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

Conformations of DNA inside the phage are crucial in the ejection dynamics. The equilibrium conformation of DNA inside the viral capsid is determined by the shape of the capsid. As there are diverse shapes of viral capsid in nature, one should consider capsid-shapes to understand ejection dynamics. In this study, we investigate the effects of the capsid-shape on the conformation of a polymer and its ejection rate by Langevin Dynamics simulations. We perform ejection simulations of three capsid-shapes; 1) sphere 2) cube and 3) cuboid. From our results, a polymer is ejected faster in case of the sphere compared to other shapes of capsids. Polymer chain ejects 2 and 1.5 times faster from the sphere than the cube and cuboid, respectively. Collective rotational motion of a polymer chain is available inside the sphere confinement, whereas only threading motion is available inside the cube or cuboid confinement. The collective rotational motion increase the mobility of the polymer chain, thus accelerating the ejection process.