1分子時系列情報に基づく革新的マルチスケールモデリング

• Project Area: Innovative nanoscience of supermolecular motor proteins working in biomembranes
• Project/Area Number: 21023001
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Hokkaido University
• Principal Investigator: 李 振風 北海道大学, 電子科学研究所, 准教授 (90397795)
• Co-Investigator(Kenkyū-buntansha): 小松崎 民樹 北海道大学, 電子科学研究所, 教授 (30270549)
• Project Period (FY): 2009 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥6,400,000 (Direct Cost: ¥6,400,000); Fiscal Year 2010: ¥3,200,000 (Direct Cost: ¥3,200,000); Fiscal Year 2009: ¥3,200,000 (Direct Cost: ¥3,200,000)
• Keywords: 生体生命情報学 / 生物物理 / ナノバイオ / 分子モーター / 蛋白質

Research Abstract

我々の目的は、新規な非線形時系列解析に基づくモデル化手法の開発を通して、F1回転子の多様な時空間スケールで繰り広げられる化学・力学カップリングの動力学を抽出し、その化学エネルギーを力学エネルギーに変換する機構を明らかにすることである。当該年度は、μ秒の時間解像度をもつF1回転子の階段状になっている回転角度の時系列データからF1回転子が止まっている「停止」状態、回転している「回転」状態、それぞれの滞留時間をトレンド/変化点検出法を用いて同定した。この研究により、F1の回転している状態の統計的性質および相関が初めて明らかにされた。また、「停止」状態、「回転」状態のそれぞれの滞留時間の時系列データが得られたことで、我々が開発した速度論的スキームを構築する手法をF1回転子の時系列データに対しても適用することができるようになった。
よく知られているように、一つの与えられた滞留時間の時系列に対し、その時系列がもつすべての統計的相関を正しく与える速度論的スキームは一通りとは限らず、複数存在する可能性がある。当然ながら複数存在する場合には、速度論的スキームは滞留時間の時系列が持つ相関だけからは一義的に定めることができない。我々は「与えられた滞留時間の時系列が持つすべての統計的相関を保持する速度論的スキーム全体の集合の中で、もっとも単純で偏りのない速度論的スキームはどれか?」という問いを立てることで、速度論的スキームを一義的に定める方法論を情報理論に基づき開発した。この手法は、滞留時間の時系列データからその時系列が持つすべての統計的相関の情報を過不足無く保持する唯一の速度論的スキームを抽出するものである。この手法は、一切の経験的パラメータに依存しない、という特徴をもつ。構成された本速度論的スキームを用いることで、実験により得られる滞在時間の時系列に観測される相関、記憶等と速度論的スキームのネットワーク構造との対応関係を明らかにすることができるものと期待される(PNAS投稿予定)。

