1.
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2021/03
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Article
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Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution Physical Review Letters 126,pp.128101 (Collaboration)
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2.
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2020/06
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Article
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Mutation-induced change in chignolin stability from π-turn to α-turn RSC Advances 10,pp.22797-22808 (Collaboration)
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3.
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2019/11
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Article
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Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory Biophysics and Physicobiology 16,pp.407-429 (Collaboration)
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4.
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2019/07
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Article
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Folding pathways of NuG2-a designed mutant of protein G-using relaxation mode analysis JOURNAL OF CHEMICAL PHYSICS 151,pp.044117 (Collaboration)
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5.
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2019/02
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Article
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Identification of slow relaxation modes in a protein trimer via positive definite relaxation mode analysis JOURNAL OF CHEMICAL PHYSICS 150,pp.084113 (Collaboration)
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6.
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2018/10
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Article
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Conformational change of a biomolecule studied by the weighted ensemble method: Use of the diffusion map method to extract reaction coordinates JOURNAL OF CHEMICAL PHYSICS 149,pp.134112 (Collaboration)
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7.
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2018/04
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Article
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Relaxation mode analysis for molecular dynamics simulations of proteins Biophys Rev. 10,pp.375-389 (Collaboration)
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8.
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2018
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Article
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Analysis of Structural Stability of Chignolin JOURNAL OF PHYSICAL CHEMISTRY B 122,pp.3801-3814 (Collaboration)
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9.
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2018
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Article
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Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy J. Compt. Chem. 39,pp.202-217 (Collaboration)
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10.
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2017/12
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Article
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Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation Phys Rev E 96,pp.062408 (Collaboration)
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11.
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2017
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Article
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Stability of Unfolded and Folded Protein Structures Using a 3D-RISM with the RMDFT J. Phys. Chem. B 121(42),pp.9881-9885 (Collaboration)
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12.
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2016/06
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Article
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A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution Journal of Chemical Physics 144 (Collaboration)
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13.
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2015/09
|
Article
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Relaxation mode analysis and markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature Journal of Chemical Physics 143 (Single)
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14.
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2015/06
|
Article
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A solvation-free-energy functional: A reference-modified density functional formulation Journal of Computational Chemistry 36,pp.1359-1369 (Collaboration)
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15.
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2014/05
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Article
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Liquid-solid and solid-solid phase transition of monolayer water: High-density rhombic monolayer ice The Journal of Chemical Physics 140 (Collaboration)
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16.
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2013/08
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Article
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New Computational Approach to Determine Liquid-Solid Phase Equilibria of Water Confined to Slit Nanopores JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9(8),pp.3299-3310 (Collaboration)
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17.
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2013/02
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Article
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Effective sampling algorithms and analysis method for biomolecular simulations The 4th International Symposium on Slow Dynamics in Complex Systems 1518,pp.598-601 (Single)
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18.
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2013/02
|
Article
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Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of Human Lysozyme J. Phys. Soc. Jpn 82,pp.023803 (Collaboration)
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19.
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2012
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Book
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Biomolecular Simulations: Methods and Protocols (Collaboration)
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20.
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2012
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Article
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Multibaric-multithermal ensemble study of liquid-solid phase transition in Lennard-Jones particles J. Phys. Soc. Japan 81,pp.SA014 (Collaboration)
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21.
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2011/10
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Article
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Relaxation mode analysis of a peptide system: comparison with principal component analysis Journal of Chemical Physics 135,pp.164102(15 pages) (Collaboration)
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22.
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2011/09
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Article
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Generalized-ensemble simulations in protein science Proceedings of MSSMBS 10 pp.46-60 (Collaboration)
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23.
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2011/08
|
Article
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Size dependent phase changes in water cluster Journal of Chemical Theory and Computation 7,pp.3083-3087 (Collaboration)
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24.
|
2011/03
|
Article
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Multicanonical molecular dynamics simulation study of the liguid-solid and solid-solid transitions Lennard-Jones clusters The 8th ASME/JSME Thermal Engineering Joint Conference pp.T30089 (Collaboration)
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25.
|
2010
|
Book
|
Multi-dimensional multicanonical algorithm, simulated
tempering, replica-exchange method, and all that Physics Procedia/Recent Developments in Computer Simulation Studies in Condensed Matter Physics 4,pp.89-105 (Collaboration)
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26.
|
2009/08
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Article
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Simulated-tempering replica-exchange method for the multidimensional version Journal of Chemical Physics (Vir. J. Bio. Phys. Res. 18 (6) Quantum Mechanical Dynamics にも掲載) 131,pp.094105 (Single)
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27.
