AbstractsEngineering

The dynamics of single DNA molecules in micro/nanofluidics has attracted a great deal of attention due to its importance in the biomedical applications such as DNA separation, gene mapping, and gene therapy. The conformation change of these single long chain molecules in different hydrodynamic flows (pure extensional and simple shear flows) was first observed with the fluorescence microscopy in experiments. The Brownian dynamics simulation was then carried out and it successfully explained the interesting phenomena in experimental observation. In this dissertation, two major flows (i.e., generated by either the hydrodynamic or electrokinetic forces) to control the DNA dynamics are thoroughly investigated. The main effort is concentrated on the electrokinetic micro-flows produced by different microfluidic patterns. The finite element method is used to simulate the electrokinetic flows and the solutions are used as inputs for the coarse-grained Brownian dynamics simulation, which can capture the dynamics of single DNA molecules. In the electrokinetic flows, the electroosmotic and electrophoretic interactions affect the flow patterns of charged particles. When the electrophoretic mobility of a charged particle is higher than the surface electroosmotic mobility, the flows in the microfluidic devices are essentially the electrophoresis-dominated extensional flows even with surface charge patterning. To avoid this limitation, a novel design of a five-cross microfluidic device is proposed based on simulations. This design can generate and maintain different particle flow patterns even when the electrophoretic mobility is much higher than the electroosmotic mobility. Different responses of single DNA molecules under various hydrodynamic and electrokinetic flows are also studied. The complicated DNA molecule is simplified as either a bead-spring or a bead-rod chain in the Brownian dynamics simulations. Different forces in the governing equation of a bead-spring or bead-rod chain are discussed thoroughly. Different time-marching schemes are used and compared in the simulation of the dynamics of single DNA molecules. The simulations of DNA dynamics in the hydrodynamic and electrokinetic flows agree well with the experiments and the previous simulation results.