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Exploration of Systems Biology of Molecular Individuality

Research Project

Project/Area Number 25650044
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Biophysics
Research InstitutionHokkaido University

Principal Investigator

Komatsuzaki Tamiki  北海道大学, 電子科学研究所, 教授 (30270549)

Co-Investigator(Renkei-kenkyūsha) LI Chun-Biu  北海道大学, 電子科学研究所, 准教授 (90397795)
KAWAI Shinnosuke  北海道大学, 電子科学研究所, 特任助教 (90624065)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2013: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywords分子個性 / 情報理論 / F1-ATPase / ネットワーク / 1分子計測 / 変化点解析 / 反応ネットワーク / 経路の多重性 / ノイズ除去 / 遷移状態 / 自由エネルギー地形 / 一分子計測 / 非平衡定常状態反応ネットワーク / システム生物学
Outline of Final Research Achievements

From single molecule finite time series that changes discretely such as opened or closed, (substrate) bound or unbound, we developed a novel analysis method that objectively elucidates the state of molecules in terms of network representation and enables us to predict the future output of the molecular data in time. In addition, by developing a novel data analysis method that does not assume a form of function of likelihood, we revealed the molecular mechanism of efficient energy conversion in F1-ATPase that synthesizes “energy money”inside cell, ATP, and ATP hydrolysis designs the order of reactions.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (96 results)

All 2016 2015 2014 2013 Other

All Journal Article (13 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 13 results,  Open Access: 7 results,  Acknowledgement Compliant: 5 results) Presentation (75 results) (of which Int'l Joint Research: 8 results,  Invited: 25 results) Book (1 results) Remarks (7 results)

  • [Journal Article] Extracting subcellular fibrillar alignment with error estimation: Application to microtubules2016

    • Author(s)
      Satoru Tsugawa, Nathan Hervieux, Olivier Hamant, Arezki Boudaoud, Richard S. Smith, Chun-Biu Li and Tamiki Komatsuzaki
    • Journal Title

      Biophys. J

      Volume: 印刷中

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] ATP hydrolysis assists Phosphate release and promotes reaction ordering in F1-ATPase2015

    • Author(s)
      Li, C. B., Ueno, H., Watanabe, R., Noji, H., & Komatsuzaki, T.
    • Journal Title

      Nature Communications

      Volume: 6 Issue: 1 Pages: 10223-10223

    • DOI

      10.1038/ncomms10223

    • NAID

      120005702360

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Deciphering Time Scale Hierarchy in Reaction Networks2015

    • Author(s)
      Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 120 Issue: 8 Pages: 1961-1971

    • DOI

      10.1021/acs.jpcb.5b09941

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Kinetic Analysis for the Multistep Profiles of Organic Reactions: Significance of the Conformational Entropy on the Rate Constants of the Claisen Rearrangement2015

    • Author(s)
      Yosuke Sumiya, Yutaka Nagahata, Tamiki Komatsuzaki, Tetsuya Taketsugu, Satoshi Maeda
    • Journal Title

      The Journal of Physical Chemistry

      Volume: 119 Issue: 48 Pages: 11641-11649

    • DOI

      10.1021/acs.jpca.5b09447

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series2015

    • Author(s)
      J. Nicholas Taylor, Chun-Biu Li, David R. Cooper, Christy F. Landes, Tamiki Komatsuzaki
    • Journal Title

      Scientific Reports

      Volume: 5 Issue: 1 Pages: 9174-9174

    • DOI

      10.1038/srep09174

    • NAID

      120005600754

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] トップダウンとボトムアップの橋渡し2014

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

      生体の科学

      Volume: 65 Pages: 444-445

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging2014

    • Author(s)
      Hideyuki Yaginuma, Shinnosuke Kawai, Kazuhito V. Tabata, Keisuke Tomiyama, Akira Kakizuka, Tamiki Komatsuzaki, Hiroyuki Noji, and Hiromi Imamura
    • Journal Title

      Scientific Reports

      Volume: 4 Issue: 1 Pages: 6522-6522

    • DOI

      10.1038/srep06522

    • NAID

      120005575159

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Handling Noisy Data from Single Molecule Experiments2014

