Translocation Time through a Nanopore with an Internal Cavity Is Minimal for Polymers of Intermediate Length

Abstract

The translocation of polymers through nanopores with large internal cavities bounded by two narrow pores is studied via Langevin dynamics simulations. The total translocation time is found to be a nonmonotonic function of polymer length, reaching a minimum at intermediate length, with both shorter and longer polymers taking longer to translocate. The location of the minimum is shown to shift with the magnitude of the applied force, indicating that the pore can be dynamically tuned to favor different polymer lengths. A simple model balancing the effects of entropic trapping within the cavity against the driving force is shown to agree well with simulations. Beyond the nonmonotonicity, detailed analysis of translocation uncovers rich dynamics in which factors such as going to a high force regime and the emergence of a tail for long polymers dramatically change the behavior of the system. These results suggest that nanopores with internal cavities can be used for applications such as selective extraction of polymers by length and filtering of polymer solutions, extending the uses of nanopores within emerging nanofluidic technologies.

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

“…The structure of a flexible or semiflexible linear chain confined in simple geometries such as a slit [3,4,5,6,7,8,9], channel [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29] or spherical cavity [30,31,32,33,34] has been well explored using extensive theoretical, simulation and experimental studies. The related issues also include the translocation of a chain through a pore between interconnected cavities [35,36,37,38,39,40] mimicking the translocation of biomacromolecules across biological membrane or transport mechanism of drug delivery, and the entropy-driven segregation of polymer chains in confining spaces relevant to bacterial chromosome replication and separation upon cell division. Although biomacromolecules of circular topology such as a bacterial DNA or mitochondrial DNA of eukaryotes are quite abundant in biological systems, much less attention is paid to circular polymers in the scientific community.…”

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

“…Presently, the structure of flexible and semiflexible chains confined in objects of simple geometry such as a slit [12][13][14][15][16][17], channel [7,8,[18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35], or sphere [36][37][38][39][40] are well explored at the theoretical, simulation and experimental level. A great deal of attention has been also paid to the translocation of a chain through a pore between interconnected cavities [41][42][43][44][45][46]. This issue is related to the translocation of biomacromolecules across biological membranes, transport mechanism of drug delivery or entropy-driven segregation of polymer chains under geometrical confinement relevant to bacterial chromosome replication and separation upon cell division.…”

Translocation through a narrow pore under a pulling force

“…In the process, the biopolymer must overcome the entropy barrier [1,[26][27][28]. Hence, the methods of PT through the nanopores include the use of external force which is one of the most common methods used both in the laboratory and computational simulations [5,6,[29][30][31][32]. However, in vivo PT driven by assisted proteins called chaperone is proposed [4, [33][34][35][36][37].…”