Nanoscale molecular architecture controls calcium diffusion and ER replenishment in dendritic spines

We present here the simulation codes associated with publication [1] written in Python and Mathematica. The simulations concern calcium dynamics in dendritic spines, where each ion motion is modeled as Brownian. Spines have a geometry of a spherical head attached to a cylindrical neck, while spine apparatus, its internal calcium stores are located inside with a similar structure.

[1] Basnayake, K., Mazaud, D., Kushnireva, L., Bemelmans, A., Rouach, N., Korkotian, E. & Holcman, D. (2021) Nanoscale molecular architecture controls calcium diffusion and ER replenishment in dendritic spines. Science Advances, 7(38): eabh1376.