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2010 Fiscal Year Final Research Report

New Development of Kramers-Fokker-Planck Equation of Polyatomic Molecules

Research Project

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Project/Area Number 20550011
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionNagoya University

Principal Investigator

NAGAOKA Masataka  Nagoya University, 情報科学研究科, 教授 (50201679)

Project Period (FY) 2008 – 2010
Keywords化学反応 / 計算科学 / 化学物理 / 原子・分子物理 / シミュレーション工学 / 自己組織化 / 非平衡
Research Abstract

How is the dynamics in condensed system recognized? We tried to understand its characteristics from the viewpoint of energy relaxation processes from an HF molecule to its surrounding water solvent system.
Since the dynamics in condensed system should be considered on the basis of stochastic theory, observables must be statistically calculated. Therefore, the super-multi concurrent molecular dynamics simulation system was developed.
From those simulations of energy relaxation process using the system involved, it is found that solvated water molecules around the vibrationally excited HF molecule requires their internal vibrational modes for energy transfer. Such energy transfer pathway depends on vibrational vector of excitation mode of the HF molecule. It is concluded that intra-molecular vibrational couplings are dominant on the energy relaxation process.
In relation to the Kramers-Fokker-Planck equation modeled condensed systems, furthermore, it was investigated to select which coordinates systems could represent molecular dynamics. We considered that time scales of observables should be introduced in correspondence with molecular fluctuation. It was found that the characteristics depend properly on the time window size.

  • Research Products

    (21 results)

All 2010 2009 2008

All Journal Article (5 results) (of which Peer Reviewed: 5 results) Presentation (14 results) Book (2 results)

  • [Journal Article] A MinimalImplementation of the AMBER-GAUSSIAN Interface for Ab Initio QM/MM-MD Simulation2010

    • Author(s)
      T.Okamoto, K.Yamada, Y.Koyano, T.Asada, N.Koga, M.Nagaoka
    • Journal Title

      Journal of Computational Chemistry 32

      Pages: 932-942

    • Peer Reviewed
  • [Journal Article] Influence of Hydrostatic Pressure on Dynamics and Spatial Distribution of Protein Partial Molar Volume : Time-Resolved Surficial Kirkwood-Buff Approach2010

    • Author(s)
      I.Yu, T.Tasaki, K.Nakada, M.Nagaoka
    • Journal Title

      The Journal of Physical Chemistry B 114

      Pages: 12392-12397

    • Peer Reviewed
  • [Journal Article] Structural Dynamics of Clamshell Rotation during the Incipient Relaxation Process of Photodissociated Carbonmonoxymyoglobin : Statistical Analysis by Perturbation Ensemble Method2010

    • Author(s)
      M.Takayanagi, C.Iwahashi, M.Nagaoka
    • Journal Title

      The Journal of Physical Chemistry B 114

      Pages: 12340-12348

    • Peer Reviewed
  • [Journal Article] Intrinsic Alteration in the Partial Molar Volume on the Protein Denaturation : Surficial Kirkwood-Buff Approach2009

    • Author(s)
      I.Yu, M.Takayanagi, M.Nagaoka
    • Journal Title

      Journal of Physical Chemistry B 113

      Pages: 3543-3547

    • Peer Reviewed
  • [Journal Article] Surficial Kirkwood-Buff Approach on the Preferential Interaction of Urea and Ectoine with Protein2008

    • Author(s)
      I.Yu, M.Nagaoka
    • Journal Title

      Proceedings of International Symposiumon Frontiers of Computational Science 2008

      Pages: 9-14

    • Peer Reviewed
  • [Presentation] Anisotropic Relaxation Pathway of Excess Energy of Photolyzed MbCO by Perturbation Ensemble Method2010

    • Author(s)
      高柳昌芳, 長岡正隆
    • Organizer
      The Fourth Asian Pacific Conference of Theoretical & Computational Chemistry
    • Place of Presentation
      Port Dickson/Malaysia.
    • Year and Date
      2010-12-22
  • [Presentation] Molecular Picture of Protein Volume Paradox : A Study by Surficial Kirkwood-Buff Integral Method2010

    • Author(s)
      優乙石, 長岡正隆
    • Organizer
      The Fourth Asian Pacific Conference of Theoretical & Computational Chemistry
    • Place of Presentation
      Port Dickson/Malaysia.
    • Year and Date
      2010-12-22
  • [Presentation] Ammonia dissolution process into water : An approach by the free energy gradient method.2010

