Binding to Sliding Nucleosomes

Linear polymer model with sliding binding sites.

Setup

1. Clone this repository to your local machine.

$ git clone https://github.com/JosephWakim/sliding_nucleosome.git

2. Navigate to the repository on your local machine.

$ cd sliding_nucleosome

3. We manage dependencies with Anaconda. Please install Anaconda before installing this codebase. Details for installing Anaconda can be found here. With Anaconda installed, please run the make.sh script to create a new conda environment called slide with all dependencies. Please note that this will overwrite any existing conda environment called slide.

$ bash make.sh

4. Activate the slide conda environment.

$ conda activate slide

Theory

For the derivation of the theory underlying the sliding nucleosome and associated binding models, please visit this link.

Examples

Using our theory, we simulate ensembles of linear, euchromatic fibers, and we evaluate the resulting linker-length distributions. These examples are implemented in Jupyter notebooks in the examples/ directory of this repository.