Free energy landscape for the translocation of polymer through an interacting pore

Sun, Li‐Zhen; Cao, Wei-Ping; Luo, Meng‐Bo

doi:10.1063/1.3264944

Cited by 45 publications

(47 citation statements)

References 42 publications

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“…We find that the translocation time τ is strongly dependent on E. For the unbiased case (F = 0) and weak driving cases (F = 0.1 and 0.2), τ first decreases fast with E and then increases slowly with E, and a minimum is found near E = −1. The reason for such a nonmonotonic dependence is that the free-energy landscape or the translocation is dependent on the polymer-pore interaction [46]. It was found that a free-energy barrier for a noninteracting or weak attractive pore will change to a free-energy well for a strong attractive pore.…”

Section: Model and Simulation Methodsmentioning

confidence: 99%

“…The interaction can change the free-energy landscape for polymer translocation [45]; for instance, a free-energy barrier for a neutral pore changes to a free-energy well for a strong attractive pore [46]. Thus the translocation time was highly dependent on the interaction [46]. Up until now, the dependence of the scaling behavior of translocation time on the interaction has not been clear.…”

Section: Introductionmentioning

confidence: 94%

“…The striking difference for the translocation time distributions of polydeoxyadenylic acid [poly(dA)] and polydeoxycytidylic acid DNA molecules was attributed to the stronger attractive interaction of poly(dA) with the pore [39,40]. The interaction can change the free-energy landscape for polymer translocation [45]; for instance, a free-energy barrier for a neutral pore changes to a free-energy well for a strong attractive pore [46]. Thus the translocation time was highly dependent on the interaction [46].…”

Section: Introductionmentioning

confidence: 97%

See 2 more Smart Citations

Influence of polymer-pore interaction on the translocation of a polymer through a nanopore

Luo

Cao

2012

Phys. Rev. E

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The translocation of a bond fluctuation polymer through an interacting nanopore is studied using dynamic Monte Carlo simulation. A driving force F is applied only for monomers inside the pore. The influence of polymer-pore interaction on the scaling relation τ~N(α) is studied for both unbiased and biased translocations, with τ the translocation time and N the polymer length. Results show that the exponent α is dependent on the polymer-pore interaction. For a noninteracting pore, we find α=2.48 for unbiased translocation and α=1.35 for strong biased translocation; for strong attraction, we find α=2.35 for unbiased translocation and α=1.22 for strong biased translocation. The unbiased translocation corresponds to the low-NF regime whereas the strong biased translocation corresponds to the high-NF regime.

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Section: Model and Simulation Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 97%

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Influence of polymer-pore interaction on the translocation of a polymer through a nanopore

Luo

Cao

2012

Phys. Rev. E

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“…The polymer is thus trapped in the free-energy well, and it will cost a long time for the polymer to leave the channel. 19,37 Again, the time for the polymer translocation through the strong attractive pore is long. As a result, there is a minimum time at a proper attraction between the polymer and the pore.…”

Section: Introductionmentioning

confidence: 99%

“…And there is a free translocation point where the polymer is free of both free-energy barrier and freeenergy well. 37 For the repulsive and weak attractive pores, it is difficult for the polymer to enter the pore but is easy for the polymer to leave the pore, therefore the time for the polymer translocating from the cis side to the trans side is long. Whereas for the strong attractive pore, it is easy for the polymer to enter the channel but is difficult for it to leave.…”

Section: Introductionmentioning

confidence: 99%

Polymer translocation through a gradient channel

Zhang

Wang

Sun

et al. 2013

The Journal of Chemical Physics

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The translocation of polymer through a channel with a gradient interaction between the polymer and the channel is studied. The interaction is expressed by E = E0 + kx, where E0 is the initial potential energy at the entrance, x is the position of the monomer inside the channel, and k is the energy gradient. The mean first passage time τ is calculated by using Fokker-Planck equation for two cases (1) N > L and (2) N < L under the assumption that the diffusion rate D is a constant, here N is the polymer length and L is the length of channel. Results show that there is a minimum of τ at k = k(c) for both cases, and the value kc is dependent on E0 and driving force f. At large f, the scaling relation τ ∼ N is observed for long polymer chains. But the scaling relation is dependent on the energy gradient k for an unforced driving translocation.

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The translocation of a polymer through a nanopore with sandglass‐like geometry

Qian,

Li,

Sun

2023

Journal of Polymer Science

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In recent years, non‐uniformly geometrical nanopores, such as conical nanopores, have gained significant attention in nanopore sensing technology due to their advantages in analyte manipulation and clear output signals. This paper focuses on the polymer translocation through a sandglass‐like nanopore, characterized by a double‐conical geometry with a tip at the middle. We systematically investigate the effects of pore geometry on the translocation dynamics through computational simulations and theoretical analyses. The polymer translocation process is divided into three stages: approaching, threading, escaping, corresponding to the movement from the entry to the tip, through the tip, and from the tip to the exit, respectively. Our findings reveal that the duration of the approaching stage highly depends on the polymer conformations, while the durations of the threading and escaping stages are primarily influenced by the driving force associated with the pore geometry and the accompanying free energy change. Additionally, we report a relationship between the threading speed of the polymer at the tip and the combination of the driving force there and the free energy change during the threading stage.

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Free energy landscape for the translocation of polymer through an interacting pore

Cited by 45 publications

References 42 publications

Influence of polymer-pore interaction on the translocation of a polymer through a nanopore

Influence of polymer-pore interaction on the translocation of a polymer through a nanopore

Polymer translocation through a gradient channel

The translocation of a polymer through a nanopore with sandglass‐like geometry

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