Research Group on Natural Computing

In this paper P systems are used as a formal framework for the specification and simulation of biological systems. In particular, we will deal with gene regulation systems consisting of protein–protein and protein–DNA interactions that take place in different compartments of the hierarchical structure of the living cell or in different individual cells from a colony. We will explicitly model transcription and translation as concurrent and discrete processes using rewriting rules on multisets of objects and strings. Our approach takes into account the discrete character of the components of the system, its random behaviour and the key role played by membranes in processes involving signalling at the cell surface and selective uptake of substances from the environment. Our systems will evolve according to an extension of Gillespie’s algorithm, called Multicompartmental Gillespie’s Algorithm. The well known gene regulation system in the Lac Operon in Escherichia coli will be modelled as a case study to benchmark our approach.