Modelling and Simulation of Biochemical Processes Using Petri Nets

Abstract

Systems composed of many components which interact with each other and lead to unpredictable global behaviour, are considered as complex systems. In a biological context, complex systems represent living systems composed of a large number of interacting elements. In order to study these systems, a precise mathematical modelling was typically used in this context. However, this modelling has limitations in the structural understanding and the behavioural study. In this sense, formal computational modelling is an approach that allows to model and to simulate dynamical properties of these particular systems. In this paper, we use Hybrid Functional Petri Net (HFPN), a Petri net extension dedicated to study and verify biopathways, to model and study the Methionine metabolic pathway. Methionine and its derivatives play significant roles in human bodies. We propose a set of simulations for the purpose of studying and analysing the Methionine pathway’s behaviour. Our simulation results have shown that several important abnormalities in this pathway are related to sever diseases such as Alzheimer’s disease, cardiovascular disease, cancers and others.

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

“…The metabolic networks have been abstracted by various data structures, including substrate graphs, bipartite graphs, directed hypergraphs, reaction graphs, stoichiometric matrix, and Petri-net [39][40][41]. Directed hypergraphs can overcome the conceptual limitations of the graph modeling of biological processes such as multilateral relationships, which are not compatible with graph edges [39].…”

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

“…Metabolic networks have been abstracted by various data structures, including substrate graphs, bipartite graphs, directed hypergraphs, reaction graphs, stoichiometric matrix and petri-net [44], [45], [46]. Direced hypergraphs can overcome conceptual limitations of graph modeling of biological processes such as multilateral relationships, which are not compatible with graph edges [44].…”

Use of thiacalix[4]arene C-1193 for a directed influence on the functional activity of mitochondria and simulation of this process using a Petri nets

“…A modern variant of this approach is the use of a mathematical apparatus namely functional hybrid Petri nets, to model the dynamic states of systems. This methodology affords structural mapping, quantitative analysis, and the ability to consider activating/inhibiting effects (Formanowicz et al, 2017 ; Cherdal et al, 2018a , 2018b ; Gupta et al, 2021 ). The creation of an adequate model optimizes experimental procedures in terms of time and reagent/laboratory animal costs but also facilitates the analysis of process dynamics.…”