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2012 Fiscal Year Annual Research Report

分子系の引き込み現象発現可能性に関する理論的研究

Research Project

Project/Area Number 23655101
Research InstitutionKanazawa University

Principal Investigator

長尾 秀実  金沢大学, 数物科学系, 教授 (30291892)

Keywords引き込み現象 / 分子動力学シミュレーション / 自己組織化 / 高分子 / 脂質 / ミセル
Research Abstract

本年度は二原子分子や脂質ミセルのモデル分子を構築し、様々な条件下での引き込み現象の分子動力学シミュレーションによる研究を実施した。
前年度の研究結果では、分子密度が均一な高温状態では二原子分子振動の引き込み現象の観測は困難であった。一方、低温状態では二原子分子がクラスター化して、一部の少数分子クラスター内では分子振動に引き込み現象が観測された。本年度では二原子分子や脂質ミセルの振動モデル分子を構築し、様々な条件下での溶媒中の二個の分子間で振動引き込み現象の解析を行った。溶媒のない状態(真空中)かつ低温状態でのシミュレーション結果からは、粒子数、体積、温度が一定の条件下で振動の引き込み現象が観測できた。一方、粒子数、体積、エネルギーが一定の条件下では観測できなかった。そこで熱浴を含む粒子の運動方程式はファンデルポール方程式に帰属できることを示し、シミュレーション中の熱浴による相互作用が引き込み現象の原因であることを示した。次に溶媒中のモデル分子のシミュレーションを実施した。低密度溶媒中の分子間では引き込み現象は観測できなかったが、高密度溶媒中の二分子間では引き込み現象が誘発されることが分かった。
以上の結果から分子振動の引き込み現象は高密度の溶媒中で誘起される可能性が高いことが示すことができた。今後の課題として溶媒の粘性や物性と分子の引き込み現象に関する研究が挙げられる。

  • Research Products

    (20 results)

All 2013 2012

All Journal Article (9 results) (of which Peer Reviewed: 9 results) Presentation (11 results) (of which Invited: 4 results)

  • [Journal Article] Theoretical Study on Entrainment Phenomenon in Model Molecular Systems2013

    • Author(s)
      H. Nagao, S. Kawamoto, M. Rusmerryani, A. Purqon, K. Kawaguchi, H. Saito
    • Journal Title

      AIP Conference Proceedings

      Volume: 1518 Pages: 729-732

    • DOI

      DOI:10.1063/1.4794669

    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study on Binding Free Energy of Azurin-Cytochrome c551 Complex2012

    • Author(s)
      H. Saito, M. Iwayama, T. Mizukami, J. Kang, M.Tateno, H. Nagao
    • Journal Title

      Chemical Physics Letters

      Volume: 556 Pages: 297-302

    • DOI

      DOI:10.1016/j.cplett.2012.12.016

    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Analyses of the Dissociation Process of ADP from Hsp902012

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, M.Nishimura, T. Miyakawa, H. Saito, M. Takasu, H.Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112

    • DOI

      DOI:3791-3795,10.1002/qua.24229

    • Peer Reviewed
  • [Journal Article] Nanoscale Superconductivity2012

    • Author(s)
      Sergei P. Kruchinin, Hidemi Nagao
    • Journal Title

      International Journal Modern Physics

      Volume: 26 Pages: 12300013

    • DOI

      DOI:10.1142/S0217979212300137

    • Peer Reviewed
  • [Journal Article] Cell-Penetrating Peptide Induces Various Deformations of Lipid Bilayer Membrane: Inverted Micelle,Double Bilayer, and Transmembrane2012

    • Author(s)
      Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Shiroh Futaki, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Pages: 178-183

    • DOI

      DOI:10.1002/qua.23177

    • Peer Reviewed
  • [Journal Article] Solvation Effect on the Structural Change of Globular Protein: A Molecular Dynamics Study2012

    • Author(s)
      Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto,Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Pages: 344-350

    • DOI

      DOI:10.1002/qua.23251

    • Peer Reviewed
  • [Journal Article] Binding of Tat peptides on DOPC and DOPG lipid bilayer membrane studied by molecular dynamicssimulations2012

    • Author(s)
      Shuhei Kawamoto, Masako Takasu, Takeshi Miyakawa, Ryota Morikawa, Tatsuki Oda, Shiroh Futaki, Hidemi Nagao
    • Journal Title

      Molecular Simulation

      Volume: 38 Pages: 366-368

    • DOI

      DOI:10.1080/08927022.2010.536546

    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Structure and Lateral Pressure Profile2012

