Polyelectrolyte Translocation through a Corrugated Nanopore

Nagarajan, K.; Chen, Shing Bor

doi:10.1002/mats.202000042

Cited by 4 publications

(4 citation statements)

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“…This controlled transport of DNA molecules proved to be a success to detect various folded configurations of DNA inside conical nano capillaries [54]. In a computational study, different types of channels are modeled so far to study the effect of pore-polymer interaction on the translocation processes [55,56]. But, of all the theoretical works carried out for extended pores [33,34], very few works have been performed on the study of the translocation process via conical channels [57].…”

Section: Introductionmentioning

confidence: 99%

Translocation of polymers through a wide-open conical pore

Sharma

2024

Phys. Scr.

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The transport of biomolecules across a cell membrane is an important phenomenon that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through a conical channel, directed from the wider opening to the narrow end of the conical channel. We use the molecular dynamics approach to study the problem. The effect of the different conical pore geometry and polymer lengths on translocation dynamics is determined from the behavior of the total translocation time, τ, and the waiting time distributions, w(s). The escape of polymer segments from the narrow end of the conical channel is tracked by studying the escape velocity profile (v(i)). To demonstrate the asymmetric pore effects on the translocation dynamics, we compare the translocation process from both the narrow and wider ends of the conical channel. We find striking differences in the translocation dynamics for both processes, which are in agreement with the experimental study. We have accounted for the effect of various rigidity, and increasing length of a polymer chain, on both types of processes. This computational study can be used to underline the translocation process from different conical pores.

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Section: Introductionmentioning

confidence: 99%

Translocation of polymers through a wide-open conical pore

Sharma

2024

Phys. Scr.

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“…This controlled transport of DNA molecules proved to be a success to detect various folded configurations of DNA inside conical nano capillaries [23]. In computational study, different types of channels are modeled so far to study the effect of pore-polymer interaction on the translocation processes [24,25]. But, of all the theoretical works carried out for extended pores, very few works have been performed on the study of translocation process via conical channels [26].…”

Section: Introductionmentioning

confidence: 99%

Translocation through conical pores: A direction-dependent process

Sharma¹

2022

Preprint

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The transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through a conical channel, directed from the wider opening to the narrow end of the conical channel. We use the molecular dynamics approach to study the problem. The effect of the different conical pore geometry and polymer lengths on translocation dynamics is determined from the behavior of the total translocation time, τ , and waiting time distributions, w(s). The escape of polymer segments from the narrow end of the conical channel is tracked by studying their velocity profile (vs). To demonstrate the asymmetric pore effects on the translocatin dynamics, we compare the translocation process from both the ends of the conical channel. We find striking differences in the translocation dynamics for both processes, which are in agreement with the experimental study. We have accounted the effect of various rigidity, and increasing length of a polymer chain, on both types of processes. The study can be used to find the transition from a directional dependent to a directional independent translocation process through a asymmetric channel.

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“…[ 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 ]…”

Section: Introductionmentioning

confidence: 99%

“…[ 60 ] Moreover, the authors also employed LD simulations to investigate star polymer translocation into a spheroidal cavity subject to an external electric field inside the pore. [ 61 ] For a fixed value of the chain total mass, they found that 〈τ〉 displays non‐monotonic variation with respect to f for large cavities, while it decreases monotonically with f for sufficiently small cavities.…”

Section: Introductionmentioning

confidence: 99%

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

Tilahun

Tatek

2021

Macro Theory & Simulations

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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...

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Polyelectrolyte Translocation through a Corrugated Nanopore

Cited by 4 publications

References 36 publications

Translocation of polymers through a wide-open conical pore

Translocation of polymers through a wide-open conical pore

Translocation through conical pores: A direction-dependent process

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

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