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Abstract

In this work, we explore the 3D shape of cells and organoids in structured environments. Understanding the physical determinants of cell shape regulation in structured environments is vital as it plays a crucial role in essential biological processes, including migration, division and tissue development. The cellular Potts model (CPM) has emerged as a powerful computational framework for simulating cell behavior and morphodynamics in complex biological systems. Our research focuses on utilizing the CPM to model 3D single cells on 2D micropatterns and in 3D structured environments. We explicitly consider intracellular structures such as the nucleus and stress fibers and model their impact on cell shape. This allows us to predict morphology and trajectories during the single cell spreading process on micropatterns and demonstrates the effect of nucleus and stress fibers on these processes. Through systematic simulations and comparison with surface minimization approaches and experimental data, we demonstrate the ability of our model to accurately predict cell shapes under different spatial constraints. Additionally, we model the optic cup evagination in fish retina organoids with explicit representation of Matrigel at the surface of the organoid. The findings shed light on the mechanistic basis underlying the shape changes observed in multicellular systems.