    • Author(s)
      Chun-Biu Li, Tamiki Komatsuzaki
    • Journal Title

      Seibutsu Butsuri

      Volume: 54 Issue: 5 Pages: 257-258

    • DOI

      10.2142/biophys.54.257

    • NAID

      130004794709

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis2014

    • Author(s)
      Bo Shuang, David Cooper, J. Nick Taylor, Lydia Kisley, Jixin Chen, Wenxiao Wang, Chun Biu Li, Tamiki Komatsuzaki, Christy F. Landes
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 5 Issue: 18 Pages: 3157-3161

    • DOI

      10.1021/jz501435p

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Numerical Construction of Estimators for Single-Molecule Fluorescence Measurements2013

    • Author(s)
      Shinnosuke Kawai, David Cooper, Christy F. Landes, Henning D. Mootz, Haw Yang, Tamiki Komatsuzaki
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 117 Issue: 27 Pages: 8061-8074

    • DOI

      10.1021/jp402328m

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Aggregated Markov Model Using Time Series of Single Molecule Dwell Times with Minimum Excessive Information2013

    • Author(s)
      Chun-Biu Li, Tamiki Komatsuzaki
    • Journal Title

      Physical Review Letters

      Volume: 111 Issue: 5 Pages: 058301-058301

    • DOI

      10.1103/physrevlett.111.058301

    • NAID

      120005333588

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Spatio-temporal Hierarchy in the Dynamics of a Minimalist Protein Model2013

    • Author(s)
      Yasuhiro Matsunaga, Akinori Baba, Chun Biu Li, John Straub, Mikito Toda, Tamiki Komatsuzaki, R. Berry
    • Journal Title

      The Journal of Chemical Physics

      Volume: 139 Issue: 21 Pages: 215101-215101

    • DOI

      10.1063/1.4834415

    • NAID

      120005385312

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non-Markovian Properties and Multiscale Hidden Markovian Network Buried in Single Molecule Time Series2013

    • Author(s)
      Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, Tamiki Komatsuzaki
    • Journal Title

      The Journal of Chemical Physics

      Volume: 139 Issue: 24 Pages: 245101-245101

    • DOI

      10.1063/1.4848719

    • NAID

      120005385318

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Molecular Data Science Perspectives for Individuality Covering from Molecules to Cells2016

    • Author(s)
      小松崎 民樹
    • Organizer
      統合生命医科学研究センター疾患生物学セミナー
    • Place of Presentation
      理化学研究所横浜キャンパス(神奈川県横浜市)
    • Year and Date
      2016-03-18
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Toward deciphering cell individuality in systems biology2015

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Symposium #137 Life at Small Copy Numbers (The 2015 International Chemical Congress of Pacific Basin Societies)
    • Place of Presentation
      Hawaii, USA
    • Year and Date
      2015-12-19
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Energy landscapes and conformation network learned from single molecule time series2015

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Symposium #121 Deciphering molecular complexity from protein functions to cellular network (The 2015 International Chemical Congress of Pacific Basin Societies)
    • Place of Presentation
      Hawaii, USA
    • Year and Date
      2015-12-15
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Kinetics of Multiple conductance levels of Mechanosensitive Ion Channel2015

    • Author(s)
      Genming Wang, Chun-Biu Li, Hitoshi Tatsumi, Tamiki Komatsuzaki
    • Organizer
      The 16th RIES-Hokudai International Symposium
    • Place of Presentation
      Chateraise Gateaux Kingdom Sapporo, Sapporo, Hokkaido
    • Year and Date
      2015-11-10
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The Onset of Non-equilibrium Effects at High Temperature in the Reaction Kinetics of F1-ATPase2015

    • Author(s)
      Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    • Organizer
      The 16th RIES-Hokudai International Symposium
    • Place of Presentation
      Chateraise Gateaux Kingdom Sapporo, Sapporo, Hokkaido
    • Year and Date
      2015-11-10
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] マルコフ連鎖の時間階層的クラスタリング2015

    • Author(s)
      永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 武次 徹也, 小松崎 民樹
    • Organizer
      ERATO湊離散構造処理系プロジェクト 「2015年度 秋のワークショップ」
    • Place of Presentation
      丸駒温泉(北海道千歳市)
    • Year and Date
      2015-11-08
    • Related Report
      2015 Annual Research Report
  • [Presentation] Single Molecule Biophysics: How can One Dig the Underlying Network from Noisy and Short Time Series?2015

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      International Conference on “Challenges in Data Science: a Complex Systems Perspective
    • Place of Presentation
      Torino, Italy
    • Year and Date
      2015-10-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 1分子時系列データから解読するエネルギー地形とネットワーク2015