Research Products

• [Journal Article] Derivation of the Generalized Langevin Equation in Non-stationary environments (2011)
  • Author(s): S.Kawai, T.Komatsuzaki
  • Journal Title: Journal of Chemical Physics Volume: 134
  • NAID: 120002893836
  • Peer Reviewed
• [Journal Article] Phase Space Geometry of Dynamics Passing through Saddle Coupled with Spatial Rotation (2011)
  • Author(s): S.Kawai, T.Komatsuzaki
  • Journal Title: Journal of Chemical Physics Volume: 134
  • NAID: 120002834760
  • Peer Reviewed
• [Journal Article] A Dynamical Switching of a Reaction Coordinate to Carry the System Through to a Different Product State at High Energies (2011)
  • Author(s): H.Teramoto, M.Toda, T.Komatsuzaki
  • Journal Title: Physical Review Letters Volume: 106
  • NAID: 120002834723
  • Peer Reviewed
• [Journal Article] Quantum Reaction Boundary to Mediate Reactions in Laser Fields (2011)
  • Author(s): S.Kawai, T.Komatsuzaki
  • Journal Title: Journal of Chemical Physics Volume: 134
  • NAID: 120002834746
  • Peer Reviewed
• [Journal Article] Extracting the Underlying Effective Free Energy Landscape From Single-Molecule Time Series-Local Equilibrium States and their Network (2011)
  • Author(s): A.Baba, T.Komatsuzaki
  • Journal Title: Physical Chemistry Chemical Physics Volume: 13 Pages: 1395-1406
  • Peer Reviewed
• [Journal Article] Robustness and Diversity of Transitions in a Sea of Chaos and Stochastic Fluctuation (2010)
  • Author(s): T.Komatsuzaki, CB.Li, S.Kawai
  • Journal Title: AIP Conference Proceedings "International Conference of Numerical Analysis and Applied Mathematics 2010" Volume: 1281 Pages: 1582-1584
• [Journal Article] How does a choice of Markov partition affect the resultant symbolic dynamics? (2010)
  • Author(s): H.Teramoto, T.Komatsuzaki
  • Journal Title: Chaos Volume: 20
  • NAID: 120002548786
  • Peer Reviewed
• [Journal Article] Dynamical Reaction Coordinate in Thermally Fluctuating Environment in the Framework of Multidimensional Generalized Langevin Equations (2010)
  • Author(s): S.Kawai, T.Komatsuzaki
  • Journal Title: Physical Chemistry Chemical Physics Volume: 12 Pages: 15382-15391
  • Peer Reviewed
• [Journal Article] Robust Existence of a Reaction Boundary to Separate the Fate of a Chemical Reaction (2010)
  • Author(s): S.Kawai, T.Komatsuzaki
  • Journal Title: Physical Review Letters Volume: 105
  • NAID: 120002277520
  • Peer Reviewed
• [Journal Article] Cooperativity at different space and time scales in multiscale protein dynamics (2010)
  • Author(s): Y.Matsunaga, CB.Li, T.Komatsuzaki
  • Journal Title: Physical Review E Volume: 82
  • Peer Reviewed
• [Journal Article] Hierarchy of Reaction Dynamics in a Thermally Fluctuating Environment (2010)
  • Author(s): S.Kawai, T.Komatsuzaki
  • Journal Title: Physical Chemistry Chemical Physics Volume: 12 Pages: 7626-7635
  • NAID: 120002893806
  • Peer Reviewed
• [Journal Article] Nonlinear Dynamical Effects on Reaction Rates in Thermally Fluctuating Environments (2010)
  • Author(s): S.Kawai, T.Komatsuzaki
  • Journal Title: Physical Chemistry Chemical Physics Volume: 12 Pages: 7636-7647
  • NAID: 120002893807
  • Peer Reviewed
• [Journal Article] 多自由度Hamilton系における安定/不安定多様体の可能な折り畳みパターンとそれらの力学系の性質との関係 (2010)
  • Author(s): 寺本央、小松崎民樹
  • Journal Title: 双曲型力学系から大自由度力学系へ(数理解析研究所講究録) Volume: 1688 Pages: 26-38
• [Journal Article] New Quantification of Local Transition Heterogeneity of Multiscale Complex Networks Constructed from Single-Molecule Time Series (2009)
  • Author(s): C.B.Li, H.Yang, T.Komatsuzaki
  • Journal Title: Journal of Physical Chemistry B 113 Pages: 14732-14741
  • Peer Reviewed
• [Journal Article] Bifurcation of Transition States in Many-Degrees of Freedom Chemical Reactions (2009)
  • Author(s): C.B.Li, M.Toda, T.Komatsuzaki
  • Journal Title: Journal of Chemical Physics 130 Pages: 124116-124122
  • Peer Reviewed
• [Presentation] The Hidden Markov Modeling with Exact Information Content of Dwell-Time Time Series (2011)
  • Author(s): C.B.Li
  • Organizer: Dynamics of Complex Systems 2011
