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

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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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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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