Modelling and simulating reaction-diffusion systems using coloured Petri nets

Area of Science:

• Systems Biology
• Computational Biology
• Biophysics

Background:

• Reaction-diffusion systems are crucial for understanding developmental processes in systems biology.
• Traditional modeling methods require advanced mathematical and computational skills, posing a barrier for many biologists.
• A need exists for accessible, high-level modeling tools for complex biological systems.

Purpose of the Study:

• To present a Coloured Petri Net (CPN) framework for modeling and simulating reaction-diffusion processes.
• To integrate deterministic, stochastic, and hybrid formalisms within a unified CPN approach.
• To facilitate the study of multiscale reaction-diffusion systems coupled with biological pathways.

Main Methods:

• Development of a novel Coloured Petri Net framework.
• Integration of deterministic, stochastic, and hybrid simulation algorithms.
• Application to basic diffusion scenarios and the established Brusselator model.

Main Results:

• Demonstration of the framework's capability to model and simulate reaction-diffusion systems.
• Successful integration of multiple modeling formalisms within the CPN approach.
• Validation against a standard biological model (Brusselator) and basic diffusion scenarios.

Conclusions:

• Coloured Petri Nets offer an approachable and powerful alternative for modeling complex reaction-diffusion systems.
• The proposed framework simplifies simulation for biologists lacking extensive computational expertise.
• This approach supports the investigation of multiscale biological phenomena, including signaling, metabolism, and gene expression.