Summary of deterministic and stochastic model processes.

RNAP elongation, termination, and SC diffusion are simulated deterministically. Elongation occurs at a rate of vRNAP when the upstream and downstream SC levels are within an acceptable range, and stalls otherwise. Termination occurs instantaneously when an RNAP reaches the terminator. SC diffusion occurs instantaneously whenever topoisomerases act or RNAPs bind, unbind, or elongate. Initiation, topoisomerase binding, and RNA decay are simulated stochastically. Initiation occurs at a rate with a negatively sloped sigmoidal dependence on the local SC density, σ. This sigmoidal curve is defined by its midpoints, σi, and width, βi. Gyrase binding has a positively sloped sigmoidal SC dependence defined by similar parameters σG and βG, and TopoI binding has a negatively sloped sigmoidal SC dependence defined by σT and βG. RNA decay occurs according to a Poisson process with rate tRNA-1.