Date of Award


Document Type

Thesis open access



First Advisor

Orrin A Shindell


Most bacteria, including the well-studied Escherichia coli, exist in two modes of life: individual cells swimming in bulk fluid, and cells that have aggregated on surfaces in relatively immotile communities. In bulk fluid, E. coli swims in relatively straight paths. However, as E. coli approaches a surface, hydrodynamic interactions between the bacterium and the surrounding fluid change, causing the bacterium to acquire circular trajectories. This near-surface swimming behavior provides a measure of what bacteria experience as they transition from free swimming to surface aggregation, which is an important step in early biofilm formation.

Here we examine the near-surface dynamics of E. coli. We present a new method for imaging and analyzing near-surface swimming dynamics involving TIRF microscopy and computational image analysis. TIRF microscopy is used to record E. coli swimming near a surface. The raw TIRF microscopy data is passed to custom MATLAB code that tracks the bacteria, reconstructs their trajectories in three dimensions, and extracts measurements of near-surface dynamics. We aim to validate our methodology by measuring cell motility near glass surfaces, which has been previously studied and quantified for E. coli. Once we validate our methodology, we plan to expand the scope of our experiment to study how properties of the surface affect near-surface motility. We present a plan to synthesize new biomimetic surfaces with tunable viscosity and outline methods to characterize the surfaces. These biomimetic surfaces will be used in future bacterial motility experiments to examine the relationship between near-surface dynamics and surface viscosity.

Creative Commons License

Creative Commons Attribution-NonCommercial 4.0 International License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License