title: In silico single-molecule manipulation of DNA with rigid body dynamics.
abstract: We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally.
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Paris, France ; Institut de Génétique Humaine (IGH), CNRS UPR 1142, Montpellier, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Carrivain
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Paris, France.
authors.forename: Maria
authors.initials: M
authors.lastname: Barbi
authors.affiliation: Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Paris, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Victor
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D055672:Static Electricity
chemical_list: D004247:DNA