Polyhedral geometry and combinatorics of an autocatalytic ecosystem

DOI10.1007/S10910-024-01576-XMaRDI QIDQ6203913zbMATH OpenFDO

Authors

Publication date 8 April 2024

Published in Journal of Mathematical Chemistry (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2303.14238

zbMATH Keywords

linear programmingpolyhedral geometrychemical reaction networksautocatalysis

Mathematics Subject Classification ID

Linear programming (90C05) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Abstract: Developing a mathematical understanding of autocatalysis in chemical reaction networks has both theoretical and practical implications. For a class of autocatalysis, which we term 'stoichiometric autocatalysis', we show that it is possible to classify them in equivalence classes and develop mathematical results about their behavior. We also provide a linear-programming algorithm to exhaustively enumerate them and a scheme to visualize their polyhedral geometry and combinatorics. We then define cluster chemical reaction networks, a framework for coarse-graining realistic chemical reactions using conservation laws. We find that the list of minimal autocatalytic subnetworks in a maximally connected cluster chemical reaction network with one conservation law grows exponentially in the number of species. We end our discussion with open questions concerning autocatalysis and multidisciplinary opportunities for future investigation.

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