ArticleBulletin of mathematical biology2024
Convex Representation of Metabolic Networks with Michaelis-Menten Kinetics.
Article in Bulletin of mathematical biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Model-guided chemical environment and metabolic network design to couple pathways with cell fitness.Metabolic engineering communications · 2025Article
- Global constraint principle for microbial growth laws.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine.Briefings in bioinformatics · 2025Review
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Abstract
Polyhedral models of metabolic networks are computationally tractable and can predict some cellular functions. A longstanding challenge is incorporating metabolites without losing tractability. In this paper, we do so using a new second-order cone representation of the Michaelis-Menten kinetics. The resulting model consists of linear stoichiometric constraints alongside second-order cone constraints that couple the reaction fluxes to metabolite concentrations. We formulate several new problems around this model: conic flux balance analysis, which augments flux balance analysis with metabolite concentrations; dynamic conic flux balance analysis; and finding minimal cut sets of networks with both reactions and metabolites. Solving these problems yields information about both fluxes and metabolite concentrations. They are second-order cone or mixed-integer second-order cone programs, which, while not as tractable as their linear counterparts, can nonetheless be solved at practical scales using existing software.
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