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Simulating 3D Cell Shape with the Cellular Potts Model.

Rabea Link^1,2, Ulrich S Schwarz^3,4

¹Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany.

Methods in Molecular Biology (Clifton, N.J.)

|December 31, 2022

Summary

Computer simulations in mechanobiology can predict cell shape and forces. This guide details the Cellular Potts Model for 3D cell simulations on micropatterns, aiding research in cell mechanics.

Keywords:

Cell adhesion Cell shape Cellular Potts model Computer simulations Micropatterns Modelling

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Area of Science:

Computational mechanobiology
Biophysics
Cellular modeling

Background:

Computer simulations are integral to mechanobiology.
Predicting cell behavior based on the extracellular environment is a key challenge.
Various models exist for simulating cell and tissue shapes.

Purpose of the Study:

To provide an overview of common mechanobiology models.
To detail the Cellular Potts Model (CPM) as a lattice-based framework.
To offer a practical guide for simulating 3D cell shapes on micropatterns using CPM.

Main Methods:

Overview of existing cell simulation models.
Detailed explanation of the Cellular Potts Model (CPM).
Implementation guide for 3D CPM simulations in open-source software.

Main Results:

CPM simulations can model cell shape and position changes.
The energy function incorporates cell volume, surface area, and cell interactions.
Successful simulation of a single cell on a 3D micropattern is demonstrated.

Conclusions:

The Cellular Potts Model is a versatile framework for simulating cell mechanics.
CPM simulations can effectively predict cell behavior in response to environmental cues.
This guide facilitates the application of CPM for mechanobiology research.