Simulations of Spherical Cells on 3D Scaffolds

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.