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Nonlinear breathing modes at a defect

Wattis, Jonathan A.D.


Professor of Applied Mathematics


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.


Wattis, J. A. (2004). Nonlinear breathing modes at a defect. Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 362,

Journal Article Type Article
Publication Date Jan 1, 2004
Deposit Date Aug 15, 2008
Publicly Available Date Aug 15, 2008
Journal Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Electronic ISSN 1364-503X
Publisher The Royal Society
Peer Reviewed Peer Reviewed
Volume 362
Keywords Localisation, defect, lattice model, breathers
Public URL
Publisher URL
Additional Information Published as: Nonlinear breathing modes due to a defect in a DNA chain.


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