Journal article

Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data

Peter J Gawthrop, Michael Pan, Edmund J Crampin

JOURNAL OF THE ROYAL SOCIETY INTERFACE | ROYAL SOC | Published : 2021

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 thermodynamic principles and kinetic modelling. We demonstrate how the bond graph approach intrinsically enforces thermodynamic constraints, provides a mod..

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Grants

Awarded by Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology


Funding Acknowledgements

This research was in part conducted and funded by the Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology (project no. CE140100036)