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Stochastic Simulation of the Phage Lambda System and the Bioluminescence System Using the Next Reaction Method

Ananthanpillai, Balaji
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1259080814

Abstract Details

2009, MS, University of Cincinnati, Engineering : Electrical Engineering.
A biological pathway represents a network of complex reactions at the molecular level of living cells. Pathways model how biological molecules interact to carry out a biological function and how they respond to external stimuli. The pathway models are derived through scientific experimentation and data analysis. Modeling biochemical reactions is a component in studying and analyzing biological pathways. The modeling and control of biological pathways is extremely important in understanding various biological phenomena. Biological pathways can be controlled in the laboratory and this process has applications in medicine and also in the invention of certain biologically based components for computer circuits or bio-circuits. However, direct experimental study of the pathways is expensive and also time consuming. Mathematical modeling and stochastic simulation techniques provide an affordable and easy to use experimental platform. Mathematical modeling and stochastic simulations, based on biochemical rate equations, provide us with rigorous tools to understand the intricacies involved in biological pathways. In this thesis we model the Phage Lambda system, which functions as a biological switch, and the Bioluminescence system, which provides a model of communication. We use the stochastic simulation techniques based on Gibson and Bruck’s Next Reaction Method. We compare our results with the results of simulations using Gillespie’s Algorithm and with the results from an agent-based model. We also provide easy-to-use templates for the simulations to support future research in this area.
Carla Purdy, C, PhD (Committee Chair)
Wen-Ben Jone, PhD (Committee Member)
George Purdy, PhD (Committee Member)
118 p.
Electrical Engineering
Phage Lambda; Bioluminescence; Next Reaction Method; Gillespie Algorithm; ODE; Stochastic simulation

Recommended Citations

Citations

  • Ananthanpillai, B. (2009). Stochastic Simulation of the Phage Lambda System and the Bioluminescence System Using the Next Reaction Method [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1259080814

    APA Style (7th edition)

  • Ananthanpillai, Balaji. Stochastic Simulation of the Phage Lambda System and the Bioluminescence System Using the Next Reaction Method. 2009. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1259080814.

    MLA Style (8th edition)

  • Ananthanpillai, Balaji. "Stochastic Simulation of the Phage Lambda System and the Bioluminescence System Using the Next Reaction Method." Master's thesis, University of Cincinnati, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1259080814

    Chicago Manual of Style (17th edition)

ucin1259080814
809
© 2009, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.