Simulations of Spherical Cells on 3D Scaffolds

This MATLAB simulation models the movement of spherical "cells" constrained to travel along a 3D scaffold represented by an STL mesh. It mimics how particles behave when moving in constrained environments such as porous scaffolds, common in biomedical or soft matter applications. The code calculates mean squared displacement, first time passage, shortest traversal distance and path length. Any .STL file may be uploaded as the scaffold environment, and there are options for producing images and videos of the simulations. This code is fully parallelised.

Each cell:
• Begins its motion by either falling under gravity or being initialized on the scaffold.
• Moves randomly with a user-defined maximum velocity.
• Snaps to the nearest point on the scaffold at every time step.
• Avoids overlapping with other cells based on a "squish" tolerance.
• Logs its trajectory and outputs metrics like motility and first passage time.
The simulation is repeated for a set number of runs, and each run exports trajectory plots, Excel files with data, and optionally images and videos of movement over time.