Modelling and Simulation of Biochemical Processes Using Petri Nets

Hybrid simulation of biochemical systems using hybrid adaptive Petri nets

Due to the heterogeneity of many real biochemical systems, stochastic simulation methods do not scale well as systems become more complex and larger, whereas approximations provided by continuous models fail to capture the stochastic behavior of molecular species at very low numbers. A hybrid simulation method is a natural idea to resolve this dilemma. In this paper, we propose a novel notion o...

Ontology Driven Simulation of Biochemical Pathways Using Hybrid Petri Nets

Glycans are known to change in the earliest stage of cell development in complex living organisms. Glycoproteins and glycolipids effect the abundance level of cell surface glycans. Thus, the study of production and consumption of glycoproteins and glycolipids are important. In this paper, we present the Glycomics Modeling pathway simulation environment (GlyMpse), an ontology driven simulation m...

Stochastic Petri Nets: Modelling, Stability, Simulation

Modelling Opacity Using Petri Nets

We consider opacity as a property of the local states of the secure (or high-level) part of the system, based on the observation of the local states of a low-level part of the system as well as actions. We propose a Petri net modelling technique which allows one to specify different information flow properties, using suitably defined observations of system behaviour. We then discuss expressiven...

Modelling Gradients using Petri Nets

Motivated by the graded posteriorization during the AP axis development in the frog Xenopus laevis, we propose an abstract Petri net model for the formation of a gradient of proteins in a chain of cells.