ArticleProceedings. Mathematical, physical, and engineering sciences2017
Energy-based analysis of biomolecular pathways.
Article in Proceedings. Mathematical, physical, and engineering sciences, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A thermodynamically consistent approach to modeling epithelial solute and water transport in the proximal convoluted tubule.Journal of biological physics · 2026Article
- Energy-based bond graph models of glucose transport with SLC transporters.Biophysical journal · 2025Article
- Energy-based modelling of single actin filament polymerization using bond graphs.Journal of the Royal Society, Interface · 2025Article
- Whole-cell energy modeling reveals quantitative changes of predicted energy flows in RAS mutant cancer cell lines.iScience · 2023Article
- Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance.Molecular systems biology · 2023Article
- A modular and reusable model of epithelial transport in the proximal convoluted tubule.PloS one · 2022Review
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
- Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data.Journal of the Royal Society, Interface · 2021Article
- Network Thermodynamical Modeling of Bioelectrical Systems: A Bond Graph Approach.Bioelectricity · 2021Article
- Bond graph modelling of the cardiac action potential: implications for drift and non-unique steady states.Proceedings. Mathematical, physical, and engineering sciences · 2018Article
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2 authors.
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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.
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