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

On the Controllable Soft-Templating Approach to Mesoporous Silicates

A mean-field phase diagram for conformationally symmetric diblock melts using the standard Gaussian polymer model is presented. Our calculation, which traverses the weak- to strong-segregation regimes, is free of traditional approximations. Regions of stability are determined for disordered (DIS) melts and for ordered structures including lamellae (L), hexagonally packed cylinders (H), body-centered cubic spheres (QIm3m), close-packed spheres (CPS), and the bicontinuous cubic network with Ia3d symmetry (QIa3d). The CPS phase exists in narrow regions along the order−disorder transition for χN ≥ 17.67. Results suggest that the QIa3d phase is not stable above χN ∼ 60. Along the L/QIa3d phase boundaries, a hexagonally perforated lamellar (HPL) phase is found to be nearly stable. Our results for the bicontinuous Pn3m cubic (QPn3m) phase, known as the OBDD, indicate that it is an unstable structure in diblock melts. Earlier approximation schemes used to examine mean-field behavior are reviewed, and compa...

Unifying Weak- and Strong-Segregation Block Copolymer Theories

We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physicochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the introduction of parallel tempering, and we suggest several promising avenues for future research.

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Parallel tempering: Theory, applications, and new perspectives

2.3. Amorphous Minerals 4354 3. Biological Routes to Controlling Morphology 4354 3.1. General Mechanisms 4356 3.1.1. Soluble and Insoluble Organic Molecules 4356 3.1.2. Control over Crystal Polymorph 4357 3.1.3. Control over Crystal Orientation 4359 3.2. Single-Crystal Biominerals 4359 3.2.1. Organic and Inorganic Soluble Additives 4360 3.2.2. Templating of Single-Crystal Morphologies 4361 3.3. Polycrystalline Biominerals 4366 3.3.1. Nacre Formation in Mollusks 4366 3.3.2. ForaminiferasA Biogenic Mesocrystal 4368 3.4. Amorphous Biominerals 4370 3.4.1. Silicification in Diatoms 4370 3.4.2. In Vitro Studies of Silicification in Diatoms 4371 4. Bioinspired Routes to Controlling Crystal Morphologies 4371

Controlling Mineral Morphologies and Structures in Biological and Synthetic Systems

In a physically confined environment, interfacial interactions, symmetry breaking, structural frustration and confinement-induced entropy loss can play dominant roles in determining molecular organization. Here we present a systematic study of the confined assembly of silica-surfactant composite mesostructures within cylindrical nanochannels of varying diameters. Using exactly the same precursors and reaction conditions that form the two-dimensional hexagonal SBA-15 mesostructured thin film, unprecedented silica mesostructures with chiral mesopores such as single- and double-helical geometries spontaneously form inside individual alumina nanochannels. On tightening the degree of confinement, a transition is observed in the mesopore morphology from a coiled cylindrical to a spherical cage-like geometry. Self-consistent field calculations carried out to account for the observed mesostructures accord well with experiment. The mesostructures produced by confined syntheses are useful as templates for fabricating highly ordered mesostructured nanowires and nanowire arrays.

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Composite mesostructures by nano-confinement.

We present a theoretical framework and computer simulation methodology for investigating the equilibrium structure and properties of mesostructured polymeric fluids with embedded colloids or nanoparticles. The method is based on a field-theoretic description of the fluid in which particle coordinates and chemical potential field variables are simultaneously updated. The fluid model can contain polymers of arbitrary chemical and architectural complexity, along with particles of all shapes, sizes, and surface treatments. Simulation results are compared with experiments conducted on polystyrene (PS)-functionalized Au nanoparticles in a PS-P2VP diblock copolymer melt.

Hybrid particle-field simulations of polymer nanocomposites.

An efficient algorithm is presented for numerically evaluating a self-consistent field theoretic (SCFT) model of an AB diblock copolymer that incorporates continuous polydispersity in one of the blocks. An interesting segregation effect is found in which chains of intermediate molecular weight are concentrated at domain interfaces. This model of continuous polydispersity is also implemented in the random phase approximation (RPA) to study the order-disorder transition and predicts that the stability of the disordered, homogeneous phase decreases as the polydispersity in one of the blocks increases. The RPA predictions are confirmed by SCFT calculations. Our approach and results are particularly relevant to block copolymers prepared by quasiliving synthesis techniques, where the polymerization of one block is much more controlled than the other block.

Continuous polydispersity in a self-consistent field theory for diblock copolymers

Evidence for capillary waves at a liquid/vapor interface are presented from extensive molecular dynamics simulations of a system containing up to 1.24 million Lennard-Jones particles. Careful measurements show that the total interfacial width depends logarithmically on L{sub {parallel}}, the length of the simulation cell parallel to the interface, as predicted theoretically. The strength of the divergence of the interfacial width on L{sub {parallel}} depends inversely on the surface tension {gamma}. This allows us to measure {gamma} two ways since {gamma} can also be obtained from the difference in the pressure parallel and perpendicular to the interface. These two independent measures of {gamma} agree provided that the interfacial order parameter profile is fit to an error function and not a hyperbolic tangent, as often assumed. We explore why these two common fitting functions give different results for {gamma}.

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Scott W. Sides

Papers

Composite mesostructures by nano-confinement.

Hybrid particle-field simulations of polymer nanocomposites.

Continuous polydispersity in a self-consistent field theory for diblock copolymers

Capillary waves at liquid-vapor interfaces: a molecular dynamics simulation.

Parallel algorithm for numerical self-consistent field theory simulations of block copolymer structure