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

Luo, Meng‐Bo; Cao, Wei-Ping

doi:10.1103/physreve.86.031914

Cited by 28 publications

(26 citation statements)

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“…Polymer translocation has a lot of technological applications, such as rapid DNA sequencing and gene therapy [4,5], controlled drug delivery [6], size exclusion chromatography [7], etc. Since the process of polymer translocation is important in science and technology, it has been studied extensively in experiments [4,5,[8][9][10], theories [11][12][13][14][15][16], and computer simulations [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

“…The process of polymer translocation is dependent on many factors, such as pore structure [8,9,20], polymer-pore interaction [8,15,20,26,29,33], solvent properties [27], polymer concentration [22,28], and so on. However, one can qualitatively understand the behavior of polymer translocation from two important ingredients: the free-energy landscape [14,17] and the external driving force [34,35].…”

Section: Introductionmentioning

confidence: 99%

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Translocation of polymers into crowded media with dynamic attractive nanoparticles

2015

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The translocation of polymers through a small pore into crowded media with dynamic attractive nanoparticles is simulated. Results show that the nanoparticles at the trans side can affect the translocation by influencing the free-energy landscape and the diffusion of polymers. Thus the translocation time τ is dependent on the polymer-nanoparticle attraction strength ɛ and the mobility of nanoparticles V. We observe a power-law relation of τ with V, but the exponent is dependent on ɛ and nanoparticle concentration. In addition, we find that the effect of attractive dynamic nanoparticles on the dynamics of polymers is dependent on the time scale. At a short time scale, subnormal diffusion is observed at strong attraction and the diffusion is slowed down by the dynamic nanoparticles. However, the diffusion of polymers is normal at a long time scale and the diffusion constant increases with the increase in V.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Translocation of polymers into crowded media with dynamic attractive nanoparticles

2015

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“…35 The translocation of polymer is also dependent on the interaction between polymer and pore. 19,23,26,30,36 It was found that a free-energy barrier at repulsive and weak attractive polymer-pore interactions changes to a free-energy well at strong attractions. And there is a free translocation point where the polymer is free of both free-energy barrier and freeenergy well.…”

Section: Introductionmentioning

confidence: 98%

“…23 Many studies also pointed out that the polymerpore interaction could affect the dynamics of polymer translocation. 19,23,26,36,[38][39][40] In experiments, the interaction between polymer and α-HL pore can be tuned via protonation of charged amino acid residues of the α-HL pore. 41 It was found that the translocation time is dependent on the value of the pH gradient by tuning the pH at the trans side.…”

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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“…Chaperones, binding proteins, exist only in the trans(right) side and have the same size of λσ in which λ supposed to be an integer Abdolvahab et al (2011b); Ambjrnsson and Metzler (2004)(see the figure 1). The wall has not any width and its average effect on polymer translocation is contained in polymer diffusion constant Sun et al (2011);Luo and Cao (2012). Chaperones will bind (unbind) to (from) the polymer continuously in each step of the polymer translocation.…”

Section: Introducing Modelmentioning

confidence: 99%

Chaperone-driven polymer translocation through nanopore: Spatial distribution and binding energy

Abdolvahab

2017

Eur. Phys. J. E

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Chaperones are binding proteins which work as a driving force to bias the biopolymer translocation by binding to it near the pore and preventing its backsliding. Chaperones may have different spatial distribution. Recently we show the importance of their spatial distribution in translocation and how it effects on sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. As a result of the exponential distribution of chaperones, energy dependency of the translocation time will changed and one see a minimum in translocation time versus effective energy curve. The same trend can be seen in scaling exponent of time versus polymer length, β (T ∼ β). Interestingly in some special cases e.g. chaperones of size λ = 6 and with exponential distribution rate of α = 5, the minimum reaches even to amount of less than 1 (β < 1). We explain the possibility of this rare result and base on a theoretical discussion we show that by taking into account the velocity dependency of the translocation on polymer length, one could truly predict the amount of this minimum.

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

Cited by 28 publications

References 50 publications

Translocation of polymers into crowded media with dynamic attractive nanoparticles

Translocation of polymers into crowded media with dynamic attractive nanoparticles

Polymer translocation through a gradient channel

Chaperone-driven polymer translocation through nanopore: Spatial distribution and binding energy

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