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PyColi

Simple model of E. coli in a nutrient soup.

I cover the results of simulations in my substack article Life Without a Brain.

Usage

Clone the repository
Install the requirements with pip3 install -r requirements.txt
Run python3 main.py to run the simulation

To change the parameters of the simulation, update via the command line arguments:

--time_steps to change the number of simulation steps
--grid_size_x and --grid_size_y to change the size of the grid
--move_function to change the movement function of the bacteria. See Move section below
--placement to change the initial placement of the bacteria (random or center)

Example: python3 main.py --grid_size_x 100 --grid_size_y 100 --consumption_rate 0.1 --placement center

The script will run the simulation and save the movement in a gif

At some point I will try and see if I can visually replicate this video of E. coli in a nutrient soup: https://youtu.be/F6QMU3KD7zw?si=3CpUbphJo2pg7ATN

Move Functions

random_walk - Randomly move in any direction
biased_random_walk - Randomly move in any direction, but with a bias towards higher nutrient concentrations
biased_random_walk_with_memory - biased random walk with memory of the previous nutrient concentration and additional bias to higher concentrations

Results

Random Walk

Biased Random Walk

Biased Random Walk with Memory