Dynamics of Polymer Translocation through Nanopores: Theory Meets Experiment

Matysiak, Silvina; Montesi, Alberto; Pasquali, Matteo; Kolomeisky, Anatoly B.; Clementi, Cecilia

doi:10.1103/physrevlett.96.118103

Cited by 131 publications

(116 citation statements)

References 29 publications

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“…In particular, by applying a constant electric voltage between the ends of the channel we found that MFTT increases with the chain length, according to previous experimental results [22]. Moreover, by considering a polymer with fixed length we found that the MFTT decreases with the increasing electric voltage [11].…”

Section: Discussionsupporting

confidence: 86%

“…4 of Ref. [11]. In panels (b), (c), (d), the PDF of the FTTs follows an opposite behaviour with respect to that observed for increasing length of the polymeric chain: larger values of the voltage determine narrower distributions of the values of FTT.…”

Section: Static Electric Voltagementioning

confidence: 82%

“…2 of Ref. [11]). In particular, for N = 5, 10, 15, 20 monomers, the polymer extensions are 28, 58, 88, 118 Å, that is less or comparable with the channel length.…”

Section: Static Electric Voltagementioning

confidence: 88%

“…Because of their relevance, polymers were widely investigated in a large number of experimental, theoretical and numerical studies (see Refs. [1,2,[6][7][8][9][10][11][12][13][14][15][16][17] and references therein). A fundamental work on polymer translocation, forced by an electric field, showed that during the passage across a nanopore, the single-stranded DNA molecule significantly reduces the single-channel ion current.…”

Section: Introductionmentioning

confidence: 99%

“…As a consequence, the mean translocation time, defined as the average duration time of the current drops, linearly increases with the polymer length [9]. Experiments and simulations based on molecular dynamics showed that the translocation time increases with the chain length and decreases with the increase of a static electric voltage applied through the nanopore [9,11]. By means of theoretical approaches, it was proved that the geometric structure of the environment strongly affects the translocation dynamics through membrane pores in biological systems [18].…”

Section: Introductionmentioning

confidence: 99%

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Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

et al. 2012

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Abstract:Polymer translocation through the nanochannel is studied by means of a Monte Carlo approach, in the presence of a static or oscillating external electric voltage. The polymer is described as a chain molecule according to the two-dimensional "bond fluctuation model". It moves through a piecewise linear channel, which mimics a nanopore in a biological membrane. The monomers of the chain interact with the walls of the channel, modelled as a reflecting barrier. We analyze the polymer dynamics, concentrating on the translocation time through the channel, when an external electric field is applied. By introducing a source of coloured noise, we analyze the effect of correlated random fluctuations on the polymer translocation dynamics. PACS

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Section: Discussionsupporting

confidence: 86%

Section: Static Electric Voltagementioning

confidence: 82%

“…2 of Ref. [11]). In particular, for N = 5, 10, 15, 20 monomers, the polymer extensions are 28, 58, 88, 118 Å, that is less or comparable with the channel length.…”

Section: Static Electric Voltagementioning

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

et al. 2012

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Simulating Transport of Soft Matter in Micro/Nano Channel Flows with Dissipative Particle Dynamics

Yang

Zhu

et al. 2018

Advcd Theory and Sims

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The flow-induced transport of various soft matter systems through a fluidic channel has recently attracted great interest due to its significance ranging from the understanding of several chemical and biological processes to potential industrial and technical applications. Dynamic simulation and modeling can yield an insight into the detailed conformational, dynamical, and transport properties of soft matter systems, which is necessary to understand the transport properties of biological macromolecules in living organisms. As a mesoscopic particles-based simulation technique, dissipative particle dynamics (DPD) has quickly been adopted as a promising approach for simulating dynamic and rheological properties of simple and complex fluids as well as the events taking place inside the fluidic channels. Here, the DPD method widely used in predicting the channel flow containing various soft matter systems is reviewed. The general aspect and basic formulations of DPD are introduced, and different boundary conditions are presented for wall-bounded flows. In addition, the models based on DPD developed to simulate flow-induced transport through fluidic channels for some typical soft matter systems are discussed, including red blood cells, vesicles, polymers, and biomacromolecules. Finally, the future directions to signify the framework in enhancing the design of novel functional systems and beyond are discussed.

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Coarse Grained Molecular Dynamics Simulation of Electromechanically‐Gated DNA Modified Conical Nanopores

Höfler

Gyurcsányi

2008

Electroanalysis

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Nanopore-based devices are emerging as tools for single molecule manipulation, characterization and chemical analysis. Single or random arrays of chemically modified nanopores have been established as platforms for selective chemical and biosensing. However, it is little known about the orientation and behavior of surface tethered species in the nanopore environment as function of applied transpore voltages. In this study we report on coarse grained modeling of short (5-, 15-mer) DNA modified conical gold nanopores subjected to electrical field gradients of 5 and 50 mV/nm. An electromechanical gating effect in the single stranded DNA modified conical nanopores is predicted, which is due to the obstruction of the tip entrance by DNA strands oriented by the external electrical field. The magnitude of the rectification effect increases with increasing DNA length and decreasing tip diameter of the conical nanopore. The direction of on/off switching was found to be dependent on the location of the immobilized DNAs on the membrane supporting the nanopore.

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Dynamics of Polymer Translocation through Nanopores: Theory Meets Experiment

Cited by 131 publications

References 29 publications

Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

Simulating Transport of Soft Matter in Micro/Nano Channel Flows with Dissipative Particle Dynamics

Coarse Grained Molecular Dynamics Simulation of Electromechanically‐Gated DNA Modified Conical Nanopores

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