A coarse-grain elastic lattice polymer model of bacterial chromosomes

Supercoiled DNA, often adopt tree-like double-folded, randomly branching configurations. In this context, we studied an elastic lattice polymer model for tightly double-folded ring polymers. This model includes the spontaneous creation and deletion of side branches, which move along the tree graph structure due to local mass transport diffusion. We used Monte Carlo simulations to study systems falling into different universality classes: ideal double-folded rings without excluded volume interactions, self-avoiding double-folded rings, and double-folded rings in the melt state. The static properties are in good agreement with exact results, simulations, and predictions of Flory theory. For example, in the melt state rings adopt compact configurations and exhibit territorial behavior. In particular, we show that the emergent dynamics is in excellent agreement with a recent scaling theory. 

We extended our elastic lattice polymer model to investigate structure properties of the supercoiled bacterial chromosome. In particular, we captured universal properties of bacterial DNA from approximately 100 kb to 1 Mb scale using polymer physics. To this end, we rationalized contact properties between chromosomal loci measured in Hi-C methods.