出立兼一

高須大輔 arrow_blank.PNG 塚本貴志
卒業年度2009年度
修得学位博士
 

在学時の研究テーマ

  • 分子シミュレーションによるDNAの電気伝導特性の解析
  • 分子シミュレーションによるタンパク質とリガンドの特性解析

研究業績

国際学術雑誌に発表した論文

  1. "Ab initio fragment molecular orbital calculations on specific interactions between aryl hydrocarbon receptor and dioxin",
    S. Miyagi, S. Sawamura, E. Yoshikawa, K. Dedachi, S. Itoh, M. Ishihara-Sugano, N. Kurita,
    International Journal of Quantum Chemistry, 2012, 112, 289-299.
  2. "Specific interactions and binding energies between thermolysin and potent inhibitors: Molecular simulations based on ab initio molecular orbital method",
    T. Hirakawa, S. Fujita, T. Ohyama, K. Dedachi, M. T. H. Khan, I. Sylte, N. Kurita,
    Journal of Molecular Graphics and Modelling, 2012, 33, 1-11.
  3. "Structure-based analysis of the molecular recognitions between HIV-1 TAR-RNA and transcription factor nuclear factor-kappaB (NFkB)",
    M. T. H. Khan, C. Mischiati, A. Ather, T. Ohyama, K. Dedachi, M. Borgatti, N. Kurita, R. Gambari,
    Journal Current Topics in Medicinal Chemistry, 2011, in press.
  4. "Specific interactions and binding free energies between thermolysin and dipeptides: Molecular simulations combined with Ab initio molecular orbital and classical vibrational analysis",
    K. Dedachi, T. Hirakawa, S. Fujita, M. T. H. Khan, I. Sylte, N. Kurita,
    Journal of Computational Chemistry, 2011, 32, 3047–3057.
  5. "Specific interactions between aryl hydrocarbon receptor and dioxin congeners: Ab itinio fragment molecular orbital calculations",
    E. Yoshikawa, S. Miyagi, K. Dedachi, S. Itoh, M. Ishihara-Sugano, N. Kurita,
    Journal of Molecular Graphics and Modelling, 2010, 29, 197-205.
  6. "Structure-based Analysis of the Molecular Recognitions between HIV-1 TAR-RNA and Transcription Factor NFkB",
    MTH, Khan, C. Mischiati, A. Ather, T. Ohyama, K. Dedachi, N. Kurita, R. Gambari,
    Cellular and Molecular Life Sciences, 2010, in press.
  7. "A combined simulation with ab initio MO and classical vibrational analysis on the specific interactions between thermolysin and dipeptide ligands",
    K. Dedachi, M. T. H. Khan, I. Sylte, N. Kurita,
    Chemical Physics Letters, 2009, 479, 290-295.
  8. "Hybrid QM/MM calculations on the structure and electronic properties of hydrated RNA base pair",
    K. Dedachi, Y. Ishikawa, T. Nakatsu, T. Natsume, T. Tsukamoto, N. Kurita,
    Journal of Molecular Structure: THEOCHEM, 2008, 854, 70-75.
  9. "A combined molecular dynamics/density-functional theoretical study on the structure and electronic properties of hydrating water molecules in the minor groove of decameric DNA duplex",
    T. Tsukamoto, Y. Ishikawa, T. Natsume, K. Dedachi, N. Kurita,
    Chemical Physics Letters, 2007, 441, 136-142.
  10. "Charge transfer through single- and double-strand DNA: Simulations based on molecular dynamics and molecular orbital methods",
    K. Dedachi, T. Natsume, T. Nakatsu, S. Tanaka, Y. Ishikawa, N. Kurita,
    Chemical Physics Letters, 2007, 436, 244-251.
  11. "Hybridization energies of double strands composed of DNA, RNA, PNA and LNA",
    T. Natsume, Y. Ishikawa, K. Dedachi, T. Tsukamoto, N. Kurita,
    Chemical Physics Letters, 2007, 434, 133-138.
  12. "Electronic properties of solvated duplex DNAs by DFT calculations",
    T. Tsukamoto, Y. Ishikawa, M. J. Vilkas, T. Natsumea, K. Dedachi, N. Kurita,
    Lecture Series on Computer and Computational Sciences, 2007, 7, 1022-1025.
  13. "Density-functional theoretical study on hydrated DNA duplex: Effect of hydrating water molecules on HOMO distribution in DNA",
    T. Tsukamoto, Y. Ishikawa, M.J. Vilkas, T. Natsume, K. Dedachi, N. Kurita,
    Chemical Physics Letters, 2006, 429, 563-569.
  14. "A DFT study on the electronic properties of DNA-DNA and PNA-DNA Double Strands",
    T. Natsume, Y. Ishikawa, K. Dedachi, T. Tsukamoto, N. Kurita,
    International Journal of Quantum Chemistry, 2006, 106, 3278-3287.
  15. "Density functional molecular orbital calculations on DNA-DNA, PNA-DNA and PNA-PNA double strands",
    T. Natsume, Y. Ishikawa, K. Dedachi, N. Kurita,
    Proceedings of the International Symposium on Frontiers of Computational Science 2005, 2006, 299-303.
  16. "Charge transfer in single- and double-strand DNAs: theoretical analysis based on molecular orbital method",
    K. Dedachi, Y. Ishikawa, T. Natsume, T. Nakatsu, N. Kurita,
    International Journal of Quantum Chemistry, 2006, 106, 3270-3277.
  17. "Density-functional calculations on DNA-DNA, PNA-DNA and PNA-PNA double strands"
    T. Natsume, Y. Ishikawa, K. Dedachi, N. Kurita,
    Chemical Physics Letters, 2006, 418, 239-244.
  18. "Charge transfer through double-strand DNA and its base-mismatched ones: theoretical analysis based on semiempirical molecular orbital calculations",
    T. Natsume, K. Dedachi, S. Tanaka, T. Higuchi, N. Kurita,
    Chemical Physics Letters, 2005, 408, 381-388.

