Hisashi Okumura

14 papers Journal 14
YearRankTypeTitle / Venue / Authors
2023 J jnl
Effective mechanical potential of cell-cell interaction explains three-dimensional morphologies during early embryogenesis.
PLoS Comput. Biol.
Hiroshi Koyama, Hisashi Okumura, Atsushi M. Ito, Kazuyuki Nakamura, Tetsuhisa Otani, Kagayaki Kato, Toshihiko Fujimori
2023 J jnl
Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.
J. Comput. Chem.
Daiki Fukuhara, Masataka Yamauchi, Satoru G. Itoh, Hisashi Okumura
2022 J jnl
Implementations of replica-permutation and replica sub-permutation methods into LAMMPS.
Comput. Phys. Commun.
Masataka Yamauchi, Giovanni La Penna, Satoru G. Itoh, Hisashi Okumura
2021 J jnl
Dimerization of α-Synuclein Fragments Studied by Isothermal-Isobaric Replica-Permutation Molecular Dynamics Simulation.
J. Chem. Inf. Model.
Masataka Yamauchi, Hisashi Okumura
2019 J jnl
Replica sub-permutation method for molecular dynamics and monte carlo simulations.
J. Comput. Chem.
Masataka Yamauchi, Hisashi Okumura
2016 J jnl
Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density-functional tight-binding theory and particle mesh Ewald method.
J. Comput. Chem.
Hiroaki Nishizawa, Hisashi Okumura
2015 J jnl
Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms.
J. Comput. Chem.
Yoshiharu Mori, Hisashi Okumura
2014 J jnl
Transformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations.
J. Comput. Chem.
Hsin-Lin Chiang, Chun-Jung Chen, Hisashi Okumura, Chin-Kun Hu
2013 J jnl
Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules.
J. Comput. Chem.
Satoru G. Itoh, Hisashi Okumura
2013 J jnl
Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.
J. Comput. Chem.
Satoru G. Itoh, Hisashi Okumura
2013 J jnl
On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics.
J. Comput. Chem.
Tetsuya Morishita, Satoru G. Itoh, Hisashi Okumura, Masuhiro Mikami
2010 J jnl
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting.
J. Comput. Chem.
Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy
2006 J jnl
Multibaric-multithermal ensemble molecular dynamics simulations.
J. Comput. Chem.
Hisashi Okumura, Yuko Okamoto
2005 J jnl
Molecular simulations in the multibaric-multithermal ensembles.
Comput. Phys. Commun.
Hisashi Okumura, Yuko Okamoto