Transport and Mixing with Swimming Microorganisms in Chaotic Flows

Microorganisms, primitive unicellular forms of life, form the basis of the food web and play crucial roles in the Earth's biogeochemical cycles. Habitats of microorganisms, from oceans and lakes to soil and human intestines, are often characterized by constant fluid motion. Fluid flow exerts forces and torques on microorganisms that affect their movement and distribution, and transports essential chemicals on which they rely for sensing, foraging, and mating. As a result, flow has a broad range of effects on the behaviors of microorganisms, including their locomotion, reproduction, nutrient uptake, and communication. Despite many efforts to understand microbiology in aquatic environments, it remains a challenge to interpret the physical and biological behaviors of microorganisms in the presence of fluid flows, particularly unsteady and chaotic flows. In this thesis, I investigate the interaction between motile microorganisms and dynamical structures in chaotic flows, and the effects of such interaction on transport and mixing. The flow dynamical structures investigated here are known as the Lagrangian coherent structures (LCSs). First, I characterize the transport and mixing in a spatially periodic chaotic flow with swimming Escherichia coli. The microorganisms are found to align and accumulate near structures of strong stretching of fluid parcels, or namely, the hyperbolic LCSs. Such alignment and accumulation of microorganisms lead to reduction in large-scale transport but enhancement in small-scale mixing. Second, I examine the transport and mixing with E. coli in a more complex spatially aperiodic chaotic flow. The microorganisms are found to escape and deplete in vortex-like dynamical structures known as the elliptic LCSs. The depletion leads to enhanced transport barriers into which the transport of diffusive chemicals is much slower. Lastly, I investigate the mixing in the self-generated chaotic flows of swarming Serratia marcescens and show that dilute polymers can substantially enhance mixing induced by collective behaviors. Overall, this dissertation elucidates the nontrivial effects of the interaction between microorganisms and flow structures on transport and mixing.