Dynamics of DNA knots and links in ionized fluid

Knotted and linked DNA occurs as a result of cellular replication and DNA compaction processes. The goal of this work is to model the dynamics of knotted and linked DNA in ionized fluid. We explore stable equilibrium configurations of knotted DNA plasmids and Hopf links of kinetoplast DNA. We build upon two existing immersed boundary methods of DNA modeled as an elastic rod in fluid. The first is a deterministic model accounting for mechanical and electrostatic interactions of DNA with Navier-Stokes flow. The second is a stochastic model additionally accounting for thermal fluctuations with Stokes flow.