    • Author(s)
      小松崎 民樹
    • Organizer
      「データ駆動科学の新展開」ミニ研究会
    • Place of Presentation
      北海道大学 百年記念会館(北海道札幌市)
    • Year and Date
      2015-09-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 非平衡効果が引き起こすF1分子モーターの非アレニウス型温度依存性2015

    • Author(s)
      田宮 裕治, Chun-Biu Li, 渡邉 力也, 野地 博行, 小松崎 民樹
    • Organizer
      第9回分子科学討論会
    • Place of Presentation
      東京工業大学大岡山キャンパス(東京都目黒区)
    • Year and Date
      2015-09-16
    • Related Report
      2015 Annual Research Report
  • [Presentation] 複雑分子系の異性化反応ネットワークに埋め込まれた時間階層構造の解読2015

    • Author(s)
      永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    • Organizer
      第9回分子科学討論会
    • Place of Presentation
      東京工業大学 大岡山キャンパス(東京都目黒区)
    • Year and Date
      2015-09-16
    • Related Report
      2015 Annual Research Report
  • [Presentation] 複合化学反応系の分子シミュレーション-第一原理シミュレーションから分子技術へ-2015

    • Author(s)
      永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 武次 徹也, 小松崎 民樹
    • Organizer
      化学反応経路探索のニューフロンティア
    • Place of Presentation
      大井町駅前品川区立総合区民会館きゅりあん(東京都大井町)
    • Year and Date
      2015-09-15
    • Related Report
      2015 Annual Research Report
  • [Presentation] 複雑反応ネットワークに埋め込まれた時間階層構造の解読2015

    • Author(s)
      Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
    • Organizer
      第53回日本生物物理学会
    • Place of Presentation
      金沢大学角間キャンパス自然科学本館(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 植物の中の局所微小管と細胞成長の関係について2015

    • Author(s)
      Satoru Tsugawa, Chun-Biu Li, Tamiki Komatsuzaki
    • Organizer
      第53回日本生物物理学会
    • Place of Presentation
      金沢大学角間キャンパス自然科学本館(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 非平衡効果が引き起こすF1分子モーターの非アレニウス型温度依存性2015

    • Author(s)
      Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    • Organizer
      第53回日本生物物理学会
    • Place of Presentation
      金沢大学角間キャンパス自然科学本館(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Single Molecule Time Series Analysis of F1-ATPase to Unravel the Role of Bound-ATP Hydrolysis2015

    • Author(s)
      Chun-Biu Li, Tamiki Komatsuzaki
    • Organizer
      第53回日本生物物理学会
    • Place of Presentation
      金沢大学角間キャンパス自然科学本館(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 複雑な異性化反応ネットワークに埋め込まれた時間階層構造の解読法の開発2015

    • Author(s)
      永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    • Organizer
      日本化学会北海道支部 2015年 夏季研究発表会
    • Place of Presentation
      北海道教育大学函館校(北海道函館市)
    • Year and Date
      2015-07-18
    • Related Report
      2015 Annual Research Report
  • [Presentation] Sumi-Marcus 型ポテンシャルモデルを用いた F1分子モーターの反応速度定数の解析2015

    • Author(s)
      田宮 裕治, Chun-Biu Li, 渡邉 力也, 野地 博行, 小松崎 民樹
    • Organizer
      日本化学会北海道支部 2015年 夏季研究発表会
    • Place of Presentation
      北海道教育大学函館校(北海道函館市)
    • Year and Date
      2015-07-18
    • Related Report
      2015 Annual Research Report
  • [Presentation] 一細胞計測で見えてきたバクテリア細胞内ATP濃度の多様性2015

    • Author(s)
      柳沼 秀幸, 河合 信之輔, 田端 和仁, 冨山 佳祐, 垣塚 彰, 小松崎 民樹, 岡田 康志, 野地 博行, 今村 博臣
    • Organizer
      第67回日本細胞生物学会大会
    • Place of Presentation
      タワーホール船堀(東京都江東区)
    • Year and Date
      2015-06-30
    • Related Report
      2015 Annual Research Report
  • [Presentation] How can we define a transition state over a network?2015

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      R. Stephen Berry Tribune Symposium
    • Place of Presentation
      Telluride, CO, U.S.
    • Year and Date
      2015-06-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A kinetic disconnectivity graph to decode timescale hierarchy buried in reaction networks2015

