Date of Award


Document Type

Honors Thesis (Colby Access Only)


Colby College. Computer Science Dept.


Eric Aaron

Second Advisor

Suegene Noh


Infectious bacteria Burkholderia and social amoebas D. discoideum have been used as a case study to study the underlying evolutionary mechanisms of symbiotic relationships, chemotaxis, and collective social behaviors. The project has primarily focused on implementing a computational simulation model in order to decrease the amount of time and effort for systematic biological analysis. The model is designed to capture the essential features of symbiotic interaction for both D. discoideum and Burkholderia. The simulation model is capable of handling a wide range of simulation procedures and compatible with generalized comparative analysis. We primarily relied on a rule-based Cellular Automata model that includes essential topics, such as infection transmission and inheritance, chemotaxis, food consumption, and social behaviors of competition and altruism. Our primary research question is to explore the relationships between morbidity and mortality rates to community infection proportions. We performed a comparative analysis with varying mortality rates and observed a non-monotonic relationship. We are also interested in comparative analysis of homogeneous and heterogeneous simulations, looking for differences in collective social behaviors. All three heterogeneous trials should similar population trajectory over time. Varying infection death rates in the heterogeneous environment have shown significant differences in mound formation and community mortality rates. The results show significantly effective early community prevention from local infections. We have also designed a multi-scale simulation that is essential if we intend to expand the simulation modeling to a much larger scale in the future.


Cellular Automata, Computational Modeling, Symbiotic Biology, Social Amoeba, Data Analysis