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This paper presents general information about ARUZ, a scalable, fully parallel data processing system equipped with low-latency communication channels, designed for simulations of interactions among huge number of relatively simple elements. ARUZ consists of approximately 26 000 FPGAs and it can represent a system composed of several million elements consuming barely tens of kilowatts of power. It can be seen as a powerful machine for a wide range of applications. Currently, it implements the Dynamic Lattice Liquid algorithm, which enables studies of dynamic processes and phenomena in dense macromolecular systems. A performance estimation for liquid water shows that in one day ARUZ can model the diffusion of 1.5 million water molecules ongoing in reality for approximately 0.7 ms. [ABSTRACT FROM AUTHOR]

In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Program summary: Program title: FindClosestAtom Catalogue identifier: AEPZ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations to find which is the closest atom containing an arbitrary point in space. Atom sizes are according to the corresponding van der Waals radii. Restrictions: The geometrical model presented here does not include the chromosome organization level but it could be easily build up by using fragments of the 30 nm chromatin fiber. Unusual features: To our knowledge, this is the first open source atomic-resolution DNA geometrical model developed for DNA–radiation interaction Monte Carlo simulations. In our tests, the current model took into account the explicit position of about 56×106 atoms, although the user may enhance this amount according to the necessities. Running time: This subroutine can process about 2 million points within a few minutes in a typical current computer. [ABSTRACT FROM AUTHOR]

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: A new code, named MAP, is written in FORTRAN language for magnetohydrodynamics (MHD) simulations with the adaptive mesh refinement (AMR) and Message Passing Interface (MPI) parallelization. There are several optional numerical schemes for computing the MHD part, namely, modified Mac Cormack Scheme (MMC), Lax–Friedrichs scheme (LF), and weighted essentially non-oscillatory (WENO) scheme. All of them are second-order, two-step, component-wise schemes for hyperbolic conservative equations. The total variation diminishing (TVD) limiters and approximate Riemann solvers are also equipped. A high resolution can be achieved by the hierarchical block-structured AMR mesh. We use the extended generalized Lagrange multiplier (EGLM) MHD equations to reduce the non-divergence free error produced by the scheme in the magnetic induction equation. The numerical algorithms for the non-ideal terms, e.g., the resistivity and the thermal conduction, are also equipped in the code. The details of the AMR and MPI algorithms are described in the paper. [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]