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2005 Fiscal Year Final Research Report Summary

Dynamical Emergence Principle of Reaction Selectivity and Molecular Memory in Chemical Reactions' and Biomolecular Systems

Research Project

Project/Area Number 15540394
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics/Chemical physics
Research InstitutionKobe University

Principal Investigator

KOMATSUZAKI Tamiki  Kobe University, Faculty of Science, Associate Professor, 理学部, 助教授 (30270549)

Project Period (FY) 2003 – 2005
KeywordsChemical Reaction Dynamics / Normally hyperbolic invariant manifold / Dynamical Systems / Phase space geometry / Normal form theory / Transition state
Research Abstract

No-return transition states (TSs) defined in multidimensional phase space, where recrossing trajectories through the commonly used ‘configuration' TS pass only once, robustly exist up to moderately high energy regime above the reaction threshold even when nonlinear resonances among the bath degrees of freedom perpendicular to the reaction coordinate result in local chaos. However, at much higher energy when global chaos appears in the bath space, the separability of the reaction coordinate from the bath degrees of freedom ceases to hold locally. In the phase space near the saddles, it is found that the slower the system passes the TS, the more recrossing trajectories reappear. Their implications and mechanisms are discussed concerning to what extent one can define no-return TSs in high energy regime above the reaction threshold.
We also developed a new empirical self-consistent scheme to elucidate the local ergodic state distribution function and construct effective multidimensional free energy landscape from an ensemble of short single molecule time series. It is possible to capture not the entire topography of the multidimensional free energy landscape but the regions where the system wanders frequently. Using local ergodicity ansatz as a 0^<th> order description, we constructed the multidimensional "free energy" landscape where several local ergodic states are linked with introducing a "distance" among them. Evaluating on the probability of transition sequences sampled in an ensemble of single molecule time series, one can analyze non-Markovianity along several transition paths. e.g., relationship between memory and length of transition paths. As a function of n_s time window to estimate the short time distribution, we can also assign the number of accessible superbasins (a set of states) within time n_s.

  • Research Products

    (33 results)

All 2006 2005 2004 Other

All Journal Article (32 results) Book (1 results)

  • [Journal Article] 複雑な多谷ポテンシャルエネルギー面上で生起する動力学諸問題III-タンパク質とその周辺-(研究会報告)2006

    • Author(s)
      渕上壮太郎編
    • Journal Title

      物性研究 86

      Pages: 37-154

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Geometrical Structure buried in the phase space of Stochastic Structural Transition2006

    • Author(s)
      Chun Biu Li
    • Journal Title

      物性研究 86

      Pages: 77-81

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] タンパク質エネルギー地形における構造多様性と多次元エネルギー地形の新しい可視化手法2006

    • Author(s)
      星野恭子
    • Journal Title

      物性研究 86

      Pages: 117-122

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] 水の場としての集団運動と生体分子の構造転移ダイナミックス2006

    • Author(s)
      納多哲史
    • Journal Title

      物性研究 86

      Pages: 123-129

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Dynamical Hierarchy in Transition States of Reactions2006

    • Author(s)
      Chun Biu Li
    • Journal Title

      Few-Body Systems (印刷中)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Wavelet Analysis and Arnold Web Picture for Detecting Energy Transfer in Hamiltonian Dynamical System2006

    • Author(s)
      Akira Shojiguchi
    • Journal Title

      Laser Physics (印刷中)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Dynamical Foundation and Limitations of Statistical Reaction Theory2006

    • Author(s)
      Akira Shojiguchi
    • Journal Title

      Communications in Nonlinear Science and Numerical Simulation (印刷中)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Proceeding Reports on Dynamical Problems on Lugged Energy Landscapes I-Proteins and the surroundings2006

    • Author(s)
      Sotaro Fuchigami, Tamiki Komatsuzaki, Mikito Toda
    • Journal Title

      Bussei Kenkyu (Kyoto) 86(1)

      Pages: 37-154

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Geometrical Structure buried in the phase space of Stochastic Structural Transition2006

    • Author(s)
      Chun Biu Li, Yasuhiro Matsunaga, Mikito Toda, Tamiki Komatsuzaki
    • Journal Title

      Bussei Kenkyu (Kyoto) 86(1)

      Pages: 77-81

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Structural Diversity of Protein Enertgy Landscape and New Visualization2006

    • Author(s)
      K.Hoshino, Y.Matsunaga, Gareth J.Rylance, Roy L.Johnston, D.J.Wales, Tamiki Komatsuzaki
    • Journal Title

      Bussei Kenkyu (Kyoto) 86(1)

      Pages: 117-122

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Collective Motion of Water Field and Structural Transition of Biomolecule2006

    • Author(s)
      Satoshi Noda, Akinori Baba, Tamiki Komatsuzaki
    • Journal Title

      Bussei Kenkyu (Kyoto) 86(1)

      Pages: 123-129

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Regularity in Chaotic Transitions on Two-Basin Lands2005

    • Author(s)
      Tamiki Komatsuzaki
    • Journal Title

      Advances in Chemical Physics 130 A

      Pages: 143-170

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Regularity in Chaotic Transitions on Multi-Basin Lands capes2005

    • Author(s)
      Tamiki Komatsuzaki
    • Journal Title

      Advances in Chemical Physics 130 B

      Pages: 257-313

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] How Many Dimension is Required to Approximate Potential Energy Landscape of A Model Protein?2005

    • Author(s)
      Tamiki Komatsuzaki
    • Journal Title

      Journal of Chemical Physics 122

      Pages: 084714-1-084714-9

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Phase Space Reaction Network on a Multisaddle Energy Landscape : HCN isomerization2005

