{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/hierarchical-bond-graph-modelling-of","title":"Hierarchical Bond Graph Modelling of Biochemical Networks","arxiv_id":"1503.01814","date":"2015-10-26","proceeding":null,"authors":[],"abstract":"The bond graph approach to modelling biochemical networks is extended to\nallow hierarchical construction of complex models from simpler components. This\nis made possible by representing the simpler components as thermodynamically\nopen systems exchanging mass and energy via ports. A key feature of this\napproach is that the resultant models are robustly thermodynamically compliant:\nthe thermodynamic compliance is not dependent on precise numerical values of\nparameters. Moreover, the models are reusable due to the well-defined interface\nprovided by the energy ports.\n  To extract bond graph model parameters from parameters found in the\nliterature, general and compact formulae are developed to relate free-energy\nconstants and equilibrium constants. The existence and uniqueness of solutions\nis considered in terms of fundamental properties of stoichiometric matrices.\nThe approach is illustrated by building a hierarchical bond graph model of\nglycogenolysis in skeletal muscle.","url_abs":"http://arxiv.org/abs/1503.01814v2","url_pdf":"http://arxiv.org/pdf/1503.01814v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"hierarchical-bond-graph-modelling-of","repo_url":"https://github.com/uomsystemsbiology/energetic_cost_reference_environment","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}