Protocol for simulating cell-contact dynamics of proliferating epithelia using the vertex model

Vertex models simulate epithelial mechanics at single-cell resolution but represent cell division as a single in-plane split, agnostic to the differential apicobasal geometry of mitotic cells. Here, we present a protocol that simulates basal mitosis as two sequential changes: basal-cell diminution followed by daughter-cell reinsertion. Apical-side simulations can be performed with minimal code modification. We provide instructions for generating initial configurations, running simulations, and quantifying mechanical and topological rearrangements using command-line operations accessible to experimental biologists. For complete details on the use and execution of this protocol, please refer to Ramanathan et al.¹.