Base pairs opening and bubble transport in damped DNA dynamics with transport memory effects.

Transport memory effects on nonlinear wave propagation are addressed in a damped Peyrard-Bishop-Dauxois model of DNA dynamics. Under the continuum and overdamped limits, the multiple-scale expansion method is employed to show that an open-state configuration of the DNA molecule is described by a complex nonlinear Schrödinger equation. For the latter, solutions are proposed as bright solitons, which suitably represent the open-state configuration that takes place along the DNA molecule in the form of bubbles. A good agreement between numerical experiments and analytical predictions on the impact of memory effects on the angular frequency, velocity, width, and amplitude of the moving bubble is obtained. It also appears that memory effects can modify qualitatively and quantitatively the nonlinear dynamics of DNA, including the energy brought by enzymes for the initiation of the processes of replication and transcription.