Confinement dynamics of a semiflexible chain inside nano-spheres

TL;DR

This study investigates how a semiflexible chain, modeled after DNA, adopts different conformations inside nano-spheres under two confinement methods, revealing spiral and tennis-ball structures influenced by confinement process and rate.

Contribution

It introduces a detailed molecular dynamics simulation of DNA-like chains confined in nano-spheres, comparing two confinement procedures and their effects on chain conformations.

Findings

Chains form spiral or tennis-ball structures inside nano-spheres.

Tennis-ball structures are more common in tighter confinements.

Confinement process and rate significantly influence chain structure.

Abstract

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the chain for two different sizes of the spheres are studied in both procedures. It is shown that for the confined chains in the sphere sizes of our study, they appear in spiral or tennis-ball structures, and the tennis-ball structure is more likely to be observed in more compact confinements. Our results also show that the dynamical procedure of confinement and the rate of the confinement are influential parameters of the structure of the chain inside spherical cavities.