The effects of the structure of a confinement on the ejection rate of a polymer chain from a nanopore

Conformations of DNA inside the phage are crucial to the ejection dynamics of the DNA. The equilibrium conformation of DNA inside the viral capsid is determined by the shape of the capsid (confinement): a concentric spool DNA and a folded twist DNA are considered equilibrium conformations in a spherical capsid and an elongated capsid, respectively. Because there are a variety of viral capsids in nature, the correlation between the capsid shape and the ejection dynamics should be a topic of interest. In this study, we investigate the effects of the capsid shape on the conformation of a polymer and its ejection rate by performing Langevin Dynamics simulations. We employed two different types of capsid: 1) sphere and 2) cube capsids. We find that a polymer chain ejects out of the capsid faster in case of the sphere than the cube capsid and that the ejection rate becomes faster by up to 35% as the rigidity of the polymer increases. The segments of the polymer near the wall of the capsid travel faster than other segments, regardless of the capsid shape. However, a larger fraction of the monomers are distributed near the wall in case of the sphere capsid than the cube capsid.