Simulating Dynamic Chromosome Compaction: Methods for Bridging In Silico to In Vivo

Area of Science:

• Biophysics
• Computational Biology
• Genetics

Background:

• Chromosome structure and dynamics are crucial for cellular functions.
• Polymer models offer a powerful framework to study these properties.
• Existing molecular dynamics studies are distinct from polymer-based approaches.

Purpose of the Study:

• To develop and present a polymer dynamics model for simulating budding yeast chromatin.
• To incorporate features for modeling the nucleolus and transient chromosomal cross-links.
• To provide a predictive, stochastic model for analyzing chromosome spatiotemporal organization.

Main Methods:

• Utilized well-established bead-spring polymer models.
• Developed a C++ simulation environment with DataTank as a user interface.
• Simulated chromatin fibers in a viscous nuclear environment.

Main Results:

• The model successfully simulates budding yeast chromatin fibers.
• Features for nucleolus creation and protein-mediated cross-links were implemented.
• The simulation provides real-time visualization and data analytics via DataTank.

Conclusions:

• The polymer physics model offers versatile analyses of chromosome spatiotemporal organization.
• The simulation pipeline provides insights into the entangled chromosome milieu.
• Generated simulated chromosome data can be directly compared with experimental observations.