Processivity

The processive grappling motor model for active chromosome.

✨ Features

• Simulates the processive grappling motor
• Implements Condensin I / II motor activity models with residence time and extrusion speed.
• Compatible with OVITO for visualization of .dump and .data trajectory files

📦 Dependencies

• CUDA ≥ 11.2
• Make ≥ 4.2.1
• gcc (GCC) 9.3.1
• OS: CentOS Linux 7 (Core) 7.9.2009

🚀 Usage

Clone the repository and compile the code:

git clone git@github.com:CaOaC/Processivity.git


cd Processsivity/src

# Prepare the input and output folders (准备输入和输出文件夹)

mkdir Input Output


# Compile and run the program (构建并运行程序)
make -j8

./kickModel

📺 Demo

You can load the following files from the Output Output directory into OVITO to visualize the simulation trajectory.

• .dump file: trajectory animation
• .data file: topological structure

🎞️ movie

Visualize for the mitotic chromosome folding by processive grappling motors

Visualize for the steady states

🧾 Information

Here we provide the codes for the manuscript "Theory of Chromosome Structural Dynamics by Processive Loop Extrusion". The provided files contain the codes that were developed based on the processive grappling motor model to study chromatin jets and mitotic chromosome folding.