This Dune module contains programs to simulate the intra- and extracellular potential generated by a neuronal membrane. It implements the numerical solution of different mathematical models for the electric potential, most importantly the PNP (Poisson-Nernst-Planck) system of electrodiffusion. There are additional implementations to solve the VC (volume conductor) model and the electroneutral model by Yoichiro Mori that allow for comparison as in my 2016 Journal of Integrative Neuroscience paper. All this is implemented using a simple, cylinder-symmetrical axon model.
This module was developed as part of my PhD project in the working group of Prof. Peter Bastian at the Interdisciplinary Center for Scientific Computung at Heidelberg University. Since this code was meant for my own use only, it might be hard to understand for someone not familiar with the background or the Dune framework. In fact, it is messy, unorganized, poorly commented and it may contain an indefinite amount of bugs. Some theoretical and technical background can be found in a 2013 Biophysical Journal paper and in my PhD thesis. I strongly recommend reading the latter for some information on the code structure and numerical subtleties.
Please note that I have made this code publicly available for future reference, but I will not be able to continue development or provide support for this specific module. However, if you have questions regarding the Dune framework in general, there is an active and responsive development community on the mailing lists or the user wiki.
The main simulation from my 2013 paper can be pulled and run as a Docker image. See DOCKER.md for details.
It does not (yet) contain further simulations setups from my PhD thesis or the 2016 paper. If you are interested in those, please open an issue.
Please check out my Zenodo project containing raw simulation data in HDF5 format.
Not for the faint of heart!
For rudimentary installation instructions, see INSTALL.md. An even more rudimentary documentation can be found in DOCUMENTATION.md, which mainly lists the compile- and run-time configuration options without giving any explanation of the code structure, class design or functionality. For this, please refer to the (largely undocumented) code or contact me.
This module is free software under the BSD 3-clause license. Copyright information is stated in the file AUTHORS, the used BSD 3-clause license can be found in LICENSE.
Please be aware that the other Dune modules required by this module may be licensed differently, so please make sure you satisfy the requirements of all modules when using the complete stack.