%0 Journal Article
%T Evolution of metabolic networks: a computational frame-work
%A Christoph Flamm
%A Alexander Ullrich
%A Heinz Ekker
%A Martin Mann
%A Daniel H£żgerl
%A Markus Rohrschneider
%A Sebastian Sauer
%A Gerik Scheuermann
%A Konstantin Klemm
%A Ivo L Hofacker
%A Peter F Stadler
%J Journal of Systems Chemistry
%D 2010
%I BioMed Central
%R 10.1186/1759-2208-1-4
%X We describe here a simulation environment that implements all these components in a simplified way so that large-scale evolutionary studies are feasible. We employ an artificial chemistry that views chemical reactions as graph rewriting operations and utilizes a toy-version of quantum chemistry to derive thermodynamic parameters. Minimalist organisms with simple string-encoded genomes produce model ribozymes whose catalytic activity is determined by an ad hoc mapping between their secondary structure and the transition state graphs that they stabilize. Fitness is computed utilizing the ideas of metabolic flux analysis. We present an implementation of the complete system and first simulation results.The simulation system presented here allows coherent investigations into the evolutionary mechanisms of the first steps of metabolic evolution using a self-consistent toy universe.Computer models of the transition between an abiotic chemosphere and a primitive biosphere are plagued by the complexity of the systems and processes that need to be integrated into a coherent picture. Individual aspects and components, such as thermodynamic boundary conditions, the dynamics of self-replication, the effects of coding [1], the influence of spatial organization and compartmentalization, can be -- and have been -- tackled with their own specific minimal models. Much of the most successful modeling e orts have been invested in early systems of information propagation. The success of these approaches can at least in part be explained by the fact that generic behavioral regularities can be extracted independent of physical details. It is entirely sufficient to consider linear sequences that can be copied, mutated, ligated, and cleaved according to rules that do not have to recurse explicitly to underlying physics and chemistry [2-5].We argue here that the situation becomes fundamentally different once we become interested in metabolic evolution. Then, chemistry (and in particular the
%U http://www.jsystchem.com/content/1/1/4