Issue 40, 2016

Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel

Abstract

The combined effects of the channel asymmetry and the closed chain topology on the chain extension, structure factor, and the orientation correlations were studied using coarse-grained molecular dynamics simulations for moderate chain lengths. These effects are related to applications in linearization experiments with a DNA molecule in nanofluidic devices. According to the aspect ratio, the channels are classified as a stripe or slabs. The chain segments do not have any freedom to move in the direction of the narrowest stripe size, being approximately the same size as the segment size. The chains of both ring and linear topologies are extended more in a stripe than in a slab; this effect is strengthened for a ring. For a ring in a stripe, the extension–confinement strength dependence leads to effective Flory exponents even larger than 3/4, which is characteristic for a self-avoiding two-dimensional chain. While the chain extension–confinement strength dependence for both topologies conforms to the de Gennes regime in a stripe, a linear chain undergoes gradual transition to the pseudoideal regime as the slab height increases in the slab-like confinement. For a confined circle, the onset of the pseudoideal regime is shifted to larger slab heights. The structure factor confirms the absence of the pseudoideal and extended de Gennes regime in a stripe and the transition from the extended to the pseudoideal regime of a circular and linear chain upon increasing the slab heights.

Graphical abstract: Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel

Article information

Article type
Paper
Submitted
30 Jun 2016
Accepted
06 Sep 2016
First published
06 Sep 2016

Soft Matter, 2016,12, 8425-8439

Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel

Z. Benková, P. Námer and P. Cifra, Soft Matter, 2016, 12, 8425 DOI: 10.1039/C6SM01507G

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements