Mesoscopic modelling of epithelial tissues

TL;DR

This paper reviews various mesoscopic simulation methods for epithelial tissues, discussing their features, efficiency, and coarse-graining choices, and provides detailed guidance on implementing the Vertex Model for tissue simulation.

Contribution

It offers a comprehensive overview of mesoscopic epithelial tissue models and detailed instructions for implementing the Vertex Model, aiding researchers in choosing and applying simulation techniques.

Findings

Comparison of simulation methods based on efficiency and scale

Detailed implementation guidance for the Vertex Model

Identification of common pitfalls in tissue simulation

Abstract

Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed computational resources), the amount of cells/the size of tissues that can be simulated, the time scale of the simulated dynamics and the coarse grained level of precision. Choosing the right algorithm for the simulation of epithelial cells and tissues is a compromise between each of these key elements. Irrespective of the method, each algorithm includes part, or all, of the following features: short-range membrane-mediated attraction between cells, soft-core repulsion between cells, cell proliferation, cell death, cell motility, fluctuations, etc. We will first give a non-exhaustive overview of commonly used modeling approaches for tissues at a mesoscopic level, giving a rough idea of the coarse-graining decisions made for every one of them. Then we will dive into greater detail on how to implement a relaxation procedure according to the Vertex Model, refreshing aspects of the theoretical groundwork, describing required data structures and simulation steps and pointing out details of the simulation that can present pitfalls to a first-time implementation of the model.