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

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

Intermolecular And Surface Forces

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

Molecular imprinting science and technology: a survey of the literature for the years up to and including 2003

We present a density functional theory of nonuniform ionic fluids. This theory is based on the application of the electrostatic contribution to the free energy functional arising from mean spherical approximation for a bulk restricted primitive model and from the energy route bulk equation of state. In order to employ this functional we define a reference fluid and additional averaged densities, according to the approach introduced by Gillespie, Nonner and Eisenberg [J. Phys.: Condens. Matter 14, 12129 (2002)]. In the case of bulk systems the proposed theory reduces to the mean spherical approximation equation of state, arising from the energy route and thus it predicts the first-order phase transition. We use this theory to investigate the effects of confinement on the liquid–vapor equilibria. Two cases are considered, namely an electrolyte confined to the pore with uncharged walls and with charged walls. The dependence of the capillary evaporation diagrams on the pore width and on the electrostatic potential is determined.

Phase behavior of ionic fluids in slitlike pores: a density functional approach for the restricted primitive model.

A detailed study of the microscopic structure of an electrolyte solution, cesium chloride (CsCl) in water, is presented. For revealing the influence of salt concentration on the structure, CsCl solutions at concentrations of 1.5, 7.5, and 15 mol % are investigated. For each concentration, we combine total scattering structure factors from neutron and X-ray diffraction and 10 partial radial distribution functions from molecular dynamics simulations in one single structural model, generated by reverse Monte Carlo modeling. This combination of computer modeling methods is capable of (a) showing the extent to which simulation results are consistent with experimental diffraction data and (b) tracking down distribution functions in computer simulation that are the least comfortable with diffraction data. For the present solutions, we show that the level of consistency between simulations that use simple pair potentials and experimental structure factors is nearly quantitative. Remaining inconsistencies seem to ...

Understanding the structure of aqueous cesium chloride solutions by combining diffraction experiments, molecular dynamics simulations, and reverse Monte Carlo modeling.

Density profiles of chemically reacting simple fluids near impenetrable surfaces

We apply recently developed version of a density functional theory [Z. Wang, L. Liu, and I. Neretnieks, J. Phys.: Condens. Matter 23, 175002 (2011)]10.1088/0953-8984/23/17/175002 to study adsorption of a restricted primitive model for an ionic fluid in slit-like pores in the absence of interactions induced by electrostatic images. At present this approach is one of the most accurate theories for such model electric double layers. The dependencies of the differential double layer capacitance on the pore width, on the electrostatic potential at the wall, bulk fluid density, and temperature are obtained. We show that the differential capacitance can oscillate as a function of the pore width dependent on the values of the above parameters. The number of oscillations and their magnitude decrease for high values of the electrostatic potential. For very narrow pores, close to the ion diameter, the differential capacitance tends to a minimum. The dependence of differential capacitance on temperature exhibits maxi...

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Orest Pizio

Papers

Phase behavior of ionic fluids in slitlike pores: a density functional approach for the restricted primitive model.

Understanding the structure of aqueous cesium chloride solutions by combining diffraction experiments, molecular dynamics simulations, and reverse Monte Carlo modeling.

Density profiles of chemically reacting simple fluids near impenetrable surfaces

Electric double layer capacitance of restricted primitive model for an ionic fluid in slit-like nanopores: A density functional approach

Water-like fluid in the presence of Lennard–Jones obstacles: predictions of an associative replica Ornstein–Zernike theory☆