Abstract
The National Institutes of Health states that about 65% of all microbial infections and up to 80% of chronic infections are accompanied by biofilms. Biofilms are a community of microorganisms contained in a self-produced extracellular polymeric substance (EPS). This matrix of EPS allows the cells to adhere to non-living and living surfaces with high resilience. These colonies are infamous for their resilience to antibiotics and the immune system, which generates an imperative hazard to public health. A biofilm can lead to infection, blockage of medical equipment such as IV tubes, or problems in mechanical machinery associated with biological organism. The formation of a biofilm is a multistep process lead by the attachment of microbes to a surface followed by a growth of a micro-colony. The area of study for biofilms is growing and a greater understanding of their development under various conditions is needed to develop novel and effective techniques to rectify their involvement in infection. The goal of this thesis was to build a computational framework, Bacterial Simulation Tool (BST), that would simulate the interaction between a growing biofilm and fluid flow. The BST is focused on fast prototyping, as current simulation tools are complicated and require a lot of time. The BST handles multiple user editable variables such as stress on the biofilm and various growth factors that may inhibit or accelerate growth. Moreover, the goal was to produce an architecture that would allow qualitatively accurate predictions, but that at the same time would run quickly enough to allow for generating simulations within minutes. This would have the future benefit of running parallel simulations to perform parameters sweeps. Current work in this field is time gated, many simulation tools take a significant amount of time, this one is designed to be quicker.