We address the problem of phase transitions in random site graphs. Such graphs were recently proposed as more useful abstractions of proteins and their network of interactions than standard graphs. A set of binding reactions between proteins give rise to the stochastic assembly of protein complexes. We use a rule-based language to represent and simulate such systems. Based on methods from statistical physics we investigate the dependency of the asymptotic size distribution of such complexes with respect to the site configuration and binding affinities of and between proteins, respectively. In particular we discuss a liquidity index of such abstract protein networks and apply it to the problem of chemoreceptor clustering in E. coli.
|Title of host publication||Proceedings of Sixth International Workshop on Computational Systems Biology, WCSB 2009|
|Number of pages||4|
|Publication status||Published - 2009|