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Information thermodynamics for biochemical signal transduction

Research Project

Project/Area Number 16K17780
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionThe University of Tokyo (2018)
Hokkaido University (2017)
Tokyo Institute of Technology (2016)

Principal Investigator

Ito Sosuke  東京大学, 大学院理学系研究科(理学部), 講師 (00771221)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2018: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2017: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords情報熱力学 / シグナル伝達 / 情報幾何 / 不確定性関係 / オンサーガ相反関係 / 移動エントロピー / 熱力学第二法則 / 非平衡統計力学 / 酵素反応 / 量子速度限界 / 熱力学 / 大腸菌走化性 / Markovネットワーク / Onsager相反関係 / 生物物理
Outline of Final Research Achievements

In this study, we construct the unified theory of information and thermodynamics called information thermodynamics as a fundamental theory of biological information processing. We have derived the generalization of the Onsager reciprocal relation with information flow and the second law of thermodynamics in terms of the Granger causality. We have also derived a thermodynamic uncertainty relationship between thermodynamic cost and the speed from a view point of information geometry, that is a differential geometry of information theory. Our result is generally useful to understand the biological sensory adaptation and the enzyme reaction quantitatively.

Academic Significance and Societal Importance of the Research Achievements

本研究成果は、情報理論と熱力学の融合理論である情報熱力学を発展させ、生体内のシグナル伝達の定量的な理解に役立てるための理論的な基盤を作ることである。この研究の発展によって、生体内で伝達される情報について熱力学的なコストとの関係から定量的に理解が可能となる。この研究の方向性は、低エネルギーコストで効率的な生体システムの理解に役立ち、工学的な実装の礎になると考えている。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (41 results)

All 2019 2018 2017 2016 Other

All Int'l Joint Research (2 results) Journal Article (10 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 3 results,  Acknowledgement Compliant: 2 results) Presentation (24 results) (of which Int'l Joint Research: 8 results,  Invited: 11 results) Book (2 results) Remarks (3 results)

  • [Int'l Joint Research] AMOLF(オランダ)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] FOM Institute AMOLF(オランダ)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Stochastic thermodynamic interpretation of information geometry2018

    • Author(s)
      Sosuke Ito
    • Journal Title

      Physical Review Letters

      Volume: 121 Issue: 3 Pages: 030605-030605

    • DOI

      10.1103/physrevlett.121.030605

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Stochastic time-evolution, information geometry and the Cramer-Rao Bound2018

    • Author(s)
      Sosuke Ito and Andreas Dechant
    • Journal Title

      arXiv (preprint)

      Volume: 1810 Pages: 06832-06832

    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Journal Article] Unified framework for the second law of thermodynamics and information thermodynamics based on information geometry2018

    • Author(s)
      Sosuke Ito
    • Journal Title

      arXiv (preprint)

      Volume: 1810 Pages: 09545-09545

    • NAID

      130008147772

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Stochastic thermodynamic interpretation of information geometry2017

    • Author(s)
      Sosuke Ito
    • Journal Title

      arXiv (preprint)

      Volume: 1712 Pages: 04311-04311

    • Related Report
      2017 Research-status Report
  • [Journal Article] < 講義ノート> ネットワーク上の情報熱力学とその生体情報処理への応用 (第 62 回物性若手夏の学校 集中ゼミ)2017

    • Author(s)
      伊藤 創祐
    • Journal Title

      物性研究

      Volume: 6. 4

    • NAID

      120006384206

    • Related Report
      2017 Research-status Report
  • [Journal Article] 最近の研究から ネットワーク上の情報熱力学とその生体情報処理への応用2017

    • Author(s)
      伊藤創祐. 沙川貴大
    • Journal Title

      日本物理学会誌

      Volume: 72(9), Pages: 658-662

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] ネットワーク上の情報熱力学とその生体情報処理への応用2017

    • Author(s)
      伊藤創祐, 沙川貴大
    • Journal Title

      日本物理学会誌

      Volume: 印刷中

    • NAID

      130007418934

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Linear irreversible thermodynamics and Onsager reciprocity for information-driven engines2016

    • Author(s)
      Shumpei Yamamoto, Sosuke Ito, Naoto Shiraishi, and Takahiro Sagawa
    • Journal Title

      Phyical Review E

      Volume: 94 Issue: 5 Pages: 052121-052121

    • DOI

      10.1103/physreve.94.052121

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Backward transfer entropy: Informational measure for detecting hidden Markov models and its interpretations in thermodynamics, gambling and causality2016

    • Author(s)
      Sosuke Ito
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 36831-36831

    • DOI

      10.1038/srep36831

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] 適応センサー中のマクスウェルのデーモン2016

    • Author(s)
      伊藤創祐
    • Journal Title

      生物物理

      Volume: 56 Pages: 232-233

    • NAID

      130005165629

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Thermodynamic speed limits for biochemical reaction and its information geometric interpretation2019

    • Author(s)
      Sosuke Ito
    • Organizer
      Winter Q-bio
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Stochastic thermodynamic interpretation of information geometry2018

    • Author(s)
      Sosuke Ito
    • Organizer
      Big data analysis from a dynamical systems point of view
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Stochastic thermodynamics and information geometry2018

    • Author(s)
      Sosuke Ito
    • Organizer
      APEF 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Information geometry and thermodynamic uncertainty for biochemical process2018

    • Author(s)
      Sosuke Ito
    • Organizer
      The 56th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2018 Annual Research Report
  • [Presentation] 情報幾何とマルコフ過程の熱力学2018

