ArticleJournal of the Royal Society, Interface2021
Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data.
Article in Journal of the Royal Society, Interface, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Thermodynamically consistent, reduced models of gene regulatory networks.Royal Society open science · 2025Article
- Energy-based analysis of biochemical oscillators using bond graphs and linear control theory.Royal Society open science · 2025Article
- Energy-based modelling of single actin filament polymerization using bond graphs.Journal of the Royal Society, Interface · 2025Article
- Foundations of a Compositional Systems Biology.ArXiv · 2024Article
- Sensitivity analysis of biochemical systems using bond graphs.Journal of the Royal Society, Interface · 2023Article
- Article
- Analysing and simulating energy-based models in biology using BondGraphTools.The European physical journal. E, Soft matter · 2021Article
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Renewed interest in dynamic simulation models of biomolecular systems has arisen from advances in genome-wide measurement and applications of such models in biotechnology and synthetic biology. In particular, genome-scale models of cellular metabolism beyond the steady state are required in order to represent transient and dynamic regulatory properties of the system. Development of such whole-cell models requires new modelling approaches. Here, we propose the energy-based bond graph methodology, which integrates stoichiometric models with thermodynamic principles and kinetic modelling. We demonstrate how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems. The approach is illustrated using a well-established stoichiometric model of
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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.