Brownian Dynamics Simulation of Dps:DNA Condensate Formation in Starved E. Coli

The spatial organization of membraneless organelles and biomolecules is essential for bacterial function. In this study, we develop a minimal 3D biophysical model to investigate how starved E. coli re-organizes its DNA using Dps proteins. We model DNA as polymers made of beads connected by springs, with stretching and bending informed by experiments, and represent Dps proteins as spherical particles. We use the Lennard-Jones potential for Dps-DNA interactions to describe short range repulsion and long range attraction forces. Interactions between Dps-Dps and DNA-DNA are described using a Weeks-Chandler-Andersen for a purely repulsive interaction. We simulate the system’s evolution using overdamped Langevin dynamics, and explore condensate formation and morphology. We analyze the emergent structures through spatial morphologies, spatial correlation functions, and Dps particle trajectories. Our results show that condensate formation depends on the concentrations of Dps and DNA, as well as their interaction strength. Low Dps concentrations lead to network-like structures, while higher concentrations result in condensates, with larger DNA concentrations producing larger condensates. Finally, our results qualitatively replicate condensate morphologies observed in experiments.