Hierarchical bond graph modelling of biochemical networks

DOI10.1098/RSPA.2015.0642MaRDI QIDQ5363476zbMATH OpenOpenAlexFDO

Authors Joseph Cursons, Peter J. Gawthrop, Edmund J. Crampin

Publication date 29 September 2017

Published in Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1503.01814

zbMATH Keywords

biochemical networksfree-energy constants

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

Abstract: The bond graph approach to modelling biochemical networks is extended to allow hierarchical construction of complex models from simpler components. This is made possible by representing the simpler components as thermodynamically open systems exchanging mass and energy via ports. A key feature of this approach is that the resultant models are robustly thermodynamically compliant: the thermodynamic compliance is not dependent on precise numerical values of parameters. Moreover, the models are reusable due to the well-defined interface provided by the energy ports. To extract bond graph model parameters from parameters found in the literature, general and compact formulae are developed to relate free-energy constants and equilibrium constants. The existence and uniqueness of solutions is considered in terms of fundamental properties of stoichiometric matrices. The approach is illustrated by building a hierarchical bond graph model of glycogenolysis in skeletal muscle.

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(10)

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