Modeling and simulation of cellular metabolism and energy production by mitochondria

Abstract

It is the intent of this thesis to investigate and develop a simulation model for metabolic pathways in the cells, namely, Glycolysis and Krebs cycle, using the DEVS formalism and the CD++ tool, then to further improve it to complete virtual mitochondrion. The hierarchical nature of DEVS makes it ideal for describing naturally hierarchical systems as the Cell, while its discrete-event approach improves performance due to the asynchronous nature of the events occurring in the cell. Simultaneously, as DEVS is a timed-based modeling approach, timing of the chemical reactions can be adequately represented. The models were developed using the CD++ toolkit, a modeling tool for simulation of complex physical systems that can be used to simulate a variety of models. CD++ server permits the execution and visualization of the results with sophisticated and easy-to-use Graphical User Interfaces. A precise and easy to use simulation environment for biological models of glycolysis and Krebs cycle was created, and the results presented show the potential of this approach.