Abstract:The structural properties of a flexible and semiflexible circular chain confined in an array of parallel nanoposts with a square lattice cross-sectional projection were studied using coarse-grained molecular dynamics simulations. To address the effect of the circular topology, a comparison with linear analogs was also carried out. In the interpretation of the chain structural properties, the geometry of the post array is considered as a combination of a channel approximating the interstitial volume with the diameter d c and a slit approximating the passage aperture with the width w p . The number of interstitial volumes occupied by a chain monotonically increases with the decreasing ratio d c /w p regardless of the way the geometry of the post array is varied. However, depending on how the array geometry is modified, the chain span along the posts displays a monotonic (constant post separation) or a non-monotonic behavior (constant passage width) when plotted as a function of the post diameter. In the case of monotonic trend, the width of interstitial spaces increases with the increasing chain occupation number, while, in the case of non-monotonic trend, the width of interstitial spaces decreases with the increasing chain occupation number. In comparison with linear topology, for circular topology, the stiffness affects more significantly the relative chain extension along the posts and less significantly the occupation number. The geometrical parameters of the post arrays are stored in the single-chain structure factors. The characteristic humps are recognized in the structure factor which ensue from the local increase in the density of segments in the circular chains presented in an interstitial volume or from the correlation of parallel chain fragments separated by a row of posts. Although the orientation correlations provide qualitative information about the chain topology and the character of confinement within a single interstitial volume, information about the array periodicity is missing.

Equilibrium conformation of a semiflexible macromolecule in an array of nanoposts exhibits a non-monotonic behavior both at variation of the chain stiffness and increased crowding imposed by nanoposts. This is a result of the competition between the axial chain extension in channel-like interstitial volumes between nanoposts and the chain partitioning among these volumes. The approximation of a nanopost array as a combination of a quasi-channel and a quasi-slit like geometry semi-qualitatively explains the behavior of a chain in the array. In this approximation, the interstitial spaces are viewed as being of the channel geometry, while the passages between two adjacent posts are viewed as being of the slit geometry. Interestingly, the stiffer chains tend to penetrate more readily through the passage apertures, in the direction perpendicular to the post axes, and thus to occupy more interstitial volumes. This is consistent with the prediction of the free-energy penalty that is lower for a stiffer chain at strong slit-like confinement. These findings can find applications in the control of macromolecular conformations in recent nanotechnological techniques with bio-macromolecules such as a DNA.

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