(248b) DNA Dynamics in Nanoslits and Nanochannels : Roles of Semi-Flexibility and Hydrodynamic Screening
AIChE Annual Meeting
Tuesday, November 10, 2009 - 12:45pm to 1:00pm
Classical polymer physics has been shown to be extremely successful in predicting flexible polymer conformation and dynamics in confined environments. Less is understood about the dynamics of confined semi-flexible chains. In sub-100nm channels, nano-fabrication has facilitated studies of DNA conformation and dynamics near and below the DNA persistence length ($\sim$50nm), which provides a good model for studying semi-flexible polymer dynamics. We investigate semi-flexible chain dynamics in nanochannels and nanoslits with Brownian dynamics simulations, Monte Carlo simulations, and optical microscopy. Our study explores how the bending energy, the conformational entropy, and the DNA-surface interactions affect the macromolecular conformation. The importance of intra-chain hydrodynamic interactions and how hydrodynamic screening affect chain dynamics is examined. Our study finds that the competition between chain semi-flexibility and confinement can lead to damping of low frequency chain relaxation modes.