Simulation study of extracellular potential from axon in tunnel.

All simulations can be executed through the script run_all.sh

A neural simulation of an axon (based on axon model from Hallermann et al. 2012).
First the NEURON mechanisms must be compiled by executing 'nrnivmodl'
in the folder HallermannEtAl2012, assuming NEURON is installed.
The neural simulation can then be executed by:
python neural_simulation.py
The positions and transmembrane currents are saved to file.

For the Finite Element Method simulations, the mesh must first be
created:
cd mesh_nmi_tunnel/
sh mesh_it.sh

All Finite Element simulations and plotting can then be done by running:
cd ../MEA_tunnel_FEM
python FEM_simulations.py

This will find the FEM solution for each time step.

NOTE: In more advanced cases, it might be best to use the reciprocity
principle, where a point source is positioned at each electrode site,
and simulated for a unitary charge.
This can be used as a mapping for finding the potential at the electrodes
for an arbitrary distribution of point currents in the volume,
and for arbitrary time courses.