Molecular simulations in the multibaric-multithermal ensembles. - Hisashi Okumura; Yuko Okamoto (Comput. Phys. Commun., 2005)

Multibaric-multithermal ensemble molecular dynamics simulations. - Hisashi Okumura; Yuko Okamoto (J. Comput. Chem., 2006)

Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. - Hisashi Okumura; Emilio Gallicchio; Ronald M. Levy (J. Comput. Chem., 2010)

Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules. - Satoru G. Itoh; Hisashi Okumura (J. Comput. Chem., 2013)

Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides. - Satoru G. Itoh; Hisashi Okumura (J. Comput. Chem., 2013)

On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics. - Tetsuya Morishita; Satoru G. Itoh; Hisashi Okumura; Masuhiro Mikami (J. Comput. Chem., 2013)

Transformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations. - Hsin-Lin Chiang; Chun-Jung Chen; Hisashi Okumura; Chin-Kun Hu (J. Comput. Chem., 2014)

Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms. - Yoshiharu Mori; Hisashi Okumura (J. Comput. Chem., 2015)

Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density-functional tight-binding theory and particle mesh Ewald method. - Hiroaki Nishizawa; Hisashi Okumura (J. Comput. Chem., 2016)

Replica sub-permutation method for molecular dynamics and monte carlo simulations. - Masataka Yamauchi; Hisashi Okumura (J. Comput. Chem., 2019)

Dimerization of α-Synuclein Fragments Studied by Isothermal-Isobaric Replica-Permutation Molecular Dynamics Simulation. - Masataka Yamauchi; Hisashi Okumura (J. Chem. Inf. Model., 2021)

Implementations of replica-permutation and replica sub-permutation methods into LAMMPS. - Masataka Yamauchi; Giovanni La Penna; Satoru G. Itoh; Hisashi Okumura (Comput. Phys. Commun., 2022)

Effective mechanical potential of cell-cell interaction explains three-dimensional morphologies during early embryogenesis. - Hiroshi Koyama; Hisashi Okumura; Atsushi M. Ito; Kazuyuki Nakamura; Tetsuhisa Otani; Kagayaki Kato; Toshihiko Fujimori (PLoS Comput. Biol., 2023)

Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency. - Daiki Fukuhara; Masataka Yamauchi; Satoru G. Itoh; Hisashi Okumura (J. Comput. Chem., 2023)