# Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction

@article{Gawthrop2017BondGM, title={Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction}, author={Peter J. Gawthrop}, journal={IEEE Transactions on NanoBioscience}, year={2017}, volume={16}, pages={177-188} }

Engineering systems modeling and analysis based on the bond graph approach has been applied to biomolecular systems. In this context, the notion of a Faraday-equivalent chemical potential is introduced which allows chemical potential to be expressed in an analogous manner to electrical volts thus allowing engineering intuition to be applied to biomolecular systems. Redox reactions, and their representation by half-reactions, are key components of biological systems which involve both electrical…

## 26 Citations

### Bond graph modelling of chemoelectrical energy transduction

- Engineering, Chemistry
- 2017

An energy based model of action potentials is presented, which can be directly used to compute energy consumption in both healthy and diseased neurons and contributes to the current debate on the trade-off between the speed of an action potential event and energy consumption.

### Network Thermodynamical Modeling of Bioelectrical Systems: A Bond Graph Approach.

- BiologyBioelectricity
- 2021

Network Thermodynamics, as implemented with bond graphs, provide one approach to creating physically compatible mathematical models of bioelectrical systems, illustrated using simple models of ion channels, redox reactions, proton pumps and electrogenic membrane transporters, demonstrating that the approach can be used to build mathematical and computer models of a wide range of bioElectrical systems.

### Network Thermodynamics of Biological Systems: A Bond Graph Approach

- MathematicsbioRxiv
- 2022

Edmund Crampin (1973-2021) was at the forefront of Systems Biology research and his work will influence the field for years to come. This paper brings together and summarises the seminal work of his…

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

- BiologyJournal of the Royal Society Interface
- 2021

It is demonstrated how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems.

### A bond graph approach to integrative biophysical modelling

- Biology
- 2019

Methods based on the bond graph framework to facilitate model reuse and integration are developed and used to facilitate the development of simple, thermodynamically consistent models of enzymes that are easily incorporated into larger models.

### Modular Dynamic Biomolecular Modelling: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data

- Biology, EngineeringbioRxiv
- 2021

It is demonstrated how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems.

### Analysing and simulating energy-based models in biology using BondGraphTools

- EngineeringbioRxiv
- 2021

BondGraphTools, a Python library for constructing and analysing bond graph models for energy-based modelling is introduced and examples from biochemistry are used to illustrate how BondGraphTools can be used to automate model construction in systems biology while maintaining consistency with the laws of physics.

### SBML to bond graphs: from conversion to composition

- Computer SciencebioRxiv
- 2022

A framework to convert suitable SBML models of biochemical networks into bond graphs is developed, which imposes energy conservation laws on these models, resulting in physically plausible coupled models.

### The Energetic Cost of the Action Potential: Bond Graph Modelling of Electrochemical Energy Transduction in Excitable Membranes

- Biology
- 2015

An energy based model of action potentials is presented that can be directly used to compute energy consumption in both healthy and diseased neurons and these results are illustrated by comparing the energy consumption of healthy and degenerative retinal ganglion cells using both simulated and in vitro data.

### Bond Graph Representation of Chemical Reaction Networks

- Chemistry, EngineeringIEEE Transactions on NanoBioscience
- 2018

This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction network concept of complexes by illustrated using a simple enzyme-catalyzed reaction and a trans-membrane transporter.

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An energy based model of action potentials is presented, which can be directly used to compute energy consumption in both healthy and diseased neurons and contributes to the current debate on the trade-off between the speed of an action potential event and energy consumption.

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