avishaibarnoy/caveolindisk

Caveolin-1 in Caveolae simulation

About

2D simulation of caveolin-1 on caveolae surface

Description

caveolin is modelled as a disk and are connected to each other by membrane. Differnet combination of connectiong between neighborig caveolin are computed, and the geometry is minimized with respect to an ideal angle between edges.

How to use

Running simulation

In the generate_geom.py file edit the following parameters:

• n_disks number of proteins in calculations.
• L half-distance between proteins in simulation.
• r_disk radius of proteins.

1. Run generate_geom.py to generate geometries and place them in correct folders
2. Run run_simulation.sh to go through folders and optimize each geometry

Analysis

To be added in the future

Development

In the future I will add an input file and rearrange some of the functions.

Thanks

Thanks for Itai Knaan-Harpaz for the algorithm for the initial geometry