@article{GawCudCra20,
title = {Physically-Plausible Modelling of Biomolecular Systems: A Simplified, Energy-Based Model of the Mitochondrial Electron Transport Chain},
journal = {Journal of Theoretical Biology},
pages = 110223,
volume = 493,
year = 2020,
issn = {0022-5193},
doi = {10.1016/j.jtbi.2020.110223},
author = {Peter J. Gawthrop and Peter Cudmore and Edmund J. Crampin},
keywords = {Systems biology, Thermodynamical modelling, Bond graph, Computational biology},
abstract = {Advances in systems biology and whole-cell modelling demand increasingly comprehensive mathematical models of cellular biochemistry. Such models require the development of simplified representations of specific processes which capture essential biophysical features but without unnecessarily complexity. Recently there has been renewed interest in thermodynamically-based modelling of cellular processes. Here we present an approach to developing of simplified yet thermodynamically consistent (hence physically plausible) models which can readily be
incorporated into large scale biochemical
descriptions but which do not require full
mechanistic detail of the underlying processes. We
illustrate the approach through development of a simplified, physically plausible model of the mitochondrial electron transport chain and show that the simplified model behaves like the full system.}
}
@article{PanGawCur20,
author = {Michael Pan and Peter J. Gawthrop and Joseph Cursons and Kenneth Tran and Edmund J. Crampin},
title = {{The cardiac Na+/K+ ATPase: An updated, thermodynamically consistent model}},
year = 2020,
month = 8,
journal = {Physiome},
url = {https://physiome.figshare.com/articles/journal_contribution/The_cardiac_Na_K_ATPase_An_updated_thermodynamically_consistent_model/12871070},
doi = {10.36903/physiome.12871070.v1},
abstract = {
The Na+/K+ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na+ and K+ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte Na+/K+ ATPase to study extracellular potassium accumulation during ischaemia, demonstrating the ability to recapitulate a wide range of experimental data, but unfortunately there was no archived code associated with the original manuscript. Here we detail an updated version of the model and provide CellML and MATLAB code to ensure reproducibility and reusability. We note some errors within the original formulation which have been corrected to ensure that the model is thermodynamically consistent, and although this required some reparameterisation, the resulting model still provides a good fit to experimental measurements that demonstrate the dependence of Na+/K+ ATPase pumping rate upon membrane voltage and metabolite concentrations. To demonstrate thermodynamic consistency we also developed a bond graph version of the model. We hope that these models will be useful for community efforts to assemble a whole-cell cardiomyocyte model which facilitates the investigation of cellular energetics.
}
}
@article{GawPan20,
author = {Gawthrop, Peter J.
and Pan, Michael},
title = {Network Thermodynamical Modeling of Bioelectrical Systems: A Bond Graph Approach},
journal = {Bioelectricity},
year = 2021,
month = {Mar},
day = 01,
publisher = {Mary Ann Liebert, Inc., publishers},
volume = 3,
number = 1,
pages = {3--13},
abstract = {Interactions among biomolecules, electrons, and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance understanding but also to enable computer models to complement in vitro and in vivo experiments. Such models can never be entirely accurate; it is nevertheless important that the models are compatible with physical principles. Network Thermodynamics, as implemented with bond graphs, provide one approach to creating physically compatible mathematical models of bioelectrical systems. This is illustrated using simple models of ion channels, redox reactions, proton pumps, and electrogenic membrane transporters thus demonstrating that the approach can be used to build mathematical and computer models of a wide range of bioelectrical systems.},
issn = {2576-3105},
doi = {10.1089/bioe.2020.0042},
note = {Published Online: 18 Dec 2020}
}
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