Thesis (M.S., Bioinformatics & Computational Biology) -- University of Idaho, 2014 | Bacterial plasmids are extra-chromosomal, typically circular DNA elements that require a bacterial host to survive, but replicate separately from the host chromosome. Plasmids may confer host-beneficial traits to and co-evolve with their hosts, yet many of the underlying genetic mechanisms of plasmid-host adaptation are still unknown. The work highlighted here revolved around the creation of a computer model to simulate plasmid evolution in bacterial hosts and observe the underlying mechanisms of adaptation and the impact of different plasmid characteristics on population diversity. This was done by changing features of the ancestral plasmid (i.e. cost, stability, and transferability and mutations rates) and monitoring the effect on the population over time. The output of the simulation was comparable to results of published experimental evolution studies. This model can now be used to help explain experimentally observed plasmid evolution dynamics and generate hypotheses about plasmid evolution that may later be tested empirically.