Since it is difficult or impossible to generate turbulent flow in a highly viscous fluid or a microfluidic system, efficient mixing becomes a challenge. However, it is possible in a laminar flow to generate chaotic particle trajectories (well-known as chaotic advection), that can lead to effective mixing. This dissertation studies mixing in flows with the limiting case of zero Reynolds numbers that are called Stokes flows and illustrates the practical use of different theories, namely the topological chaos theory, the set-oriented analysis and lobe dynamics in the analysis, design and optimization of different laminar-flow mixing systems. In a recent development, the topological chaos theory has been used to explain the chaos built in the flow only based on the topology of boundary motions. Without considering any details of the fluid dynamics, this novel method uses the Thurston-Nielsen (TN) classification theorem to predict and describe the stretching of material lines both qualitatively and quantitatively. The practical application of this theory toward design and optimization of a viscous-flow mixer and the important role of periodic orbits as "ghost rods" are studied. The relationship between stretching of material lines (chaos) and the homogenization of a scalar (mixing) in chaotic Stokes flows is examined in this work. This study helps determining the extent to which the stretching can represent real mixing. Using a set-oriented approach to describe the stirring in the flow, invariance or leakiness of the Almost Invariant Sets (AIS) playing the role of ghost rods is found to be in a direct relationship with the rate of homogenization of a scalar. The mixing caused by these AIS and the variations of their structure are explained from the point of view of geometric mechanics using transport through lobes. These lobes are made of segments of invariant manifolds of the periodic points that are generators of the ghost rods. A variety of the concentration-based measures, the important parameters of their calculation, and the implicit effect of diffusion are described. The studies, measures and methods of this dissertation help in the evaluation and understanding of chaotic mixing systems in nature and in industrial applications. They provide theoretical and numerical grounds for selection of the appropriate mixing protocol and design and optimization of mixing systems, examples of which can be seen throughout the dissertation. / Ph. D.

The dynamics of a complex system can be understood by analyzing the phase space structure of that system. We apply geometric and statistical techniques to two Hamiltonian systems to find and exploit structure in the phase space that helps us get qualitative and quantitative results about the phase space transport. While the structure can be revealed by the study of invariant manifolds of fixed points and periodic orbits in the first system, there do not exist any fixed points (and hence invariant manifolds) in the second system. The use of statistical (or measure theoretic) and topological methods reveals the phase space structure even in the absence of fixed points or stable and unstable invariant manifolds. The first problem we study is the four-body problem in the context of a spacecraft in the presence of a planet and two of its moons, where we exploit the phase space structure of the problem to devise an intelligent control strategy to achieve mission objectives. We use a family of analytically derived controlled Keplerian Maps in the Patched-Three-Body framework to design fuel efficient trajectories with realistic flight times. These maps approximate the dynamics of the Planar Circular Restricted Three Body Problem (PCR3BP) and we patch solutions in two different PCR3BPs to form the desired trajectories in the four body system. The second problem we study concerns phase space mixing in a two-dimensional time dependent Stokes flow system. Topological analysis of the braiding of periodic points has been recently used to find lower bounds on the complexity of the flow via the Thurston-Nielsen classification theorem (TNCT). We extend this framework by demonstrating that in a perturbed system with no apparent periodic points, the almost-invariant sets computed using a transfer operator approach are the natural objects on which to pin the TNCT. / Ph. D.