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Dynamics and Logic in Evolutions of Ecosystems and Proteins

Research Project

Project/Area Number 11837010
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research InstitutionOsaka University

Principal Investigator

KIKOCHI Macoto  Graduate School of Science, Osaka University Professor, サイバーメディアセンター, 教授 (50195210)

Co-Investigator(Kenkyū-buntansha) CHAWANYA Tsuyoshi  Graduate School of Science, Osaka University Lecturer, 大学院・理学研究科, 講師 (80294148)
TOKITA Kei  Graduate School of Science, Osaka University Research Associate, サイバーメディアセンター, 助教授 (00263195)
Project Period (FY) 1999 – 2000
Project Status Completed (Fiscal Year 2000)
Budget Amount *help
¥4,100,000 (Direct Cost: ¥4,100,000)
Fiscal Year 2000: ¥1,300,000 (Direct Cost: ¥1,300,000)
Fiscal Year 1999: ¥2,800,000 (Direct Cost: ¥2,800,000)
Keywordsecosystem / protein / evolution / dynamical system / extinction / diversity / folding / レプリケーター方程式 / 計算機シミュレーション / フォールディング / 生体系
Research Abstract

1. Extinction and Speciation Dynamics of Large-scale Ecosystem
Introducing the effect of extinction into the so-called replicator equations, we constructed a general model where the diversity of species is a dynamical variable. The system shows very different behavior from the original equation and leads to mass extinction when the system initially has high diversity. We further introduced the effects of invasion and mutation into the system and obtained the following conclusions : (1) interspecies interactions become more symbiotic under the pressure of natural selection ; (2) a complex ecosystem can emerge when temporally neutral mutants are introduced ; (3) such ecosystem possesses strong resistance to invasion ; (4) a typical process of fixation of mutants is realized through the rapid growth of a group of symbiotic mutants with higher fitness than majority species ; (5) a hierarchical taxonomic structure (like family-genus-species) emerges ; and (6) the relative abundance of specie … More s exhibits a typical pattern widely observed in nature.
2. Dynamical Structure of Large-scale Ecosystem
We investigated the dynamical structure related to spontaneous interchange of major species and found that this structure is relevant to several other systems. We proposed a new mechanism for maintaining diversity in systems dominated by competing interactions.
3. Role of Non-native Interaction in the Evolution of Protein
β-lactoglobulin is known to exhibit an anomalous folding process in which an accumulation of non-native α-helices is observed in the folding intermediate while the native state is β-sheet dominated. Our principal question here is why the non-native intermediate state has not been eliminated in the course of the Darwinian evolution. Based on lattice model simulations, we found that the free-energy landscape bears a highly "non-funnel" nature and the intermediate state is "on-pathway". The result indicate that the folding intermediate have some active role in the folding process, and has thus been conserved through the evolution. Less

Report

(3 results)
  • 2000 Annual Research Report   Final Research Report Summary
  • 1999 Annual Research Report
  • Research Products

    (24 results)

All Other

All Publications (24 results)

