Bond Graphs Unify Stoichiometric Analysis and Thermodynamics

2020/07/31 by P.J. Gawthrop, Gawthrop, Peter J.
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #FOS: Biological sciences #Gene Regulatory Network Analysis #Microbial Metabolic Engineering and Bioproduction #Molecular Networks (q-bio.MN)

paper · pdf · doi:10.48550/arxiv.2007.15917

openalex publication_date 2020/07/31 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

Whole-cell modelling is constrained by the laws of nature in general and the laws of thermodynamics in particular. This paper shows how one prolific source of information, stoichiometric models of biomolecular systems, can be integrated with thermodynamic principles using the bond graph approach to network thermodynamics.

Related

• Biomolecular System Energetics
• Characterisation of conserved and reacting moieties in chemical reaction networks
• The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics
• Computing fluxes and chemical potential distributions in biochemical networks: energy balance analysis of the human red blood cell
• The Essential Role of Thermodynamics in metabolic network modeling: physical insights and computational challenges