This project implements the Gillespie algorithm to simulate a chemical reaction network consisting of three species: A, B, and C. The simulation runs for a total time of 50.0 seconds and outputs the molecule counts for each species at every second.
- Implementation of the Gillespie algorithm for simulating chemical reactions
- Support for customizing the rate constants, initial molecule counts, and simulation time
- Outputs the molecule counts for each species at every second during the simulation
- Uses NumPy for efficient array operations
- Includes a visualization of the simulation using Matplotlib
- Clone this repository and install the required dependencies:
git clone https://github.com/your-username/gillespie-algorithm-simulation.git
cd gillespie-algorithm-simulation
pip install -r requirements.txt- Run the simulation using the following command:
python simulate.py- The output will be saved in a CSV file named** **
output.csv. You can view the plot of the simulation by running:
python plot.py- To customize the simulation parameters, modify the corresponding variables at the beginning of the** **
simulate.pyfile.
rate_A_to_B: the rate constant for the reaction A -> B (default: 1.0)rate_B_to_C: the rate constant for the reaction B -> C (default: 0.5)initial_A: the initial number of molecules of species A (default: 100)initial_B: the initial number of molecules of species B (default: 0)initial_C: the initial number of molecules of species C (default: 0)simulation_time: the duration of the simulation (default: 50.0)
Contributions are welcome! If you would like to contribute to this project, please fork it and submit a pull request with your changes.
This project is licensed under the MIT License. See LICENSE.txt for details.
Thanks, Dr.William Richardson, University of Arkansas for his contributions and support.