Efficient Parallelization of Short-Range Molecular Dynamics Simulations on Many-Core Systems

This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly inhomogeneous systems like nanodevices or nanostructured materials. In the proposed scheme the calculation of the forces and the generation of neighbor lists is divided into small tasks. The tasks are then executed by a thread pool according to a dependent task schedule. This schedule is constructed in such a way that a particle is never accessed by two threads at the same time.Benchmark simulations on a typical 12 core machine show that the described algorithm achieves excellent parallel efficiencies above 80 % for different kinds of systems and all numbers of cores. For inhomogeneous systems the speedups are strongly superior to those obtained with spatial decomposition. Further benchmarks were performed on an Intel Xeon Phi coprocessor. These simulations demonstrate that the algorithm scales well to large numbers of cores.Comment: 12 pages, 8 figure

Lattice Dynamics of Martensitic Transformations Examined by Atomistic Simulations

We have performaed molecular dynamics simulations of Fe(80)Ni(20) alloys using an inter-atomic potential of the EAM-type which allows the simulation of the martensite-austenite transition. We present results, showing the development of an inhomogeneous shear system on a nanoscale during the thermally induced austenitic transition. In addition to this we obtained the phonon dispersion relations of the martensite phase by calculating the dynamical structure factor from our simulation results. On approaching the transition temperature the phonon dispersion shows anomalies which might be connected with the formation of the microstructure during the austenitic transition.Comment: 7 pages, 4 figures, Contribution submitted to the "IV European Symposium on Martensitic Transformations" (ESOMAT 97), July 1-5, 1997, Enschede (The Netherlands

Coordinated oscillations in cortical actin and Ca2+ correlate with cycles of vesicle secretion.

The actin cortex both facilitates and hinders the exocytosis of secretory granules. How cells consolidate these two opposing roles was not well understood. Here we show that antigen activation of mast cells induces oscillations in Ca(2+) and PtdIns(4,5)P(2) lipid levels that in turn drive cyclic recruitment of N-WASP and cortical actin level oscillations. Experimental and computational analysis argues that vesicle fusion correlates with the observed actin and Ca(2+) level oscillations. A vesicle secretion cycle starts with the capture of vesicles by actin when cortical F-actin levels are high, followed by vesicle passage through the cortex when F-actin levels are low, and vesicle fusion with the plasma membrane when Ca(2+) levels subsequently increase. Thus, cells employ oscillating levels of Ca(2+), PtdIns(4,5)P(2) and cortical F-actin to increase secretion efficiency, explaining how the actin cortex can function as a carrier as well as barrier for vesicle secretion

High-Precision Thermodynamics and Hagedorn Density of States

We compute the entropy density of the confined phase of QCD without quarks on the lattice to very high accuracy. The results are compared to the entropy density of free glueballs, where we include all the known glueball states below the two-particle threshold. We find that an excellent, parameter-free description of the entropy density between 0.7Tc and Tc is obtained by extending the spectrum with the exponential spectrum of the closed bosonic string.Comment: 4 pages, 3 figure

Liapunov functions for the problem of Lurie

Popov criteria for asymptotic stability of Lurie system of differential equations and Liapunov function

IMPLICATIONS FOR TRADE TENSIONS AND DISPUTES FROM STRUCTURAL IMPACTS OF THE NAFTA: A U.S. PORK INDUSTRY PERSPECTIVE

International Relations/Trade,