Polymer confinement and translocation

Single polymer passage through geometrically confined regions is ubiquitous in biology. Recent technological advances have made the direct study of its dynamics possible. We studied the capture of DNA molecules by the electroosmotic flow of a nanopore induced by its surface charge under an applied electric field. We showed theoretically that the DNA molecules underwent coil-stretch transitions at a critical radius around the nanopore and the transition assisted the polymer passage through the pore. To understand how a polymer worms through a narrow channel, we investigated the translocation dynamics of a Gaussian chain between two compartments connected with a cylindrical channel. The number of segments inside the channel changed throughout the translocation process according to the overall free energy of the chain. We found a change in the entropic driving force near the end of the process due to the partitioning of the chain end into the channel rather than the initial compartment. We also developed a theory to account for the electrophoretic mobility of DNA molecules passing through periodic confined regions. We showed that the decrease in the translocation time with the molecular weight was due to the propensity of hairpin entries into the confined regions. To further explore the dynamics of polymer translocation through nanopores, we performed experimental studies of sodium polystyrene sulfonate translocation through α-hemolysin protein nanopores. By changing the polymer-pore interaction using different pH conditions, we identified the physical origins of the three most common event types. We showed that increasing the polymer-pore attraction increased the probability of successful translocation. Motivated by understanding the dynamics of a polymer in a crowded environment, we investigated the dynamics of a chain inside a one dimensional array of periodic cavities. In our theory, the chain occupied different number of cavities according to its confinement free energy which consisted of entropic and excluded volume parts. By assuming that the chain moved cooperatively, the diffusion constant exhibited Rouse dynamics. Finally, we performed computer simulations of a chain inside a spherical cavity. We found that the confinement effect was best described by the hard sphere chain model. We further studied the escape dynamics of the chain out of the cavity through a small hole. The equilibrium condition of the chain during the escape was discussed