The effects of packaging on the ejection rate of a polymer from a nanopore

DNA ejection and packaging are related in terms of DNA conformation. As the DNA becomes jammed, it cannot undergo dramatic conformational change in the capsid. That is, final conformation after packaging may be correlated with the conformation right before ejected. Then, a scientific question arises; whether a packaging process affects the ejection rate or not. In this work, we find three regimes of ejection processes: (1) knot dominant, (2) non-equilibrium dominant and (3) effective-ejection regime. We perform Langevin dynamics simulations of a semi-flexible single chain with 660 monomers. We package the chain with different packaging rates into a nanopore and eject the chain subsequently. If the chain is packaged slowly enough to be knotted, its ejection process becomes slow (~35%). Also, if the chain is packaged too fast to relax its conformation, its ejection rate decreases (~20%). Then, if a packaging rate is moderate (3), where DNA can relax but cannot be knotted, DNA ejects faster than other regimes. Our results show that ejection dynamics is determined by the history of packaging and suggest that there could be most effective packaging rate for ejection process in nature.