title: Dynamical simulations of DNA supercoiling and compression.
abstract: In the present article, we summarize our recent studies of DNA dynamics using the generalized immersed boundary method. Our analysis of the effects of electrostatic repulsion on the dynamics of DNA supercoiling revealed that, after perturbation, a pre-twisted DNA collapses into a compact supercoiled configuration that is sensitive to the initial excess link and ionic strength of the solvent. A stochastic extension of the generalized immersed boundary method shows that DNA in solution subjected to a constant electric field is compressed into a configuration with smaller radius of gyration and smaller ellipticity ratio than those expected for such a molecule in a thermodynamic equilibrium.
authors.affiliation: Department of Mathematics, University of Pittsburgh, 511 Thackeray Hall, Pittsburgh, PA 15260, U.S.A. swigon@pitt.edu
authors.forename: David
authors.initials: D
authors.lastname: Swigon
authors.forename: Sookkyung
authors.initials: S
authors.lastname: Lim
authors.forename: Yongsam
authors.initials: Y
authors.lastname: Kim
mesh_terms: D003198:Computer Simulation; D004278:DNA, Superhelical / Q000737:chemistry*; D004560:Electricity; D008958:Models, Molecular; D013269:Stochastic Processes
chemical_list: D004278:DNA, Superhelical