Hisashi Okumura

发表

Molecular dynamics simulations in the multibaric–multithermal ensemble

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2004 .

Simulated tempering based on global balance or detailed balance conditions: Suwa–Todo, heat bath, and Metropolis algorithms

Yoshiharu Mori, Hisashi Okumura, H. Okumura, 2015, J. Comput. Chem..

Generalized-Ensemble Algorithms for Simulations of Complex Molecular Systems

Yuko Okamoto, Hisashi Okumura, Satoru G. Itoh, 2012 .

Generalized-ensemble algorithm with suwa-Todo algorithm : Replica-Permutation Method

Hisashi Okumura, Itoh Satoru.G., H. Okumura, 2013 .

Multibaric–multithermal ensemble molecular dynamics simulations

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2006, J. Comput. Chem..

Conformational populations of ligand‐sized molecules by replica exchange molecular dynamics and temperature reweighting

Ronald M. Levy, Emilio Gallicchio, Hisashi Okumura, 2009, J. Comput. Chem..

Generalized-ensemble algorithms for molecular dynamics simulations

Yuko Okamoto, Hisashi Okumura, Satoru G. Itoh, 2007 .

Authentifizierbares printed material and process for its manufacture

Kazuhiko Shimada, Hisashi Okumura, Masato Kiuchi, 2001 .

Hamiltonian replica‐permutation method and its applications to an alanine dipeptide and amyloid‐β(29–42) peptides

Hisashi Okumura, Satoru G. Itoh, H. Okumura, 2013, J. Comput. Chem..

1516 Multi-Hierarchy Molecular Dynamics Simulation with Affine Coupling Method

Hiroaki Nakamura, Seiki Saito, Hisashi Okumura, 2011 .

Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density‐functional tight‐binding theory and particle mesh Ewald method

Hisashi Okumura, Hiroaki Nishizawa, H. Okumura, 2016, J. Comput. Chem..

1P045 Efficient sampling for biomolecules by the replica-permutation method(01B. Protein:Structure & Function,Poster)

Hisashi Okumura, Satoru G. Itoh, 2013 .

Replica sub‐permutation method for molecular dynamics and monte carlo simulations

Hisashi Okumura, Masataka Yamauchi, H. Okumura, 2019, J. Comput. Chem..

Molecular simulations in the multibaric-multithermal ensembles

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2005, Comput. Phys. Commun..

On‐the‐fly reconstruction of free‐energy profiles using logarithmic mean‐force dynamics

Masuhiro Mikami, Tetsuya Morishita, Hisashi Okumura, 2013, J. Comput. Chem..

Coulomb replica‐exchange method: Handling electrostatic attractive and repulsive forces for biomolecules

Hisashi Okumura, Satoru G. Itoh, H. Okumura, 2013, J. Comput. Chem..

Transformation between α‐helix and β‐sheet structures of one and two polyglutamine peptides in explicit water molecules by replica‐exchange molecular dynamics simulations

Chun-Jung Chen, Chin-Kun Hu, Hisashi Okumura, 2014, J. Comput. Chem..

Temperature and pressure dependence of alanine dipeptide studied by multibaric-multithermal molecular dynamics simulations.

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2008, The journal of physical chemistry. B.

Pressure-Induced Helical Structure of a Peptide Studied by Simulated Tempering Molecular Dynamics Simulations.

Yoshiharu Mori, Hisashi Okumura, H. Okumura, 2013, The journal of physical chemistry letters.

Generalized-ensemble molecular dynamics and Monte Carlo algorithms beyond the limit of the multicanonical algorithm

Hisashi Okumura, H. Okumura, 2010 .

Liquid-Gas Phase Transitions Studied by Multibaric-Multithermal Monte Carlo Simulations

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2004 .

Monte Carlo simulations in generalized isobaric-isothermal ensembles.

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles.

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2007, The Journal of chemical physics.

Liquid–vapor coexistence curves of several interatomic model potentials

Hisashi Okumura, Fumiko Yonezawa, H. Okumura, 2000 .

Explicit Symplectic Integrators of Molecular Dynamics Algorithms for Rigid-Body Molecules in the Canonical, Isothermal-Isobaric, and Related Ensembles

Yuko Okamoto, Hisashi Okumura, Satoru G. Itoh, 2006 .

Dimerization process of amyloid-β(29-42) studied by the Hamiltonian replica-permutation molecular dynamics simulations.

Hisashi Okumura, H. Okumura, S. Itoh, 2014, The journal of physical chemistry. B.

Structural basis of TRPA1 inhibition by HC-030031 utilizing species-specific differences

Rupali Gupta, Yoshiharu Mori, Hisashi Okumura, 2016, Scientific Reports.

Molecular dynamics study of liquid–vapor coexistence curves and supercritical fluids

Hisashi Okumura, Fumiko Yonezawa, H. Okumura, 2001 .

Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric‐multithermal molecular dynamics method

Hisashi Okumura, H. Okumura, 2012, Proteins.

Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.

Hisashi Okumura, H. Okumura, 2008, The Journal of chemical physics.

Amyloid fibril disruption by ultrasonic cavitation: nonequilibrium molecular dynamics simulations.

Hisashi Okumura, Satoru G. Itoh, H. Okumura, 2014, Journal of the American Chemical Society.

Manifold Correction Method for the Nosé–Hoover and Nosé–Poincaré Molecular Dynamics Simulations

Toshio Fukushima, Atsushi M. Ito, Hisashi Okumura, 2014 .

Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation.

Hisashi Okumura, H. Okumura, S. Itoh, 2013, Physical chemistry chemical physics : PCCP.

Multibaric–Multithermal Molecular Dynamics Simulation of Alanine Dipeptide in Explicit Water

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2007 .

Replica-Permutation Method with the Suwa-Todo Algorithm beyond the Replica-Exchange Method.

Hisashi Okumura, H. Okumura, S. Itoh, 2012, Journal of chemical theory and computation.

Comparison of Replica-Permutation Molecular Dynamics Simulations with and without Detailed Balance Condition

Hisashi Okumura, Hiroaki Nishizawa, H. Okumura, 2015 .

Molecular simulations by generalized-ensemble algorithms in isothermal–isobaric ensemble

Yoshiharu Mori, Hisashi Okumura, Masataka Yamauchi, 2019, Biophysical Reviews.

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

Yuko Okamoto, Hisashi Okumura, Y. Okamoto, 2009, The Journal of chemical physics.

Reliable Determination of the Liquid-Vapor Critical Point by the NVT Plus Test Particle Method.

Hisashi Okumura, Fumiko Yonezawa, H. Okumura, 2001 .

Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.

Hisashi Okumura, H. Okumura, 2011, Physical chemistry chemical physics : PCCP.

Decomposition-order effects of time integrator on ensemble averages for the Nosé-Hoover thermostat.

Tetsuya Morishita, Hisashi Okumura, H. Okumura, 2013, The Journal of chemical physics.

Theoretical approaches for dynamical ordering of biomolecular systems.

Hirofumi Sato, Hisashi Okumura, Masahiro Higashi, 2018, Biochimica et biophysica acta. General subjects.

Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulations predict only one end has open conformations

Hisashi Okumura, Satoru G. Itoh, H. Okumura, 2016, Scientific Reports.

Comparisons between molecular dynamics and hydrodynamics treatment of nonstationary thermal processes in a liquid.

Hisashi Okumura, H. Okumura, D. Heyes, 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.