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

A. Alvarez·F. R. Romero·J. F. R. Archilla·J. Cuevas·P. V. Larsen
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Abstract

We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are oriented in opposite directions. The Hamiltonian of the Peyrard--Bishop model is augmented with a term that includes the dipole--dipole coupling between base pairs. Numerical simulations show the existence of two dynamical regimes. If the translational kinetic energy of a moving breather launched towards the interface is below a critical value, it is trapped in a region around the interface collecting vibrational energy. For an energy larger than the critical value, the breather is transmitted and continues travelling along the double strand with lower velocity. Reflection phenomena never occur. The same study has been carried out when a single dipole is oriented in opposite direction to the other ones. When moving breathers collide with the single inverted dipole, the same effects appear. These results emphasize the importance of this simple type of local inhomogeneity as it creates a mechanism for the trapping of energy. Finally, the simulations show that, under favorable conditions, several launched moving breathers can be trapped successively at the interface region producing an accumulation of vibrational energy. Moreover, an additional colliding moving breather can produce a saturation of energy and a moving breather with all the accumulated energy is transmitted to the chain.

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A. Alvarez, F. R. Romero, J. F. R. Archilla, J. Cuevas, P. V. Larsen. 2006-03-27. Breather trapping and breather transmission in a DNA model with an interface. https://doi.org/10.1140/epjb%2Fe2006-00191-0

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