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bioRxiv · 10.1101/2021.03.24.436792

Modular Dynamic Biomolecular Modelling: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data.

Gawthrop, P.·Pan, M.·Crampin, E.
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Abstract

Renewed interest in dynamic simulation models of biomolecular systems has arisen from advances in genome-wide measurement and applications of such models in biotechnology and synthetic biology. In particular, genome-scale models of cellular metabolism beyond the steady state are required in order to represent transient and dynamic regulatory properties of the system. Development of such whole-cell models requires new modelling approaches. Here we propose the energy-based bond graph methodology, which integrates stoichiometric models with thermo-dynamic principles and kinetic modelling. We demonstrate how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems. The approach is illustrated using a well-established stoichiometric model of Escherichia coli (E. coli) and published experimental data.

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Gawthrop, P., Pan, M., Crampin, E.. 2021-03-25. Modular Dynamic Biomolecular Modelling: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data.. https://doi.org/10.1101/2021.03.24.436792

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