Prerequisites

This project requires Python 3.8+ and the following packages:

• numpy
• vispy
• dataclasses (for Python versions < 3.7, where it's not built-in)

You can install the required packages using pip:

pip install numpy vispy dataclasses

Vesicle Diffusion Prototype

This project is a fast and modular prototype for simulating vesicle diffusion within a 2D triangular mesh — a simplified abstraction of vesicle transport along biological membranes.

The simulation was developed in response to a scientific paper shared as part of an interview preparation, aiming to demonstrate understanding of spatial diffusion, geometric sampling, and efficient real-time computation.

Key Features

• Vesicles modeled as circular particles with membrane sample points
• Triangle occupancy detection using a fully vectorized 2D side-test
• Brownian motion (diffusion) with rejection sampling for spatial exclusion
• Per-vesicle diffusion coefficients
• Real-time interactive visualization using Vispy
• Ready for GPU acceleration using CuPy or PyTorch
• Modular design, easily extendable to tetrahedral 3D meshes and reaction models

Reference

This prototype was inspired by:

Iain Hepburn et al., "Vesicle and reaction-diffusion hybrid modeling with STEPS"
Communications Biology, 2024
https://doi.org/10.1038/s42003-024-06276-5

The current code implements a simplified 2D equivalent of the tetrahedral diffusion model described in the paper, using triangle meshes and point-based surface sampling for efficiency.