alihashmiii/3d-vertex-model

vertex model implementation to simulate biological tissue in 3D

3D Vertex Model

The project contains an implementation of a vertex model to simulate biological tissues in 3D. The repository currently houses the Mathematica notebook (PDF) for simulating an infinite sheet of cells in a monolayer. However, this code can be easily modified to simulate cells in 3D agglomerates/aggregates - which are essentially easier to simulate than an infinite sheet. In this implementation the cells can exchange neighbours (T1 transitions).

vertex model sim - contains the code for modeling infinite sheet of cells

multilayer sim - contains code for modeling multilayered tissue structure

sanity checks for functions - contains test modules to check whether functions are performing correctly

To-Do List:

• cell division event to create a new polyhedron
• cell death to remove a polyhedron from the mesh

Notes

• If you use or modify the code to disseminate the results in a publication, you would need to cite the author's repository and explicitly ask for permission. Ofcourse I will not decline any request

• The code is based on and is a modification of Okuda et al 2012, "Reversible network reconnection model for simulating large deformation in dynamic tissue morphogenesis"

• install IGraphM to use the SubIsomorphicQ function