Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction. Gawthrop, P. J. IEEE Transactions on NanoBioscience, 16(3):177-188, April, 2017. Available at arXiv:1611.04264doi abstract bibtex 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 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 analyzed using the Faraday-equivalent chemical potential approach and engineering intuition is used to guide affinity equalisation: a energy based analysis of the mitochondrial electron transport chain.
@article{Gaw17a,
author = {P. J. Gawthrop},
journal = {IEEE Transactions on NanoBioscience},
title = {Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction},
year = 2017,
volume = 16,
number = 3,
pages = {177-188},
abstract = { 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
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
analyzed using the Faraday-equivalent chemical
potential approach and engineering intuition is used
to guide affinity equalisation: a energy based
analysis of the mitochondrial electron transport
chain. },
keywords = {Analytical models;Biological system modeling;Chemicals;Computational modeling;Context;Electric potential;Protons;Biological system modeling;computational systems biology;systems biology},
doi = {10.1109/TNB.2017.2674683},
issn = {1536-1241},
month = {April},
archiveprefix = {arXiv},
eprint = {1611.04264},
note = {Available at {arXiv:1611.04264}}
}
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Redox reactions, and their representation by half-reactions, 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 analyzed using the Faraday-equivalent chemical potential approach and engineering intuition is used to guide affinity equalisation: a energy based analysis of the mitochondrial electron transport chain. ","keywords":"Analytical models;Biological system modeling;Chemicals;Computational modeling;Context;Electric potential;Protons;Biological system modeling;computational systems biology;systems biology","doi":"10.1109/TNB.2017.2674683","issn":"1536-1241","month":"April","archiveprefix":"arXiv","eprint":"1611.04264","note":"Available at arXiv:1611.04264","bibtex":"@article{Gaw17a,\n author = {P. J. Gawthrop},\n journal = {IEEE Transactions on NanoBioscience},\n title = {Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction},\n year = 2017,\n volume = 16,\n number = 3,\n pages = {177-188},\n abstract = { Engineering systems modeling and analysis based on the bond\n graph approach has been applied to biomolecular\n systems. In this context, the notion of a\n Faraday-equivalent chemical potential is introduced\n which allows chemical potential to be expressed in\n an analogous manner to electrical volts thus\n allowing engineering intuition to be applied to\n biomolecular systems. Redox reactions, and their\n representation by half-reactions, are key components\n of biological systems which involve both electrical\n and chemical domains. A bond graph interpretation of\n redox reactions is given which combines bond graphs\n with the Faraday-equivalent chemical potential. This\n approach is particularly relevant when the\n biomolecular system implements chemoelectrical\n transduction – for example chemiosmosis within the\n key metabolic pathway of mitochondria: oxidative\n phosphorylation. 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