Brownian Dynamics of a Microsphere attached to a Worm-like Chain polymer

WLC-BD is a Python implementation of the Brownian Dynamics Simulation for the Worm-Like Chain (WLC) model.

Overview

This script performs a simulation of the Worm-Like Chain (WLC) model for a magnetic bead system. It calculates the force-extension relation and simulates traces for different forces using the Milstein solver. The simulation parameters and global constants are defined at the beginning of the script. The simulation results are saved in a pickle file named tracesimulations.pickle.

This script requires the autograd, scipy, and multiprocessing libraries to be installed.

Model

The model assumes the worm-like chain is attached to a hard wall located at $$z=0$$, The other end of the chain is attached to a microsphere which is pulled along the positive $$z$$-axis with a force $$F_{mag}$$. The hydrodynamic effect of the hard wall is modelled by the Faxén correction of the Stoke's drag.

Features

• Simulates the Brownian motion of the microsphere using Milstein method.
• Automatically choses the time step to be 2 orders of magnitude smaller than the charactristic time of the motion

Usage

Modify the "Global Parameters for the simulation" given at the beginning of WLC_BD_simulation.py and to run a simulation, use the following command:

python WLC_BD_simulation.py

License

This project is licensed under the MIT License. See the LICENSE file for details.

Contact

For any questions or suggestions, please open an issue or contact the repository owner.