Condensation dynamics of sticky and anchored flexible biopolymers

TL;DR

This study uses simulations and a free-energy model to understand how long, anchored biopolymers like DNA condense over time through ripening and merging pathways, revealing key factors influencing gene regulation.

Contribution

It introduces a minimal mechanistic free-energy model that captures the dynamics of biopolymer condensation, advancing understanding beyond equilibrium theories.

Findings

Identified two main dynamical pathways: ripening and merging.

Demonstrated how kinetic parameters and mechanical constraints influence condensation.

Provided a scaling law for the condensation process.

Abstract

Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use coarse-grained 3D Brownian-dynamics simulations to study how long, end-anchored biopolymers condense over time due to transient crosslinking. By tracking how clusters nucleate, merge, and disappear, we identify two dominant dynamical pathways, ripening and merging, that govern the progression from an uncompacted chain to a single condensate. We show how microscopic kinetic parameters, protein density, and mechanical constraints shape these pathways. Using insights from the simulations, we construct a minimal mechanistic free-energy model that captures the observed scaling behavior. Together, these results clarify the dynamical determinants of DNA and chromatin reorganization on timescales relevant to gene regulation.