Energy localization in an anharmonic twist-opening model of DNA dynamics

    Research output: Contribution to journalArticle

    14 Citations (Scopus)

    Abstract

    Energy localization is investigated in the framework of the anharmonic twist-opening model proposed by Cocco and Monasson. This model includes the coupling between opening and twist that result from the helicoidal geometry of B-DNA. I first reduce the corresponding two-component model to its amplitude equations, which have the form of coupled discrete nonlinear Schr̈odinger (DNLS) equations, and I perform the linear stability analysis of the plane waves, solutions of the coupled DNLS equations. It is shown that the stability criterion deeply depends on the stiffness of the molecule. Numerical simulations are carried out in order to verify analytical predictions. It results that increasing the value of the molecule stiffness makes the energy patterns long-lived and highly localized. This can be used to explain the way enzymes concentrate energy on specific sequences of DNA for the base-pairs to be broken. The role of those enzymes could therefore be to increase the stiffness of closed regions of DNA at the boundaries of an open state.

    Original languageEnglish
    Article number414107
    JournalJournal of Physics Condensed Matter
    Volume22
    Issue number41
    DOIs
    Publication statusPublished - Oct 20 2010

    Fingerprint

    Schrodinger equation
    stiffness
    DNA
    deoxyribonucleic acid
    Stiffness
    B-Form DNA
    nonlinear equations
    enzymes
    Enzymes
    Base Pairing
    Linear stability analysis
    Molecules
    Stability criteria
    energy
    molecules
    plane waves
    Geometry
    Computer simulation
    geometry
    predictions

    All Science Journal Classification (ASJC) codes

    • Materials Science(all)
    • Medicine(all)
    • Condensed Matter Physics

    Cite this

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    title = "Energy localization in an anharmonic twist-opening model of DNA dynamics",
    abstract = "Energy localization is investigated in the framework of the anharmonic twist-opening model proposed by Cocco and Monasson. This model includes the coupling between opening and twist that result from the helicoidal geometry of B-DNA. I first reduce the corresponding two-component model to its amplitude equations, which have the form of coupled discrete nonlinear Schr̈odinger (DNLS) equations, and I perform the linear stability analysis of the plane waves, solutions of the coupled DNLS equations. It is shown that the stability criterion deeply depends on the stiffness of the molecule. Numerical simulations are carried out in order to verify analytical predictions. It results that increasing the value of the molecule stiffness makes the energy patterns long-lived and highly localized. This can be used to explain the way enzymes concentrate energy on specific sequences of DNA for the base-pairs to be broken. The role of those enzymes could therefore be to increase the stiffness of closed regions of DNA at the boundaries of an open state.",
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    Energy localization in an anharmonic twist-opening model of DNA dynamics. / Tabi, Conrad Bertrand.

    In: Journal of Physics Condensed Matter, Vol. 22, No. 41, 414107, 20.10.2010.

    Research output: Contribution to journalArticle

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