This is a MATLAB/Netlogo code for the paper "Beyond microtubules: The cellular environment at the endoplasmic reticulum attracts proteins to the nucleus, enabling nuclear transport" by Chae et al. (2023) submitted in iScience. The code simulates the protein diffusion in a heterogeneous intracellular environment with physical interaction with the ER.
Protein diffusion under the presence of obstacles.
- ABM_ERbinding.nlogo
Code for protein diffusion in an intracellular environment with obstacles. Binding and unbinding of proteins with obstacles are implemented. Biologically relevant parameters (protein radius, cell radius) are used. Proteins are magnified by 20 times.
Effective PDE describing diffusion in the heterogeneous intracellular environment.
- pde_simulation_by_time.m
PDE simulation code for Chapman's law. Provides the distribution fo protein (p(x,t)) over time and the flux map.
- diffusion2d_high_hetero.m
MATLAB function code required for implementing pde_simulation_by_time.m This function calculates the flux and spatial derivative of PDE based on Chapman's law in the highly heterogeneous intracellular environment.
Simulating ABM equivalent to effective PDE (Chapman's law)
- hetero_diffusion_ellipse_v1.nlogo
Simulates effective diffusion following Chapman's law in an elliptic-shaped cell.
- hetero_diffusion_various_ER_v1.nlogo
Simulates effective diffusion following Chapmna's law with a complex structured ER.