Discrete event, multi-level simulation of metabolite channeling

• Published in: BioSystems 2004-07, Vol.75 (1), p.29-41
• Main Authors: Degenring, Daniela, Röhl, Mathias, Uhrmacher, Adelinde M
• Format: Article
• Language: English
• Subjects: Computer Simulation; Discrete event simulation; Metabolism; Metabolite channeling; Models, Biological; Models, Molecular; Multi-level simulation; Systems Biology - methods; Tryptophan synthase; Tryptophan Synthase - metabolism
• ISSN: 0303-2647; 1872-8324
• DOI: 10.1016/j.biosystems.2004.03.008

Typically differential equations are employed to simulate cellular dynamics. To develop a valid continuous model based on differential equations requires accurate parameter estimations; an accuracy which is often difficult to achieve, due to the lack of data. In addition, processes in metabolic pathways, e.g. metabolite channeling, seem to be of a rather qualitative and discrete nature. With respect to the available data and to the perception of the underlying system, a discrete rather than a continuous approach to modeling and simulation seems more adequate. A discrete approach does not necessarily imply a more abstract view on the system. If we move from macro to micro and multi-level modeling, aspects of subsystems and their interactions, which have been only implicitly represented, become an explicit part of the model. To start exploring discrete event phenomena within metabolite channeling we choose the tryptophan synthase. Based on a continuous macro model, a discrete event, multi-level model is developed which allows us to analyze the interrelation between structural and functional characteristics of the enzymes.