Writhe, Twist and Radius of Gyration Analysis on Course-Grained Supercoiled DNA Models

DNA replication, translation, and storage are essential to the functions of life. DNA storage and packing impact gene expression in both prokaryotic and eukaryotic cells. Chromosomal DNA is an exotic and poorly understood phase of soft matter. From experiment, we know that the density of DNA packing reached, requires the help of proteins referred to as nucleoid-associated proteins (NAPS). We simulated simple circular bacterial chromosomes with varying amounts of NAPS. Using a course-grained DNA model, we have performed molecular dynamics methods using the LAMMPS software. We have analyzed our simulations to determine the writhe, twist, and radius of gyration of DNA for varying NAPs concentrations. These techniques allow us to see details which no microscope or experimental method can uncover. This is a first step towards our ultimate goal of producing a physically, chemically, and biology accurate simulation of the entire DNA condensing and division process of a prokaryotic cell.