I. References to the papers:

The below talk about the constitutive model of the muscle

1) http://physbam.stanford.edu/~fedkiw/papers/stanford2004-06.pdf
2) https://www.math.ucla.edu/~jteran/papers/TSNF03.pdf

This discusses how to robustly handle inverting elements

3)https://www.math.ucla.edu/~jteran/papers/ITF04.pdf

II. The code :

All the simulation is written as the functions of SimMesh class, found in the mesh.hpp & mesh.cpp files. The code for handling inversion is in the CalculateStresses() function

To run the code, you need to have GLM and Eigen libraries in the src folder, and compile using make to generate the executable.