DEVS modelling and simulation of the cellular metabolism by mitochondria

Abstract

We present a method for modelling and simulating metabolic pathways in the cells (namely, the glycolysis and Krebs' cycle), using the discrete event system specification (DEVS) formalism. 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 involved. DEVS time-based nature can adequately represent the timing of the chemical reactions. We show how this methodology enables creating a precise and easy way to model and simulate biological systems, including advanced visualisation of the experiments. The results presented, which focus on the simulation of the cellular metabolism pathways in mitochondria, show the potential of our approach.

Keywords:

• DEVS
• CD++
• mitochondria
• glycolysis
• Krebs' cycle

Acknowledgements

This work has been partially funded by the NSERC, and by Prof. Tofy Mussivand at the Ottawa Heart Institute. Rhys Goldstein (Autodesk Research) has provided useful feedback in the later version of the manuscript.

Notes

1. [email protected]

Additional information

Notes on contributors

Roxana Djafarzadeh

1 1. [email protected]