# LUTsyn model demonstration files
by Duy-Tan Jonathan Pham (duytanph@usc.edu)  
August 11, 2021

See paper: "Bridging hierarchies in multi-scale models of neural systems: Look-up tables enable computationally efficient simulations of nonlinear synaptic dynamics" (Pham et al., 2021)

## Running Instructions

- [Download look-up table files (LUTs.zip)](/data/267103/LUTs.zip)  
  - ensure the two folders containing the LUT files are located in your working directory
- Execute terminal command `nrnivmodl` within the working directory that contains all files including `.mod` files
- Execute terminal command `python LUTsyn_example_main.py` to run example code that compares multiple synapse model outputs

## Description of included files

- `LUTsyn_example_main.py`  
  This file contains the main Python script to run a demonstration of the LUTsyn model, as well as the kinetic and exponential models and plots a comparison between the models. Both AMPA and NMDA receptors are simulated and compared. This was tested using Python 3.5 and NEURON v7.6.7.  
  - **NOTE:** Please be sure to run `nrnivmodl` in terminal/command prompt in your working directory that contains the `.mod` files before running this script.

- `LUTsyn_example_functions.py`  
  This file contains the supporting functions that are used in `LUTsyn_example_main.py` which take care of executing NEURON simulations and instantiating the synapse mechanisms.

- `AMPA16v8_noNetCon.mod`  
  `.mod` file that implements the 16 state kinetic model for AMPA

- `E3_NMDA_v2.mod`  
  `.mod` file that implements NMDA dynamics using a linear triple exponential

- `exp2syn_v2.mod`  
  A modified version of NEURON's native `exp2syn` mechanism to represent AMPA dynamics using a linear double exponential function

- `LUTsyn_AMPA_4th_E3_dtc.mod`  
  Implementation of the AMPA LUTsyn model.

- `LUT_AMPA_kinetic_g_4th_M300ms_d1ms_NT0.1_DIFF_v3.npy`  
  This file represents the look-up table data structure that holds the amplitude values for the AMPA LUTsyn model.

- `LUTsyn_NMDA_5th_E3_dtc.mod`  
  Implementation of the NMDA LUTsyn model.

- `LUT_NMDA_kinetic_OSP_5th_M1000ms_d5ms_NT0.1_DIFF_v3.npy`  
  This file represents the look-up table data structure that holds the amplitude values for the NMDA LUTsyn model.

- `negative_init.hoc`  
  File that implements an initial simulation that has reached steady-state

- `NMDA_v6_3_opt.mod`  
  `.mod` file that implements the 15 state kinetic model for NMDA

- `NTDiffusion.mod`  
  `.mod` file that implements presynaptic glutamate release (concentration). This mechanism runs in series with the kinetic models.

- `vecstim.mod`  
  `.mod` file for creating vectors that contain stimulation patterns

## Changelog

- 2022-12: Updated MOD files to contain valid C++ and be compatible with the upcoming versions 8.2 and 9.0 of NEURON.
- 2025-10-17: Fixed data download link and converted readme to markdown.