@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}}
}

{"_id":"FiSaMxRKHsJ3MCB6R","bibbaseid":"gawthrop-bondgraphmodelingofchemiosmoticbiomolecularenergytransduction-2017","author_short":["Gawthrop, P. J."],"bibdata":{"bibtype":"article","type":"article","author":[{"firstnames":["P.","J."],"propositions":[],"lastnames":["Gawthrop"],"suffixes":[]}],"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","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. An alternative way of implementing\n computational modularity using bond graphs is\n introduced and used to give a physically based model\n of the mitochondrial electron transport chain To\n illustrate the overall approach, this model is\n analyzed using the Faraday-equivalent chemical\n potential approach and engineering intuition is used\n to guide affinity equalisation: a energy based\n analysis of the mitochondrial electron transport\n chain. },\n keywords = {Analytical models;Biological system modeling;Chemicals;Computational modeling;Context;Electric potential;Protons;Biological system modeling;computational systems biology;systems biology},\n doi = {10.1109/TNB.2017.2674683},\n issn = {1536-1241},\n month = {April},\n archiveprefix = {arXiv},\n eprint = {1611.04264},\n note = {Available at {arXiv:1611.04264}}\n}\n\n","author_short":["Gawthrop, P. 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