An elastic lattice polymer model of bacterial chromosomes

Bacterial DNA often adopts tree-like double-folded branching configurations due to DNA supercoiling. In this context, we propose a framework to generate expected bacterial chromosome structures at multiple scales. To this end, we extend our previous model of elastic polymer chains on an FCC lattice for tightly double-folded ring polymers [1] to include the degree of freedom associated with the length of branches. Namely, the model includes the spontaneous creation and deletion of side branches, which move along the tree graph structure due to local mass transport diffusion, and a chemical potential to control the length of branches. The model parameters can then be adjusted to simulate conditions similar to the environment of bacterial chromosomes in terms of DNA concentration, self-avoiding interactions and cylindrical confinement. By introducing a real-space renormalization of branching tree melts, we were able to coarse-grain our model to capture the universal properties of the DNA from 10 kb to 4 Mb scale. As a result, we are able to rationalize from first principles contact properties between bacterial chromosomal loci as measured from high-throughput conformation capture (Hi-C) methods.