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Chemistry & Dynamics in Complex Environments
    • Place of Presentation
      Telluride, CO, U.S.
    • Year and Date
      2015-06-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Energy Landscapes learned from Single-Molecule Time-Series: Dimensionality and Disconnectivity Graph2015

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      The Complexity of Dynamics Kinetics from Single Molecules to Cells
    • Place of Presentation
      Telluride, CO, U.S.
    • Year and Date
      2015-06-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] マルコフ連鎖の時間階層的クラスタリング2015

    • Author(s)
      永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 武次 徹也, 小松崎 民樹
    • Organizer
      ERATO湊離散構造処理系プロジェクト 「2015年度 初夏のワークショップ」
    • Place of Presentation
      北海道大学情報科学研究科 ERATO 会議室(北海道札幌市)
    • Year and Date
      2015-06-11
    • Related Report
      2015 Annual Research Report
  • [Presentation] Energy landscapes derived from single molecule spectroscopy and complex networks2015

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Architecture, dynamics, and functionality of molecular biosystems
    • Place of Presentation
      The Institute for Molecular Science(愛知県岡崎市)
    • Year and Date
      2015-03-31
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis2015

    • Author(s)
      B. Shuang, D. Cooper, J. N. Taylor, L. Kisley, J. Chen, W. Wang, C.-B. Li, T. Komatsuzaki, and C. F. Landes
    • Organizer
      2015 Oil & Gas High Performance Computing Workshop
    • Place of Presentation
      Houston, USA
    • Year and Date
      2015-03-05
    • Related Report
      2014 Research-status Report
  • [Presentation] Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis2015

    • Author(s)
      Bo Shuang, David Cooper, J. Nick Taylor, Lydia Kisley, Jixin Chen, Wenxiao Wang, Chun Biu Li, Tamiki Komatsuzaki, Chrisy Landes
    • Organizer
      The 2015 Quantitative BioImaging Conference
    • Place of Presentation
      Paris, France
    • Year and Date
      2015-01-07
    • Related Report
      2014 Research-status Report
  • [Presentation] Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series2015

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      The 8th biennial workshop on Single Molecule Biophysics (SMB)
    • Place of Presentation
      Aspen, USA
    • Year and Date
      2015-01-04
    • Related Report
      2014 Research-status Report
  • [Presentation] An extraction of embedded timescale hierarchies buried in complex reaction network2014

    • Author(s)
      Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
    • Organizer
      The 15th Ries-Hokudai International Symposium 響[hibiki]
    • Place of Presentation
      CHATERAISE Gateaux Kingdom SAPPORO(北海道札幌市)
    • Year and Date
      2014-12-16
    • Related Report
      2014 Research-status Report
  • [Presentation] A kinetic disconnectivity graph to decode timescale hierarchy buried in reaction networks2014

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      XIXth International Workshop on Quantum Systems in Chemistry, Physics and Biology
    • Place of Presentation
      New Taipei City, Taiwan
    • Year and Date
      2014-11-16
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Data Driven Approach to Dynamics of Protein Motor2014

    • Author(s)
      Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    • Organizer
      New Challenges in Complex Systems Science
    • Place of Presentation
      Nishiwaseda Campus, Waseda University(東京都新宿区)
    • Year and Date
      2014-10-25
    • Related Report
      2014 Research-status Report
  • [Presentation] Challenges in Understanding Complex Systems at the Single Molecule Level2014

    • Author(s)
      Chun-Biu Li, and Tamiki Komatsuzaki
    • Organizer
      New Challenges in Complex Systems Science
    • Place of Presentation
      Nishiwaseda Campus, Waseda University(東京都新宿区)
    • Year and Date
      2014-10-25
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 複雑分子系の構造異性化反応ネットワークに埋め込まれた時間階層構造の抽出2014

    • Author(s)
      永幡 裕, 寺本 央, Chun-Biu Li, 小松崎 民樹
    • Organizer
      研究会「理論と実験」2014
    • Place of Presentation
      広島大学理学部(広島県東広島市)
    • Year and Date
      2014-10-10
    • Related Report
      2014 Research-status Report
  • [Presentation] 分子個性と少数性2014

    • Author(s)
      小松崎 民樹
    • Organizer
      第52回日本生物物理学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道札幌市)
    • Year and Date
      2014-09-26
    • Related Report
      2014 Research-status Report
  • [Presentation] 複雑分子系の異性化反応ネットワークに埋め込まれた時間階層構造の抽出2014

