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

Tilahun, Mesay; Tatek, Yergou B.

doi:10.1002/mats.202000090

Cited by 4 publications

(2 citation statements)

References 68 publications

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“…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 ].…”

Section: Polymer Translocation: Highlights From Theoretical Developmentmentioning

confidence: 99%

“…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.…”

Section: Controlling the Speed Of Translocationmentioning

confidence: 99%

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

Singh

Chauhan

Bharadwaj

et al. 2023

IJMS

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Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

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“…The first theoretical study of pulled polymer translocation was performed by Kantor and Kardar [ 55 ], predicting

Section: Polymer Translocation: Highlights From Theoretical Developmentmentioning

confidence: 99%

Section: Controlling the Speed Of Translocationmentioning

confidence: 99%

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

Singh

Chauhan

Bharadwaj

et al. 2023

IJMS

View full text Add to dashboard Cite

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Transport of a comb-like polymer across a nanochannel subject to a pulling force

Adane,

Tatek,

Tilahun

2024

J. Phys.: Condens. Matter

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We investigate the dynamics of comb-like polymer translocation through a nanochannel using three-dimensional Langevin dynamics simulations based on a coarse-grained chain model. A comprehensive set of simulations are performed to examine the effects of system parameters such as the grafting density $\rho$ of the side chains, the polymer chain length, the nanochannel dimensions, and the magnitude of the pulling force on the translocation dynamics. For a given polymer chain length, keeping the backbone length is constant while varying $\rho$, we have found that the dependence of the mean translocation time $\left\langle \tau\right\rangle $ on $\rho$ is non-monotonic, with a maximum translocation time for a specific $\rho$ at which the translocation is the slowest.The simulation results also show that $\left\langle \tau\right\rangle $ is not significantly affected by the channel width above a certain radius, while the comb-like polymer translocation is hindered by a narrower channel due to increased interactions between the chain monomers and the channel. In addition, $\left\langle \tau\right\rangle $ increases linearly with the nanochannel length.A linear scaling relationship between the mean translocation time $\left\langle \tau\right\rangle$ and the chain length $N$ of polymer is obtained, $\left\langle \tau\right\rangle \sim N$. Similarly, the dependence of $\left\langle \tau\right\rangle$ on the backbone chain size $N_{bb}$ has a quasi-linear dependence, $\left\langle \tau\right\rangle \sim N_{bb}$. On the other hand, the translocation velocity $v$ follows a power-law relationship with the polymer chain length $N$ as $v \sim N^{-1}$. The mean translocation time also shows an inverse linear relationship with the magnitude of the pulling force $F$, $\left\langle \tau\right\rangle \sim F^{-1}$. The power-law relationships discovered in this study contribute to the fundamental understanding of the comb polymer translocation dynamics and to establishing a framework for further investigations in this field.

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A Monte Carlo study on a 3-dimensional comb polymer translocation through a nanopore driven by an electric field

Bruh,

Tatek

2024

Modelling Simul. Mater. Sci. Eng.

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A lattice Monte Carlo simulation study of the translocation of comb polymers through a nanopore subjected to an electric field is presented. The translocation dynamics was extensively studied in terms of the applied electric field strength, the pore size, and the comb polymer topology. The variations of the most probable translocation time $\tau_p$ and the mean translocation time \mt\ as a function of the applied electric field strength show distinct features, the latter exhibiting a nonmonotonic dependence on the electric field. We were able to show the existence of a critical field strength $\delta \epsilon_c$ defined by the narrowest distribution of the translocation time, which is closely related to the size of the nanopore. In addition, we have found that the critical field strength also defines a transition point between two regimes of translocation: a smooth translocation for a field strength below $\delta \epsilon_c$ and a chaotic translocation for a field strength above $\delta \epsilon_c$. Moreover, for the smallest pore size ($r_p = 1$), monomers can only cross the nanopore in a single file, while for larger pores different modes of polymer translocation are identified. Finally, the dependence of the mean translocation time on the backbone length is governed by a power law relationship $\left < \tau \right > \sim {N_B}^{\alpha}$, where the scaling exponent $\alpha$ is found to be in the range of 1.3--1.7 for the set of side chain lengths and nanopore sizes investigated. As for the side chain length $N_S$, the mean translocation time is found to follow a linear dependence $\left < \tau \right > \sim {N_S}$.

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

Cited by 4 publications

References 68 publications

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

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

Transport of a comb-like polymer across a nanochannel subject to a pulling force

A Monte Carlo study on a 3-dimensional comb polymer translocation through a nanopore driven by an electric field

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