Biophysics research boosted with data-era computational tools and algorithms.
Simulated molecular dynamics and organization on the postsynaptic membrane using Gillespie's
algorithm. Implemented and unit-tested in Python 3.8, parallelized using Ray.
Accelerated counting of nearest neighbors using CNN-like vectorization; see src/im2col.py and src/Synapse.py.
- Run from
simulate.py - "Content" of each simulation instance described in
single_trial.py
Run pytest from the repo's root directory.