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Nonequilibrium thermodynamics for fluctuations of biopolymers

Research Project

Project/Area Number 19540392
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Mathematical physics/Fundamental condensed matter physics
Research InstitutionIbaraki University

Principal Investigator

NAKAGAWA Naoko  Ibaraki University, 理学部, 准教授 (60311586)

Project Period (FY) 2007 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2010: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2009: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2008: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2007: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywords統計物理学 / 非平衡・非線形物理学 / 非平衡定常系 / クラウジウス関係式 / エントロピー / 熱と仕事の相関 / 揺らぎ / タンパク質 / 折りたたみ転移 / 4点相関関数 / 熱力学第二法則 / 過剰熱 / 熱力学関数 / 統計力学 / inherent structures / 分布関数 / エントロピー生成 / 局所詳細釣り合い / ボルツマン因子 / 軌道平均
Research Abstract

Aiming at the construction of the formulation to describe the working mechanism of biopolymers, we study nonequilibrium steady states analytically. We obtain a concise expression for the probability distribution function correct up to the second order of the degree of nonequilibrium. From this expression, we arrive at a naturally extended Clausius relation to nonequilibrium. We next extend the relation to the second order of the degree of nonequilibrium and find that we should include a twist term, which especially appears in nonlinear nonequilibrium. From a different point of view to examine proteins' dynamics, we study slow fluctuations in a protein model and characterize them by a four-point correlation-functions.

Report

(6 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report   Self-evaluation Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (32 results)

All 2011 2010 2009 2008 2007 Other

All Journal Article (19 results) (of which Peer Reviewed: 19 results) Presentation (9 results) Remarks (4 results)

  • [Journal Article] Entropy and nonlinear nonequilibrium thermodynamic relation for heat conducting steady states2011

    • Author(s)
      Teruhisa S.Komatsu, Naoko Nakagawa, Shin-ichi Sasa, Hal Tasaki
    • Journal Title

      Journal of Statistical Physics vol.142

      Pages: 127-153

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Entropy and nonlinear nonequilibrium thermodynamic relation for heat conducting steady states2011

    • Author(s)
      T.S.Komatsu, N.Nakagawa, S-i.Sasa, H.Tasaki
    • Journal Title

      Journal of Statistical Physics

      Volume: 142 Pages: 127-153

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Stationary distribution and thermodynamic relation in nonequilibrium steady states2010

    • Author(s)
      Teruhisa S.Komatsu, Naoko Nakagawa, Shin-ichi Sasa, Hal Tasaki, N.Ito
    • Journal Title

      Progress of Theoretical Physics, Supplement vol.184

      Pages: 329-338

    • NAID

      110007703098

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Stationary distribution and thermodynamic relation in nonequilibrium steady states2010

    • Author(s)
      T.S.Komatsu, N.Nakagawa, S-i.Sasa, H.Tasaki, N.Ito
    • Journal Title

      Progress of Theroretical Physics、Supplement

      Volume: 184 Pages: 329-338

    • NAID

      110007703098

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Representation of nonequilibrium steady states in large mechanical systems2009

    • Author(s)
      Teruhisa S.Komatsu, Naoko Nakagawa, Shin-ichi Sasa, Hal Tasaki
    • Journal Title

      Journal of Statistical Physics vol.134

      Pages: 401-423

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Representation of nonequilibrium steady states in large mechanical systems2009

    • Author(s)
      Teruhisa S. Komatsu, Naoko Nakagawa, Shin-ichi Sasa, Hal Tasaki
    • Journal Title

      Journal of Statistical Physics vol. 134

      Pages: 401-423

    • Related Report
      2009 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Critical examination of the inherent-structure-landscape analysis of two-state folding proteins2009

    • Author(s)
      Johannes-Geert Hagmman, Naoko Nakagawa, Michel Peyrard
    • Journal Title

      Physical Review E 80

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Representation of nonequilibrium steady states in large mechanical systems2009

    • Author(s)
      T.S.Komatsu, N.Nakagawa, S.Sasa and H.Tasaki
    • Journal Title

      Journal of Statistical Physics 134

      Pages: 401-423

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Steady-State Thermodynamics for Heat Conduction : Microscopic Derivation2008

    • Author(s)
      Teruhisa S.Komatsu, Naoko Nakagawa, Shin-ichi Sasa, Hal Tasaki
    • Journal Title

      Physical Review Letters vol.100

      Pages: 230602-230602

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Expression for the Stationary Distribution in Nonequilibrium Steady States2008

    • Author(s)
      Teruhisa S.Komatsu, Naoko Nakagawa
    • Journal Title

      Physical Review Letters vol.100

      Pages: 30601-30601

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Steady-State Thermodynamics for Heat Conduction : Microscopic Derivation2008

    • Author(s)
      Teruhisa S. Komatsu, Naoko Nakagawa, Shin-ichi Sasa, Hal Tasaki
    • Journal Title

      Physical Review Letters vol. 100

      Pages: 230602-230602

    • Related Report
      2009 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Expression for the Stationary Distribution in Nonequilibrium Steady States2008

