Peer-reviewedCC BY-NC-ND 4.0STAR Protocols
Protocol for simulating cell-contact dynamics of proliferating epithelia using the vertex model
4 affiliations
- 1Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA.
- 2Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
- 3Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
- 4Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA. Electronic address: [email protected].
Abstract
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
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BibTeX
@article{sarkar2026protocol,
title = {{Protocol for simulating cell-contact dynamics of proliferating epithelia using the vertex model}},
author = {Tanmoy Sarkar and Jeffrey J Lovelace and Matej Krajnc and Rosemary Mwithiga and Subramanian P Ramanathan},
journal = {STAR Protocols},
year = {2026},
month = oct,
doi = {10.1016/j.xpro.2026.104909},
url = {https://doi.org/10.1016/j.xpro.2026.104909},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Protocol for simulating cell-contact dynamics of proliferating epithelia using the vertex model
AU - Tanmoy Sarkar
AU - Jeffrey J Lovelace
AU - Matej Krajnc
AU - Rosemary Mwithiga
AU - Subramanian P Ramanathan
PY - 2026
DA - 2026/10/19
JO - STAR Protocols
DO - 10.1016/j.xpro.2026.104909
UR - https://doi.org/10.1016/j.xpro.2026.104909
AB - 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
SN - 2666-1667
ER -