Conformation of Flexible and Semiflexible Chains Confined in Nanoposts Array of Various Geometries

The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular dynamics simulations. The geometry of the nanopost array was varied at the constant post diameter d_p and the ensuing modifications of the chain conformation were compared with the structural behavior of the chain in the series of nanopost arrays with the constant post separation S_p as well as with the constant distance between two adjacent post walls (passage width) w_p. The free energy arguments based on an approximation of the array of nanopost to a composite of quasi-channels of diameter d_c and quasi-slits of height w_p provide semiqualitative explanations for the observed structural behavior of both chains. At constant post separation and passage width, the occupation number displays a monotonic decrease with the increasing geometry ratio d_c/w_p or volume fraction of posts, while a maximum is observed at constant post diameter. The latter finding is attributed to a relaxed conformation of the chains at small d_c/w_p ratio, which results from a combination of wide interstitial volumes and wide passage apertures. This maximum is approximately positioned at the same d_c/w_p value for both flexible and semiflexible chains. The chain expansion from a single interstitial volume into more interstitial volumes also starts at the same value of d_c/w_p ratio for both chains. The dependence of the axial chain extension on the d_c/w_p ratio turns out to be controlled by the diameter of the interstitial space and by the number of monomers in the individual interstitial volumes. If these two factors act in the same way on the axial extension of chain fragments in interstitial volumes the monotonic increase of the axial chain extension with the d_c/w_p in the nanopost arrays is observed. At constant w_p, however, these two factors act in opposite way and the axial chain extension plotted against the d_c/w_p ratio exhibits a maximum. In the case of constant post diameter, the characteristic hump in the single chain structure factor whose position correlates with the post separation is found only in the structure factor of the flexible chain confined in the nanopost array of certain value of S_p. The structure factor of the flexible chain contains more information on the monomer organization and mutual correlations than the structure factor of the semiflexible chain. The stiffer chain confined in the nanopost array is composed of low number of statistical segments important for the presence of respective hierarchical regimes in the structure factor.