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2008 Fiscal Year Final Research Report

Establishment of Dynamical Foundations of Selectivity and Stochasticity in Biomolecule Functions and Chemical Reaction Networks

Research Project

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Project/Area Number 18340124
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics/Chemical physics
Research InstitutionHokkaido University (2007-2008)
Kobe University (2006)

Principal Investigator

KOMATSUZAKI Tamiki  Hokkaido University, 電子科学研究所, 教授 (30270549)

Co-Investigator(Kenkyū-buntansha) LI Chun Biu  北海道大学, 電子科学研究所, 准教授 (90397795)
BABA Akinori  北海道大学, 電子科学研究所, 博士研究員 (50397840)
Project Period (FY) 2006 – 2008
Keywords化学反応動力学 / 力学系理論 / 一分子計測 / エネルギー地形学
Research Abstract

相空間構造に立脚して熱的環境において、頑健に存在し得る反応の選択性の起源とその崩壊原理を解明した。また、1分子の挙動の時系列データを通して、背後に存在する自由エネルギー地形および状態遷移ネットワーク構造をできるだけ自然な形で得る汎用なダイナミックス基盤を開発した。この方法論を用いて、将来的には、例えばアルツハイマー病の原因であるアミロイド凝集体の形成機構の解明などへの展開が期待される。

  • Research Products

    (50 results)

All 2009 2008 2007 2006 Other

All Journal Article (23 results) (of which Peer Reviewed: 18 results) Presentation (26 results) Remarks (1 results)

  • [Journal Article] Bifurcation of no-return transition states in many-body chemical reactions2009

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

      Journal of Chemical Physics 130

      Pages: 124116-124122

    • Peer Reviewed
  • [Journal Article] Exploring Remnant of Invariants Buried in a Deep Potential Well in Chemical Reactions2008

    • Author(s)
      Hiroshi Teramoto and Tamiki Komatsuzaki
    • Journal Title

      Journal of Chemical Physics 129

      Pages: 094302-094310

    • Peer Reviewed
  • [Journal Article] Probing Remnants of Invariants to Mediate Energy Exchange in Highly-Chaotic Many-dimensional Systems2008

    • Author(s)
      Hiroshi Teramoto and Tamiki Komatsuzaki
    • Journal Title

      Physical Review E 78

      Pages: 017202-017205

    • Peer Reviewed
  • [Journal Article] 1分子時系列情報から我々は何を学び取ることができるか?2008

    • Author(s)
      小松崎民樹
    • Journal Title

      物性研究 91

      Pages: 121-130

  • [Journal Article] 1分子時系列情報から読み解く生体分子の状態遷移ネットワーク2008

    • Author(s)
      小松崎民樹
    • Journal Title

      日本生物物理学会生物物理 48(5)

      Pages: 282-283

    • Peer Reviewed
  • [Journal Article] 高分子とカオス-異常拡散と階層的規則性-2008

    • Author(s)
      松永康佑・小松崎民樹
    • Journal Title

      日本高分子学会誌高分子 57(2)

      Pages: 58-61

    • Peer Reviewed
  • [Journal Article] Multiscale Complex Network of Protein Conformational Fluctuation Buried in Single Molecule Time Series2008

    • Author(s)
      Chun Biu Li, Haw Yang, and Tamiki Komatsuzaki
    • Journal Title

      Proceedings of National Academy of Sciences USA 105

      Pages: 536-541

    • Peer Reviewed
  • [Journal Article] Dynamical Foundation and Limitations of Statistical Reaction Theory2008

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

      Communications in Nonlinear Science and Numerical Simulation 13

    • Peer Reviewed
  • [Journal Article] Fractional Behavior in Multi-Dimensional Hamiltonian Systems Describing Reactions2007

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

      Physical Review E76

      Pages: 056205(14pages)

    • Peer Reviewed
  • [Journal Article] Construction of effective free energy landscape from single molecule time series2007

