Peristalsis in perivascular networks

This repo contains the code used for the results in the manuscript "The directional flow generated by perisalsis in perivascular networks - theoretical and numerical reduced order descriptions" by Ingeborg Gjerde, Marie Rognes and Antonio Sanchez.

Centrally, the code computes net flow driven by peristalsis. This can be done both analytically and numerically; simulation/run_comparison.py validates these two approaches against each other.

Dependencies

The code is based on models and methods provided in graphnics, which in turn depends on

• FEniCS
• networkx

We recommend using the provided docker image for running the code.

Running the code

Docker image

The container can be built and run locally by executing

git clone https://github.com/scientificcomputing/perivascular-peristalsis/tree/main
cd perivascular-peristalsis
docker build --no-cache -t graphnics . # build the docker image
cd ..
docker run --name graphnics-container -v "$(pwd):/home/fenics/shared" -d -p 127.0.0.1:8888:8888 graphnics 'jupyter-notebook --ip=0.0.0.0'

Notebooks can then be accessed by executing

docker logs graphnics-container

and opening the link provided in the output.

To run scripts natively, open a terminal in the container by executing

docker exec -it graphnics-container /bin/bash

and enter the shared folder containing the code

cd shared

Reproducing the results in the paper

The comparison between the analytical and numerical approach on a single vessel can be run by executing

python3 simulation/run_comparison.py --betas 2 --Ls 1 --ts_per_cycle 25 --lambdas 0.1 1 2 10 

The number of arguments given to --betas and --Ls determines the number of vessel segments; running e.g.

python3 simulation/run_comparison.py --betas 2 2 2 --Ls 1 1 1 --ts_per_cycle 25 --lambdas 0.1 1 2 10 

repeats the same experiment on a Y-birucation.

The simulation of interacting cardiac and vasomotion waves can be run by executing

python3 simulation/run_interacting_waves.py