Study of ejection dynamics of a semi-flexible polymer from a nano-sphere using molecular dynamics simulation compared with theory

Abstract

There are many biological phenomena and novel applications that require confinement of polymer and then its ejection from spherical geometries, such as the gene ejection from its capsid in gene therapy or the ejection of the genetic substance of the virus from its capsule. DNA is one of the most important biopolymers, which is confined within a (three-dimensional) restriction or the nucleus of the cell. To investigate the dynamics of the ejection of these confined chains, one can consider a semi-flexible polymer chain confined inside a nano-sphere. Sakaue described static configurations of a semi-flexible polymer chain with length L and width b confined in a nanosphere with diameter D in a wide range of persistence lengths l within five different regimes [1]. In our past studies, we presented a theory to describe the ejection dynamics of a semi-flexible polymer chain from the sphere. Accordingly, the ejection times of a semi-flexible polymer were calculated for the five regimes [2]. In the present study, using molecular dynamics simulations, the ejection of semi-flexible polymer in the regime (V), the so-called bending regime, is investigated. The bending regime is mostly applicable for biological structures, because the persistence length of the double-stranded DNA is large. The boundaries for this regime is shown by the relation (Lb^2 )^(1/3)