Investigating polymer physics with single molecule experiment and Brownian dynamics simulation

Flexible polymer molecules exhibit complex dynamical behavior when subjected to hydrodynamic forces in flow. In this work, we investigate the behavior of DNA chains using both single molecule experiments via epifluorescence microscopy and Brownian dynamics (BD) simulations.; Intramolecular hydrodynamic interactions (HI) in flexible polymer chains influence both the equilibrium and non-equilibrium physical properties of macromolecules. To experimentally investigate the role of HI on non-equilibrium polymer behavior, we directly observed the dynamics of DNA ranging in contour length from 150 to 1300 microns in planar extensional flow. Polymer models are also employed to explore the role of intramolecular HI. A semi-implicit bead-spring BD algorithm with fluctuating HI and excluded volume (EV) interactions is developed.; Highly extensible E. coli DNA molecules were observed to exist in either a coiled or highly extended conformation for a narrow range of flow strengths in planar extensional flow. Therefore, the conformation of a single polymer chain strongly depends on its deformation history. This conformation hysteresis persists for many polymer relaxation times and is due to conformation-dependent hydrodynamic forces. Polymer conformational energy landscapes were calculated from computer simulations and show two minima for flow strengths near the coil-stretch transition.; BD simulation results for 84 micron DNA in shear flow are presented for both free-draining bead-spring models and for models including both HI and EV interactions. Good agreement between recent experiments and BD simulations is obtained for ensemble average measurements of polymer extension, orientation angle, viscosity, and first normal stress coefficient over a wide range of flow strengths.; We also show that the motion of both free and tethered flexible polymer molecules and rigid Brownian rods in unbounded shear flow is characterized by a clear tumbling frequency. The frequency of tumbling motion scales sub-linearly with shear rate and in all cases we develop scaling law analyses for these physical systems.; Finally, we investigate the role of intramolecular HI on polymer dynamics for long DNA molecules in linear, two-dimensional mixed flows near the tri-critical point. Conformational state hopping, where a single polymer chain preferentially samples both coiled and highly extended states during steady flows, is observed and characterized.