# README for Crbl_tDCS_Zhang2021 Simulation code for Zhang, X., Hancock, R., and Santaniello, S. (2021) Transcranial Direct Current Stimulation of Cerebellum Alters Spiking Precision in Cerebellar Cortex: A Modeling Study of Cellular Responses. PLoS Comp Biol. DOI: 10.1371/journal.pcbi.1009609.

Dependencies:

• NEURON v.7.7 or later (may run on some older versions)
• MATLAB r2017a or later (may run on some older versions)

The codes were executed on Windows 10. Not tested on other operating systems (Unix/macOS etc).

To run simulations for granule cells:

1. Compile NEURON mechanisms in the (./Granule/mod_files/) folder using the mknrndll executable; copy the generated nrnmech.dll file to the (./Granule/) folder.
2. In MATLAB, run the script "tDCSsearch_GrC.m", which sets parameters for the tDCS-induced electric field intensity and filenames. It then calls the NEURON script "mosinit_tDCS_synapse_189-1-33dw.hoc" which simulates the granule cell activity under synaptic inputs under the given tDCS settings.

To run simulations for deep cerebellar nuclear cells:

1. Compile NEURON mechanisms in the (./DCN/mod_files/) folder using the mknrndll executable; copy the generated nrnmech.dll file to the (./DCN/) folder.
2. In MATLAB, run the script "tDCSsearch_DCN.m", which sets parameters and calls the NEURON script "mosinit_tDCS_synapse_189-1-33dw.hoc". The latter simulates the DCN activity during rebound spiking under the given tDCS settings.

To run simulations for Purkinje cells:

1. Compile NEURON mechanisms in the (./Purkinje/mod_files/) folder using the mknrndll executable; copy the generated nrnmech.dll file to the (./Purkinje/) folder.
2. In MATLAB, run the script "tDCSsearch_dend_train_delayedonset.m", which sets parameters and calls the NEURON script "mosinit_tDCS_synapse_189-1-33dw.hoc". The latter simulates the Purkinje cell activity under mossy fiber inputs under the given tDCS settings.
3. Run the script "tDCSsearch_1cs.m", which sets parameters and calls the NEURON script "mosinit_tDCS_1cs.hoc". The latter simulates the Purkinje cell activity under climbing fiber inputs under the given tDCS settings.
4. Run the script "tDCSsearch_caspike.m", which sets parameters and calls the NEURON script "mosinit_tDCS_caspike.hoc". The latter simulates the Purkinje cell calcium bursting activity under the given tDCS settings.
5. Run the script "Vshift_search_calcium.m", which sets parameters and calls the NEURON script "mosinit_calcium_soma_vshift.hoc" or "mosinit_calcium_dend_vshift.hoc". The latter two simulate the Purkinje cell calcium bursting activity under voltage shifts applied to soma or dendritic compartments.

Scripts used to generate all the figures in the article, including estimated EF values and simulated values for all voxels in head models accrue to over 4 GB and are available at the link: https://drive.google.com/drive/folders/1udxxdToV9zuXK7h27znhCWIkQHau0D2w?usp=sharing