A Traffic Flow Model for Bio-Polymerization Processes
Bio-polymerization processes like transcription and translation are central to proper function of a cell. The speed at which the bio-polymer grows is affected both by the number of pauses of elongation machinery, as well the number of bio-polymers due to crowding effects. In order to quantify these effects in fast transcribing ribosome genes, we rigorously show that a classical traffic flow model is the limit of a mean occupancy ODE model. We compare the simulation of this model to a stochastic model and evaluate the combined effect of the polymerase density and the existence of pauses on the instantaneous transcription rate of ribosomal genes.
Davis, Lisa, Tomáš Gedeon, Jakub Gedeon, and Jennifer Thorenson. “A Traffic Flow Model for Bio-Polymerization Processes.” Journal of Mathematical Biology 68, no. 3 (February 13, 2013): 667–700. doi:10.1007/s00285-013-0651-0.