  • Place of Presentation: Hokkaido University(招待,口頭 招待講演)
• [Presentation] Innovative Single Molecule Time Series Analysis of Supermolecular Motor Proteins (2011)
  • Author(s): C.B.Li, T.Komatsuzaki
  • Organizer: 2nd International Symposium on Photonic Bioimaging
  • Place of Presentation: Niseko, Hokkaido(一般,ポスター)
• [Presentation] Single Molecule Time Series Analysis of Supermolecular Motor Proteins (2010)
  • Author(s): C.B.Li
  • Organizer: Graduate Student Seminar
  • Place of Presentation: Radboud University Nijmegen, the Netherlands(招待,口頭 招待講演)
  • Year and Date: 2010-08-03
• [Presentation] Time-dependent Perturbation Analysis of Small Nonintegrable Hamiltonian System (2010)
  • Author(s): C.B.Li
  • Organizer: Dynamics of Complex Systems Seminar
  • Place of Presentation: Department of Mathematics, Hokkaido University(招待,口頭 招待講演)
  • Year and Date: 2010-06-09
• [Presentation] Transition to Chaos above the Reaction Threshold : Bifureations, Resonances and Future Challenges (2010)
  • Author(s): C.B.Li
  • Organizer: Workshop on Dynamical System Theory and Reaction Dynamics toward Large Systems
  • Place of Presentation: Kyoto University(口頭)
  • Year and Date: 2010-01-05
• [Presentation] When one plus one is more than two : Theoretical challenges in learning from the next generation single- and multiple-molecule experiments (2010)
  • Author(s): C.B.Li
  • Organizer: 48^<th> annual meeting of Biophysical Society of Japan
  • Place of Presentation: Tohoku University(招待,口頭 招待講演)
• [Presentation] 一分子時系列情報に基づく革新的モデリング (2010)
  • Author(s): C.B.Li, T.Komatsuzaki
  • Organizer: 革新的ナノバイオ終了シンポジウム
  • Place of Presentation: Osaka University(一般,ポスター)
• [Presentation] 膜超分子モーターの革新的時系列解析 (2010)
  • Author(s): C.B.Li, T.Komatsuzaki
  • Organizer: 革新的ナノバイオ第5回班会議
  • Place of Presentation: Gakushuin University(一般,口頭)
• [Presentation] A Handy Guide to Analyze Time Series from Biological Systems : Some Simple but Powerful Tools (2009)
  • Author(s): C.B.Li
  • Organizer: Graduate student seminar
  • Place of Presentation: University of Fukui, Faculty of Medical Science(口頭)
  • Year and Date: 2009-12-15
• [Presentation] Quantifying the Local Transition Heterogeneity of Multiscale Complex Networks Reconstructed from Single-Molecule Time Series (2009)
  • Author(s): C.B.Li, H.Yang, T.Komatsuzaki
  • Organizer: 47^<th> Annual Meeting of Biophysical Society of Japan
  • Place of Presentation: Tokushima(ポスター)
  • Year and Date: 2009-11-01
• [Presentation] What is the Relevant Information in Modeling the Dynamics of Complex Systems from Measurements (2009)
  • Author(s): C.B.Li
  • Organizer: Symposium of Dynamics of complex systems 2009
  • Place of Presentation: Hokkaido University(口頭)
  • Year and Date: 2009-08-31
• [Presentation] Challenges in Modeling the Dynamics of Multiscale Complex Bio-Systems (2009)
  • Author(s): C.B.Li
  • Organizer: Telluride Workshop on "The Complexity of Dynamics and Kinetics in Many Dimensions"
  • Place of Presentation: Telluride, USA(口頭)
  • Year and Date: 2009-06-29
• [Book] "Extracting the Underlying Unique Reaction Scheme from a Single-Molecule Time Series", Cell Signaling Reactions : Single-Molecular Kinetic Analysis (2010)
  • Author(s): C.B.Li, T.Komatsuzaki
  • Total Pages: 330
  • Publisher: Springer
• [Book] "Dynamical Reaction Theory based on Geometric Structures of Phase Space" Advances in Chemical Physics (2010)
  • Author(s): S.Kawai, H.Teramoto, C.B.Li, T.Komatsuzaki, M.Toda
  • Total Pages: 60
  • Publisher: John-Wiley & Sons, Inc.(印刷中)
• [Book] "Non-Brownian Phase Space Dynamics of Molecules, the Nature of their Vibrational States, and non-RRKM Kinetics" Advances in Chemical Physics (2010)
  • Author(s): D.M.Leitner, Y.Matsunaga, A.Shojiguchi, C.B.Li, T.Komatsuzaki
  • Total Pages: 50
  • Publisher: John-Wiley & Sons, Inc.(印刷中)
• [Book] "Extracting the Underlying Unique Reaction Scheme from a Single-Molecule Time Series" in Cell Signaling Reactions : Single-Molecular Kinetic Analysis (2010)
  • Author(s): C.B.Li, T.Komatsuzaki
  • Total Pages: 43
  • Publisher: Springer(印刷中)