Effect of Inhomogeneity in Translocation of Polymers through Nanopores

Details Effect of Inhomogeneity in Translocation of Polymers through Nanopores Effect of Inhomogeneity in Translocation of Polymers through Nanopores

2006-06-28

arxiv.org/abs/cond-mat/0606739v1

Physics

Condensed Matter

Statistical Mechanics

12 pages, 5 figures, submitted to J. Chem. Phys

Scientific paper

10.1063/1.2338539

The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the single-stranded chain can go through the nanopore the double-stranded segment has to unzip before the translocation. Utilizing a simple analytical model, translocation times are calculated explicitly for different polymer orientations, i.e., when the single-stranded block enters the pore first and when the double-stranded segment is a leading one. The dependence of the translocation dynamics on external fields, energy of interaction in the double-stranded segment, size of the polymer and the fraction of double-stranded monomers is analyzed. It is found that the order of entrance into the pore has a significant effect on the translocation dynamics. The theoretical results are discussed using free-energy landscape arguments.

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