High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, +6

PLoS Computational Biology

EngineeringHit IdentificationMolecular BiologyComputational ChemistryMolecular Dynamics +15

42 TFlops hierarchical <i>N</i> -body simulations on GPUs with applications in both astrophysics and turbulence

Tsuyoshi Hamada, Tetsu Narumi, Rio Yokota, +3

Vortex ParticlesEngineeringGpu BenchmarkingComputer ArchitectureParticle Method +19

Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations

Tetsu Narumi, Ryutaro Susukita, Toshikazu Ebisuzaki, +2

Molecular Simulation

Molecular Dynamics MachineEngineeringPhysicsNatural SciencesMolecular Biology +13

Protein Explorer

Makoto Taiji, Tetsu Narumi, Yousuke Ohno, +4

EngineeringComputational BiologyComputer EngineeringMolecular Dynamics SimulationsProtein Modeling +11

DS-CUDA: A Middleware to Use Many GPUs in the Cloud Environment

Minoru Oikawa, Atsushi Kawai, Kentaro Nomura, +3

Cluster ComputingEngineeringGpu BenchmarkingComputer ArchitectureMolecular Dynamics +15

Petascale turbulence simulation using a highly parallel fast multipole method on GPUs

Rio Yokota, Lorena A. Barba, Tetsu Narumi, +1

Computer Physics Communications

EngineeringPhysicsAerospace EngineeringNatural SciencesFluid Mechanics +11

Hardware accelerator for molecular dynamics: MDGRAPE-2

Ryutaro Susukita, Toshikazu Ebisuzaki, Bruce G. Elmegreen, +8

Computer Physics Communications

EngineeringMolecular ComputingComputational ChemistryMolecular DynamicsBiophysics +1

Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models

Ryuji Sakamaki, Amadeu K. Sum, Tetsu Narumi, +1

The Journal of Chemical Physics

Thermodynamic properties of methane/water interface predicted by molecular dynamics simulations

Ryuji Sakamaki, Amadeu K. Sum, Tetsu Narumi, +2

The Journal of Chemical Physics

EngineeringComputational ChemistryChemistryNatural Gas HydrateMolecular Dynamics +14

Gordon Bell finalists II---A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3

Tetsu Narumi, Makoto Taiji, Mitsuru Ikei, +8

EngineeringProtein AssemblyMolecular BiologyAnalytical UltracentrifugationMolecular Dynamics +22