Bacterial flows: Mixing and pumping in microfluidic systems using flagellated bacteria

The objective of the proposed thesis is to demonstrate the use of bacteria as controllable elements of a microfluidic network in micro-engineered systems. We utilize flagellated bacteria (Escherichia coli and Serratia marcescens) whose motors are extremely powerful and reasonably well understood. We are strongly against the removal of the motor from the bacterium or the fabrication to mimic the microflagellar system since the full organism is already naturally designed to accomplish many engineering tasks. The core of the proposed study relies on the use of flagellated bacteria to actuate surrounding fluid in a controlled and directed manner. Flagellated bacteria are used both as individual actuators and in arrays (bacterial carpet), where the collective effort of the organisms can be applied to complete microfluidic systems such as a chaotic mixer and a fluidic pump. The effect of bacterial motion on the diffusion of a molecule of high molecular weight is studied by observing the mixing of two streams of fluid in a microfluidic flow cell. The presence of motile E. coli bacteria in one of the streams results in a remarkable increase in the effective diffusion coefficient. If a large number of Serratia marcescens are encouraged to dock to the walls of a microchannel, then a flagellar carpet is created with unique properties. The activity of the bacterial carpet can be used to enhance the mixing between two streams of fluid. Furthermore, we observe that the diffusion process is also shown to undergo a change from standard Fickian diffusion to superdiffusive behavior in both cases. Another exciting property of a bacterial carpet in a microfluidic system is the observation that it can pump fluid autonomously at speeds as high as 25 microns per second. The bacteria draw their propulsion energy from the nutrients in the motile buffer and hence the system is a self-contained microfluidic component. Factors governing the behavior of the bacteria-powered pump are tested to determine pumping characteristics as well as the durability of the bacterial motor array under a wide variety of external stimuli (food, temperature, geometry). Lastly, we investigate the mechanisms that lead to the onset and decay of self-organization and coordination of the flagella over length scales hundreds of times larger than the size of the individual cells.