Hisashi Okumura

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 6

Top Topics

Data Generation

Chemical Compounds

Molecular Dynamics

Top Venues

J. Comput. Chem.

Comput. Phys. Commun.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Daiki Fukuhara, Masataka Yamauchi, Satoru G. Itoh, Hisashi Okumura
Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency. J. Comput. Chem. 44 (4) (2023)
Hiroshi Koyama, Hisashi Okumura, Atsushi M. Ito, Kazuyuki Nakamura, Tetsuhisa Otani, Kagayaki Kato, Toshihiko Fujimori
Effective mechanical potential of cell-cell interaction explains three-dimensional morphologies during early embryogenesis. PLoS Comput. Biol. 19 (8) (2023)
Masataka Yamauchi, Giovanni La Penna, Satoru G. Itoh, Hisashi Okumura
Implementations of replica-permutation and replica sub-permutation methods into LAMMPS. Comput. Phys. Commun. 276 (2022)
Masataka Yamauchi, Hisashi Okumura
Dimerization of α-Synuclein Fragments Studied by Isothermal-Isobaric Replica-Permutation Molecular Dynamics Simulation. J. Chem. Inf. Model. 61 (3) (2021)
Masataka Yamauchi, Hisashi Okumura
Replica sub-permutation method for molecular dynamics and monte carlo simulations. J. Comput. Chem. 40 (31) (2019)
Hiroaki Nishizawa, Hisashi Okumura
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. 37 (31) (2016)
Yoshiharu Mori, Hisashi Okumura
Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms. J. Comput. Chem. 36 (31) (2015)
Hsin-Lin Chiang, Chun-Jung Chen, Hisashi Okumura, Chin-Kun Hu
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. 35 (19) (2014)
Tetsuya Morishita, Satoru G. Itoh, Hisashi Okumura, Masuhiro Mikami
On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics. J. Comput. Chem. 34 (16) (2013)
Satoru G. Itoh, Hisashi Okumura
Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides. J. Comput. Chem. 34 (29) (2013)
Satoru G. Itoh, Hisashi Okumura
Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules. J. Comput. Chem. 34 (8) (2013)
Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J. Comput. Chem. 31 (7) (2010)
Hisashi Okumura, Yuko Okamoto
Multibaric-multithermal ensemble molecular dynamics simulations. J. Comput. Chem. 27 (3) (2006)
Hisashi Okumura, Yuko Okamoto
Molecular simulations in the multibaric-multithermal ensembles. Comput. Phys. Commun. 169 (1-3) (2005)