Dynamical scaling exponents for polymer translocation through a nanopore

Luo, Kuntian; Ollila, Santtu T. T.; Huopaniemi, Ilkka; Ala-Nissilä, Tapio; Pomorski, Paweł; Karttunen, Mikko; Ying, S. C.; Bhattacharya, Aniket

doi:10.1103/physreve.78.050901

Cited by 100 publications

(90 citation statements)

References 30 publications

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“…If so, this would weaken the analogy between the translocation and the anomalous diffusion of a monomer. (The accuracy of these claims is questioned in further work [39]. )…”

Section: Discussionmentioning

confidence: 98%

Anomalous diffusion with absorbing boundary

Kantor

Kardar²

2007

Phys. Rev. E

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In a very long Gaussian polymer on time scales shorter that the maximal relaxation time, the mean squared distance travelled by a tagged monomer grows as ∼ t1/2 . We analyze such sub-diffusive behavior in the presence of one or two absorbing boundaries and demonstrate the differences between this process and the sub-diffusion described by the fractional Fokker-Planck equation. In particular, we show that the mean absorption time of diffuser between two absorbing boundaries is finite. Our results restrict the form of the effective dispersion equation that may describe such sub-diffusive processes.

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“…If so, this would weaken the analogy between the translocation and the anomalous diffusion of a monomer. (The accuracy of these claims is questioned in further work [39]. )…”

Section: Discussionmentioning

confidence: 98%

Anomalous diffusion with absorbing boundary

Kantor

Kardar²

2007

Phys. Rev. E

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“…In the case of a strong polymer-pore interaction and a weak driving force, the translocation and the residence times depend nonmonotonically on the polymer length. A combination of MC and LD simulations in two and three dimensions investigated the scaling of the translocation time with the length of the threaded polymer and revealed a variety of distinct scaling exponents for both unbiased and driven translocation, 53 raising a new debate on the scaling exponents and their theoretical explanation.…”

Section: Numerical Simulationsmentioning

confidence: 99%

Translocation of biomolecules through solid‐state nanopores: Theory meets experiments

Fyta

Melchionna

Succi

2011

J Polym Sci B Polym Phys

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ABSTRACT:The interest in polynucleotide translocation through nanopores has moved from purely biological to the need of realizing nanobiotechnological applications related to personalized genome sequencing. Polynucleotide translocation is a process in which biomolecules, like DNA or RNA, are electrophoretically driven through a narrow pore and their passage can be monitored by the change in the ionic current through the pore. Such a translocation process, which will be described here offers a very promising technology aiming at ultra-fast low-cost sequencing of DNA, though its realization is still confronted with challenges and drawbacks. In this review, we present the main aspects involved in the polynucleotide translocation through solid-state nanopores by discussing the most relevant experimental, theoretical, and computational approaches and the way these can supplement each other. The discussion will expose the goals that have been reached so far, the open questions, and contains an outlook to the future of nanopore sequencing.

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“…Because of this, much simulation work has been performed with different simulation methods and simulation models, such as Langevin dynamics(LD) [8][9][10][11][12][13][14] , Monte Carlo (MC) simulation [15][16][17] , molecular dynamics(MD) [18][19][20] , Brownian dynamics(BD) [21] , Disipative particle dynamics (DPD) [22,23] , and Lattice Boltzmann method(LBM) [24,25] . In principle, these methods and models studied the effects of factors, e.g., external field [13] , polymer-pore interactions [10] , and chain length [14,18] .…”

Section: Introductionmentioning

confidence: 99%

Effect of hydrodynamic interaction on flow-induced polymer translocation through a nanotube

Ding

Duan

Yuyuan

et al. 2015

Chem. Res. Chin. Univ.

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We investigated the effect of hydrodynamic interaction(HI) on flow-induced polymer translocation through a nanotube by Brownian dynamics simulations. Whether there is HI in the simulation system is separately controlled by using different diffusion tensors. It is found that HI has no effect on critical velocity flux for long polymer chains due to the competition between more drag force and the hindrance of chain stretching from HI, however, HI broadens the transition interval. In addition, for flow-induced polymer translocation with HI, the critical velocity flux firstly slowly decreases with the increase of chain length and then becomes identical to that of it without HI, that is, the critical velocity flux is independent of chain length. At the same time, HI also accelerates the translocation process and makes the relative variation amplitude of single bead translocation time smaller. In fact, HI can enhance the intrachain cooperativity to make the whole chain obtain more drag force from fluid field and hinder chain stretching, both of which play an important role in translocation process.

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Dynamical scaling exponents for polymer translocation through a nanopore

Cited by 100 publications

References 30 publications

Anomalous diffusion with absorbing boundary

Anomalous diffusion with absorbing boundary

Translocation of biomolecules through solid‐state nanopores: Theory meets experiments

Effect of hydrodynamic interaction on flow-induced polymer translocation through a nanotube

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