Effect of chain stiffness for semiflexible macromolecules in array of cylindrical nanoposts

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.