditions.

Water conduction through the hydrophobic channel of a carbon nanotube

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

Gold is known as a shiny, yellow noble metal that does not tarnish, has a face centred cubic structure, is non-magnetic and melts at 1336 K. However, a small sample of the same gold is quite different, providing it is tiny enough: 10 nm particles absorb green light and thus appear red. The meltingtemperature decreases dramatically as the size goes down. Moreover, gold ceases to be noble, and 2–3 nm nanoparticles are excellent catalysts which also exhibit considerable magnetism. At this size they are still metallic, but smaller ones turn into insulators. Their equilibrium structure changes to icosahedral symmetry, or they are even hollow or planar, depending on size. The present tutorial review intends to explain the origin of this special behaviour of nanomaterials.

Size matters: why nanomaterials are different

http://kbose.weebly.com/uploads/1/0/4/9/10492046/force-distance_curves_by_atomic_force_microscopy_1.pdf

Force-distance curves by atomic force microscopy

We review the current state of knowledge of phase separation and phase equilibria in porous materials. Our emphasis is on fundamental studies of simple fluids (composed of small, neutral molecules) and well-characterized materials. While theoretical and molecular simulation studies are stressed, we also survey experimental investigations that are fundamental in nature. Following a brief survey of the most useful theoretical and simulation methods, we describe the nature of gas‐liquid (capillary condensation), layering, liquid‐liquid and freezing/melting transitions. In each case studies for simple pore geometries, and also more complex ones where available, are discussed. While a reasonably good understanding is available for phase equilibria of pure adsorbates in simple pore geometries, there is a need to extend the models to more complex pore geometries that include effects of chemical and geometrical heterogeneity and connectivity. In addition, with the exception of liquid‐liquid equilibria, little work has been done so far on phase separation for mixtures in porous media.

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Phase separation in confined systems

We have prepared a series of molecular models of porous glass using a recently developed procedure (Gelb, L. D.; Gubbins, K. E. Langmuir 1998, 14, 2097) that mimics the experimental processes that produce Vycor and controlled-pore glasses. We calculate nitrogen adsorption isotherms in these precisely characterized model glasses using Monte Carlo simulations. These isotherms are analyzed using the Barrett−Joyner−Halenda (BJH) method to yield pore size distributions, which are tested against exact pore size distributions directly measured from the pore structures. The BJH method yields overly sharp distributions that are systematically shifted (by about 1 nm) to lower pore sizes than those from our geometric method.

Pore size distributions in porous glasses : A computer simulation study

We have developed a realistic model for studying adsorption in porous glasses which reproduces the complex structure of these materials. The model porous material is generated by a quench molecular dynamics procedure which mimics the processes by which Vycor glass and controlled-pore glasses are produced. We examine this procedure and the resulting model materials by a variety of methods and find that they have porosities, pore sizes, and surface areas very similar to the real glasses. These simulated glasses have precisely known properties (surface area, pore size distribution, etc.), in contrast to experimental glasses; computer experiments on such model glasses can therefore be used to test new and existing experimental methods of characterization. We calculate the adsorption isotherms for a model of nitrogen adsorbing onto these materials and analyze these data using the BET isotherm. The BET monolayer density exhibits systematic variations with both the average pore size and the porosity of the model...

Characterization of Porous Glasses: Simulation Models, Adsorption Isotherms, and the Brunauer−Emmett−Teller Analysis Method

We report both experimental measurements and molecular simulations of the melting and freezing behavior of simple fluids in porous media. The experimental studies are for carbon tetrachloride and nitrobenzene in controlled pore glass (CPG) and Vycor. Differential scanning calorimetry (DSC) was used to determine the melting point in the porous materials for each of the glass samples. In the case of nitrobenzene (which has a nonzero dipole moment), dielectric spectroscopy was also used to determine melting points. Measurements by the two methods were in excellent agreement. The melting point was found to be depressed relative to the bulk value for both fluids. With the exception of smallest pores, the melting point depression was proportional to the reciprocal of the pore diameter, in agreement with the Gibbs-Thomson equation. Structural information about the different confined phases was obtained by measuring the dielectric relaxation times using dielectric spectroscopy. Monte Carlo simulations were used to determine the shift in the melting point, T m , for a simple fluid in pores having both repulsive and strongly attractive walls. The strength of attraction to the wall was shown to have a large effect on the shift in T m , with T m being reduced for weakly attracting walls. For strongly attracting walls, such as graphitic carbon, the melting point increases for slit-shaped pores. For such materials, the adsorbed contact layer is shown to melt at a higher temperature than the inner adsorbed layers. A method for calculating the free energies of solids in pores is presented, and it is shown that the solid-liquid transition is first order in these systems.

Phase Transitions in Pores: Experimental and Simulation Studies of Melting and Freezing†

We have performed large-scale molecular dynamics simulations of the polymerization of silicic acid in aqueous solution using the potential developed by Fueston and Garofalini [J. Phys. Chem. 1990, 94, 5351]. Seventeen simulations, with different water-to-silicon ratios and silicic acid concentrations, were each run for between 1.6 and 12.5 ns, at temperatures of 1500, 2000, and 2500 K. Water clearly acts as a catalyst in these simulations. When the water-to-silicon ratio is large, we find that the initial stages of the polymerization process are dominated by the conversion of monomers to dimers and addition of monomers to small clusters, while at longer times cluster−cluster aggregation is observed. Using data from simulations at different temperatures, the activation energies of condensation between silicic acid monomers were calculated at different water-to-silicon ratios and found to compare favorably with experimental results; an extrapolation (at constant density) of simulated reaction rates to ambie...

Molecular dynamics simulations of the polymerization of aqueous silicic acid and analysis of the effects of concentration on silica polymorph distributions, growth mechanisms, and reaction kinetics

Lev D. Gelb

Papers

Phase separation in confined systems

Pore size distributions in porous glasses : A computer simulation study

Characterization of Porous Glasses: Simulation Models, Adsorption Isotherms, and the Brunauer−Emmett−Teller Analysis Method

Phase Transitions in Pores: Experimental and Simulation Studies of Melting and Freezing†

Molecular dynamics simulations of the polymerization of aqueous silicic acid and analysis of the effects of concentration on silica polymorph distributions, growth mechanisms, and reaction kinetics