Simulation and validation of molecular genetic triggers networks with timed hybrid Petri Nets

Abstract

In this paper a bistable self-organizing genetic structure with two alternative stable states (true and false) – one-dimensional molecular-genetic trigger (1D MGT) – is modeled with Timed Hybrid Petri Nets. It has been proved that the gene expression regulation process of lexA recA genetic systems with regulatory enzymes is controlled by 1D MGT. 1D MGT can be switched from one stable state to another one as a response to internal and external factors (i.e., temperature, UV radiation, pH, concentrations of specific molecules etc.) considered as input signals. These two stable states correspond to activated and to repressed states of recA gene, respectively. It is shown that 1D MGT being a self-organizing nanostructures occurred in living cells can fulfill the logical function NOT. The simulation of 1D MGT networks is implemented in the Visual Petri Nets tool using Timed Hybrid Petri Nets. Networks of two sequentially connected 1D MGTs with repressor and activator links are modeled. They can fulfill the logical functions OR and NAND.