Journal article
Analysing and simulating energy-based models in biology using BondGraphTools
P Cudmore, M Pan, PJ Gawthrop, EJ Crampin
European Physical Journal E | SPRINGER | Published : 2021
Abstract
Abstract: Like all physical systems, biological systems are constrained by the laws of physics. However, mathematical models of biochemistry frequently neglect the conservation of energy, leading to unrealistic behaviour. Energy-based models that are consistent with conservation of mass, charge and energy have the potential to aid the understanding of complex interactions between biological components, and are becoming easier to develop with recent advances in experimental measurements and databases. In this paper, we motivate the use of bond graphs (a modelling tool from engineering) for energy-based modelling and introduce, BondGraphTools, a Python library for constructing and analysing bo..
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Awarded by Australian Research Council
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 number CE140100036). PJG would like to thank the Faculty of Engineering and Information Technology, University of Melbourne, for its support via a Professorial Fellowship. The authors would like to thank the reviewers for their constructive feedback, which have helped to improve both the paper and the software.