Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere

Area of Science:

• Biophysics
• Computational Biology
• Cell Biology

Background:

• Chromatin, the complex of DNA and proteins, undergoes dynamic rearrangements within the cell nucleus.
• Active processes, driven by molecular motors, are crucial for chromatin organization and function.
• Understanding chromatin dynamics in confined cellular environments is essential for cell biology.

Purpose of the Study:

• To model and analyze the hydrodynamic behavior of active chromatin within a confined geometry simulating the cell nucleus.
• To investigate chromatin polymer dynamics driven by polar-symmetry motors in both linear and nonlinear regimes.
• To elucidate the influence of boundaries on chromatin flow patterns.

Main Methods:

• Development of a hydrodynamic model for active chromatin dynamics.
• Application of analytical and numerical methods to solve the model.
• Utilizing vector spherical harmonics to describe flow geometry in confinement.

Main Results:

• Identified steady, transverse chromatin flows circulating around the spherical domain in the long-term nonlinear regime.
• Demonstrated that these circulating flows are robust to perturbations.
• Established that the characteristic size of these flows is determined by the domain size.

Conclusions:

• Confinement in a cell nucleus leads to robust, circulating chromatin flows driven by active motor processes.
• Vector spherical harmonics provide a powerful tool for analyzing confined active matter systems.
• The findings offer foundational insights for more complex models of active chromatin dynamics within the nucleus.