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2009/06
|
Article
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Multidimensional generalized-ensemble algorithms for complex systems Journal of Chemical Physics 130(21),pp.214105 (Collaboration)
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28.
|
2009/04
|
Article
|
From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering Physical Review E (Vir. J. Bio. Phys. Res. 17 (8) Statistical and Nonlinear Physics にも掲載) 79,pp.047701 (Collaboration)
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29.
|
2008
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Book
|
Combination of generalized-ensemble algorithms for protein folding simulations (Collaboration)
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30.
|
2007
|
Article
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Combination of generalized-ensemble algorithms and reference interaction site model theory Condensed Matter Physics 10(4),pp.495 (Collaboration)
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31.
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2005
|
Article
|
Generalized-ensemble simulations of biomolecular system Biophysical J. pp.513A-513A Part 2 Suppl. (Single)
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32.
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2004
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Article
|
Combination of the replica-exchange Monte Carlo method and the reference interaction site model theory for simulating a peptide molecule in aqueous solution J. Phys. Chem. B 108,pp.19002-19012 (Collaboration)
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33.
|
2004
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Article
|
Generalized-ensemble Monte Carlo algorithms for simulations of proteins AIP Conference Proceedings:Slow Dynamics in Complex Systems, edited by M. Tokuyama and I. Oppenheim 708,pp.350-351 (Collaboration)
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34.
|
2004
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Article
|
Replica-exchange extensions of simulated tempering method J. Chem. Phys. (Vir. J. Bio. Phys. Res. 8 (3) Protein Conformational Dynamics/Folding にも掲載) 121,pp.2491-2504 (Collaboration)
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35.
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2003
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Article
|
Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory Chem. Phys. Lett. 380,pp.609-619 (Collaboration)
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36.
|
2003
|
Article
|
Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of small peptides II. Application to a more complex system J. Chem. Phys. (Vir. J. Bio. Phys. Res. 5(7) Fundamental Polymer Statics/Dynamics にも掲載) 118,pp.6676-6688 (Collaboration)
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37.
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2003
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Article
|
Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of small peptides. I. Formulation and benchmark test J. Chem. Phys. (Vir. J. Bio. Phys. Res. 5(7) Fundamental Polymer Statics/Dynamics にも掲載) 118,pp.6664-6675 (Collaboration)
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38.
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2002
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Article
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A pH-dependent variation in alpha-helix structure of the S-peptide of ribonuclease studied by Monte Carlo simulated annealing Biopolymers 63,pp.273-279 (Collaboration)
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39.
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2002
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Article
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Generalized-ensemble simulations of spin systems and protein systems Phys. Commun. 146,pp.69-76 (Collaboration)
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40.
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2001
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Article
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Generalized-ensemble algorithms for molecular simulations of biopolymers Biopolymers (Peptide Science) 60,pp.96-123 (Collaboration)
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41.
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2000
|
Article
|
Helix-coil transitions of amino-acid homo-oligomers in aqueous solution studied by multicanonical simulations J. Chem. Phys. (Vir. J. Bio. Phys. Res. 1 (6) Protein Conformational Dynamics/Folding にも掲載) 112,pp.10638-10647 (Collaboration)
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42.
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2000
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Article
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Multicanonical algorithm combined with the RISM theory for simulating peptides in aqueous solution Chem. Phys. Lett. 329,pp.295-303 (Collaboration)
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43.
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2000
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Article
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Replica-exchange simulated tempering method for simulations of frustrated systems Chem. Phys. Lett. 332,pp.131-138 (Collaboration)
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44.
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1999
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Article
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Alpha-Helix propensities of homo-oligomers in aqueous solution studied。。by multicanonical algorithm Chem. Phys. Lett. 309,pp.95-100 (Collaboration)
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45.
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1999
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Article
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Classification of low-energy conformations of Met-enkephalin in the gas phase and in a model solvent based on the extended scaled particle theory B. Chem. Soc. Jpn. 72,pp.1717-1729 (Collaboration)
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46.
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1998
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Article
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Temperature dependence of distributions of conformations of a small peptide J. Mol. Graph. Model 16,pp.226-238; 262-263 (Collaboration)
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47.
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1996
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Article
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A method for calculating the eigenvalues of large Hermitian matrices by second-order recursion formulae Comput. Phys. Commun. 96,pp.217-231 (Collaboration)
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