1. Convex Representation of Metabolic Networks with Michaelis–Menten Kinetics.
- Author
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Taylor, Josh A., Rapaport, Alain, and Dochain, Denis
- Subjects
- *
COUPLING reactions (Chemistry) , *METABOLIC models , *CELL physiology , *PROBLEM solving , *INTERIOR-point methods , *POLYHEDRAL functions - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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