A Computational Approach to Extinction Events in Chemical Reaction Networks with Discrete State Spaces
Abstract
Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist of a series of systems of equalities and inequalities on the edges of a modified reaction network called a domination-expanded reaction network. In this paper, we present a computational implementation of these conditions written in Python and apply the program on examples drawn from the biochemical literature, including a model of polyamine metabolism in mammals and a model of the pentose phosphate pathway in Trypanosoma brucei. We also run the program on 458 models from the European Bioinformatics Institute's BioModels Database and report our results.
Keywords
Cite
@article{arxiv.1701.02014,
title = {A Computational Approach to Extinction Events in Chemical Reaction Networks with Discrete State Spaces},
author = {Matthew D. Johnston},
journal= {arXiv preprint arXiv:1701.02014},
year = {2017}
}
Comments
27 pages