Integrating genome-scale metabolic models into multi-scale simulations

Genome-scale metabolic models can predict how individual cells allocate resources and respond to their environment, yet few frameworks link single-cell metabolism to the spatial organisation of multicellular systems. Here we introduce PhysiCelldFBA, an extension of the PhysiCell agent-based framework that couples genome-scale dynamic flux balance analysis to off-lattice multicellular simulations. Each simulated cell carries its own metabolic model, allowing local environmental conditions to shape metabolism while metabolic activity feeds back on the surrounding environment, cellular behaviour, and spatial organisation. We first validate this coupling by showing that glucose consumption, CO ₂ production, and biomass accumulation remain mass-balanced in a closed E. coli system, with simulated biomass agreeing with analytical predictions to within 1%. We then demonstrate how metabolic phenotypes emerge from this coupling across microbial and mammalian systems. Spatial nutrient gradients generate metabolic stratification and acetate cross-feeding in growing E. coli colonies; diffusion-limited metabolism produces proliferative, hypoxic, and necrotic zones across a broad panel of metabolites in a tumour-like tissue; distinct, organism-specific metabolic networks give rise to syntrophic cross-feeding and spatial niche formation in a two-species consortium; and metabolic state couples energy availability to transitions between cellular motility and growth. Across these examples, metabolic stratification, cross-feeding, and phenotypic adaptation emerge from local metabolic optimisation and environmental feedback rather than being explicitly prescribed. PhysiCelldFBA therefore provides a general framework for simulating genome-scale metabolism at single-cell resolution and linking intracellular metabolic state to cellular behaviour and emergent organisation across scales.