A Graph Grammar for Modelling RNA Folding
Adane Letta Mamuye (School of Science, Technology, University of, Camerino), Emanuela Merelli (School of Science, Technology, University of, Camerino), Luca Tesei (School of Science, Technology, University of, Camerino)
TL;DR
This paper introduces a graph grammar-based model for RNA folding, capturing the process as a self-adaptive system driven by free energy minimization, enabling precise simulation of RNA structural evolution.
Contribution
It presents a novel graph grammar framework to model RNA folding dynamics, integrating energy considerations into graph transformations.
Findings
Effective representation of RNA configurations as graphs
Rules accurately simulate folding guided by free energy
Framework supports analysis of folding pathways
Abstract
We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour resembles the one of a self-adaptive system. Each RNA configuration is a graph and the evolution of configurations is constrained by precise rules that can be described by a graph grammar.
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