The complexity of biochemical networks necessitates the use of computational and mathematical frameworks to accurately characterize and study these systems. However, modern frameworks developed for this task have inadequacies that limit their accuracy or scalability. In this report, a mathematical model of the canonical enzyme substrate binding network is developed, and, using estimated true and maximal reaction rates, a methodology utilizing principles of flux balance analysis is developed to deduce the individual reaction rate constants in the network. It is then shown that these two reaction rates are not sufficient to unambiguously define a mass action kinetic model of this network. Nevertheless, the methodology developed greatly reduces the degrees of freedom of the system, and, as a result, the solution space of the network can be examined computationally and analytically revealing several non-intuitive sensitivities.
This project was mentored by Dr. Michael A. Mackey, PhD at the University of Iowa. http://ir.uiowa.edu/honors_theses/177/
The repository contains the code used to perform a rigorious quantitative analysis of enzyme substrate binding.
Please enter the MassActionModelingOfCatalysis directory to read the finished work and view the code!