    • Author(s)
      伊藤創祐
    • Organizer
      2019年電子情報通信学会総合大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 情報幾何の確率的熱力学による解釈と熱力学不確定性関係2018

    • Author(s)
      伊藤創祐
    • Organizer
      日本物理学会 2018年 秋季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 熱力学第二法則と情報熱力学第二法則の情報幾何による統一的フレームワーク2018

    • Author(s)
      伊藤創祐
    • Organizer
      日本物理学会 第74回年次大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Stochastic thermodynamics of information2018

    • Author(s)
      Sosuke Ito
    • Organizer
      Frontiers of complex systems science: soft matter, biophysics, and statistical physics
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Stochastic Thermodynamic Interpretation of Information Geometry2018

    • Author(s)
      伊藤創祐
    • Organizer
      若手研究会「統計物理学とその周辺」
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 情報熱力学の進展:細胞内ネットワーク及び情報幾何への拡張2018

    • Author(s)
      伊藤創祐
    • Organizer
      東北大学数理科学連携研究センター・ワークショップ 細胞内ネットワークのダイナミクス~生物学と数理科学の協働~
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 情報理論と熱力学2018

    • Author(s)
      伊藤 創祐
    • Organizer
      北海道大学電子科学研究所 平成29年度 研究交流会
    • Related Report
      2017 Research-status Report
  • [Presentation] 情報熱力学の展開と生体系への応用2017

    • Author(s)
      伊藤創祐
    • Organizer
      日本物理学会 2017年 春季大会 若手奨励賞受賞記念講演
    • Place of Presentation
      大阪大学
    • Year and Date
      2017-03-17
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] 情報熱力学とギャンブルの情報理論のアナロジー2017

    • Author(s)
      伊藤創祐
    • Organizer
      日本物理学会 2017年 春季大会
    • Place of Presentation
      大阪大学
    • Year and Date
      2017-03-17
    • Related Report
      2016 Research-status Report
  • [Presentation] Thermodynamics of information on biochemical signaling networks2017

    • Author(s)
      Sosuke Ito
    • Organizer
      Deciphering complex energy landscape and kinetic network from single molecules to cells: a new challenge to make theories meet experiments
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 生化学系の情報熱力学2017

    • Author(s)
      伊藤創祐
    • Organizer
      第60回自動制御連合講演会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Langevin系における熱力学, 情報熱力学2017

    • Author(s)
      伊藤創祐
    • Organizer
      Perspectives of Nonlinear Phenomena in Random and Non-autonomous Dynamics
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 生化学時計の情報熱力学2017

    • Author(s)
      伊藤創祐
    • Organizer
      研究会「理論と実験」2017
    • Related Report
      2017 Research-status Report
  • [Presentation] 生化学時計の情報熱力学2017

    • Author(s)
      Sosuke Ito and Pieter rein ten Wolde
    • Organizer
      日本物理学会2017年秋季大会
    • Related Report
      2017 Research-status Report
  • [Presentation] Information thermodynamic study of biochemical clock2017

    • Author(s)
      Sosuke Ito and Pieter rein ten Wolde
    • Organizer
      第55回日本生物物理学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] 生体適応センサーの情報熱力学2017

    • Author(s)
      伊藤創祐
    • Organizer
      日本神経回路学会 時限研究会2017
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] ネットワーク上の情報熱力学と生体シグナル伝達への応用2017

    • Author(s)
      伊藤創祐
    • Organizer
      第62回物性若手夏の学校
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Thermodynamics and information geometry2017

    • Author(s)
      Sosuke Ito
    • Organizer
      The 18th RIES-Hokudai International Symposium
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Maxwell's demon in biochemical signal transduction with feedback loop2016

    • Author(s)
      Sosuke Ito and Takahiro Sagawaq
    • Organizer
      DutchBiophysics 2016
    • Place of Presentation
      Veldhoven, Netherlands
    • Year and Date
      2016-10-03
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Backward transfer entropy: Informational measure of non hidden-Markov property2016

    • Author(s)
      Sosuke Ito
    • Organizer
      Statphys26
    • Place of Presentation
      Lyon, France
    • Year and Date
      2016-06-18
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Book] information thermodynamics on causal networks and its application to biochemical signal transduction2016

    • Author(s)
      Sosuke Ito
    • Total Pages
      133
    • Publisher
      Springer
    • Related Report
      2016 Research-status Report
  • [Book] Chapter 3 "Information flow and entropy production on Bayesian networks" in "Mathematical Foundations and Applications of Graph Entropy"2016

    • Author(s)
      Sosuke Ito and Takahiro Sagawa (Edited by Matthias Dehmer, Frank Emmert-Streib, Zengqiang Chen, Xueliang Li and Yongtang Shi)
    • Total Pages
      296
    • Publisher
      Wiely-VCH
    • Related Report
      2016 Research-status Report
  • [Remarks] Prof. Pieter rein ten Wolde

    • URL

      https://amolf.nl/people/pieter-rein-ten-wolde

    • Related Report
      2016 Research-status Report
  • [Remarks] Prof. Tom Shimizu

    • URL

      https://amolf.nl/people/tom-shimizu

    • Related Report
      2016 Research-status Report
  • [Remarks] Dr. Keita Kamino

    • URL

      https://amolf.nl/people/keita-kamino

    • Related Report
      2016 Research-status Report

URL: 

Published: 2016-04-21   Modified: 2020-03-30  

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