Microtubule dynamics simulation

Simulation of microtubule growth dynamics in the presence and absence of physical obstacles.

Work done by:

• Simulation code: Florian Huber and Maurits Kok
• Experiments run by: Maurits Kok and Svenja-Marei Kalisch
• Marileen Dogterom

Simulation code

The full simulation code used to produce the results as published in [coming soon] is provided.\ in this repository.
The code consits of the main simulation code (simulation_main.py and simulation_functions.py). Simulation parameters are specified in simulation_parameters.py. Functions for plotting the results are provided in plotting_functions.py.

Requirements

Python version 3.6 or higher.

Installation

If you work with Anaconda you choose to create an own environment for mtdynamics bu running the following commands:

# install mtdynamics in a new virtual environment to avoid dependency clashes
conda create --name mtdynamics python=3.7
conda activate mtdynamics
pip install mtdynamics
pip install jupyter  # Optional, if you want to run jupyter notebooks from this environment
conda install -c anaconda pywin32  # Optional, if you run into win32api error (e.g. when using Python 3.8)

Or simply install mtdynamics in your already existing environment:

pip install mtdynamics

Runing the simulation

Jupyter notebook(s) are provided to illustrate how to run the simlation. They can be found in the folder \notebooks.