    • Author(s)
      H. Saito, M. Iwayama, H. Takagi, M. Nishimura, T. Miyakawa, K. Kawaguchi, M. Takasu, T. Mizukami, H. Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Pages: 3834-3839

    • DOI

      10.1002/qua.24248

    • Peer Reviewed
  • [Journal Article] Molecular Dynamics Studies of Lipid Bilayer with Gramicidin A: Effects of Gramicidin A on Membrane Structure and Hydrophobic Match2012

    • Author(s)
      Hiroaki Saito, Taku Mizukami, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Pages: 161-170

    • DOI

      10.1002/qua.23252

    • Peer Reviewed
  • [Presentation] Hras-GTP内におけるGTP周辺にある水分子の分子動力学法による研究2013

    • Author(s)
      宮川毅, 森河良太, 高須昌子, 杉森公一, 川口一朋, 齋藤大明, 長尾秀実
    • Organizer
      第68回 日本物理学会 春季大会
    • Place of Presentation
      広島
    • Year and Date
      20130326-29
  • [Presentation] Molecular dynamics analyses of dissociation process of ADP from Hsp902013

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, H. Saito, H. Nagao
    • Organizer
      International Symposium On Computational Science 2013
    • Place of Presentation
      Kanazawa
    • Year and Date
      20130218-20130221
    • Invited
  • [Presentation] Theoretical studies on oxidation of molecules by combining MD and QM/MM calculations2013

    • Author(s)
      Masashi Iwayama, Isman Kurniawan, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
    • Organizer
      The 53rd Sanibel Symposium
    • Place of Presentation
      Florida, USA
    • Year and Date
      20130217-22
  • [Presentation] Theoretical study on entrainment phenomenon in model molecular systems2012

    • Author(s)
      Hidemi Nagao, Michke Rusmerryani, Acep Pruqon, Kazutomo Kawaguchi, Hiroaki Saito
    • Organizer
      The 4th International Symposium on Slow Dynamics in Complex Systems
    • Place of Presentation
      Sendai
    • Year and Date
      20121202-20121207
  • [Presentation] Binding Free Energy of Azurin-Cytochrome c551 Complex by all-atom Molecular Dynamics Simulation2012

    • Author(s)
      H. Saito, M. Iwayama, T. Mizukami, K. Kawaguchi, Hidemi Nagao
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      Kobe
    • Year and Date
      20121014-20121018
  • [Presentation] Free energy profile of Hsp90-ADP binding by molecular dynamics simulations2012

    • Author(s)
      K. Kawaguchi, H. Saito, Hidemi Nagao
    • Organizer
      Conference on Computational Physics (CCP2012)
    • Place of Presentation
      Kobe
    • Year and Date
      20121014-18
  • [Presentation] Free energy profile for binding of ADP to Hsp90 with molecular dynamics simulation2012

    • Author(s)
      K. Kawaguchi, H. Takagi, M. Iwayama, M. Nishimura, H. Saito, Hidemi Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Year and Date
      20120922-20120924
  • [Presentation] Structure and lateral pressure profile of lipid bilayer containing gramicidin A by molecular dynamics simulation2012

    • Author(s)
      H. Saito, M. Iwayama, M. Nishimura, H. Takagi, K. Kawaguchi, H. Nagao
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Year and Date
      20120922-20120924
  • [Presentation] THEORETICAL STADIES ON SUPERCONDUCTIVITY IN ULTRASMALL GRAIN2012

    • Author(s)
      H.Nagao
    • Organizer
      9th International Conference on New Theories, Discoveries, and Applications of Superconductors and Related Materials
    • Place of Presentation
      Rome, Italy
    • Year and Date
      20120916-20120920
    • Invited
  • [Presentation] Molecular dynamics study of gramicidin A in lipid bilayer: structure and lateral pressure profile2012

    • Author(s)
      Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Kazutomo Kawaguchi, and Hidemi Nagao
    • Organizer
      The 5th International Symposium on Computational Sciences (ISCS) 2012
    • Place of Presentation
      Yogyakarta, Indonesia
    • Year and Date
      20120515-20120516
    • Invited
  • [Presentation] Free energy profile for binding of ADP to Hsp90 by molecular dynamics simulation2012

    • Author(s)
      Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Hiroaki Saito, and Hidemi Nagao
    • Organizer
      The 5th International Symposium on Computational Sciences (ISCS) 2012
    • Place of Presentation
      Yogyakarta, Indonesia
    • Year and Date
      20120515-20120516
    • Invited

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Published: 2014-07-24  

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