Active viscous shell

active_viscous_shell is distributed as a supplemental material to the paper:

Borja da Rocha, H., Bleyer, J., & Turlier, H. (2021). A viscous active shell theory of the cell cortex. arXiv preprint arXiv:2110.12089.

The code is based on the FEniCS software package for the finite-element implementation, Gmsh for the meshing and the Mmg platform for adaptive remeshing.

Theory and implementation

See the Theory and implementation document.

Requirements

• FEniCS (>= 2019.1.0, Python 3), see installation instructions here.
• Gmsh, see Download here.
• the meshio package for mesh conversion (version 5.0 at least)

pip install meshio==5.*

• the mmgs application of the MMG library, Download here.

Usage

First, you should specify in the paths.json files the path corresponding to the gmsh and mmgs_O3 application on your system such as:

{
    "gmsh": "/path/to/gmsh",
    "mmg": "/path/to/mmgs_O3"
}

We use configuration files named config.conf for specifying the simulation parameters. Each example is in the folder ./Examples, including:

• ./Examples/HyperOsmoticShock
• ./Examples/HypoOsmoticShock
• ./Examples/Cytokinesis

To run one of the examples, first activate the FEniCS environment if you used a virtual environement based installation (e.g. conda activate fenicsproject). Then:

cd ./Examples/HyperOsmoticShock 
python3 ../../main.py