Simulating bacterial transcription and translation in a stochastic π calculus

Abstract

Stochastic simulation of genetic networks based on models in the stochastic π-calculus is a promising recent approach. This paper contributes an extensible model of the central mechanisms of gene expression i.e. transcription and translation, at the prototypical instance of bacteria. We reach extensibility through object-oriented abstractions, that are expressible in a stochastic π-calculus with pattern guarded inputs. We illustrate our generic model by simulating the effect of translational bursting in bacterial gene expression. © Springer-Verlag Berlin Heidelberg 2006.