Prof. Yasushige Yonezawa

Email: yonezawa2ipr@gmail.com

Qualifications

1991 Ph.D., Physics, Tsukuba Univercity, Japan

Publications

1. 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)
2. 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
3. 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
4. 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.
5. 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
6. 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
7. 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
8. Enhanced free-energy calculation using multi-scale simulation. H. Shimoyama,Y. Yonezawa, H. Nakamura. J. Chem. Phys. 133, 135101, 2010
9. 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
10. 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.
11. 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.
12. 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
13. 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.
14. 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
15. 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
16. 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
17. 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
18. 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
19. 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
20. 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.
21. 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
22. 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.
23. 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.
24. 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.
25. The Structural Information on the DNA Binding Protein HU in Solution Obtained by the Small Angle Neutron Scattering Experiments.S Fujiwara ,Y.Yonezawa