Prof. Yasushige Yonezawa
Kinki University, Japan
Professor
Email: yonezawa2ipr@gmail.com
Qualifications
1991 Ph.D., Physics, Tsukuba Univercity, Japan
1981-1985 B.S., Department of Applied Physics, National Defense Academy of Japan, Japan
Publications
-
Molecular Dynamics Scheme for Precise Estimation of Electrostatic Interaction via Zero-Dipole Summation Principle, I. Fukuda,Y. Yonezawa, and H. Nakamura J. Chem. Phys. 134, 164107 (2011)
-
Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method.Y. Yonezawa, I. Fukuda, N. Kamiya, H. Shimoyama, and H. Nakamura, J. Chem. Theor. Comput. Vol. 7, Issue 5, p1484-1493
-
Degree of pyramidality governs the height and peak position of the free-energy-barrier for thecis–transisomerization ofN-Methylacetamide.Yasushige Yonezawa, Daron M. Standley, Haruki Nakamura Chem. Phys. Lett., Vol. 503, Issues 1-3, 2011, p139-144
-
Electronic structures of a [4Fe–4S] cluster, [Fe4S4(SCH3)3(CH3COO)], in dark-operative protochlorophyllide oxidoreductase (DPOR). Yu Takano,Yasushige Yonezawa, Yuichi Fujita, Genji Kurisu, Haruki Nakamura. Chem. Phys. Lett., vol.503, 2011, p296-300.
-
Multicanonical molecular dynamics simulations combined with metadynamics for the free energy landscape of a biomolecular system with High Energy BarriersY. Yonezawa, H. Shimoyama, H. Nakamura Chem. Phys. Lett. vol. 501, p598-602, 2011
-
Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation. H. Shimoyama, H. Nakamura,Y. Yonezawa. J. Chem. Phys. 134, 024109, 2011
-
Theory for Trivial Trajectory Parallelization of Multicanonical Molecular Dynamics and Application to a Polypeptide in Water, J.Ikeba, K. Umezawa, N. Kamiya, T. Sugihara, Y. Yonezawa, Y. Takano, H. Nakamura, J. Higo, J. Comput. Chem. vol. 32, p1286-1297, 2011
-
Enhanced free-energy calculation using multi-scale simulation. H. Shimoyama,Y. Yonezawa, H. Nakamura. J. Chem. Phys. 133, 135101, 2010
-
Intra- and Intermolecular Interaction Inducing Pyramidalization on both sides of a Proline Di-peptide during Isomerization: an ab Initio QM/MM Molecular Dynamics Simulation Study in explicit water,Yonezawa Y.; Nakata K.; Sakakura, K; Takada T.; Nakamura H., J. Am. Chem. Soc. 2009,131(12), pp 4535–4540
-
Membrane attachment facilitates ligand access to active site in Monoamine Oxidase A, Apostolov, R.;Yonezawa, Y.; Standley, D.; Kikugawa, G.; Takano, Y.; Nakamura, H., Biochemistry, 48, 5864-5873, 2009.
-
Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit waterJ. Higo, N. Kamiya, T. Sugihara,Y. Yonezawa,H. NakamuraChemical Physics Letter, 2009, vol. 473, p326-329.
-
Resonating Coupled-Cluster CI approach to ion-radical systems: Comparison with the unrestricted coupled-cluster approach. S. Yamanaka, Satomichi. Nishihara, K. Nakata,Y. Yonezawa, Mitsutaka Okumura, T. Takada, H. Nakamura, Kizashi Yamaguch, Int J of Quant Chem, Volume 109 Issue 15, 3811-3818,2009
-
A resonating broken-symmetry CI study of cationic states of phenalenyl dimeric compounds, Nishihara S.; Yamanaka S.; Kusakabe K.; Nakata K.;Yonezawa Y.; Nakamura H.; Takada T.; Yamaguchi K., Polyhedron , vol. 28, Issue 9-10, 22, 1628-1633, 2009.
-
A resonating broken symmetry configuration interaction approach for double-exchange magnetic systems, Nishikawa S.; Yamanaka S.; Kusakabe K.; Nakata K.;Yonezawa Y.; Nakamura H.; Takada T. and Yamaguchi K., J. Phys. Condens. Matter, , 21, 064227-064231, 2009
-
Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems.Kikugawa G,Apostolov R,Kamiya N,Taiji M,Himeno R,Nakamura H,Yonezawa Y.J Comput. Chem. Jan 15;30(1):110-8, 2009
-
Resonating Broken Symmetry CI Approach for Ion-Radical Systems: Comparison With UHF, Hybrid-DFT, and CASSCF-DFT, Nishikawa S.; Yamanaka S.; Ukai T.; Nakata K.; Kusakabe K.;Yonezawa Y.; Nakamura H.; Takada T.; Yamaguchi K.,Int. J. Quant. Chem. , Vol 108, p2966-2977, 2008
-
Consistent Molecular Dynamics Scheme Applying the Wolf Summation for Calculating Electrostatic Interaction of Particles.Fukuda I.,Yonezawa Y., Nakamura H.,Journal of the Physical Society of Japan, , Vol. 77, No. 11, p114301-114305, 2008
-
Protein-inhibitor Flexible Docking by a Multicanonical Sampling: Native Complex Structure with the Lowest Free Energy and a Free-energy Barrier Distinguishing the Native Complex from the Others Kamiya N.,Yonezawa Y., Nakamura H., Higo J., PROTEINS: Structure, Function, and Bioinformatics , Jan 1, 70(1), 41-53, 2008
-
Opal OP: An Extensible Grid-Enabling Wrapping Approach for Legacy Applications", Ichikawa K.; Date S.; Krishnan S.; Li W.; Nakata K.;Yonezawa Y.;Nakamura H.; Shinji Shimojo: 3rd Workshop on Grid Computing & Applications (GCA2007), Jun. 2007
-
Molecular dynamics simulation study on water associated with π-electrons of benzene by using QM/MM potentialYonezawa Y.; Nakata K.; Takada T. and Nakamura H., Chemical Physics Letters, Volume 428, Issues 1-3, Pages 73-77, 2006.
-
Flexible docking of an amyloid-forming peptide from β2-microglobulin Standley D.M.,Yonezawa Y.; Goto Y.; and Nakamura H. FEBS Letters, Volume 580, Issue 26, 13 November, Pages 6199-6205, 2006
-
Effects of salt concentration on association of the amyloid protofilaments of hen egg white Lysozyme studied by time-resolved neutron scattering."S. Fujiwara, F. Matsumoto,Y. Yonezawa,(2003)J. Mol.Biol.331 (1), 21-28.
-
An insight into the pathway of the amyloid fibril formation of hen egg white Lysozyme obtained from a small-angle X-ray and neutron scattering study.Y. Yonezawa, S. Tanaka, T. Kubota, K. Wakabayashi, K. Yutani, S. Fujiwara, (2002)J. Mol. Biol.323 (2), 237-251.
-
Denaturation and Aggregation of Hen Egg Lysozyme in Aqueous EthanolSolution Studied by Dynamic Light Scattering.S. Tanaka, Y. Oda, M. Ataka, K. Onuma, S. Fujiwara,Y. Yonezawa.(2001)Biopolymers Oct. 15;59(5),370-379.
-
The Structural Information on the DNA Binding Protein HU in Solution Obtained by the Small Angle Neutron Scattering Experiments.S Fujiwara ,Y.Yonezawa