title: Hydrodynamics of DNA confined in nanoslits and nanochannels.
abstract: Modeling the dynamics of a confined, semi exible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and "read" a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirk-wood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA.
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Dorfman
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA.
authors.forename: Damini
authors.initials: D
authors.lastname: Gupta
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA.
authors.forename: Aashish
authors.initials: A
authors.lastname: Jain
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA.
authors.forename: Abhiram
authors.initials: A
authors.lastname: Muralidhar
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA ; Materials Research Laboratory, University of California - Santa Barbara, Santa Barbara, CA 93106 USA.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Tree