Biomolecular Systems and Bond Graphs
- Publications
- Software
- Tutorials - jupyter notebooks
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stoich :
Stoichiometric analysis
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svgBondGraph:
Conversion of bond graph diagram in SVG (scaleable vector graphics) to BondGraphTools
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Complexes:
Using extensions to BondGraphTools to illustrate the notion of complexes.
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Linearisation:
Using extensions to BondGraphTools to illustrate
linearisation of systems described by bond graphs.
- Papers - jupyter notebooks
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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.
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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.
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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.
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GawPan22:
Peter J. Gawthrop and Michael Pan.
Network thermodynamics of biological systems: A bond graph
approach.
Mathematical Biosciences, 352:108899, 2022.
doi.
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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.
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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.