    • Author(s)
      永幡 裕、前田 理、寺本 央、Chun-Biu Li、堀山 貴史、武次 徹也、小松崎 民樹
    • Organizer
      第8回分子科学討論会
    • Place of Presentation
      広島大学東広島キャンパス(広島県東広島市)
    • Year and Date
      2014-09-21
    • Related Report
      2014 Research-status Report
  • [Presentation] 少数性の生物学において顕在化する分子個性2014

    • Author(s)
      小松崎 民樹
    • Organizer
      日本物理学会2014年秋季大会
    • Place of Presentation
      中部大学春日井キャンパス(愛知県春日井市)
    • Year and Date
      2014-09-09
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Energy landscapes learned from time series and networks2014

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Energy Landscapes : From Single Molecules to Soft Matter
    • Place of Presentation
      Durham, UK
    • Year and Date
      2014-08-20
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 複雑分子系における構造異性化反応ネットワークの理解に向けて2014

    • Author(s)
      永幡 裕, 寺本 央, Chun-Biu Li, 小松崎 民樹
    • Organizer
      第54回 分子科学若手の会 夏の学校
    • Place of Presentation
      いこいの村能登半島(石川県羽咋郡志賀町)
    • Year and Date
      2014-08-18
    • Related Report
      2014 Research-status Report
  • [Presentation] Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series2014

    • Author(s)
      J.N. Taylor, Chun Biu Li, and Tamiki Komatsuzaki
    • Organizer
      Macromolecular dynamics: structure, function and diseases
    • Place of Presentation
      Beijing, China
    • Year and Date
      2014-07-03
    • Related Report
      2014 Research-status Report
  • [Presentation] Extracting Cooperative modes between a biological molecule and water molecules2014

    • Author(s)
      Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    • Organizer
      International Workshop "Over the Barriers of Transition Paths: Dynamical Processes in Proteins and Complex Molecular Systems"
    • Place of Presentation
      Tokyo Institute of Technology(神奈川県横浜市)
    • Year and Date
      2014-06-28
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Energy Landscapes Constructed From Single-molecule Time Series And Reaction Networks2014

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Macromolecular dynamics: structure, function and diseases
    • Place of Presentation
      Beijing, China
    • Year and Date
      2014-06-27
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Theories Should Meet Experiments: What Can We Extract From Time Series Data?2014

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Beijing Computational Science Research Center (CSRC) Seminar
    • Place of Presentation
      Beijing, China
    • Year and Date
      2014-06-23
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series2014

    • Author(s)
      J.N. Taylor, Chun Biu Li, and Tamiki Komatsuzaki
    • Organizer
      ICBP 8th IUPAP international conference on biological physics
    • Place of Presentation
      Beijing, China
    • Year and Date
      2014-06-21
    • Related Report
      2014 Research-status Report
  • [Presentation] 複雑分子系における構造異性化反応ネットワークの理解に向けて2014

    • Author(s)
      永幡 裕、前田 理、寺本 央、Chun-Biu Li、堀山 貴史、武次 徹也、小松崎 民樹
    • Organizer
      第17回理論化学討論会
    • Place of Presentation
      名古屋大学(東山キャンパス)ES総合館(愛知県名古屋市)
    • Year and Date
      2014-05-23
    • Related Report
      2014 Research-status Report
  • [Presentation] 生体分子と水の過渡的な集団運動の抽出2014

    • Author(s)
      寺本央、戸田幹人、小松崎民樹
    • Organizer
      第17回理論化学討論会
    • Place of Presentation
      名古屋大学(東山キャンパス)ES総合館(愛知県名古屋市)
    • Year and Date
      2014-05-22
    • Related Report
      2014 Research-status Report
  • [Presentation] Energy Landscapes Constructed From Single-Molecule Time Series and Reaction Networks2014

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      The 2014 Les Houches - TSRC Protein Dynamics Workshop
    • Place of Presentation
      Les Houches, France
    • Year and Date
      2014-05-21
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] ノイジーなFRETデータから多重経路を考慮に入れた自由エネルギー地形を抽出する2014

    • Author(s)
      小松崎 民樹
    • Organizer
      理研シンポジウム:細胞システムの動態と論理Ⅵ
    • Place of Presentation
      理化学研究所和光本所(埼玉県和光市)
    • Year and Date
      2014-04-04
    • Related Report
      2014 Research-status Report
  • [Presentation] タンパク質の時系列から得られたMarkov連鎖の解析に向けて:グラフの分割とクラスタリングで定義する複雑な化学反応における状態とその時間階層構造2014

