Glutamate Diffusion and Receptor Activation Model

Computational model for simulating glutamate diffusion in extracellular space and subsequent NMDA/AMPA receptor activation with biophysically realistic kinetics.

This repository contains MATLAB code supporting a study submitted to Nature Communications.

🚀 Quick Start

For MATLAB Users

git clone https://github.com/RusakovLab/NatureComm.git
cd NatureComm

1. Open MATLAB R2022b
2. Add the main directory to your MATLAB path
3. Configure InputParametersSR.m and statisticSR.txt
4. Run DiffusionGlutamateBalls.m

For Non-MATLAB Users (Demo)

1. Navigate to Demo/ directory
2. Install MATLAB Runtime R2022b from MATLAB_Runtime_R2022b_Update_10_win64.zip
3. Run DiffusionGlutamateBalls.exe

📋 System Requirements

Component	Requirement
OS	Windows 10/11 (64-bit recommended)
MATLAB	R2022b (required for .m files)
RAM	16 GB+ recommended
Storage	~1 GB for full output
Processor	Tested on Intel i9-12900K & UCL HPC Cluster

⏱️ Performance Benchmarks

System	Configuration	Particles	Runtime
Local PC (i9-12900K)	Demo executable	100	~20 min
Local PC (i9-12900K)	Full MATLAB simulation	5,000	~8 hours
UCL HPC Cluster	Full MATLAB simulation	5,000	~2 hours

🔬 Model Components

Glutamate Diffusion

• Primary script: DiffusionGlutamateBalls.m
• Simulates molecular diffusion in extracellular space
• Accounts for spherical obstacles and adhesion binding

Receptor Models

NMDA Receptors

• Script: NMDA_SpaceSR.m
• Biophysically realistic kinetics

AMPA Receptors

• Main script: RunAmpa.m → calls Unified_AMPA_SpaceSR.m
• Three kinetic models:
  • Patneau-Mayer (AMPA.m): 6-state model
  • Raman-Trussell (AMPA1.m): Dual open-state model
  • GluR1-based (AMPA2.m): 12-state ligand binding model

📊 Output Files

File Pattern	Content
Balls distribution *.txt	Spherical obstacle coordinates & radii
DistanceFree *.txt	Free glutamate space-time distribution
DistanceBound *.txt	Bound glutamate space-time distribution
PD 0.1/0.3/1/3 ms *.txt	Molecular positions at specific timepoints

🛠️ Usage Workflow

Step 1: Configure Parameters

Edit simulation settings in:

• InputParametersSR.m - Core parameters (domain size, molecule count, release radius)
• statisticSR.txt - Statistical parameters (trials, adhesion probabilities)

Step 2: Run Diffusion Simulation

DiffusionGlutamateBalls.m

Step 3: Simulate Receptor Dynamics

% For NMDA receptors
NMDA_SpaceSR.m

% For AMPA receptors (all models)
RunAmpa.m

Step 4: Visualize Results

PlotDataControl.m

⚙️ Configuration Options

Switching Between Free/Bound Molecules

In Unified_AMPA_SpaceSR.m, modify the filePattern:

% For free glutamate molecules
filePattern = fullfile(myFolder, 'DistanceFree*.txt');

% For adhesion-bound molecules  
filePattern = fullfile(myFolder, 'DistanceBound*.txt');

📈 Reproducing Manuscript Results

1. Run diffusion simulations with N = 1,000 and N = 5,000 particles:

   DiffusionGlutamateBalls.m

2. Simulate receptor activation:

   RunAmpa.m        % For AMPA receptors
   NMDA_SpaceSR.m   % For NMDA receptors

3. Analyze and compare using test data from DataforAMPAandNMDATesting/ folder

4. Generate visualizations:

   PlotDataControl.m

📁 Repository Structure

NatureComm/
├── Demo/
│   ├── DiffusionGlutamateBalls.exe
│   └── MATLAB_Runtime_R2022b_Update_10_win64.zip
├── DataforAMPAandNMDATesting/
├── InputParametersSR.m
├── statisticSR.txt
├── DiffusionGlutamateBalls.m
├── NMDA_SpaceSR.m
├── RunAmpa.m
├── Unified_AMPA_SpaceSR.m
├── AMPA.m / AMPA1.m / AMPA2.m
└── PlotDataControl.m

📝 License

This MATLAB 2022b was used under the University College London academic use license.

📚 Citation

If you use this code in your research, please cite the associated paper submitted to Nature Communications.

🤝 Contributing

This repository supports a specific research publication. For questions or collaboration inquiries, please contact the corresponding author.

📞 Contact

Corresponding Author: Leonid Savchenko
Institution: UCL Institute of Neurology
Repository: https://github.com/RusakovLabMonteCarloSynapse

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