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Correction published on 1 December 2017, see Polymers 2017, 9(12), 665.

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Polymers 2017, 9(8), 313; https://doi.org/10.3390/polym9080313

Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts

1
Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 41 Bratislava, Slovakia
2
LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre 687, 4168-007 Porto, Portugal
*
Author to whom correspondence should be addressed.
Received: 2 July 2017 / Revised: 24 July 2017 / Accepted: 25 July 2017 / Published: 28 July 2017
(This article belongs to the Special Issue Knotted and Catenated Polymers)
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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 dc and a slit approximating the passage aperture with the width wp. The number of interstitial volumes occupied by a chain monotonically increases with the decreasing ratio dc/wp 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. View Full-Text
Keywords: semiflexible circular chain; array of nanoposts; confinement; DNA; molecular dynamics; microfluidic devices semiflexible circular chain; array of nanoposts; confinement; DNA; molecular dynamics; microfluidic devices
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
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Benková, Z.; Rišpanová, L.; Cifra, P. Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts. Polymers 2017, 9, 313.

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