Polyhedral geometry and combinatorics of an autocatalytic ecosystem

DOI10.1007/S10910-024-01576-XarXiv2303.14238MaRDI QIDQ6203913FDOQ6203913

Authors:

Publication date: 8 April 2024

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

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.

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

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zbMATH Keywords

linear programmingpolyhedral geometrychemical reaction networksautocatalysis

Mathematics Subject Classification ID

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

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