Nonlinear breathing modes at a defect

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.

Asymptotic analysis of combined breather-kink modes in a Fermi-Pasta-Ulam chain

We find approximations to travelling breather solutions of the one-dimensional Fermi-Pasta-Ulam (FPU) lattice. Both bright breather and dark breather solutions are found. We find that the existence of localised (bright) solutions depends upon the coefficients of cubic and quartic terms of the potential energy, generalising an earlier inequality derived by James [CR Acad Sci Paris 332, 581, (2001)]. We use the method of multiple scales to reduce the equations of motion for the lattice to a nonlinear Schr{\"o}dinger equation at leading order and hence construct an asymptotic form for the breather. We show that in the absence of a cubic potential energy term, the lattice supports combined breathing-kink waveforms. The amplitude of breathing-kinks can be arbitrarily small, as opposed to traditional monotone kinks, which have a nonzero minimum amplitude in such systems. We also present numerical simulations of the lattice, verifying the shape and velocity of the travelling waveforms, and confirming the long-lived nature of all such modes.