Network thermodynamics of biological systems: A bond graph approach

Edmund Crampin (1973-2021) was at the forefront of Systems Biology research and his work will influence the field for years to come. This paper brings together and summarises the seminal work of his group in applying energy-based bond graph methods to biological systems. In particular, this paper: (a) motivates the need to consider energy in modelling biology; (b) introduces bond graphs as a methodology for achieving this; (c) describes extensions to modelling electrochemical transduction; (d) outlines how bond graph models can be constructed in a modular manner and (e) describes stoichiometric approaches to deriving fundamental properties of reaction networks. These concepts are illustrated using a new bond graph model of photosynthesis in chloroplasts.

Automated summary

This paper summarises the significant contributions of Edmund Crampin and his group in applying energy-based bond graph methods to biological systems. It motivates the importance of considering energy in biological modelling, introduces bond graphs as a methodology, describes extensions for modelling electrochemical transduction, outlines modular construction of bond graph models, and explains stoichiometric approaches for deriving fundamental properties of reaction networks.