The effects of a knot and its conformational relaxation on the ejection of a single polymer chain from confinement
CB Park and S Kwon and BJ Sung, JOURNAL OF CHEMICAL PHYSICS, 151, 054901 (2019).
The ejection of a single polymer chain out of confinement is a ubiquitous phenomenon in various engineering and biological processes. A virus, for example, ejects a DNA from its viral capsid to a host cell in order to infect the host. The ejection of a polymer chain is often relatively fast such that the polymer hardly relaxes its conformation and stays in nonequilibrium states during the ejection. However, the effects of the nonequilibrium conformation on the ejection process still remain unanswered, especially when a complicated conformation such as a knot exists. In this study, we employ a generic coarse-grained model and perform extensive molecular simulations to investigate how the knot and its conformational relaxation would affect the kinetics of the ejection process. We find that the ejection becomes slower by a factor of nine or more when the polymer chain forms a knot conformation inside the confinement. The knot conformation makes the polymer chain highly tensed, thus hindering the polymer from being pulled from the capsid. In order to investigate the effect of the knot and its conformational relaxation systematically, we tune the molecular parameters of the polymer chain and control the degree of relaxation of the knot conformation. The relaxation of the knot conformation facilitates the ejection process significantly.
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