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21 changes: 21 additions & 0 deletions README.md
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# Reconstitution of Action Potentials in a Model of a Hippocampal Mossy Fiber from Action Potential-Evoked Sodium, Potassium and Calcium Current Waveforms as Described In

Henrik Alle, Arnd Roth and J. R. P. Geiger, Energy-efficient action potentials in hippocampal mossy fibers, *Science* 325, 1405-1408 (2009). doi: 10.1126/science.1174331

This directory contains mod and hoc files for the NEURON simulator, as well as dat files representing the conductance waveforms which are read in via the `stepforce()` function in GNa.mod, GK.mod and GCa.mod.

## To run the simulations, follow these steps:

1. Compile the mod files using `nrnivmodl` under Mac OS X and Linux, or `mknrndll` under Windows.

2. Run `reconstitution.hoc` in NEURON. This performs the simulation shown in Fig. 2A and B of the paper and plots the results using NEURON's graphical user interface.

3. If desired you can perform an automated fit of the measured action potential waveform by running `fit_th1.hoc`. This writes results to three files: `parameters1.txt`, `measuredAP1.txt`, and `modelAP1.txt` and may take several hours.

If you have questions please contact
henrik.alle@charite.de
arnd.roth@ucl.ac.uk

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2025-06-02: Converted README to Markdown.
33 changes: 0 additions & 33 deletions readme.txt

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