1.34 Tflops Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM. - Tetsu Narumi; Ryutaro Susukita; Takahiro Koishi; Kenji Yasuoka; Hideaki Furusawa; Atsushi Kawai; Toshikazu Ebisuzaki (SC, 2000)

A smooth-particle mesh Ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700. - Kholmirzo Kholmurodov; William Smith; Kenji Yasuoka; Thomas A. Darden; Toshikazu Ebisuzaki (J. Comput. Chem., 2000)

Simulations of magnetic materials with MDGRAPE-2. - Bruce G. Elmegreen; Roger H. Koch; Manfred E. Schabes; Tiffany Crawford; Toshikazu Ebisuzaki; Hideaki Furusawa; Tetsu Narumi; Ryutaro Susukita; Kenji Yasuoka (IBM J. Res. Dev., 2004)

Overheads in Accelerating Molecular Dynamics Simulations with GPUs. - Tetsu Narumi; Ryuji Sakamaki; Shun Kameoka; Kenji Yasuoka (PDCAT, 2008)

Accelerating Molecular Dynamics Simulations on PlayStation 3 Platform Using Virtual-GRAPE Programming Model. - Tetsu Narumi; Shun Kameoka; Makoto Taiji; Kenji Yasuoka (SIAM J. Sci. Comput., 2008)

42 TFlops hierarchical N-body simulations on GPUs with applications in both astrophysics and turbulence. - Tsuyoshi Hamada; Tetsu Narumi; Rio Yokota; Kenji Yasuoka; Keigo Nitadori; Makoto Taiji (SC, 2009)

Fast multipole methods on a cluster of GPUs for the meshless simulation of turbulence. - Rio Yokota; Tetsu Narumi; Ryuji Sakamaki; Shun Kameoka; Shinnosuke Obi; Kenji Yasuoka (Comput. Phys. Commun., 2009)

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach. - Tetsu Narumi; Kenji Yasuoka; Makoto Taiji; Siegfried Höfinger (J. Comput. Chem., 2009)

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3. - Tetsu Narumi; Kenji Yasuoka; Makoto Taiji; Francesco Zerbetto; Siegfried Höfinger (Comput. J., 2011)

Petascale turbulence simulation using a highly parallel fast multipole method - Rio Yokota; Tetsu Narumi; Lorena A. Barba; Kenji Yasuoka (CoRR, 2011)

DS-CUDA: A Middleware to Use Many GPUs in the Cloud Environment. - Minoru Oikawa; Atsushi Kawai; Kentaro Nomura; Kenji Yasuoka; Kazuyuki Yoshikawa; Tetsu Narumi (SC Companion, 2012)

GPU-accelerated computation of electron transfer. - Siegfried Höfinger; Angela Acocella; Sergiu C. Pop; Tetsu Narumi; Kenji Yasuoka; Titus Beu; Francesco Zerbetto (J. Comput. Chem., 2012)

Petascale turbulence simulation using a highly parallel fast multipole method on GPUs. - Rio Yokota; Lorena A. Barba; Tetsu Narumi; Kenji Yasuoka (Comput. Phys. Commun., 2013)

Comparison of the accuracy of periodic reaction field methods in molecular dynamics simulations of a model liquid crystal system. - Takuma Nozawa; Kazuaki Z. Takahashi; Tetsu Narumi; Kenji Yasuoka (J. Comput. Chem., 2015)

Multi-Step Time Series Generator for Molecular Dynamics. - Katsuhiro Endo; Katsufumi Tomobe; Kenji Yasuoka (AAAI, 2018)

Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application. - Kai Pua; Daisuke Yuhara; Sho Ayuba; Kenji Yasuoka (CoRR, 2019)

A stochastic Hamiltonian formulation applied to dissipative particle dynamics. - Linyu Peng; Noriyoshi Arai; Kenji Yasuoka (Appl. Math. Comput., 2022)

MD-GAN with multi-particle input: the machine learning of long-time molecular behavior from short-time MD data. - Ryo Kawada; Katsuhiro Endo; Daisuke Yuhara; Kenji Yasuoka (CoRR, 2022)

Prediction of transport property via machine learning molecular movements. - Ikki Yasuda; Yusei Kobayashi; Katsuhiro Endo; Yoshihiro Hayakawa; Kazuhiko Fujiwara; Kuniaki Yajima; Noriyoshi Arai; Kenji Yasuoka (CoRR, 2022)

Optimal Replica-Exchange Molecular Simulations in Combination with Evolution Strategies. - Akie Kowaguchi; Katsuhiro Endo; Paul E. Brumby; Kentaro Nomura; Kenji Yasuoka (J. Chem. Inf. Model., 2022)

An Efficient Random Number Generation Method for Molecular Simulation. - Kiyoshiro Okada; Paul E. Brumby; Kenji Yasuoka (J. Chem. Inf. Model., 2022)

Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models. - Ryo Kawada; Katsuhiro Endo; Kenji Yasuoka; Hidekazu Kojima; Nobuyuki Matubayasi (J. Chem. Inf. Model., 2023)

Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization. - Akie Kowaguchi; Paul E. Brumby; Kenji Yasuoka (J. Chem. Inf. Model., 2024)

Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model. - Hideo Doi; Tatsuya Nakano; Kota Sakakura; Kazuki Akisawa; Koji Okuwaki; Yoshinori Hirano; Eiji Yamamoto; Kenji Yasuoka; Satoshi Ohshima; Takahiro Katagiri; Yuji Mochizuki (J. Comput. Chem., 2025)