Single molecule electrophoresis of star polymers through nanopores: Simulations

Katkar, Harshwardhan H.; Muthukumar, Murugappan

doi:10.1063/1.5029980

Cited by 14 publications

(48 citation statements)

References 34 publications

(59 reference statements)

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“…To isolate the effect of the polymer architecture, the total number of monomers, N = 1 + fm, was fixed at 121 in all cases. [26][27][28] Equation 3is integrated in time using the velocity Verlet algorithm with a time-step Δt = 0.005. At the start of each simulation, the terminal bead of one arm was placed just inside the nanopore, as shown in Figure 1.…”

Section: Methodsmentioning

confidence: 99%

“…At the start of each simulation, the terminal bead of one arm was placed just inside the nanopore, as shown in Figure 1. [26,27] With this bead fixed in position, the chain was allowed to equilibrate until the radius of gyration fluctuated about an equilibrium value. Subsequently, the bead originally placed inside the nanopore was released and the external force was turned on.…”

Section: Methodsmentioning

confidence: 99%

“…For f ≤ 4, the translocation always occurs with one leading arm, in agreement with the results of Katkar and Muthukumar. [26] Due to the short pore length of σ employed in this study, the translocation may occur with multiple leading arms for f ≥ 6. [27] For 6 ≤ f ≤ 10, the number of leading arms ranges between 0.2f and 0.3f.…”

Section: Effect Of Confinement Strength For Spherical Cavitymentioning

confidence: 98%

“…[21,22] As such, the phenomenon of star polymer translocation through a nanopore has attracted increasing attention over the last decade. [21][22][23][24][25][26][27][28] One of the first studies that investigated the effect of star polymer functionality upon the translocation time, τ was electric field strength, E, upon τ. They found τ to exhibit weaker dependence upon κ for larger N and α to be sensitive to the values of κ and E.…”

Section: Introductionmentioning

confidence: 99%

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Star Polymer Translocation into a Spheroidal Cavity

Nagarajan

Chen

2020

Macro Theory & Simulations

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Star polymer translocation into a spheroidal cavity has been studied using Langevin dynamics simulations. To isolate the effect of polymer architecture, the total number of monomers, N, is kept constant while the number of arms, f, is varied. For the special case of a spherical cavity, the mean translocation time, τ, exhibits nonmonotonic variation with f for large cavities, but decreases monotonically with f for sufficiently small cavities. The value of τ for a prolate cavity is generally similar to that for a spherical cavity of similar volume. In both cases, τ decreases monotonically with f for small cavities. In contrast, τ is significantly larger for an oblate cavity and exhibits nonmonotonic variation with f. If the attraction between the monomers and the cavity wall is sufficiently strong, the effect of cavity geometry largely vanishes and τ decreases monotonically with f, regardless of the cavity shape.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Effect Of Confinement Strength For Spherical Cavitymentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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Star Polymer Translocation into a Spheroidal Cavity

Nagarajan

Chen

2020

Macro Theory & Simulations

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“…H. H. Katkar and M. Muthukumar studied the translocation of charged star polymers of constant mass driven by an externally applied electric field by varying chain functionality. [59] Their main finding is that the translocation kinetics is strongly affected by the polymer functionality with a non-monotonic dependence of the translocation time with respect to functionality and the existence of a critical functionality for which the translocation is the fastest. The authors also reported that the translocation was found to be impossible for chains above a particular functionality when the nanopore radius was sufficiently small.…”

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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Translocation of a Self-propelled Polymer through a Narrow Pore

Wang

Zhou

et al. 2022

Chin J Polym Sci

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Single molecule electrophoresis of star polymers through nanopores: Simulations

Cited by 14 publications

References 34 publications

Star Polymer Translocation into a Spheroidal Cavity

Star Polymer Translocation into a Spheroidal Cavity

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

Translocation of a Self-propelled Polymer through a Narrow Pore

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