    • Author(s)
      Chun Biu Li
    • Journal Title

      Journal of Chemical Physics 123

      Pages: 184301(1)-184301(13)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Chaotic Reaction Dynamics and the Phase Space Geometry of Multidimensional Chemical Reaction2005

    • Author(s)
      Chun Biu Li
    • Journal Title

      Bussei Kenkyu (Kyoto) 84(3)

      Pages: 481-482

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Regularity in Chaotic Transitions on Two-Basin Landscapes2005

    • Author(s)
      Tamiki Komatsuzaki, R.Stephen Berry
    • Journal Title

      Advances in Chemical Physics 130A

      Pages: 143-170

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Regularity in Chaotic Transitions on Multi-Basin Landscapes2005

    • Author(s)
      Tamiki Komatsuzaki, Kyoko Hoshino, Y.Matsunaga
    • Journal Title

      Advances in Chemical Physics 130B

      Pages: 257-313

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] How Many Dimension is Required to Approximate Potential Energy Landscape of A Model Protein?2005

    • Author(s)
      Tamiki Komatsuzaki, Kyoko Hoshino, Yasuhiro Matsunaga, Gareth J.Rylance, Roy L.Johnston, David J.Wales
    • Journal Title

      Journal of Chemical Physics 122

      Pages: 084714-1-084714-9

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Phase Space Reaction Network on a Multisaddle Energy Landscape : HCN isomerization2005

    • Author(s)
      Chun Biu Li, Yasuhiro Matsunaga, Mikito Toda, Tamiki Komatsuzaki
    • Journal Title

      Journal of Chemical Physics 123

      Pages: 184301(1)-184301(13)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Chaotic Reaction Dynamics and the Phase Space Geometry of Multidimensional Chemical Reaction2005

    • Author(s)
      Chun Biu Li, M.Toda, T.Komatsuzaki
    • Journal Title

      Bussei Kenkyu (Kyoto) 84(3)

      Pages: 481-482

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Hierarchical Regularity in Multi-Basin Dynamics on Protein Landscapes2004

    • Author(s)
      Yasuhiro Matsunaga
    • Journal Title

      AIP conference series for Slow Dynamics in Complex Systems 708

      Pages: 302-305

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Protein Folding Dynamics : Ergodic Behavior in Principal Component Space2004

    • Author(s)
      Yasuhiro Matsunaga
    • Journal Title

      AIP conference series for Slow Dynamics in Complex Systems 708

      Pages: 342-343

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] A Coarse-Graining of Energy Landscapes of Proteins -Structural Stability of the Most Stable States-2004

    • Author(s)
      Kyoko Hoshino
    • Journal Title

      AIP conference series for Slow Dynamics in Complex Systems 708

      Pages: 344-345

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Geometrical Structures of Phase Space in Multi-Dimen sional Chaos (研究会報告)2004

    • Author(s)
      戸田幹人
    • Journal Title

      物性研究 83

      Pages: 176-188

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Hierarchical Regularity in Multi-Basin Dynamics on Protein Landscapes2004

    • Author(s)
      Y.Matsunaga, K.S.Kostov, Tamiki Komatsuzaki
    • Journal Title

      AIP conference series for Slow Dynamics in Complex Systems 708

      Pages: 302-305

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Protein Folding Dynamics : Ergodic Behavior in Principal Component Space2004

    • Author(s)
      Y.Matsunaga, Tamiki Komatsuzaki
    • Journal Title

      AIP conference series for Slow Dynamics in Complex Systems 708

      Pages: 342-343

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] A Coarse-Graining of Energy Landscapes of Proteins-Structural Stability of the Most Stable States-2004

    • Author(s)
      K.Hoshino, Y.Matsunaga, M.Miller, D.J.Wales, Tamiki Komatsuzaki
    • Journal Title

      AIP conference series for Slow Dynamics in Complex Systems 708

      Pages: 344-345

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Geometrical Structures of Phase Space in Multi-Dimensional Chaos : Applications to Chemical Reaction Dynamics in Complex Systems2004

    • Author(s)
      Mikito Toda, Tamiki Komatsuzaki, Tetsuro Konishi, R.Stephen Berry, Stuart A.Rice eds.
    • Journal Title

      Bussei Kenkyu (Kyoto) 83

      Pages: 176-188

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Dynamical Hierarchy in Transition States of Reactions

    • Author(s)
      Chun Biu Li, Akira Shojiguchi, Mikito Toda, Tamiki Komatsuzaki
    • Journal Title

      Few-Body Systems (in press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Wavelet Analysis and Arnold Web Picture for Detecting Energy Transfer in Hamiltonian Dvnamical System

    • Author(s)
      Akira Shojiguchi, Akinori Baba, Chun Biu Li, Tamiki Komatsuzaki, Mikito Toda
    • Journal Title

      Laser Physics (in press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Dynamical Foundation and Limitations of Statistical Reaction Theory

    • Author(s)
      Akira Shojiguchi, Chun Biu Li, Tamiki Komatsuzaki, Mikito Toda
    • Journal Title

      Communications in Nonlinear Science and Numerical Simulation (in press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Book] Special Volume "Geometric Structures of Phase Space in Multi-Dimensional Chaos" in Advances in Chemical Physics2005

    • Author(s)
      M.Toda(共編)
    • Total Pages
      1224
    • Publisher
      John Wiley & Sons. Inc.
    • Description
      「研究成果報告書概要(和文)」より

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Published: 2007-12-13  

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