TBI-Preprint 06-03-002

[PostScript] [PDF]

A minimal and self-consistent in silico cell model based on macromolecular interactions

Christoph Flamm, Lukas Endler, Stefan Müller, Stefanie Widder, Peter Schuster

Submitted to:
Phil. Trans. R. Soc. B Special Issue on Artificial Cell 2006

A self-consistent minimal cell model with a physically motivated schema for molecular interaction is introduced and described. The genetic and metabolic reaction network of the cell is modeled by multidimensional nonlinear ODEs, which are derived from biochemical kinetics. The strategy behind this modeling approach is to keep the model sufficiently simple in order to be able to perform studies on evolutionary optimization in populations of cells. At the same time the model should be complex enough to handle the basic features of genetic control of metabolism and coupling to environmental factors. Thereby the model system will provide insight into the mechanisms leading to important biological phenomena like homeostasis, (circadian) rhythms, robustness, and adaptation to a changing environment. One example of modeling a molecular regulation mechanism, cooperative binding of transcription factors, is discussed in detail.

Biochemical ODE solver, cooperativity, genetic regulatory network, metabolic network, SBML

Return to 2006 working papers list.
Last modified: 2006-08-09 15:30:49 xtof