    • Author(s)
      Teruhisa S. Komatsu, Naoko Nakagawa
    • Journal Title

      Physical Review Letters vol. 100

      Pages: 30601-30601

    • Related Report
      2009 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Steady State Thermodynamics for Heat Conduction : Microscopic Derivation2008

    • Author(s)
      T.S.Komatsu, N.Nakagawa, S. Sasa and H.Tasaki
    • Journal Title

      Physical Review Letters 100

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 非平衡定常系のボルツマン因子2008

    • Author(s)
      小松輝久、中川尚子
    • Journal Title

      日本物理学会誌 63

      Pages: 694-697

    • NAID

      110006936676

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Expression for the Stationary Distribution in Nonequilibrium Steady States2008

    • Author(s)
      T. S. Komatsu and N. Nakagawa
    • Journal Title

      Physical Review Letters 100

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Reversibility Parameter for a Markovian Stepper2007

    • Author(s)
      Takahiro Harada, Naoko Nakagawa
    • Journal Title

      Europhysics Letters vol.78

      Pages: 50002-50002

    • NAID

      120000808031

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Confomational Temperature Characterizing the Folding of a Protein2007

    • Author(s)
      Naoko Nakagawa
    • Journal Title

      Physical Review Letters vol.98

      Pages: 128104-128104

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] A Reversibility Parameter for a Markovian Stepper2007

    • Author(s)
      Takahiro Harada, Naoko Nakagawa
    • Journal Title

      Europhysics Letters vol. 78

      Pages: 50002-50002

    • NAID

      120000808031

    • Related Report
      2009 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Confomational Temperature Characterizing the Folding of a Protein2007

    • Author(s)
      Naoko Nakagawa
    • Journal Title

      Physical Review Letters vol. 98

      Pages: 128104-128104

    • Related Report
      2009 Self-evaluation Report
    • Peer Reviewed
  • [Presentation] 非平衡定常系における熱力学関係式とオンサガーの相反関係2010

    • Author(s)
      中川尚子
    • Organizer
      日本物理学会
    • Place of Presentation
      大阪府立大学
    • Year and Date
      2010-09-24
    • Related Report
      2010 Annual Research Report 2010 Final Research Report
  • [Presentation] 「非線形非平衡」の拡張クラウジウス関係式2009

    • Author(s)
      中川尚子
    • Organizer
      日本物理学会
    • Place of Presentation
      熊本大学
    • Year and Date
      2009-09-26
    • Related Report
      2010 Final Research Report 2009 Annual Research Report 2009 Self-evaluation Report
  • [Presentation] On the Second law of Steady State Thermodynamics2009

    • Author(s)
      中川尚子
    • Organizer
      Frontiers in Nonequilibrium Physics
    • Place of Presentation
      京都大学
    • Year and Date
      2009-08-03
    • Related Report
      2010 Final Research Report 2009 Annual Research Report 2009 Self-evaluation Report
  • [Presentation] Comformational temperature characterizing the folding of a protein2008

    • Author(s)
      中川尚子
    • Organizer
      Frontier of Glassy Physics
    • Place of Presentation
      京都大学
    • Year and Date
      2008-11-20
    • Related Report
      2010 Final Research Report 2009 Self-evaluation Report 2008 Annual Research Report
  • [Presentation] 非平衡定常系における熱力学関係式とその応用32008

    • Author(s)
      中川尚子
    • Organizer
      日本物理学会
    • Place of Presentation
      岩手大学
    • Year and Date
      2008-09-23
    • Related Report
      2008 Annual Research Report
  • [Presentation] 非平衡定常系における熱力学関係式とその応用12008

    • Author(s)
      中川尚子
    • Organizer
      日本物理学会
    • Place of Presentation
      近畿大学
    • Year and Date
      2008-03-24
    • Related Report
      2010 Final Research Report 2009 Self-evaluation Report
  • [Presentation] 非平衡定常系における熱力学関係式とその応用2008

    • Author(s)
      中川 尚子
    • Organizer
      日本物理学会
    • Place of Presentation
      近畿大学
    • Year and Date
      2008-03-24
    • Related Report
      2007 Annual Research Report
  • [Presentation] 非平衡状態にあるタンパク質の構造を特徴付ける有効温度2007

    • Author(s)
      中川 尚子
    • Organizer
      日本生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] 仕事分布に現れる記憶効果と非平衡度の影響2007

    • Author(s)
      中川尚子
    • Organizer
      日本物理学会
    • Place of Presentation
      北海道大学
    • Year and Date
      2007-09-24
    • Related Report
      2010 Final Research Report 2009 Self-evaluation Report 2007 Annual Research Report
  • [Remarks]

    • URL

      http://info.ibaraki.ac.jp/scripts/websearch/index.htm

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://info.ibaraki.ac.jp/scripts/websearch/index.htm

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://info.ibaraki.ac.jp/scripts/websearch/index.htm

    • Related Report
      2008 Annual Research Report
  • [Remarks] 茨城大学研究者情報総覧

    • URL

      http://info.ibaraki.ac.jp/scripts/websearch/index.htm

    • Related Report
      2007 Annual Research Report

URL: 

Published: 2007-04-01   Modified: 2016-04-21  

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