On the relation between reactions and complexes of (bio)chemical reaction networks

DOI10.1016/J.JTBI.2012.10.016zbMATH Open1368.92072arXiv1203.5932OpenAlexW2964184662WikidataQ51308160 ScholiaQ51308160MaRDI QIDQ2013286FDOQ2013286

Authors: Jost Neigenfind, Sergio Grimbs, Z. Nikoloski 

Publication date: 17 August 2017

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the stoichiometry of the underlying interrelated components, but also on a multitude of kinetic parameters. Invariant flux ratios, obtained within flux coupling analysis, as well as invariant complex ratios, derived within chemical reaction network theory, can characterize robust properties of a system at steady state. However, the existing formalisms for the description of these invariants do not provide full characterization as they either only focus on the flux-centric or the concentration-centric view. Here we develop a novel mathematical framework which combines both views and thereby overcomes the limitations of the classical methodologies. Our unified framework will be helpful in analyzing biologically important system properties.

Full work available at URL: https://arxiv.org/abs/1203.5932

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zbMATH Keywords

metabolic networkchemical reaction network theorymass action systemflux coupling analysis

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Cites Work

• Ideals, varieties, and algorithms. An introduction to computational algebraic geometry and commutative algebra
• Chemical reaction systems with toric steady states
• Title not available (Why is that?)
• The existence and uniqueness of steady states for a class of chemical reaction networks

Cited In (7)

• On the complexity of reconstructing chemical reaction networks
• Network translation and steady-state properties of chemical reaction systems
• Biochemical reaction networks: An invitation for algebraic geometers
• Reaction network realizations of rational biochemical systems and their structural properties
• Absolute concentration robustness: algebra and geometry
• Chemical reaction network approaches to biochemical systems theory
• Absolute concentration robustness in networks with low-dimensional stoichiometric subspace

Uses Software

• efmtool

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