title: Effect of orientation in translocation of polymers through nanopores.
abstract: 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.
authors.affiliation: Department of Chemistry, Rice University, Houston, TX 77005-1892, USA.
authors.forename: Stanislav
authors.initials: S
authors.lastname: Kotsev
authors.forename: Anatoly B
authors.initials: AB
authors.lastname: Kolomeisky
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D004058:Diffusion; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009068:Movement; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*; D011108:Polymers / Q000737:chemistry*; D016062:Porosity; D013816:Thermodynamics
chemical_list: D011108:Polymers