Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: Leu-Enkephalin folding

Dmitry Nerukh, George Karvounis, Robert C. Glen

    Research output: Chapter in Book/Published conference outputConference publication


    Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated.
    Original languageEnglish
    Title of host publicationComputational life sciences II
    Subtitle of host publicationsecond international symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006. Proceedings
    EditorsMichael R. Berthold, Robert C. Glen, Ingrid Fischer
    Place of PublicationBerlin (DE)
    Number of pages12
    ISBN (Electronic)978-3-540-45768-8
    ISBN (Print)978-3-540-45767-1
    Publication statusPublished - 2006
    Event2nd International Symposium on Computational Life sciences - Cambridge, United Kingdom
    Duration: 27 Sept 200629 Sept 2006

    Publication series

    NameLecture notes in computer science
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349


    Symposium2nd International Symposium on Computational Life sciences
    Abbreviated titleCompLife 2006
    Country/TerritoryUnited Kingdom


    • folding
    • enkephalin
    • dynamic complexity
    • computational mechanics


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