Bond Graph Modelling of Chemiosmotic Biomolecular Energy Transduction
Abstract
Engineering systems modelling and analysis based on the bond graph approach has been applied to biomolecular systems. In this context, the notion of a Faradayequivalent 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 halfreactions, are key components of biological systems which involve both electrical and chemical domains. A bond graph interpretation of redox reactions is given which combines bond graphs with the Faraday equivalent chemical potential. This approach is particularly relevant when the biomolecular system implements chemoelectrical transduction  for example chemiosmosis within the key metabolic pathway of mitochondria: oxidative phosphorylation. An alternative way of implementing computational modularity using bond graphs is introduced and used to give a physically based model of the mitochondrial electron transport chain. To illustrate the overall approach, this model is analysed using the Faradayequivalent chemical potential approach and engineering intuition is used to guide affinity equalisation: a energy based analysis of the mitochondrial electron transport chain.
 Publication:

arXiv eprints
 Pub Date:
 November 2016
 arXiv:
 arXiv:1611.04264
 Bibcode:
 2016arXiv161104264G
 Keywords:

 Quantitative Biology  Molecular Networks
 EPrint:
 IEEE Transactions on NanoBioscience, 16(3):177188, April 2017