    • Author(s)
      Akinori Baba and Tamiki Komatsuzaki
    • Journal Title

      Proceedings of National Academy of Sciences USA 104(49)

      Pages: 19297-19302

    • Peer Reviewed
  • [Journal Article] Anomalous Diffusionin Folding Dynamics on Minimalist Protein Landscape2007

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

      Physical Review Letters 99

      Pages: 238103(4pages)

    • Peer Reviewed
  • [Journal Article] Development of atechnique for the investigation of folding dynamics of single proteins for extended time periods2007

    • Author(s)
      Masahito Kinoshita, Kiyoto Kamagata, Akio Maeda, Yuji Goto, Tamiki Komatsuzaki and Satoshi Takahashi
    • Journal Title

      Proceedings of National Academy of Sciences USA 104

      Pages: 10453-10458

    • Peer Reviewed
  • [Journal Article] Fractionalbehavior in nonergodic reaction processesof isomerization2007

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

      Physical Review E(rapid communication) 75

      Pages: 035204(R)(4pages)

    • Peer Reviewed
  • [Journal Article] Dimension reduction for extracting geometrical structure of multidimensional phase space : Application to fast energy exchange in the reactionO(^1D)+N_2O→NO+NO2007

    • Author(s)
      Shinnosuke Kawai, Yo Fujimura, Okitsugu Kajimoto, Takefumi Yamashita,Chun Biu Li, Tamiki Komatsuzaki, and Mikito Toda
    • Journal Title

      Physical Review A 75

      Pages: 022714(11pages)

    • Peer Reviewed
  • [Journal Article] 惑星科学と非線形科学の接点 : 化学反応から生物計算まで2007

    • Author(s)
      白川智弘・郡司ペギオ幸夫・小松崎民樹
    • Journal Title

      日本惑星科学会誌遊星人 16(4)

      Pages: 322-329

    • Peer Reviewed
  • [Journal Article] Topographical complexity of multidimensional energy landscapes2006

    • Author(s)
      Gareth J. Rylance, Roy L. Johnston, Yasuhiro Matsunaga, Chun Biu Li, Akinori Baba, Tamiki Komatsuzaki
    • Journal Title

      Proceedings of National Academy of Sciences USA 103

      Pages: 18551-18555

    • Peer Reviewed
  • [Journal Article] Wavelet Analysis and Arnold Web Picture for Detecting Energy Transfer in Hamiltonian Dynamical System2006

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

      Laser Physics 16(7)

      Pages: 1097-1106

    • Peer Reviewed
  • [Journal Article] Definability of No-return Transition States in High Energy Regime Above Threshold2006

    • Author(s)
      Chun Biu Li, Akira Shojiguchi, MikitoToda, and Tamiki Komatsuzaki
    • Journal Title

      Physical Review Letters 97

      Pages: 028302-028305

    • Peer Reviewed
  • [Journal Article] Dynamical Hierarchy in Transition States of Reactions2006

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

      Few-Body Systems 38

      Pages: 173-179

    • Peer Reviewed
  • [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・馬場昭典・小松崎民樹
    • Journal Title

      物性研究 86-1

      Pages: 123-129

  • [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・松永康佑・Gareth J. Rylance, Roy L. Johnston, David J. Wales, 小松崎民樹
    • Journal Title

      物性研究 86-1

      Pages: 117-122

  • [Journal Article] Geometrical Structure buriedin the Phase Space of StochasticStructural Transition2006

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

      物性研究 86-1

      Pages: 77-81

  • [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・小松崎民樹・戸田幹人
    • Journal Title

      物性研究 86-1

      Pages: 37-154

  • [Presentation] Exploring remnants of invariants buried in a deep potential well in chemical reactions2009

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Focus Session : The Transition State in Physics, Chemistry, and Astrophysics, APS Meeting
    • Place of Presentation
      Pittsburgh(招待)
    • Year and Date
      20090316-20
  • [Presentation] What can we learn about the mechanism of complexity in kinetics and dynamics from scalar time series?2008