    • Author(s)
      永幡 裕, 寺本 央, Chun-Biu Li, 小松崎 民樹
    • Organizer
      理研シンポジウム:細胞システムの動態と論理Ⅵ
    • Place of Presentation
      理化学研究所和光本所(埼玉県和光市)
    • Year and Date
      2014-04-04
    • Related Report
      2014 Research-status Report
  • [Presentation] タンパク質の時系列から得られたMarkov連鎖の解析に向けて:グラフの分割とクラスタリングで定義する複雑な化学反応における状態とその時間階層構造2014

    • Author(s)
      永幡 裕, 堀山 貴史, 前田 理, 寺本 央, Chun-Biu Li, 小松崎 民樹
    • Organizer
      2013 年度日本生物物理学会北海道支部例会
    • Place of Presentation
      北海道大学 シオノギ創薬イノベーションセンター(札幌市)
    • Related Report
      2013 Research-status Report
  • [Presentation] パターン形成における本質的な高次相関情報量の抽出2014

    • Author(s)
      宮川尚紀,寺本央,河合信之輔,李振風,小松崎民樹
    • Organizer
      日本物理学会 第69回年次大会
    • Place of Presentation
      東海大学湘南キャンパス(平塚市)
    • Related Report
      2013 Research-status Report
  • [Presentation] タンパク質一分子計測から得られたマルコフ連鎖がもつ時間階層構造の理解に向けて2014

    • Author(s)
      永幡裕,寺本央,Chun-Biu Li,小松崎民樹
    • Organizer
      日本物理学会 第69回年次大会
    • Place of Presentation
      東海大学湘南キャンパス(平塚市)
    • Related Report
      2013 Research-status Report
  • [Presentation] A microscopic ruler tells us the underlying networks in single molecule measurements2013

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Nanoscale Science Seminars 2013:A Microscopic ruler tells us the underlying networks in single molecule measurements
    • Place of Presentation
      Max Planck Institute(Stuttgart, Germany)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] データ駆動型モデリングと一分子動態解析における虚実2013

    • Author(s)
      小松崎 民樹
    • Organizer
      日本顕微鏡学会第69回学術講演会
    • Place of Presentation
      ホテル阪急エキスポパーク(吹田市)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Unbiased estimation of physical properties in noisy experimental data2013

    • Author(s)
      Shinnosuke Kawai, David Cooper, Christy Landes, Henning D. Mootz, Haw Yang, Tamiki Komatsuzaki
    • Organizer
      IMS Workshop on "Hierarchical Molecular Dynamics: From Ultrafast Spectroscopy to Single Molecule Measurements"
    • Place of Presentation
      NINS Okazaki Conference Center(Okazaki, Japan)
    • Related Report
      2013 Research-status Report
  • [Presentation] Revisiting Energy Landscape & Extracting it from FRET measurement2013

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      The Complexity of Dynamics and Kinetics in Many Dimensions
    • Place of Presentation
      Telluride, CO. (USA)
    • Related Report
      2013 Research-status Report
  • [Presentation] Revisiting Energy Landscape, Timescale, Coarse-Graining2013

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      Chemistry and Dynamics in Complex Environments
    • Place of Presentation
      Telluride, CO. (USA)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 実験データからノイズを取り除き背後の物理量を評価する方法2013

    • Author(s)
      河合信之輔・David Cooper・Christy Landes・Henning D. Mootz・Haw Yang・小松崎民樹
    • Organizer
      日本化学会北海道支部2013年夏季研究発表会
    • Place of Presentation
      北見工業大学(北見市)
    • Related Report
      2013 Research-status Report
  • [Presentation] Toward System Molecular Biology & Data Science2013

    • Author(s)
      Tamiki Komatsuzaki
    • Organizer
      A Symposium on Single Molecule Biophysics and Cyt c Biochemistry
    • Place of Presentation
      Jyozankei View Hotel(Sapporo, Japan)
    • Related Report
      2013 Research-status Report
  • [Presentation] Information of multi-order correlation in pattern formation2013

    • Author(s)
      Naoki Miyagawa, Hiroshi Teramoto , Chun-Biu Li, Tamiki Komatsuzaki
    • Organizer
      A Symposium on Single Molecule Biophysics and Cyt c Biochemistry
    • Place of Presentation
      Jyozankei View Hotel(Sapporo, Japan)
    • Related Report
      2013 Research-status Report
  • [Presentation] Identifying the most distinct disjoint sets to extract hierarchical structure in Markov chain steady state network extracted from time series by finding “minimum” transition probability2013

