Learn More
As an entry for the 2009 Gordon Bell price/performance prize, we present the results of two different hierarchical <i>N</i>-body simulations on a cluster of 256 graphics processing units (GPUs). Unlike many previous <i>N</i>-body simulations on GPUs that scale as <i>O</i>(<i>N</i><sup>2</sup>), the present method calculates the <i>O</i>(<i>N</i> log(More)
The cysteinyl leukotrienes (cys-LTs), leukotriene C4 (LTC4) and its metabolites, LTD4 and LTE4, are proinflammatory lipid mediators in asthma and other inflammatory diseases. They are generated through the 5-lipoxygenase/LTC4 synthase (LTC4S) pathway and act via at least two distinct G protein-coupled receptors. The inhibition of human LTC4S will make a(More)
The rapid and accurate molecular dynamics simulation of biomolecules was made possible by a special purpose computer, MD-GRAPE Ž . GRAvity PipE for Molecular Dynamics , which computes arbitrary central force and potential. A program package for the molecular dynamics simulation of Ž biological macromolecules was developed PEACH Program for Energetic .(More)
We have achieved a sustained performance of 55 TFLOPS for molecular dynamics simulations of the amyloid fibril formation of peptides from the yeast Sup35 in an aqueous solution. For performing the calculations, we used the MDGRAPE-3 system---a special-purpose computer system for molecular dynamics simulations. Its nominal peak performance was 415 TFLOPS for(More)
A new method is presented for determining the hydration site of proteins, where the effect of structural fluctuations in both protein and hydration water is explicitly considered by using molecular dynamics simulation (MDS). The whole hydration sites (HS) of lysozyme are composed of 195 single HSs and 38 clustered ones (CHS), and divided into 231 external(More)
We report on resent astrophysical N-body simulations performed on the GRAPE-4 (GRAvity PipE 4) system, a special-purpose computer for astrophysical N-body simulations. We first review the astrophysical motivation, the algorithm, the structure of the GRAPE system, and the actual performance. The GRAPE-4 system consists of 1692 pipeline processors. The peak(More)