@article{GawCra17,
  author = {Gawthrop, Peter J. and Crampin, Edmund J.},
  title = {Energy-based analysis of biomolecular pathways},
  volume = 473,
  number = 2202,
  year = 2017,
  doi = {10.1098/rspa.2016.0825},
  publisher = {The Royal Society},
  archiveprefix = {arXiv},
  eprint = {1611.02332},
  note = {Available at {arXiv:1611.02332}},
  abstract = {Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about steady-state mass flows (reaction rates) through the network. In this work, we show how pathway analysis of biomolecular networks can be extended using an energy-based approach to provide information about energy flows through the network. This energy-based approach is developed using the engineering-inspired bond graph methodology to represent biomolecular reaction networks. The approach is introduced using glycolysis as an exemplar; and is then applied to analyse the efficiency of free energy transduction in a biomolecular cycle model of a transporter protein [sodium-glucose transport protein 1 (SGLT1)]. The overall aim of our work is to present a framework for modelling and analysis of biomolecular reactions and processes which considers energy flows and losses as well as mass transport.},
  issn = {1364-5021},
  journal = {Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences}
}

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