This zip-Folder contains all NEURON simulator files used for the modeling in the Paper

Lombardi, Jedlicke, Luhmann, Kilb "Interactions between membrane resistance, GABA-A receptor properties, bicarbonate dynamics and Cl--transport shape activity-dependent changes of intra-cellular Cl- concentration." International Journal of Molecular Science 2019

Each subfolder contains the hoc and ses files required for the modeling of one subproject. In each subfolder all mod files are stored, they must be tranformed into a DLL with the MkNrnDll.exe program (windows) or equivalent on your platform (if you need more help compiling the mod files and running the model please see:
https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml

To start the model the Start_xxxx.hoc schould be started, which loads the correct cell, implemented the correct mechanisms and runs the simulations. Only some of the "isolated dendrite files" requires the manual implementation of .ses files to implement voltage-clamp.

The programs runs without GUI and the results are stored in ASCII files. Please contact me (wkilb at uni-mainz.de) for a .xls speadsheed that eases the readout of relevant values (e.g. max min) from these ASCII sheets.

Please be aware that these complex simulations with several repetitions require some time. For most simulations a status report was printed in the main NEURON screen. Most folders also provide a .ses file that can be loaded manually via the GUI and allows visualization of most relevant parameters.

Example run:
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Change directory to and compile the mod files in the Isolated_Dendrite_gPas__Fig1 folder. Start the program start_GABA_isolated_dendrite.hoc (double clicking in windows explorer) with nrngui or using the method appropriate for your platform.

Press Init & Run and select to Keep Lines in the dend.cli(0.5) graph.

NEURON Main Menu -> Tools -> Distributed Mechanisms -> Viewers -> Name Values

then double click on dend and edit the g_pas (S/cm2) text field in the new parameter window:

Change the value to 0.018:

screenshot1

the click Init & Run again and you should see an image similar to figure 1 C (top) in the paper: screenshot2