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Abstract: Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern massively concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive. This paper illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put_notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load. [Copyright &y& Elsevier]

Abstract: The paper presents an extension to the spheropolyhedra method for the simulation of granular materials comprising particles of general shapes with bonding. A bonding, cement, or cohesion model for particles sharing common faces is introduced. The bonding force is elastic and has a strain-based breaking threshold for modelling fracture. An initial study is conducted based on the Brazilian tensile test to check how the parameters of the proposed model affect the principal variables measured in this test. Afterwards, solid cubic blocks are then subjected to a triaxial test to explore the mathematical macroscopic failure model. It is found that the peak strength envelope is the product of the superposition of frictional and fracture failure mechanisms. The fracture failure is mainly produced by an avalanche of broken cohesive bonds. The intensity of the avalanche exhibits a power law distribution, as reported in previous studies. The method allows for random divisions of solid bodies without any pre-existing internal voids. It offers a natural, effective tool to model, simulate and study fragmentation processes in 3D. [Copyright &y& Elsevier]

Abstract: A Discrete Element Method (DEM) simulation program of gravity driven granular collapse is developed to compare the performance of Verlet table and linked-cell algorithms. Focusing on the simulation efficiency, the two neighbor list algorithms'' parameters are discussed such as search radius , cell edge , updating interval time step (UPTime) and the number of particles in simulation system N. The results show that appropriate parameters will improve the simulation efficiency, while the inappropriate parameters will debase the simulation efficiency, even leading to the simulation system crash. The results and discussions presented in this paper will be useful not only for parameters adjustment of DEM but also for Molecular Dynamics (MD) simulations. It will be beneficial to improving the simulation efficiency, especially for the researchers who intend to carry out DEM or MD simulation. [Copyright &y& Elsevier]

Abstract: This paper presents a molecular dynamics (MD) scheme for the automatic generation of dot patterns for the light guides used in LCD backlight modules. Several MD computational techniques are integrated with the conventional MD scheme to enable the adjustment of the dot density in specific regions of the light guide in order to create a dot distribution with a high dot density variation and a high spatial uniformity. These techniques include the cell division technique, the variable r-cut technique, the boundary smoothing technique and the reflective boundary condition. The reflective boundary condition enables a precise control of the dot density within each cell, and is instrumental in achieving a dot distribution with both a high dot density variation and a high spatial uniformity. The performance of the proposed dot generation scheme is verified by considering the practical example of the dot pattern design of a light guide with a single LED light source located in the lower-right corner. The numerical results confirm the ability of the proposed method to achieve an even luminance condition by establishing a dot pattern whose density increases concentrically with an increasing distance from the light source. [Copyright &y& Elsevier]

Abstract: This paper describes large-scale molecular dynamics simulations of liquid crystals. Simulations using simple models have been applied to colloidal systems involving one and two macroparticles. The defect structure around a macroparticle, and the solvent-mediated interactions between them have been studied. These simulations may provide input information for mesoscale models involving many more particles and much longer timescales. [Copyright &y& Elsevier]