Breather trapping and breather transmission in a DNA model with an interface

Abstract

We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a chain in which all the base pairs are identical and there exists a discontinuity in the orientation of the dipole moments within them, that is, there exists an interface such that the dipole moments at each side are oriented in opposite directions. We consider three different interfaces 1) when the dipoles have opposite orientations at each side, 2) a single dipole with opposite orientation that the rest, 3) two consecutive parallel dipoles with opposite orientation that the rest. We find that for all of them there exists a critical value of the translational energy of the breather below which the breathers are trapped and above which the breathers are transmitted. We formulate a new 'trapping hypothesis' which establishes which establishes the necessary conditions for the trapping of moving breathers when they interact with a local inhomogeneity.