We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic potentials, [F. Dominquez-Adame et al., Phys. Rev. E 52, 2183 (1995)], we analyze the behavior of lattices built from real DNA sequences obtained from human genome data. We confirm the existence of threshold forces, already found in Fibonacci sequences, and of stop positions highly dependent on the specific sequence. Another relevant conclusion is that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [Phys. Lett. A 193, 263 (1994)] is a useful tool to identify key regions that control the behaviour of a larger sequence. We then study how the fluctuations can assist the propagation process by helping the excitations to escape the stop positions. Our conclusions point out to improvements of the model which look promising to describe mechanical denaturation of DNA. Finally, we also consider how randomly distributed energy focus on the chain as a function of the sequence.
We revisit the issue of directed motion induced by zero average forces in extended systems driven by ac forces. It has been shown recently that a directed energy current appears if the ac external force, f(t), breaks the symmetry f(t) = -f(t+T/2), T being the period, if topological solitons (kinks) existed in the system. In this work, a collective coordinate approach allows us to identify the mechanism through which the width oscillation drives the kink and its relation
with the mathematical symmetry conditions. Furthermore, our theory predicts, and numerical simulations confirm, that the direction of motion depends on the initial phase of the driving, while the system behaves in a ratchet-like fashion if averaging over initial conditions. Finally, the presence of noise overimposed to the ac driving does not destroy the directed motion; on the contrary, it gives rise to an activation process that increases the velocity of the motion. We conjecture that this could be a signature of resonant phenomena at larger noises.