SurfaceBulkViscousFlows

Repository that holds the Julia software with code demonstrators of the numerical examples in the paper "Unfitted finite element modelling of surface-bulk viscous flows in animal cells". https://arxiv.org/abs/2505.05723

List of examples

Referred to the paper sections

• Section 4.1 Verification examples
  • Verification in fixed sphere
  • Verification with dynamic surface
• Section 4.2 Self-organised shape emergence
  • Shape emergence
• Section 4.3 Relaxation dynamics
  • Pear
  • Popcorn
  • Torus
• Section 4.4 Cell cleavage
  • 2D axisymmetric division
  • 3D division

Instructions to run the examples

Prerequisites

• A Julia installation (link to instructions)
• Install PETSc version 3.15.2 with mumps and let Julia find the library:

Linux instructions: On your folder of choice;

  wget https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.15.2.tar.gz
  tar -xvzf petsc-3.15.2.tar.gz
  cd petsc-3.15.2.tar.gz
  ./configure -download-mumps -download-scalapack -download-parmetis -download-metis --download-bison -download-ptscotch --download-make --with-debugging=0 --download-mpich --download-fblaslapack=1
  make PETSC_DIR=/your-folder/petsc-3.15.2 PETSC_ARCH=arch-linux-c-opt check

Note that for PETSc you might need to install missing required libraries.

Add export JULIA_PETSC_LIBRARY="/your-folder/petsc-3.15.2/arch-linux-c-opt/lib/libpetsc.so" to your .bashrc file.

Running an example

• Clone the repository at a path of your choice
• Open a Julia interactive session on the repository directory

  git clone [email protected]:ericneiva/SurfaceBulkViscousFlows.git
  cd SurfaceBulkViscousFlows
  julia --project

• Before running an example for the first time, set up the project dependencies

  julia> # press ] to enter Pkg mode...
  (SurfaceBulkViscousFlows) pkg> instantiate # Check that Julia points to your local PETSc installation

• Run the example of your choice

  julia> include("examples/Verification/VerificationInFixedSphere.jl")

• Output files are generated in the folder for inspection

How to cite this code

In order to give credit to the contributors of this software, we simply ask you to cite the references below in any publication in which you have made use of the repository.

Contact

Please, contact Eric Neiva or Hervé Turlier if you have any questions.