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Institute for Protein Research Seminar on New Approaches to Complexity of Protein Dynamics by Single Molecule Measurements : Experiments and Theories
    • Place of Presentation
      Osaka(招待)
    • Year and Date
      20081207-09
  • [Presentation] Data-driven Modeling of Single Mechanosensitive Ion Channels from Time Series Analysis2008

    • Author(s)
      Chun Biu Li
    • Organizer
      Institute for Protein Research Seminar on New Approaches to Complexity of Protein Dynamics by Single Molecule Measurements : Experiments and Theories
    • Place of Presentation
      Osaka(招待)
    • Year and Date
      20081207-09
  • [Presentation] Understanding the Multiscale Dynamics of Complex Biological Systems from Single Molecule Experiments2008

    • Author(s)
      Chun Biu Li
    • Organizer
      日本生物物理学会シンポジウム「レア・イベントから創薬へ」
    • Place of Presentation
      福岡(招待)
    • Year and Date
      20081203-05
  • [Presentation] 1分子計測から読み解く状態遷移ネットワーク-機械受容チャネルを例に2008

    • Author(s)
      清一人、馬場昭典、Chun Biu Li、小松崎民樹
    • Organizer
      日本生物物理学会シンポジウム「イオンチャネルゲーティングのダイナミクスをイメージする」
    • Place of Presentation
      福岡(招待)
    • Year and Date
      20081203-05
  • [Presentation] Multiscale Complex Network and Effective Free Energy Landscape Extracted from Single-Molecule Time Series2008

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Symposium on Linking single molecule spectroscopy and energy landscape perspectives at 46th Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Fukuoka(招待)
    • Year and Date
      20081203-05
  • [Presentation] 1分子時系列情報から読み解く生体機能の階層構造2008

    • Author(s)
      小松崎民樹
    • Organizer
      第64回日本物理学会
    • Place of Presentation
      岩手(招待)
    • Year and Date
      20080920-23
  • [Presentation] 「1分子計測から読み解く状態遷移ネットワーク-機械受容チャネルを例に」「膜機能分子ダイナミクスの分子機構解明に向けて」2008

    • Author(s)
      小松崎民樹
    • Organizer
      生理研研究会
    • Place of Presentation
      岡崎(招待)
    • Year and Date
      20080904-05
  • [Presentation] 化学反応や生体高分子の構造転移における「偶然と必然」の数理を探る2008

    • Author(s)
      小松崎民樹
    • Organizer
      Dynamics of complex systems 2008--数学的予測方式の可能性と諸分野からのニーズ
    • Place of Presentation
      北海道大学(招待)
    • Year and Date
      20080901-03
  • [Presentation] An Information-theoretic Approach to unveil the Multiscale Dynamics of Biophysical Systems : Information Flows among Different Scales2008

    • Author(s)
      Chun Biu Li
    • Organizer
      Dynamics of complex systems 2008--数学的予測方式の可能性と諸分野からのニーズ
    • Place of Presentation
      北海道大学(招待)
    • Year and Date
      20080901-03
  • [Presentation] Extracting Multiscale Complex Network of Protein Fluctuation from Single-Molecule TimeS eries, Telluride Summer Workshop2008

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Characterizing Landscapes : From Biomolecules to Cellular Networks
    • Place of Presentation
      (invited)
    • Year and Date
      20080706-12
  • [Presentation] 1分子時系列情報から生体分子機能の複雑さを解読する2008

    • Author(s)
      小松崎民樹
    • Organizer
      分子研シンポジウム
    • Place of Presentation
      岡崎(招待)
    • Year and Date
      20080613-14
  • [Presentation] Construction of an Effective Free Energy Landscape from Single-Molecule Time Series2008

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      1st Annual Protein and Peptide Conference, BIT's 4th Life Spring Forum on protein folding and diseases-celebrating 60years of Prof. Scheraga's science(1948-2008), Shenzhen
    • Place of Presentation
      invited(招待)
    • Year and Date
      20080422-24
  • [Presentation] On the search of new mathematical frameworks to unveil the multiscale dynamics of complex systems2008

