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,