A multispecies exclusion model inspired by transcriptional interference

Abstract

We introduce exclusion models of two distinguishable species of hard rods with their distinct sites of entry and exit under open boundary conditions. In the first model both species of rods move in the same direction whereas in the other two models they move in the opposite direction. These models are motivated by the biological phenomenon known as transcriptional interference. Therefore, the rules for the kinetics of the models, particularly the rules for the outcome of the encounter of the rods, are also formulated to mimic those observed in transcriptional interference. By a combination of mean-field theory and computer simulation of these models we demonstrate how the flux of one species of rods is completely switched off by the other. Exploring the parameter space of the model we also establish the conditions under which switch-like regulation of two fluxes is possible; from the extensive analysis we discover more than one possible mechanism of this phenomenon.