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A Spatial Artificial Chemistry Implementation of a Gene Regulatory Network Aimed at Generating Protein Concentration
Iliya Miralavy1, Wolfgang Banzhaf2
1Michigan State University, Department of Computer Science and Engineering, BEACON Center for the Study of Evolution in Action.
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Gene regulatory networks are networks of interactions in organisms responsible for determining the production levels of proteins and peptides. Mathematical and computational models of gene regulatory networks have been proposed, some of them rather abstract and called artificial regulatory networks. In this contribution, a spatial model for gene regulatory networks is proposed that is biologically more realistic and incorporates an artificial chemistry to realize the interaction between regulatory proteins called the transcription factors and the regulatory sites of simulated genes. The result is a system that is quite robust while able to produce complex dynamics similar to what can be observed in nature. Here an analysis of the impact of the initial states of the system on the produced dynamics is performed, showing that such models are evolvable and can be directed toward producing desired protein dynamics.
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