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)
  • 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.