title: Nonlinear irreversible thermodynamics of single-molecule experiments.
abstract: Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the nonlinear case of systems under nonequilibrium external constraints, we are able to calculate the entropy production and the general nonlinear kinetic equations for the variables involved. In particular, we analyze the case of RNA stretching protocols obtaining critical oscillations between different configurational states when forced by external means to remain in the unstable region of its free-energy landscape, as observed in experiments. We also calculate the entropy produced during these hopping events and show how resonant phenomena in stretching experiments of single RNA macromolecules may arise. We also calculate the hopping rates using Kramer's approach obtaining a good comparison with experiments.
authors.affiliation: UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México.
authors.forename: I
authors.initials: I
authors.lastname: Santamaría-Holek
authors.affiliation: UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México.
authors.forename: N J
authors.initials: NJ
authors.lastname: López-Alamilla
authors.affiliation: UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México.
authors.forename: M
authors.initials: M
authors.lastname: Hidalgo-Soria
authors.affiliation: Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Marti i Franques, 08028 Barcelona, Spain.
authors.forename: A
authors.initials: A
authors.lastname: Pérez-Madrid
mesh_terms: D001696:Biomechanical Phenomena; D019277:Entropy; D007700:Kinetics; D055595:Mechanical Phenomena; D017711:Nonlinear Dynamics; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D013269:Stochastic Processes
chemical_list: D012313:RNA