Abstract
Discrete modeling of biological mechanisms such as the lac operon is crucial in giving us a thorough understanding of their function and the related control mechanisms. This, in turn, provides us with a deeper insight into the organisms that employ these biological mechanisms as a whole. In this work, we utilize certain techniques from algebraic geometry, such as Gröbner basis, to attain a polynomial representation of the lac operon in E. coli based on its required catalysts and environmental conditions. First, we construct a Boolean network and wiring diagram of the lac operon system in order to predict the status of the system at any point in time given an initial condition. In the second part of the project, we concentrate on the time evolution of a certain state of the system and using reverse-engineering techniques, we reconstruct the polynomial equations. Finally, we compare the polynomial equations obtained in both parts.
Faculty Sponsors
Vehbi Emrah Paksoy, Ph.D.
Project Type
Event
Location
Alvin Sherman Library
Start Date
4-10-2015 1:00 PM
End Date
4-10-2015 5:30 PM
An Algebro-Geometric Approach to Reverse Engineering the Lac Operon in E. coli
Alvin Sherman Library
Discrete modeling of biological mechanisms such as the lac operon is crucial in giving us a thorough understanding of their function and the related control mechanisms. This, in turn, provides us with a deeper insight into the organisms that employ these biological mechanisms as a whole. In this work, we utilize certain techniques from algebraic geometry, such as Gröbner basis, to attain a polynomial representation of the lac operon in E. coli based on its required catalysts and environmental conditions. First, we construct a Boolean network and wiring diagram of the lac operon system in order to predict the status of the system at any point in time given an initial condition. In the second part of the project, we concentrate on the time evolution of a certain state of the system and using reverse-engineering techniques, we reconstruct the polynomial equations. Finally, we compare the polynomial equations obtained in both parts.