    • Author(s)
      Yutaka Nagahata, Hiroshi Teramoto, Takashi Horiyama, Chun-Biu Li, Tamiki Komatsuzaki
    • Organizer
      A Symposium on Single Molecule Biophysics and Cyt c Biochemistry
    • Place of Presentation
      Jyozankei View Hotel(Sapporo, Japan)
    • Related Report
      2013 Research-status Report
  • [Presentation] 時間スケールに依存して変化する実効自由度とエネルギー地形2013

    • Author(s)
      河合 信之輔,寺本 央,小松崎 民樹
    • Organizer
      第7回分子科学討論会2013京都
    • Place of Presentation
      京都テルサ(京都市)
    • Related Report
      2013 Research-status Report
  • [Presentation] 定常マルコフ連鎖から階層構造を抽出する際に生じる組み合わせ爆発2013

    • Author(s)
      永幡 裕, 寺本 央, 堀山 貴史, Chun-Biu Li, 小松崎 民樹
    • Organizer
      湊離散構造処理系プロジェクト ERATO セミナー
    • Place of Presentation
      北海道大学工学部(札幌市)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 個々の軌道の振舞いとその集団分布の振舞いの関係~一軌道レベルでのスペクトル解析法とそれによる溶質分子と水の協同運動の抽出~2013

    • Author(s)
      寺本央、戸田幹人、小松崎民樹
    • Organizer
      第36回溶液化学シンポジウム プレシンポジウム
    • Place of Presentation
      北海道大学 学術交流会館(札幌市)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Dynamic Disorder 再考:解析の虚実2013

    • Author(s)
      小松崎 民樹
    • Organizer
      研究会「理論と実験」2013
    • Place of Presentation
      広島大学理学部(東広島市)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Let Systems Tell for themselves: Energy Landscape and Complex Network2013

    • Author(s)
      James N. Taylor, Shinnosuke Kawai, Chun Biu Li, Tamiki Komatsuzaki
    • Organizer
      Technologies for Medical Diagnosis and Therapy Symposium
    • Place of Presentation
      Academia Sinica(Taipei, Taiwan)
    • Related Report
      2013 Research-status Report
  • [Presentation] Toward the Decoding of Single Nucleotides Tunneling Current by Change Point Analysis2013

    • Author(s)
      Chun-Biu Li, Tamiki Komatsuzaki
    • Organizer
      Technologies for Medical Diagnosis and Therapy Symposium
    • Place of Presentation
      Academia Sinica(Taipei, Taiwan)
    • Related Report
      2013 Research-status Report
  • [Presentation] A Multiscale Kinetic Scheme Extracted from EGFR-Grb2 Single Molecule Reaction2013

    • Author(s)
      Sultana Tahmina, Takagi Hiroaki, Morimatsu Miki, Teramoto Hiroshi, Li Chun-Biu, Sako Yasushi, Komatsuzaki Tamiki
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      国立京都国際会館(京都市)
    • Related Report
      2013 Research-status Report
  • [Presentation] 一分子時系列から抽出されたマルコフ連鎖 定常ネットワーク における遷移確率が“最小”となる分子の“状態”の同定2013

    • Author(s)
      永幡 裕, 寺本 央, Li Chun-Biu, 小松崎 民樹
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      国立京都国際会館(京都市)
    • Related Report
      2013 Research-status Report
  • [Presentation] 分子イメージングから要素間の高次相互作用の定量化に向けて2013

    • Author(s)
      小松崎 民樹
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      国立京都国際会館(京都市)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] An Information-Theoretical approach to Local Equilibrium State Analysis for Single-Molecule Time-Series2013

    • Author(s)
      J. Nick Taylor, Li Chun-Biu, Kawai Shinnosuke, Komatsuzaki Tamiki
    • Organizer
      第51回日本生物物理学会年会
    • Place of Presentation
      国立京都国際会館(京都市)
    • Related Report
      2013 Research-status Report
  • [Presentation] 分子個性(Dynamic disorder):一分子生物学から産まれた新しい概念?2013

    • Author(s)
      小松崎 民樹
    • Organizer
      第2回バイオ単分子研究会
    • Place of Presentation
      つなぎ温泉 紫苑(盛岡市)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] タンパク質一分子の計測から得られた定常マルコフ連鎖がもつ時間階層構造の理解に向けて2013

