Tetsu Narumi

TL;DR: The present method calculates the O(N log N) treecode and O (N) fast multipole method (FMM) on the GPUs with unprecedented efficiency and demonstrates the performance of the method by choosing one standard application -a gravitational N-body simulation- and one non-standard application -simulation of turbulence using vortex particles.

TL;DR: In this paper, the authors used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment performance of molecular docking and employed the molecular mechanics/Poisson Boltzmann and surface area method to estimate the binding free energies.

TL;DR: The Protein Explorer is a PC cluster equipped with special-purpose engines that calculate nonbonded interactions between atoms, which is the most time-consuming part of the simulations.

TL;DR: The Molecular Dynamics Machine (MDM) as mentioned in this paper is a special-purpose computer for classical molecular dynamics simulations that accelerates the calculation of non-bonding forces, Coulomb and van der Waals forces, because the calculation cost for Coulomb force dominates the total calculation time when we treat a large system of charged particles without truncating Coulomb forces.

TL;DR: Large-scale direct numerical simulations of homogeneous-isotropic fluid turbulence, achieving sustained performance of 1.08 petaflop/s on gpu hardware using single precision, exceeds by an order of magnitude the largest vortex-method calculations to date.