Systems biology and the silicon cell: Order out of chaos

Abstract

Abstract This paper gives an overview of the thermodynamics and kinetics background to the silicon cell (SiC!) approach. SiC! makes precise mathematical models of components of systems inclusive of their interaction properties. It then puts these component models together into a computer program and integrates the behavior. For metabolic pathways, SiC! takes the ensembles of enzyme molecules as the components. It takes the ensemble averaged metabolite concentrations as the dependent variables these components work on. We show how this approach depends on principles of non equilibrium thermodynamics and kinetics. Metabolic control analysis is an early and characteristic approach to systems biology. Using silicon cells one can do this control analysis in silico . Also this analysis also has a number of theoretical foundations, which are again close to those of non equilibrium thermodynamics. We propose that Metabolic Control Analysis is in fact the extension from equilibrium thermodynamics to non equilibrium systems that so many searched for in the second half of the previous century.