    • Author(s)
      永幡 裕, 寺本 央, Li Chun-Biu, 小松崎 民樹
    • Organizer
      ERATO湊離散構造処理系プロジェクト 「2013年度 秋のワークショップ」
    • Place of Presentation
      第一滝本館(登別市)
    • Related Report
      2013 Research-status Report
  • [Presentation] Extracting the Protein-folding Dynamics from Single Molecule Time Series2013

    • Author(s)
      Kunihiko Ibe, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    • Organizer
      The 14th RIES-HOKUDAI International Symposium 網[mou]
    • Place of Presentation
      シャトレーゼガトーキングダムサッポロ(札幌市)
    • Related Report
      2013 Research-status Report
  • [Presentation] Information of multi-order correlation in pattern formation2013

    • Author(s)
      Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, and Tamiki Komatsuzaki
    • Organizer
      The 14th RIES-HOKUDAI International Symposium 網[mou]
    • Place of Presentation
      シャトレーゼガトーキングダムサッポロ(札幌市)
    • Related Report
      2013 Research-status Report
  • [Presentation] Toward understanding hierarchical structure of complex reaction networks extracted from single molecule time series2013

    • Author(s)
      Yutaka Nagahata, Hiroshi Teramoto, Takashi Horiyama, Chun-Biu Li, Tamiki Komatsuzaki
    • Organizer
      The 14th RIES-HOKUDAI International Symposium 網[mou]
    • Place of Presentation
      シャトレーゼガトーキングダムサッポロ(札幌市)
    • Related Report
      2013 Research-status Report
  • [Presentation] Scrutiny of Heterogeneity in Memory by Extracting Reaction Network Buried in Single Molecule Time Series of EGFR and Grb22013

    • Author(s)
      Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, and Tamiki Komatsuzaki
    • Organizer
      The 14th RIES-HOKUDAI International Symposium 網[mou]
    • Place of Presentation
      シャトレーゼガトーキングダムサッポロ(札幌市)
    • Related Report
      2013 Research-status Report
  • [Presentation] An Information-Theoretical Approach to Local Equilibrium State Analysis for Single-Molecule Time-Series2013

    • Author(s)
      J. N. Taylor, C.B. Li, S. Kawai, and T. Komatsuzaki
    • Organizer
      The 14th RIES-HOKUDAI International Symposium 網[mou]
    • Place of Presentation
      シャトレーゼガトーキングダムサッポロ(札幌市)
    • Related Report
      2013 Research-status Report
  • [Book] パリティ11月号:ラグランジュ協同構造―流体の流れに隠れた骨格2013

    • Author(s)
      Thomas Peacock, George Haller : 小松崎民樹 訳
    • Total Pages
      9
    • Publisher
      丸善出版株式会社
    • Related Report
      2013 Research-status Report
  • [Remarks] 回転分子モーターF1-ATPase の化学ー力学エネルギー変換におけるATP加水分解反応の役割解明!

    • URL

      http://www.es.hokudai.ac.jp/result/2015-12-18-mlns/

    • Related Report
      2015 Annual Research Report
  • [Remarks] Single Molecule Chemo-mechanics ...

    • URL

      http://www.oia.hokudai.ac.jp/blog/31871/

    • Related Report
      2015 Annual Research Report
  • [Remarks] 北海道大学電子科学研究所分子生命数理研究分野HP

    • URL

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

    • Related Report
      2014 Research-status Report
  • [Remarks] プレス発表 ノイズを含むデータから分子の状態とそれらのネットワーク。。。

    • URL

      http://www.hokudai.ac.jp/pr/150318_es_pr.pdf

    • Related Report
      2014 Research-status Report
  • [Remarks] ノイズを含むデータから分子の状態とそれらのネットワーク。。。

    • URL

      http://www.es.hokudai.ac.jp/result/2015-03-18-mlns/

    • Related Report
      2014 Research-status Report
  • [Remarks] Novel method developed to extract ...

    • URL

      http://www.oia.hokudai.ac.jp/blog/2015/03/23/novel-method-developed-to-extract-molecular-states-and-their-network-from-noisy-single-molecule-time-series-data/

    • Related Report
      2014 Research-status Report
  • [Remarks] 北海道大学電子科学研究所、分子生命数理研究分野ホームページ

    • URL

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

    • Related Report
      2013 Research-status Report

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Published: 2014-07-25   Modified: 2019-07-29  

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