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Nonlinear breathing modes at a defect

Wattis, Jonathan A.D.

Authors

Jonathan A.D. Wattis Jonathan.Wattis@nottingham.ac.uk



Abstract

Recent molecular dynamics (MD) simulations of Cubero et al (1999) of
a DNA duplex containing the 'rogue' base difluorotoluene (F) in place of a
thymine (T) base show that breathing events can occur on the nanosecond
timescale, whereas breathing events in a normal DNA duplex take place on the microsecond timescale.
The main aim of this paper is to analyse a nonlinear Klein-Gordon lattice
model of the DNA duplex including both nonlinear interactions between
opposing bases and a defect in the interaction at one lattice site;
each of which can cause localisation of energy.
Solutions for a breather mode either side of the defect are derived using
multiple-scales asymptotics and are pieced together across the defect to
form a solution which includes the effects of the nonlinearity and the defect.
We consider defects in the
inter-chain interactions and in the along chain interactions.
In most cases we find in-phase breather modes and/or out-of-phase
breather modes, with one case displaying a shifted mode.

Journal Article Type Article
Publication Date Jan 1, 2004
Journal Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Electronic ISSN 1364-503X
Publisher Royal Society, The
Peer Reviewed Peer Reviewed
Volume 362
APA6 Citation Wattis, J. A. (2004). Nonlinear breathing modes at a defect. Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 362,
Keywords Localisation, defect, lattice model, breathers
Publisher URL http://journals.royalsociety.org/content/4qja9tmm6jnf9j8a/fulltext.pdf
Copyright Statement Copyright information regarding this work can be found at the following address: http://eprints.nottingh.../end_user_agreement.pdf
Additional Information Published as: Nonlinear breathing modes due to a defect in a DNA chain.

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://eprints.nottingham.ac.uk/end_user_agreement.pdf





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