Influence of the Location of Attractive Polymer–Pore Interactions on Translocation Dynamics

Ghosh, Bappa; Chaudhury, Srabanti

doi:10.1021/acs.jpcb.7b09208

Cited by 9 publications

(13 citation statements)

References 43 publications

(94 reference statements)

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“…In the following simulation, we have used the polymer-mediated passage of polymer through nanopores driven by the external force. In this type of translocation, several parameters, such as the length and radius of the nanopore, the applied external force, and the friction coefficient of both Cis and Trans environments, are investigated [2,[38][39][40][41]. In the meantime, one of the cases that are rarely investigated is the interaction energy (potential depth) between the nanopore wall and the polymer passing through it and its effect on the time of PT.…”

Section: Introductionmentioning

confidence: 99%

Translocation through a narrow pore under a pulling force

Hamidabad

Abdolvahab

2019

Sci Rep

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We employ a three-dimensional molecular dynamics to simulate a driven polymer translocation through a nanopore by applying an external force, for four pore diameters and two external forces. To see the polymer and pore interaction effects on translocation time, we studied nine interaction energies. Moreover, to better understand the simulation results, we investigate polymer center of mass, shape factor and the monomer spatial distribution through the translocation process. Our results reveal that increasing the polymer-pore interaction energy is accompanied by an increase in the translocation time and decrease in the process rate. Furthermore, for pores with greater diameter, the translocation becomes faster. The shape analysis of the polymer indicates that the polymer shape is highly sensitive to the interaction energy. In great interactions, the monomers come close to the pore from both sides. As a result, the translocation becomes fast at first and slows down at last. Overall, it can be concluded that the external force does not play a major role in the shape and distribution of translocated monomers. However, the interaction energy between monomer and nanopore has a major effect especially on the distribution of translocated monomers on the trans side.

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Section: Introductionmentioning

confidence: 99%

Translocation through a narrow pore under a pulling force

Hamidabad

Abdolvahab

2019

Sci Rep

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“…In the simulations, the majority of the works investigated translocation using neutral chains as the studying models. Only a few papers used charged chains with explicit ions to explore the dynamics of translocation [48,72,74,75,76,77]. As we know, the biomacromolecules concerned in the applications of translocation, such as DNA, RNA and proteins, are mostly ionizable molecules in aqueous solutions and belong to a general category of linear polymer, called “polyelectrolyte”.…”

Section: Introductionmentioning

confidence: 99%

Translocation of Charged Polymers through a Nanopore in Monovalent and Divalent Salt Solutions: A Scaling Study Exploring over the Entire Driving Force Regimes

Hsiao

2018

Polymers

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Langevin dynamics simulations are performed to study polyelectrolytes driven through a nanopore in monovalent and divalent salt solutions. The driving electric field E is applied inside the pore, and the strength is varied to cover the four characteristic force regimes depicted by a rederived scaling theory, namely the unbiased (UB) regime, the weakly-driven (WD) regime, the strongly-driven trumpet (SD(T)) regime and the strongly-driven isoflux (SD(I)) regime. By changing the chain length N, the mean translocation time is studied under the scaling form ⟨ τ ⟩ ∼ N α E − δ . The exponents α and δ are calculated in each force regime for the two studied salt cases. Both of them are found to vary with E and N and, hence, are not universal in the parameter’s space. We further investigate the diffusion behavior of translocation. The subdiffusion exponent γ p is extracted. The three essential exponents ν s , q, z p are then obtained from the simulations. Together with γ p , the validness of the scaling theory is verified. Through a comparison with experiments, the location of a usual experimental condition on the scaling plot is pinpointed.

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“…The backbone of the peptide can thus be considered as the single-file motion of the polymer through the pore. Such simple polymer models are well established in previous simulation studies on polymer translocation. ,,, …”

Section: Modelmentioning

confidence: 95%

“…The dimensionless parameters are ϵ 0 = 80, σ = 1, ε = 1, k B T = 1.2ε, R 0 = 1.5σ, . With ε LJ = 3.39 × 10 21 J, the temperature T = 300 K. The parameter values used in our simulations are in the range of benchmark parameters reported in previous translocation studies and were effective in explaining experimental results. ,,, The scaling of the driving force of the monomer in the pore is , which is about 3.39 pN. In our simulations, the external electric field E is set over a range between 0.1 and 4.…”

Section: Modelmentioning

confidence: 99%

“…Using all-atom molecular dynamics simulations, it has been shown that the alteration in the pH of the solution has a significant effect on both electroosmotic flow and the anionic selectivity of the pore . The experimental findings were explained theoretically by performing free-energy calculations and calculating the translocation time from the free-energy profile of the polymer. ,− In a recent study by Ghosh and Chaudhury, extensive molecular dynamics simulations were performed to study the effect of the strength and spatial distribution of charges across a nanopore . This study was motivated by an experimental design where the translocation of a cationic polypeptide was controlled by introducing electrostatic traps at specific regions in the pore lumen .…”

Section: Introductionmentioning

confidence: 99%

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Translocation Dynamics of an Asymmetrically Charged Polymer through a Pore under the Influence of Different pH Conditions

Ghosh

Chaudhury

2019

J. Phys. Chem. B

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We study the translocation of a polymer with oppositely charged segments at both ends of the chain passing through a pore under the effect of an external electric field in the presence of a pH gradient using Langevin dynamics simulations. As observed in experiments, the electrostatic interactions between the pore and the polymer are tuned by altering the pH gradient. Our simulation studies show that with the change in charge distribution on the polymer and the pore that can mimic different pH conditions, the external driving force and the polymer–pore electrostatic interactions play a significant role in the translocation process. The external electric forces are dominant during the entry stage, and the entry time decreases with increase in the charge asymmetry of the pore-trapped polymer. During the exit stage, the electrostatic interactions as well as the external electric field act in concert in determining the exit time through the pore. Our simulation results can capture many features observed in experiments. Our results are explained qualitatively by calculating the free-energy change of the polymer chain during the translocation process.

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Influence of the Location of Attractive Polymer–Pore Interactions on Translocation Dynamics

Cited by 9 publications

References 43 publications

Translocation through a narrow pore under a pulling force

Translocation through a narrow pore under a pulling force

Translocation of Charged Polymers through a Nanopore in Monovalent and Divalent Salt Solutions: A Scaling Study Exploring over the Entire Driving Force Regimes

Translocation Dynamics of an Asymmetrically Charged Polymer through a Pore under the Influence of Different pH Conditions

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