Forced translocation of a polymer: Dynamical scaling versus molecular dynamics simulation

Dubbeldam, Johan; Rostiashvili, V. G.; Milchev, A.; Vilgis, Thomas A.

doi:10.1103/physreve.85.041801

Cited by 70 publications

(113 citation statements)

References 37 publications

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“…As a consequence, with growing chain length N and force f , the translocation exponent α also increases from α = 2ν ≈ 1.19 to α = 1 + ν ≈ 1.59. These predictions are supported by our simulation findings [13] as well as by results of Lehtola et al [14][15][16] but differ from the results of Luo et al [17]. The tensile force propagation phenomenon treated within the iso-flux trumpet model also leads to α = 1 + ν [18].…”

Section: Introductionsupporting

confidence: 82%

“…This principle states that in the limit of very small fluctuations the FPE solution reproduces the deterministic (or quasistatic) solution s(t) = M(t) which was derived in Ref. [13]. The case of colored Gaussian statistics as well as the behavior of the VAF G(t 1 ,t 2 ) will be studied by MD simulation in Sec.…”

Section: From Langevin To Fokker-planck Equationmentioning

confidence: 99%

“…For arbitrary strong driving forces, an interesting approach based on the notion of tensile force propagation along the chain backbone has been suggested by Sakaue [9][10][11]. Sakaue's idea has been used and worked out very recently in other theoretical treatments [12,13].…”

Section: Introductionmentioning

confidence: 99%

“…We have shown [13] that for the "trumpet" case, the characteristic duration (in the case of Rouse dynamics) of the first and second stages goes as τ 1 ∝ N 1+ν /f and τ 2 ∝ N 2ν /f 1/ν , respectively, (where ν ≈ 3/5 is the Flory exponent), so that atf R def = aN ν f/k B T 1 the first stage time dominates. As a consequence, with growing chain length N and force f , the translocation exponent α also increases from α = 2ν ≈ 1.19 to α = 1 + ν ≈ 1.59.…”

Section: Introductionmentioning

confidence: 99%

“…Recently [13] we suggested a theoretical description based on the tensile (Pincus) blob picture of a pulled chain and the notion of a tensile force propagation, introduced by Sakaue [9][10][11]. Assuming that the local driving force is matched by a drag force of equal magnitude, (i.e., in a quasistatic approximation), we derived an equation of motion for the tensile front position.…”

Section: Introductionmentioning

confidence: 99%

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Driven translocation of a polymer: Fluctuations at work

et al. 2013

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The impact of thermal fluctuations on the translocation dynamics of a polymer chain driven through a narrow pore has been investigated theoretically and by means of extensive molecular dynamics (MD) simulation. The theoretical consideration is based on the so-called velocity Langevin (V-Langevin) equation which determines the progress of the translocation in terms of the number of polymer segments, s (t), that have passed through the pore at time t due to a driving force f . The formalism is based only on the assumption that, due to thermal fluctuations, the translocation velocity v =ṡ(t) is a Gaussian random process as suggested by our MD data. With this in mind we have derived the corresponding Fokker-Planck equation (FPE) which has a nonlinear drift term and diffusion term with a time-dependent diffusion coefficient D(t). Our MD simulation reveals that the driven translocation process follows a super diffusive law with a running diffusion coefficient D(t) ∝ t γ where γ < 1. This finding is then used in the numerical solution of the FPE which yields an important result: For comparatively small driving forces fluctuations facilitate the translocation dynamics. As a consequence, the exponent α which describes the scaling of the mean translocation time τ with the length N of the polymer, τ ∝ N α is found to diminish. Thus, taking thermal fluctuations into account, one can explain the systematic discrepancy between theoretically predicted duration of a driven translocation process, considered usually as a deterministic event, and measurements in computer simulations. In the nondriven case, f = 0, the translocation is slightly subdiffusive and can be treated within the framework of fractional Brownian motion (fBm).

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Section: Introductionsupporting

confidence: 82%

Section: From Langevin To Fokker-planck Equationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Driven translocation of a polymer: Fluctuations at work

et al. 2013

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Translocation of a polymer through a nanopore starting from a confining nanotube

2015

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In this manuscript, Langevin Dynamics simulations and Tension-Propagation theory are used to investigate the forced translocation of a polymer from a confining tube through a nanopore situated at one of the tube's ends. The diameter of the tube allows for a control over the polymer conformations: decreasing the tube diameter reduces the number of conformations available to the polymer chain both before and during translocation. As the tube diameter is decreased, the translocation time is observed to increase. Interestingly, while the width of the distribution of translocation times is reduced if the chain starts in a tube, it reaches a maximum for weakly confining tubes. A Tension-Propagation approach is developed for the tube-nanopore setup in the strongly driven limit. Good agreement between the simulations and the theory allows for an exploration of the underlying physical mechanisms, including the calculation of an effective pore friction and the assessing of the impact of monomer crowding on the trans side.

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Langevin dynamcis simulations of driven polymer translocation into a cross‐linked gel

Sibrac

Slater

2017

Electrophoresis

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We investigate the dynamics of driving a polyelectrolyte such as DNA through a nanopore and into a cross-linked gel. Placing the gel on the trans-side of the nanopore can increase the translocation time while not negatively affecting the capture rates. Thus, this setup combines the mechanics of gel electrophoresis with nanopore translocation. However, contrary to typical gel electrophoresis scenarios, the effect of the field is localized in the immediate vicinity of the nanopore and becomes negligible inside the gel matrix. Thus, we investigate the process by which a semiflexible polymer can be pushed into a gel matrix via a localized field and we describe how the dynamics of gel penetration depends upon the field intensity, polymer stiffness, and gel pore size. Our simulation results show that a semiflexible polymer enters the gel region with two distinct mechanisms depending upon the ratio between the bending length scale and the gel pore size. In both regimes, the gel fibers cause a net increase in the mean translocation time. Interestingly, the translocation rate is found to be constant (a potentially useful feature for many applications) during the predominant part of the translocation process when the polymer is stiff over a length scale comparable to the gel pore size.

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Forced translocation of a polymer: Dynamical scaling versus molecular dynamics simulation

Cited by 70 publications

References 37 publications

Driven translocation of a polymer: Fluctuations at work

Driven translocation of a polymer: Fluctuations at work

Translocation of a polymer through a nanopore starting from a confining nanotube

Langevin dynamcis simulations of driven polymer translocation into a cross‐linked gel

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