    • Author(s)
      長岡正隆
    • Organizer
      The International Chemical Congress of Pacific Basin Societies(Pacifichem 2010)
    • Place of Presentation
      Honolulu, Hawaii/USA.
    • Year and Date
      2010-12-16
  • [Presentation] タンパク質体積パラドックスの分子描像:表面カークウッド-バフ積分法による考察2009

    • Author(s)
      優乙石, 長岡正隆
    • Organizer
      第47回生物物理学会年会
    • Place of Presentation
      徳島
    • Year and Date
      20091031-20091101
  • [Presentation] Toward Absolute Reaction Rate Theory in Solution via Free Energy Gradient Method with Extensive QM/MM Molecular Dynamics Simulations2009

    • Author(s)
      長岡正隆
    • Organizer
      The 3rd Japan-Czech-Slovak symposium on Theoretical and Computational Chemistry
    • Place of Presentation
      Bratislava/Slovak Republic.
    • Year and Date
      2009-10-10
  • [Presentation] 溶質分子エネルギー緩和過程における溶媒熱障壁について2009

    • Author(s)
      岡本拓也, 長岡正隆
    • Organizer
      第3回分子科学討論会名古屋2009
    • Place of Presentation
      名古屋大学
    • Year and Date
      2009-09-24
  • [Presentation] 光解離MbCOヘム近傍領域への非等方的余剰エネルギー緩和過程の理論的研究2009

    • Author(s)
      高柳昌芳, 大槻進, 長岡正隆
    • Organizer
      第3回分子科学討論会名古屋2009
    • Place of Presentation
      名古屋大学
    • Year and Date
      2009-09-24
  • [Presentation] 部分モル体積の空間分布から見たタンパク質変性:カークウッド-バフ積分法による考察2009

    • Author(s)
      優乙石, 長岡正隆
    • Organizer
      第3回分子科学討論会名古屋2009
    • Place of Presentation
      名古屋大学
    • Year and Date
      2009-09-24
  • [Presentation] MbCO光解離直後に生じる非等方的緩和過程の高分解能解析2009

    • Author(s)
      高柳昌芳, 長岡正隆
    • Organizer
      第12回理論化学討論会
    • Place of Presentation
      東京大学
    • Year and Date
      2009-05-30
  • [Presentation] 表面Kirkwood-Buff積分法によるタンパク質部分モル体積不変性の微視的理解2009

    • Author(s)
      優乙石, 長岡正隆
    • Organizer
      第12回理論化学討論会
    • Place of Presentation
      東京大学
    • Year and Date
      2009-05-30
  • [Presentation] Toward Absolute Reaction Rate Theory In Solution Via Free Energy Gradient Method With Extensive Molecular Dynamics Simulations2009

    • Author(s)
      長岡正隆
    • Organizer
      ANSCSE13 (Annual Symposium on Computational Science and Engineering)
    • Place of Presentation
      Bangkok/Thailamd.
    • Year and Date
      2009-03-27
  • [Presentation] 化学反応と分子シミュレーション2008

    • Author(s)
      長岡正隆
    • Organizer
      第2回分子シミュレーションスクール
    • Place of Presentation
      岡崎コンファレンスセンター
    • Year and Date
      2008-12-24
  • [Presentation] Absolute Reaction Rates in Solution via Free Energy Gradient Method with Molecular Dynamics Simulations2008

    • Author(s)
      長岡正隆
    • Place of Presentation
      Sydney/Australia.
    • Year and Date
      2008-09-18
  • [Presentation] On the Intermolecular Energy Transfer around Vibrationally Excited Hydrogen Fluoride in Aqueous Solution : A Molecular Dynamics Simulation Study2008

    • Author(s)
      岡本拓也, 長岡正隆
    • Organizer
      World Association of Theoretical and Computational Chemists
    • Place of Presentation
      Sydney/Australia.
    • Year and Date
      2008-09-15
  • [Book] 計算科学講座(第2部 計算科学の展開 第6巻「分子システムの計算科学」第3章「化学反応の計算科学」)2010

    • Author(s)
      長岡正隆
    • Total Pages
      265-360
    • Publisher
      共立出版株式会社
  • [Book] Proteins : Energy, Heat and Signal Flow. Chapter8.Energy Flow Analysis in Proteins via Ensemble Molecular Dynamics Simulations : Time-Resolvedn Vibrational Analysis and Surficial Kirkwood-Buff Theory2009

    • Author(s)
      M.Nagaoka, I.Yu, M.Takayanagi
    • Total Pages
      169-196
    • Publisher
      CRC Press

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Published: 2012-01-26   Modified: 2016-04-21  

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