Critical evaluation of the computational methods used in the forced polymer translocation

Lehtola, Ville V.; Linna, Riku; Kaski, Kimmo

doi:10.1103/physreve.78.061803

Cited by 47 publications

(74 citation statements)

References 29 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: 81%

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: 81%

Driven translocation of a polymer: Fluctuations at work

et al. 2013

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“…We have previously shown that the forced polymer translocation takes place out of equilibrium and is mainly determined by the balance between the driving pore force and the drag force exerted on the polymer on the cis side [7,8]. The drag force magnitude was shown to change with the tension propagation, which shows as an increase in the number of moving polymer beads N m on the cis side.…”

Section: Introductionmentioning

confidence: 99%

Event distributions of polymer translocation

Linna

Kaski

2012

Phys. Rev. E

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We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of the process. We extract at a high length scale resolution distributions of polymer segments that continuously traverse through a nanoscale pore. The obtained log-normal distributions together with the characteristics of polymer translocation suggest that it is describable as a multiplicative stochastic process. In spite of its clear out-of-equilibrium nature the forced translocation is surprisingly similar to the unforced case. We find forms for the distributions almost unaltered with a common cut-off length. We show that the individual short-segment and short-time movements inside the pore give the scaling relations τ ∼ N α and τ ∼ f −β for the polymer translocation.

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“…While the characteristics of the driven translocation seem to be largely determined by the spreading of tension on the cis side part of the polymer [22][23][24][25][26]28], a detailed conclusive explanation of how the scaling τ ∼ N α changes with applied force is still missing. In capsid ejection, where the polymer is initially in a packed conformation, tension spreading inside the capsid can hardly explain the obtained scaling, at least for higher monomer densities.…”

Section: B the Asymmetrical Porementioning

confidence: 99%

“…We have previously investigated the waiting time profiles when analyzing the effect of tension spreading in the polymer segment on the cis side during translocation [23]. The waiting time profile gives the time each bead has to wait before it exits the pore.…”

Section: Waiting Time Profilesmentioning

confidence: 99%

“…We have previously shown that driven polymer translocation is a strongly out-of-equilibrium process [22,23], where the polymer is continuously lifted further out of equilibrium during translocation so that on the cis side there is an increasing region where the polymer is under tension and the monomers are in motion. This idea was earlier used by Sakaue in his analytical calculation [24].…”

Section: Introductionmentioning

confidence: 99%

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Dynamics of polymer ejection from capsid

et al. 2014

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Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the ejection times scale with polymer length, τ ∼ N α . We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) ρ inside the capsid. For very low densities ρ 0.002 the polymer is only weakly confined by the capsid, and we measure α = 1.33, which is close to α = 1.4 obtained for polymer translocation. At intermediate densities the scaling exponents α = 1.25 and 1.21 for ρ = 0.01 and 0.02, respectively. These scalings are in accord with a crude derivation for the lower limit α = 1.2. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, ρ 0.25. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.

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Critical evaluation of the computational methods used in the forced polymer translocation

Cited by 47 publications

References 29 publications

Driven translocation of a polymer: Fluctuations at work

Driven translocation of a polymer: Fluctuations at work

Event distributions of polymer translocation

Dynamics of polymer ejection from capsid

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