End‐Pulled Translocation of a Star Polymer Out of a Confining Cylindrical Cavity

Abstract

dispersant, potential drug delivery agents, thermoplastic elastomers, surfactants, and lubricants. [2,3,5] In addition, more recently, there is an increased interest in the biomedical field for using star-shaped macromolecules as drug release carriers by immobilizing biologically active molecules on their arms. [6-8] Polymer translocation through a nanopore is a fundamental process in diverse biological systems, including DNA and RNA translocation across nuclear pores, protein transport through membrane channels, and virus injections. [9-12] It also has advanced applications in rapid DNA sequencing, gene therapy, and controlled drug delivery. [13-20] Moreover, the study of translocation has involved complex setups such as gel matrix usage on different sides of a plane wall, [21-23] polymer ejection from micro-channels [24] and nanometric size channels, [25] and DNA molecules trapping inside a bounded cavity during the course of translocation. [26] In this respect, several experimental, [27-32] numerical, [33-38] and theoretical [39-51] studies have focused on the dynamical aspect of the translocation mechanism of linear chains [52-57] as well as star polymers. [58-61] Forced and unforced translocations of linear polymers through nanoscopic pores have been extensively studied and are still the topic of theoretical, numerical, and experimental investigations. [62-64] These processes are often complex by their own right, a complexity due to the great number of parameters involved. Indeed, translocation processes can be affected by different factors, such as the initial chain conformation, the size of the chain, the driving force (if any), and the confining geometry. For instance, forced translocation may involve the presence of a flowing fluid due to a chemical difference between the two sides of the pore, [65,66] of an electric field in the case of charged polymers, [67,68] or of a pulling force applied on a portion of the chain. [69,70] Huopaniemi et al. have studied the scaling relation between the mean translocation time 〈τ〉 and the chain mass N for a single linear chain subject to a pulling force F. [53] The authors suggested 〈τ〉 ≈ N 2 for both strong and moderate forces. They also found that 〈τ〉 scales with N as 〈τ〉 ≈ N 2ν + 1 for weak force regime, where ν is the Flory exponent in good solvent. The distribution of translocation times was found to be symmetric and narrow for strong F. Furthermore, they have found that the dependence of the mean translocation time on pulling force exhibits a scaling relation 〈τ〉 ≈ F −1. D. Sean and G. W. Slater A Langevin dynamics computer simulation is carried out to study the translocation of a single homogeneous star polymer out of a cylindrical cavity connected to a membrane wall with a circular nanopore along the tube axis. The ejection process is driven through an external pulling force applied on the free end monomer of the chain leading arm. The results show that, for a given chain mass and for relatively narrow pores, the mean translocation time 〈τ〉 exhibits a non-mono...

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

“…The first theoretical study of pulled polymer translocation was performed by Kantor and Kardar [ 55 ], predicting for moderate pulling forces. This was followed by a number of theoretical and numerical studies reporting the scaling behavior under different force regimes as well as different states of polymer [ 81 , 82 , 83 , 84 , 85 , 86 ]. The scaling exponents for various models, for both unbiased and driven translocation, are tabulated by Palyulin et al in their review article [ 21 ].…”

“…Chen et al [ 95 ] studied the pulled translocation of a compact globule and it was shown that the translocation could be controlled by changing the monomer–monomer interaction. Tilahun et al simulated the pulled translocation of a star polymer and studied the dependence of on the chain functionality and mass, as well as on the magnitude of the pulling force [ 86 ]. Another approach, based on the same principle as pulled translocation but less explored, involves immobilizing the DNA strand by tethering it to a bead or a probe.…”