  • [Publications] T.Shibata,T.Chawanya and K.Kaneko: "Noiseless collective motion out of Noisy Chaos"Physical Review Letters. 82. 4424-4427 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] G.Chikenji,M.Kikuchi and Y.Iba: "Multi-Self-Overlap Ensemble for Protein Folding : Ground State Search and Thermodynamics"Physical Review Letters. 83. 1886-1889 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] K.Tokita and A.Yasutomi: "Mass Extinction in a Dynamical System of Evolution with Variable Dimension"Physical Review E. 60. 842-847 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] G.Chikenji and M.Kikuchi: "What is the Role of non-native Intermediates of β-lactoglbulin in Protein Folding?"Proceedngs of National Academy of Science (USA). 97. 14273-14277 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] K.Tokita,M.Kikuchi and Y.Iba: "Dynamical Equation Approach to Protein Design"Progress of Theoretical Physics supplement. 138. 378-383 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] M.Kikuchi,G.Chikenji and Y.Iba: "Multi-Self-Overlap Ensemble Moute Carlo Method for Lattice Proteins and Heteropolymers"Progress of Theoretical Physics supplement. 138. 404-405 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] G.Chikenji and M.Kikuchi: "A Lattice Model Study of α→β Transitions in Protein Folding"Progress of Theoretical Phrsics supplement. 138. 406-407 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] R.Tatsumi,G.Chikenji,Y.Akutsu and M.Kikuchi: "The Relation among Thermodynamic Stability, Folding Dynamics, and Designability"Progress of Theoretical Physics supplement. 138. 420-421 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] T.Shibata, T.Chawanya and K.Kaneko.: "Noiseless Collective Motion out of Noisy Chaoss"Physical Review Letters. 82. 4424-4427 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] G.Chikenji, M.Kikuchi and Y.Iba: "Multi-Self-Overlap Ensemble for Protein Folding : Ground State Search and Thermodynamics"Physical Review Letters.. 83. 1886-1889 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] K.Tokita and A.Yasutomi.: "Mass Extinction in a Dynamical System of Evolution with Variable Dimesion"Physical Review. E60. 842-847 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] G.Chikenji and M.Kikuchi: "What is the Role of Non-native Intermediates of β-lactoglobulin in protein Folding?"Proceedings of National ACodemy of Science (USA). 97. 14273-14277 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] K.Tokita, M.Kikuchi and Y.Iba: "Dynamical Equation Approach to Protein Design"Progress of Theoretical Physics Supplement. 138. 378-383 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] M.Kikuchi, G.Chikenji and Y.Iba: "Multi-Self-Overlap Ensemble Monte Carlo Method for Lattice Profeins and Heteropolymers"Progress of Theoretical Physics Supplement. 138. 404-405 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] G.Chikenji and M.Kikuchi: "A Lattice Model Study of α→β Transitions in Protein Folding"Progress of Theoretical Physics Supplement. 138. 406-407 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] R.Tatsumi, G.Chikenji, Y.Akutsu and M.Kikuchi: "The Relations Among Thermodynamic Stability, Folding Dynamics, and Designability"Progress of Theoretical Physics Supplement. 138. 420-421 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2000 Final Research Report Summary
  • [Publications] G.Chikenji and M.kikuchi: "what is the role of non-native intermediutes of β-lactoglobulin in protein folding"Proceedings of National Academy of Science (USA). 97巻. 14273-14277 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] K.Tokita,M.Kikuchi and Y.Iba: "Dynamical Eguation Approach to Protein Design"Progress of Theoretical Physics supplement. 138巻. 378-383 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] M.Kikuchi,G.Chikenji and Y.Iba: "Multi-Selfoverlop-Ensemble Monte Carlo Method for Lattice Proteins and Heteropolymers"Progress of Theoretical Physics supplement. 138巻. 404-405 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] G.Chikenji and M.Kikuchi: "A Lattice Model Study of α→βTransitions in protein Folding"Progress of Theorefical Physics supplement. 138巻. 406-407 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] R.Tatsumi,G.Chikenji,Y.Akutsu and M.kikuchi: "The Relation among Thermodynamic stability, Folding Dynamics, and Desiguability"Progress of Theorefical Thysics supplement. 138巻. 420-421 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] G.Chikenji,M.kikuchi and Y.Iba: "Mult-Self-Overlap Ensemble for Protein Folding: Ground State Search and Thermodynamics"Plysical Review Letters. Vol. 83. 1886-1889 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] T.Shibata,T.Chawanya and K.Kaneko: "Noiseless Collective Motion out of Noisy Chaos"Plysical Review Letters. Vol. 82. 4424-4427 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] K.Tokita and A.Yasutomi: "Mass Extinction in a Dynamical System of Evolution with Variable Dimension"Plysical Review E. Vol. 60. 682-687 (1999)

    • Related Report
      1999 Annual Research Report

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Published: 1999-04-01   Modified: 2016-04-21  

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