Biomolecular Systems and Bond Graphs

• Publications
• Energy-based Modelling of Biological Systems. ( pdf )
• arXiv
• bioRxiv
• Tutorial
• eBook (pdf): "Metamodelling: Bond Graphs and Dynamic Systems." by P. J. Gawthrop and L. P. S. Smith.
• Software
• Bond Graph Tools (Bond Graph Software for Python)
• Model Transformation Tools (Bond Graph Software - deprecated)
• Tutorials - jupyter notebooks
• stoich : Stoichiometric analysis
• svgBondGraph: Conversion of bond graph diagram in SVG (scaleable vector graphics) to BondGraphTools
• Complexes: Using extensions to BondGraphTools to illustrate the notion of complexes.
• Linearisation: Using extensions to BondGraphTools to illustrate linearisation of systems described by bond graphs.
• Papers - jupyter notebooks
• GawPan20 : Peter J. Gawthrop and Michael Pan. Network thermodynamical modeling of bioelectrical systems: A bond graph approach. Bioelectricity, 3(1):3-13, Mar 2021. Published Online: 18 Dec 2020. doi.
• Gaw21 : P.J. Gawthrop. Energy-based modeling of the feedback control of biomolecular systems with cyclic flow modulation. IEEE Transactions on NanoBioscience, 20(2):183--192, April 2021. doi.
• GawPanCra21 : Peter J. Gawthrop, Michael Pan, and Edmund J. Crampin. Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data. Journal of The Royal Society Interface, 18(181):20210478, 2021. doi.
• GawPan22: Peter J. Gawthrop and Michael Pan. Network thermodynamics of biological systems: A bond graph approach. Mathematical Biosciences, 352:108899, 2022. doi.
• Advection22: Peter J. Gawthrop and Michael Pan. Energy-based advection modelling using bond graphs. Journal of The Royal Society Interface, 19(195):20220492, 2022. doi.
• Sensitivity23: Peter J. Gawthrop and Michael Pan. Sensitivity analysis of biochemical systems using bond graphs. Journal of The Royal Society Interface, 20(204):20230192, 2023. doi.