    • Author(s)
      Chun Biu Li
    • Organizer
      Workshop on Interfacial dynamics on the boundaries of physics, chemistry, biology and mathematics
    • Place of Presentation
      Hokkaido(招待)
    • Year and Date
      2008-11-20
  • [Presentation] 「1分子時系列情報から我々は何を学び取ることができるか?」「非線形科学と統計科学の対話」2007

    • Author(s)
      小松崎民樹
    • Organizer
      統計数理研究所研究会
    • Place of Presentation
      広尾(招待)
    • Year and Date
      20071126-28
  • [Presentation] 時系列から見る運動の階層性2007

    • Author(s)
      馬場昭典
    • Organizer
      日本物理学会第62回年次大会
    • Place of Presentation
      (招待)
    • Year and Date
      20070921-24
  • [Presentation] 生体分子時系列情報から我々は何を学び取ることができるか?2007

    • Author(s)
      小松崎民樹
    • Organizer
      分子研研究会分子科学における連成シュミュレーションの基礎理論と応用
    • Place of Presentation
      岡崎(招待)
    • Year and Date
      20070829-31
  • [Presentation] Dynamical Hierarchy of Transitions in Chemical Reactions2007

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Telluride Workshop, The Complexity of Dynamics and Kinetics in Many Dimensions
    • Place of Presentation
      CO, USA(招待)
    • Year and Date
      20070813-24
  • [Presentation] Multiple-Time-Scale State Space Landscape buried in Single Molecule Time Series2007

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Telluride Workshop, The Complexity of Dynamics and Kinetics in Many Dimensions
    • Place of Presentation
      CO, USA(招待)
    • Year and Date
      20070813-24
  • [Presentation] 生体分子の一分子時系列解析 : 局所平衡状態と自由エネルギー地形非線形振動子系の物理学 : 現代的問題とその解析2007

    • Author(s)
      馬場昭典
    • Organizer
      基礎物理学研究所
    • Place of Presentation
      京都(招待)
    • Year and Date
      20070605-07
  • [Presentation] Multiple-Time-Scale State Network Topography buried inSingle Molecule Time Series2007

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Energy Landscapes : Negotiating the Black Diamonds, Telluride
    • Place of Presentation
      CO, USA(invited)
    • Year and Date
      20070402-06
  • [Presentation] DynamicalHierarchy of Transitions in Chemical Reactions2007

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      DYNAMICS OF COMPLEX SYSTEMS-mathematical modeling, method and prediction
    • Place of Presentation
      Hokkaido University, Hokkaido, Japan(invited)
    • Year and Date
      20070319-20
  • [Presentation] What can one learn about the underlying free energy landscape or dynamical structure from single molecule time series?2006

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Discussion on "Theory and simulation of biomolecular nano-machines"
    • Place of Presentation
      Maiko Villa, Kobe(invited)
    • Year and Date
      20061212-16
  • [Presentation] A construction of the underlying free energy landscape from single molecule time series2006

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      Okinawa(invited)
    • Year and Date
      20061112-16
  • [Presentation] Extracting Conformational Dynamics on a Photon by Photon basis in Single Molecule Electron Transfer「蛋白質の機能運動と折り畳み運動」2006

    • Author(s)
      Chun Biu Li
    • Organizer
      大阪大学蛋白質研究所セミナー
    • Place of Presentation
      (招待)
    • Year and Date
      20060928-29
  • [Presentation] 1分子計測時系列情報から読み取るたんぱく質系の動的構造2006

    • Author(s)
      小松崎民樹
    • Organizer
      ダイナミクス研究会
    • Place of Presentation
      岐阜大医学部(招待)
    • Year and Date
      20060623-24
  • [Remarks]

    • URL

      http://mlns.es.hokudai.ac.jp

URL: 

Published: 2010-06-10   Modified: 2016-04-21  

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