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Preprint

Simulations

YH Ying Han
AT Ai-Hui Tang
TS Thomas Christian Südhof
BZ Bo Zhang

Last updated date: Oct 12, 2026 Views: 34 Forks: 0

original An abbreviated version of this protocol was published in Science Advances
Neuroligin-3 confines AMPA receptors into nanoclusters, thereby controlling synaptic strength at the calyx of Held synapses
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All the codes for simulations are posted on Zenodo (https://doi.org/10.5281/zenodo.6419982) and are also available on GitHub (https://github.com/Han-y/Model-of-Synapse.git). 

 

To simulate mEPSC currents, run the following files as stated in the README.txt: 

(1) make.m 

To get the .mexw64 file that can be invoked in MATLAB. This will result in three new files:  synapse_absorb_at_cleftbd_C.mexw64; synapse_absorb_at_glia_C.mexw64;  and synapse_C.c.

(Note: Those three files help run the following files)

 

(2) run_sim.m

This file allows user to change the simulation parameters (e.g. AMPAR states, glutamate states) and returns the results.

The “release_zone” in run_sim.m is set to be at 140 nm (PSD-95 synaptic cluster) in fig. S3. 

(Note: It can take hours to run over hundreds of simulations).

 

(3) (Optional) synapse_sim.m

Includes all parameters used in the simulation that can be modified.

 

(4) EPSC_generation.m

This allows users to get traces of simulation (e.g., GluAs mEPSC).

Copyright: © 2026 The Author(s); This is an open-access article under the CC BY license (https://creativecommons.org/licenses/by/4.0/).
How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Han, Y, Tang, A, Südhof, T C and Zhang, B(2026). Simulations. Bio-protocol Preprint. bio-protocol.org/prep3010.
  2. Han, Y., Cao, R., Qin, L., Chen, L. Y., Tang, A., Südhof, T. C. and Zhang, B.(2022). Neuroligin-3 confines AMPA receptors into nanoclusters, thereby controlling synaptic strength at the calyx of Held synapses. Science Advances 8(24). DOI: 10.1126/sciadv.abo4173

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