Gillessa

This project contains code implementing algorithms that simulate stochastic systems of equations, e.g. Gillespie's SSA. See models.py.

Notebooks contain basic experiments that simulate homodimerization on a 2D surface, which corresponds to a typical TIRF microscopy setup.

References

1. Exact stochastic simulation of coupled chemical reactions
2. A practical guide to stochastic simulations of reaction-diffusion processes
3. GillespieSSA: Implementing the Stochastic Simulation Algorithm in R

Repo structure

• notebooks/
  • SRDS.ipynb: simple stochastic simulations of reactions. Contains tests of objects and classes for incorporating diffusion, as well as some prelim results.
  • particle_sims.ipynb: particle-based simulations of homodimerization. Further checks to validate trajectory correlation algorithm in single-particle tracking experiments.
• models.py: models for simulating stochastic systems: SSA, FRM, MNRM, TAUL-LEAP