DNA chain dynamics and its applications to micro devices and scission

We present various aspects of DNA chain dynamics related to micro devices and chain scission. In the first half, we consider applications to micro devices, which are typically of the size of DNA chains and confinement effects are important. We study the effect of confining walls on the rheology and dynamics of dilute DNA solutions using a self consistent multiscale simulation technique.; Theoretical arguments suggest that the main consequences of confinement on chains are (a) the entropic force law is altered due to the loss of the chain configurational space, and (b) the viscous drag on the chain is increased due to hydrodynamic interactions (HI ) with the wall. The correct entropic spring force law and a new beadspring algorithm is developed in the presence of confining walls. We determine how the effective viscosity asymptotically approaches its bulk value. We also observe that the confinement results in two different measures of the chain relaxation time.; In the second half, we consider the application to DNA chain scission. Typical scission devices involve complicated flow fields which involve a variety of mixed flows. The tension induced in the chain by the flow is directly related to the chain conformation. Therefore, first, we examine the configurational phase transitions of flexible chains in mixed flows. As the flow type changes, the chain undergoes changes in configuration from the coiled state to the tumbling state and to non-tumbling extended state. We find these transitions are well characterized by the dispersion layer thickness in shear flow alone.; Finally, guided by the mixed flow study, we can predict typical DNA chain configurations in various mixed flows and we apply these findings to study the chain fragmentation process in a number of model flows including contraction flow. We confirm that previous literature estimates of the critical tension for chain scission is in good agreement with both our experiments and simulations and explain why different critical fracture rates are expected in different types of flows. Furthermore we apply this understanding to more complicated contraction flows with a number of design aspects in mind.