(30a) Hydrodynamics of DNA in Dilute Solution and Confinement

DNA plays an important role as both a model polymer and as the carrier of genetic information. As a result, its hydrodynamics have been the subject of increasing attention as experimental tools for studying its physical properties mature and new technologies, such as genome mapping in nanochannels, are coming to market. In this presentation, I will discuss our recent simulation work on two areas related to the hydrodynamics of DNA. In the first part, I will present our analysis of the diffusion of DNA in free solution. Importantly, our simulations indicate that DNA does not reach the Zimm (non-draining) limit until the megabase pair range, thereby calling into question generic conclusions about polymer transport obtained by studying small molecules such as lambda-phage DNA. In the second part, I will describe our results for DNA diffusion in channel confinement. In particular, I will show how the diffusivity of the DNA is intimately related to its configuration in confinement and the way that configuration affects the intrachain and polymer-wall hydrodynamic interactions.  These simulations have resolved an ongoing controversy surrounding DNA diffusivity in the de Gennes (blob) regime and allowed us to develop accurate descriptions for DNA diffusivity in all regimes of confinement. Our work takes advantage of a combination of Pruned-Enriched Rosenbluth Method simulations of a discrete wormlike chain model, which allows us to reach asymptotically large molecular weights while retaining a spatial resolution of 5 nm, and the Kirkwood approximation for the polymer diffusivity. In the course of explaining our methodology, I will also show that the Kirkwood approximation improves as DNA confinement increases, thereby providing a firm basis for the body of theoretical work that uses the Kirkwood approximation to describe the hydrodynamics of confined DNA.