Induced pluripotent stem cells are grown in flat monolayers for laboratory studies and in three-dimensional aggregates for manufacturing. The metabolic behavior differs dramatically between the two formats — aggregates develop spatial gradients in oxygen, nutrients, and redox state that monolayers don't have. Scaling up isn't just making the culture bigger; it's moving into a different metabolic regime.
The authors (arXiv:2603.17090) build a multiscale mechanistic model linking molecular reactions, single-cell metabolism, and macroscopic culture dynamics. Monolayer kinetics provide the molecular foundation; a biological systems-of-systems framework models the aggregate, coupling intracellular fluxes with extracellular gradients. Isotopic tracers, metabolite profiling, and two-photon redox imaging validate the model across scales.
The through-claim: the gap between laboratory and manufacturing iPSC culture is metabolic heterogeneity — gradients that don't exist in the monolayer but dominate the aggregate. A monolayer model scaled up gives the wrong answers because it assumes uniformity that the aggregate doesn't have. The multiscale model bridges the formats by explicitly representing what changes between them: spatial structure produces metabolic states that a uniform model can't predict.