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Agent Based Model of Biolumiescence in Vibrio fischeri

by Mylavarapu, Omkar Swarup

Abstract (Summary)
Agent based modeling (ABM) is a new computing paradigm for modeling complex systems using a bottom-up approach. It is emerging as a powerful tool in systems biology. Unlike conventional methods such as ordinary differential equations, ABM takes into account the spatial dynamics of interactions and the geometries of objects in a system. In ABM, all the participating entities of a system are modeled as software agents with their own sets of rules and abilities to change their state. These autonomous agents receive stimuli from the environment and other participating entities and respond based on their rule sets and states. In this thesis we describe an agent based model of bioluminescence in Vibrio fischeri bacteria. The model uses a java based ABM platform, MASON. MASON is a fast discrete event simulator that provides extensive capabilities for 3D visualization and parallel processing. The MASON environment allows us to model larger, more complex systems and will also allow us to develop parallel versions of our software. The Unified Modeling Language (UML) is used to represent system constituents and interactions. Bioluminescence observed in marine organisms due to biomolecular reactions occurring inside Vibrio fischeri, which resides in the organisms as a symbiont, is modeled. This bioluminescence, also known as quorum sensing, is an important form of cell-cell communication in bacteria. A comparison is made between a bacterial cell living in isolation and a cell living in a colony. The results from the model are compared with the results from ODE simulations and further corroborated by experimental findings. A list of parameters, for which the bioluminescence system is sensitive, is prepared and the behavior of the system is studied by varying these control parameters. Conclusions are drawn about the working of the model and some pointers for future work in this area are highlighted.
Bibliographical Information:

Advisor:

School:University of Cincinnati

School Location:USA - Ohio

Source Type:Master's Thesis

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ISBN:

Date of Publication:01/01/2008

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