Eur. Phys. J. E (2015) 38: 41
https://doi.org/10.1140/epje/i2015-15041-4

Regular Article

Thermal and inertial resonances in DNA unzipping

¹ Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, 50009, Zaragoza, Spain
² Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009, Zaragoza, Spain
³ Departamento de Física, Universidad de Oriente, 90500, Santiago de Cuba, Cuba
⁴ Escuela Politécnica Superior y Facultad de Ciencias de la Salud, Universidad San Jorge, 50830, Zaragoza, Spain
⁵ School of Mathematical Sciences, Queen Mary University of London, E1 4NS, London, UK

^* e-mail: berguesana@yahoo.es

Received: 9 January 2015
Revised: 18 March 2015
Accepted: 23 March 2015
Published online: 22 May 2015

Abstract

Single-molecule experiments combined with alternate forces are able to provide useful information not present in standard constant-force and -velocity pulling protocols. Here, we study the effects of such forces in the DNA mechanical unzipping by using an extension of the Peyrard-Bishop-Dauxois model. By changing the damping regime in the dynamical equations, we obtained two resonant mechanisms in both the mean time and the mean force of unzipping. One is thermally assisted and it is characterized by a matching between the period of the external force and the mean unzipping time of the DNA chain, while the other depends on the inertial properties of the system. Both mechanisms are studied systematically under different opening protocols and different parameters of the system. The main results here presented contribute in characterizing and finding optimized conditions in DNA unzipping experiments.