Rule Based Modeling of Gene Regulation and Biosynthesis of Tryptophan in E. coli

The genetic regulation of the Trp operon in the bacterium E. coli relies on a sophisticated control mechanism. It tightly couples the advance of transcribing RNA polymerase to the efficiency of the contemporaneous translation of the nascent transcript by a ribosome. The concurrent control of this process involves interdependencies between multiple molecular actors. Within process algebra based modeling languages focused on pairwise interaction, its representation required sophisticated coding tricks. In this work, we abstract the mechanism of transcriptional attenuation within a novel rule base modeling language. It allows non-trivial concurrent control by representing molecules as parametrized terms.