Browsing by Author "Ghosh, Dipanjan"

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    Collective motion of swimming bacteria under geometric confinement and oxygen diffusion
    (2024-12) Ghosh, Dipanjan
    Swimming bacteria navigate a myriad of physical constraints and chemical signals in their native environments. In this thesis, we combine quantitative imaging and mathematical modeling to gain insights into the behaviors of swimming bacteria in conditions relevant to their natural habitats. First, we investigate the collective swimming of the bacterium E. coli under geometric confinement relevant to their natural habitats such as pores of soil or the interstitial spaces in our bodies. Using a genetically modified strain of E. coli whose swimming speed can be controlled using light intensity, we confine a suspension of swimming bacteria in a Hele-Shaw cell with a thickness close to the cell body dimensions of the bacteria. Depending on the thickness of the Hele-Shaw cell, the bacterial cells either cross over each other in the vertical dimension or are confined to a monolayer. When they cross over each other, we find that the bacterial cells exhibit long-range nematic alignment of their cell bodies. On the other hand, when confined to a monolayer, the bacterial cells exhibit transient clusters with local polar order. Thus, we uncover a simple criterion—the ability to cross or not to cross—that dictates the large-scale motion and transport of bacterial cells under geometric confinement. Next, we study the collective response of a population of E. coli to a gradient of diffusing oxygen. In a capillary channel with a diffusing oxygen gradient, we image a suspension of swimming E. coli where a small subpopulation is fluorescently tagged. Our method enables the quantification of the bacterial dynamics at the scale of the population and the scale of an individual cell. We find that, at early times, the bacteria accumulate in a density peak at a distance away from the air-water interface and the position of this density peak evolves with time. We uncover a surprising observation—the direction of migration of the bacterial population undergoes a switch depending on the cell density. At low bacterial densities, the population migrates away from the air-water interface toward regions of low oxygen availability, whereas, at high densities, the population migrates toward the air-water interface with high oxygen availability. We use a kinetic theory describing the dynamics of run-and-tumble bacteria to understand our experimental observations. Using a minimal biophysical model, we explain the observed switch in directional migration. Then, we develop a mathematical model based on the E. coli chemical sensing pathway that offers a possible mechanism for the observed behavior at the population scale. Finally, in our experiments, we track the motion of individual cells in the dense population and provide a microscopic origin for our observed population-scale behavior. Finally, we investigate the combined effect of chemical cues and physical interactions on the swimming behavior of an individual cell in a dense population. The swimming of E. coli is powered by molecular oxygen, and the cells swim slower at low oxygen availability. In our experiments in a capillary channel with a gradient of diffusing oxygen, we find that, surprisingly, bacteria in the interior of the channel with a low oxygen availability swim faster than the bacteria at the air-water interface with the highest oxygen availability. Further, we find that the swimming speed positively correlates with the local spatial density of cells in the channel. Thus, the swimming behavior of the cells depends both on the availability of the chemical oxygen and physical interactions with its neighboring cells. We quantify the microscopic dynamics of individual cells in the dense suspension and offer a possible explanation for this anomalous observation. Taken together, our work provides novel insights into the swimming behavior of bacteria in response to chemical cues and physical interactions encountered in their native environments.