The Open-System Mass-Energy Flux Model of Human Metabolism

These supplementary materials accompany the forthcoming theoretical framework paper titled The Open System Mass Energy Flux Model of Human Metabolism. They provide the complete technical content that supports the formal model, including full mathematical derivations, extended stoichiometric calculations, mechanistic modules, measurement protocols, calibration notes, and statistical code. This package ensures transparency, reproducibility, and open scientific access to all underlying methods and calculations used in the development of the Mass Energy Flux Framework. The materials include detailed control volume mathematics, mass flux and energy flux relations, partitioning functions, hormonal gating functions, and boundary condition assumptions. Full stoichiometry is provided for oxidation pathways, including fatty acids, glucose, amino acids, and ethanol, along with atomic mass accounting and electron routing. Extended worked examples illustrate substrate specific flux behaviour, mixed meal responses, hormonal state modulation, and thermogenesis pathways. The supplementary materials also contain the complete Standard Operating Procedure index for all assays and instruments referenced in the framework, including respiratory exchange ratio measurement, carbon dioxide flux quantification, isotope tracer protocols, hormone panels, absorption assays, and microbiome sequencing. Calibration notes and quality control requirements are included for indirect calorimetry, gas analysers, isotope tracers, mass spectrometry, and sequencing platforms. A full set of simulation scripts is provided for parameter ranges, sensitivity analyses, Monte Carlo modelling, Bayesian inference for partitioning functions, error propagation, uncertainty quantification, and model stability tests. These scripts support the validation and exploration of the Mass Energy Flux Framework and allow independent researchers to reproduce or extend the model. This Zenodo record serves as the permanent, citable repository for all supplementary materials associated with the theoretical framework paper. It is not a preprint and does not contain the main manuscript. The full theoretical paper will be submitted separately to a preprint server. These materials are provided to support open science, reproducibility, and transparent model development.