国内の学術雑誌に発表した論文

  1. "Fragment MO計算によるAhRとダイオキシン間の特異的相互作用の解析",
    宮城慧, 吉川依里, 出立兼一, 伊藤聡, 石原-菅野美津子, 栗田典之
    J. Comput. Aided Chem., 2009, 10, 63-75.
  2. "細胞シミュレーションによる癌浸潤機構の解析",
    永瀬圭良, 小林浩, 永田昇, 山本史雄, 夏目貴行, 出立兼一, 塚本貴志, 栗田典之
    J. Comput. Aided Chem., 2007, 8, 75-84.
  3. "密度汎関数法による水和したDNAの電子状態解析: DNA副溝内の水和水がHOMOに与える影響",
    塚本貴志, Y. Ishikawa, 夏目貴行, 出立兼一, M.J. Vilkas, 栗田典之,
    J. Comput. Aided Chem., 2006, 7, 203-213.
  4. "1重鎖及び2重鎖DNAの電流電圧特性の理論的解析",
    出立兼一, 夏目貴行, 田中成典, 樋口高年, 栗田典之,
    J. Comput. Aided Chem., 2004, 5, 52-61.

国際学会における発表

  1. "Binding free energies between thermolysin and dipeptide ligands obtained by molecular simulations based on ab initio MO and classical vibrational methods",
    K. Dedachi, M.T.H. Khan, I. Sylte, N. Kurita,
    CBI-KSBSB Joint Conference BIOINFO 2009, 2009, November 4-7, Busan, Korea.
  2. "Molecular Mechanics and Fragment Molecular Orbital calculations on Specific Interactions between Thermolysin and Dipeptide Ligands",
    K. Dedachi, M. T. H. Khan, I. Sylteb, N. Kurita,
    International Symposium on Pathway/Network to Disease and Drug Discovery Specially Focused on Nuclear Receptors and Metabolic Syndrome , 2008, October. 22-24, Tokyo, Japan.
  3. "Molecular mechanics and molecular orbital simulations on specific interactions between thermolysin and dipeptide ligands",
    K. Dedachi, M. T. H. Khanb, I. Sylteb and N. Kurita,
    International Symposium on Multi-scale Simulations of Biological and Soft Materials , 2008, June. 18-20, Tokyo, Japan.
  4. "MP2, DFT and ONIOM calculations on the structures and electronic properties of hydrated RNA base and base pair",
    K. Dedachi, Y. Ishikawa, T. Natsume, T. Tsukamoto, N. Kurita,
    The 12th International Conference on the Applications of Density Functional Theory in Chemistry and Physics, 2007, Aug. 26-30, Amsterdam, The Netherlands.
  5. "Electronic and charge-transfer properties of single- and double-strand DNAs obtained by density functional method,"
    K. Dedachi, T. Natsume, T. Nakatsu, Y. Ishikawa, N. Kurita,
    The XIIth International Congress of Quantum Chemistry, 2006, May 21-26, Kyoto, Japan.
  6. "Charge transfer in Single- and Double-strand DNAs: Molecular Simulations Based on Molecular Orbital Method,"
    K. Dedachi, T. Natsume, T. Nakatsu, Y. Ishikawa, N. Kurita,
    2006 Sanibel Symposium, 2006, Feb. 25- March 2, Georgia, U.S.A.
  7. "Charge Transfer in Single- and Double-strand DNAs: Theoretical Analysis Based on Molecular Orbital Method,"
    K. Dedachi, T. Natsume, T. Nakatsu, N. Kurita,
    International Symposium on Frontiers of Computational Science 2005, 2005, December 12-13, Nagoya, Japan.

国内学会における発表

  1. "分子シミュレーションによる金属プロテアーゼとリガンド間の特異的相互作用の解析",
    出立兼一, M. T. H. Khan, I. Sylte, 栗田典之,
    第3回分子科学討論会, 2009, 愛知県.
  2. "分子シミュレーションによるサーモリシンとリガンド間の特異的相互作用の解析",
    出立兼一, 栗田典之, M. T. H. Khan, I. Sylte
    計算科学研究センター・ワークショップ2009, 2009, 愛知県.
  3. "MP2, DFT 及びONIOM 法を用いたウラシル塩基の水和構造の解析",
    出立兼一, 中津泰輔, 夏目貴行, 塚本貴志, Y. Ishikawa, 栗田典之,
    第10回理論化学討論会, 2007, 愛知県.
  4. "電場を考慮したDNAの電気伝導特性の解析",
    出立兼一,夏目貴行,中津泰輔,栗田典之,
    第19回分子シミュレーション討論会, 2005, 愛知県.
  5. "1重鎖及び2重鎖DNAの構造と電子物性の理論的解析",
    出立兼一, 夏目貴行, 田中成典, 栗田典之,
    分子構造総合討論会2004, 2004, 広島県.
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