ArticleIET systems biology2016
Modular bond-graph modelling and analysis of biomolecular systems.
Article in IET systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 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 analysis of biochemical oscillators using bond graphs and linear control theory.Royal Society open science · 2025Article
- 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
- Sensitivity analysis of biochemical systems using bond graphs.Journal of the Royal Society, Interface · 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
- Hierarchical semantic composition of biosimulation models using bond graphs.PLoS computational biology · 2021Article
- Network Thermodynamical Modeling of Bioelectrical Systems: A Bond Graph Approach.Bioelectricity · 2021Article
- Meeting the multiscale challenge: representing physiology processes over ApiNATOMY circuits using bond graphs.Interface focus · 2018Article
- Bond Graph Model of Cerebral Circulation: Toward Clinically Feasible Systemic Blood Flow Simulations.Frontiers in physiology · 2018Article
- Energy-based analysis of biomolecular pathways.Proceedings. Mathematical, physical, and engineering sciences · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this study suggests that they can play the same rôle in the modelling, analysis and synthesis of biomolecular systems. The particular structure of bond graphs arising from biomolecular systems is established and used to elucidate the relation between thermodynamically closed and open systems. Block diagram representations of the dynamics implied by these bond graphs are used to reveal implicit feedback structures and are linearised to allow the application of control-theoretical methods. Two concepts of modularity are examined: computational modularity where physical correctness is retained and behavioural modularity where module behaviour (such as ultrasensitivity) is retained. As well as providing computational modularity, bond graphs provide a natural formulation of behavioural modularity and reveal the sources of retroactivity. A bond graph approach to reducing retroactivity, and thus inter-module interaction, is shown to require a power supply such as that provided by the ATP ⇌ ADP + Pi reaction. The mitogen-activated protein kinase cascade (Raf-MEK-ERK pathway) is used as an illustrative example.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.