awakenedhaki / mnase-simulation

Monte Carlo simulation of 11nm DNA fibre digestion by MNase

Micrococcal Nuclease Simulation

This repository contains a Python-based simulation that models the action of Micrococcal Nuclease (MNase) on DNA 11nm fibres. The core components of the simulation include:

• Fibre Class: Represents the 11nm DNA fibre structure, including nucleosomes and linker DNA segments.

• MNase Class: Simulates the stochastic cleavage action of MNase on DNA fibres, randomly selecting nucleosomes and linkers for enzymatic digestion.

• Main Simulation Logic: Orchestrates the simulation over a series of time steps, continuously updating the state of the DNA fibres based on MNase action.

Key Features:

• Stochastic Modelling: Utilizes Monte Carlo methods to realistically simulate the random nature of enzymatic cleavage on DNA.

• Object-Oriented Approach: Employs classes to effectively represent complex biological entities and their interactions.

• Statistical Analysis: The output, consisting of the lengths of DNA fibres post-MNase treatment, is suitable for further statistical analysis to understand the distribution and average effects of the nuclease.

Objectives

• Initialize git repository
• Create boilerplate files
  • README.md
  • .gitignore
  • main.py
  • model/__init__.py
• Define classes
  • Fibre (data structure)
    • Define attributes: n_nuclesomes, left_linker, right_linker
    • Implement constructor (__init__ method)
    • Implement method to determine number of nucleotides in Fibre
  • MNase (namespace)
    • Implement method to select a random nucleosome index
    • Implement method to select either the left or right linker to cleave
    • Implement method to cleave the fibre
• Implement Visualization
  • Install matplotlib
  • Define a function to visualize distribution of fibre lengths as a histogram
  • Define a function to visualize fibre length over time