From Equilibrium to Non-equilibrium: Multiscale Modeling of Nucleoid Compaction and Separation in Escherichia coli

The organization and spatial localization of bacterial chromosomes is fundamental to cellular function, requiring DNA molecules with contour lengths of millimeters to not only compact into cells just micrometers in size, but also to separate properly during cell division — all without the membrane-bound organelles found in eukaryotes. This thesis investigates the physical mechanisms governing nucleoid compaction and separation in Escherichia coli through three complementary approaches that bridge equilibrium thermodynamics and out-of-equilibrium cellular processes.

We first develop a comprehensive free energy model to quantify the contributions of different macromolecular crowders to nucleoid compaction. We find that while polyribosomes initiate phase separation between the nucleoid and cytoplasm, cytosolic proteins primarily control the homeostatic nucleoid size, with protein concentration fluctuations near physiological levels capable of inducing rapid changes in nucleoid volume.

Next, we extend this framework to an one-dimensional reaction-diffusion model incorporating transcription, translation, and mRNA degradation to capture the spatiotemporal dynamics of DNA and ribosomes during the cell cycle. The model demonstrates that active polysome production within the nucleoid creates an instability that drives nucleoid splitting into two distinct lobes, with the accumulation of polysomes at mid-cell providing a mechanism for chromosome separation consistent with experimental observations.

To address limitations of continuum models, we implement molecular dynamics simulations in LAMMPS with explicit central dogma reactions, maintaining DNA chain connectivity and three-dimensional geometry. These simulations reveal that transcriptional activity expands the nucleoid proportionally to active RNA polymerase numbers, and that active processes are essential for complete chromosome separation. Without them, sister chromosomes remain in contact despite entropic forces. The results from the simulations also exhibits large stochastic fluctuations, which is absent in the previous one-dimensional reaction-diffusion model.

Collectively, the integration of equilibrium thermodynamics, reaction-diffusion dynamics, and molecular simulations provides a multi-scale framework demonstrating how active cellular processes couple with physical forces to organize genetic material. Our findings have implications for understanding the evolution of cellular organization of bacteria and the development of antibiotics targeting chromosome dynamics. The methodologies developed here — from analytical free energy models to large-scale molecular simulations — offer tools for investigating similar organizational principles in other cellular systems lacking membrane-bound compartments.