Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)


Mathematics and Statistics

First Advisor

Yi Jiang

Second Advisor

Vladimir Bondarenko

Third Advisor

Eric Gilbert

Fourth Advisor

Xin Qi


Bacterial biofilms are a structured population of bacteria adhered to a biotic or abiotic surface. Bacteria establish a biofilm by encasing themselves in a self-secreted matrix of extra polymeric substance. The matrix, composed primarily of polysaccharides and protein, confers to the individual bacterium enhanced protection from environmental insults. These insults would otherwise be detrimental to the bacteria if they were not part of the biofilm. To properly time when it is most beneficial to establish a biofilm and carry out other process, bacteria have developed a means to communicate using signaling molecules termed autoinducers. These signaling molecules help bacteria to make coordinated decisions.

One such decision is phenotype switching, where some bacteria in the colony change their phenotypes to ensure their survival or the survival of an entire colony. Some species of bacteria exhibit a clear delineated spatiotemporal pattern of changing their phenotype. In particular, Bacillus Subtilis forms a biofilm that exhibits spatiotemporal patterning during its development. Using an agent-based model that includes thresholds on environmental cues we reproduced the spatiotemporal behavior observed from experiments. Specifically, we incorporate thresholds on the concentration on the level of nutrient and autoinducer to reproduce the experimental pattern. This model represents the first attempt using an agent-based model to reproduce the spatiotemporal pattern exhibited experimentally where phenotype switching is induced by both nutrient and the autoinducer. The model allows us to gain an understand of the interrelatedness between autoinducer levels and nutrient availability.

The end stage of biofilm development inevitably leads to some members of the community dying or leaving through a variety of dispersal mechanisms. We developed another agent-based model to study biofilm dispersal. Dispersal is caused by the weakening of cohesive bonds within the biofilm. We study dispersal under the condition where cohesive forces are weakened to induce dispersion. The weakening of cohesive force allows us to gain insight on the benefits if any dispersal has on the development of a biofilm.