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2020 – today
- 2023
[j14]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): 534-545 (2023)- [j13]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) - 2022
- [j12]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: 108362 (2022) - 2021
- [j11]Masataka Yamauchi, Hisashi Okumura:
Dimerization of α-Synuclein Fragments Studied by Isothermal-Isobaric Replica-Permutation Molecular Dynamics Simulation. J. Chem. Inf. Model. 61(3): 1307-1321 (2021)
2010 – 2019
- 2019
- [j10]Masataka Yamauchi, Hisashi Okumura:
Replica sub-permutation method for molecular dynamics and monte carlo simulations. J. Comput. Chem. 40(31): 2694-2711 (2019) - 2016
- [j9]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): 2701-2711 (2016) - 2015
- [j8]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): 2344-2349 (2015) - 2014
- [j7]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): 1430-1437 (2014) - 2013
- [j6]Satoru G. Itoh, Hisashi Okumura:
Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules. J. Comput. Chem. 34(8): 622-639 (2013) - [j5]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): 1375-1384 (2013) - [j4]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): 2493-2497 (2013) - 2010
- [j3]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): 1357-1367 (2010)
2000 – 2009
- 2006
- [j2]Hisashi Okumura, Yuko Okamoto:
Multibaric-multithermal ensemble molecular dynamics simulations. J. Comput. Chem. 27(3): 379-395 (2006) - 2005
- [j1]Hisashi Okumura, Yuko Okamoto:
Molecular simulations in the multibaric-multithermal ensembles. Comput. Phys. Commun. 169(1-3): 317-321 (2005)
Coauthor Index
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