Dynamics of Polymer Translocation: A Short Review with an Introduction of Weakly-Driven Regime

Sakaue, Takahiro

doi:10.3390/polym8120424

Cited by 42 publications

(60 citation statements)

References 34 publications

(102 reference statements)

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“…Early computer simulations confirmed this showing that during translocation, polymer segments on both sides of the membrane are driven out of equilibrium throughout the process [4]. Sakaue formulated his tension propagation theory to completion, and an important addition was made by Rowghanian and Grosberg [2,3,[5][6][7]. It is now established that driven translocation dynamics of fully flexible polymers is determined by tension propagation on the cis side, where monomers sequentially join the dragged segment of the polymer increasing the friction.…”

Section: Introductionmentioning

confidence: 95%

“…al. showing the potential of translocation in DNA sequencing [1]. Due to the potential applications and the originally missing theoretical framework, research has mostly concerned driven polymer translocation, where force is exerted on the polymer segment residing inside the pore [2]. This force drives the polymer from the initial cis to the receiving trans side.…”

Section: Introductionmentioning

confidence: 99%

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Dynamics of driven translocation of semiflexible polymers

Suhonen¹,

Linna²

2018

Phys. Rev. E

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We study translocation of semiflexible polymers driven by force f_{d} inside a nanometer-scale pore using our three-dimensional Langevin dynamics model. We show that the translocation time τ increases with increasing bending rigidity κ. Similarly, the exponent β for the scaling of τ with polymer length N,τ∼N^{β}, increases with increasing κ as well as with increasing f_{d}. By comparing waiting times between semiflexible and fully flexible polymers we show that for realistic f_{d} translocation dynamics is to a large extent, but not completely, determined by the polymer's elastic length measured in number of Kuhn segments N_{Kuhn}. Unlike in driven translocation of flexible polymers, friction related to the polymer segment on the trans side has a considerable effect on the resulting dynamics. This friction is intermittently reduced by buckling of the polymer segment in the vicinity of the pore opening on the trans side. We show that in the experimentally relevant regime where viscosity is higher than in computer simulation models, the probability for this buckling increases with increasing f_{d}, giving rise to a larger contribution to the trans side friction at small f_{d}. Similarly to flexible polymers, we find significant center-of-mass diffusion of the cis side polymer segment which speeds up translocation. This effect is larger for smaller f_{d}. However, this speedup is smaller than the slowing down due to the trans side friction. At large enough N_{Kuhn}, the roles can be seen to be reversed, and the dynamics of flexible polymers can be reached. However, for example, polymers used in translocation experiments of DNA are elastically so short that the finite-length dynamics outlined here applies.

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Section: Introductionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Dynamics of driven translocation of semiflexible polymers

Suhonen¹,

Linna²

2018

Phys. Rev. E

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“…Such coarse-grained models are easily amenable to molecular dynamics (MD) and Monte Carlo simulations [11][12][13][14][15], but even then it is a challenge to explicitly include electrostatic polymer-membrane interactions and they are usually assumed to be negligible. On the theoretical side, a comprehensive theory for driven polymer translocation dynamics has been developed based on the idea of non-equilibrium tension propagation [16][17][18][19][20][21]. The basic idea in this theory is to focus on the dynamics of a single degree of freedom, the translocation coordinate s(t), and include all the many-body effects arising from the (non-equilibrium) chain conformations on the cis side of the membrane into a time-dependent friction η cis (t).…”

Section: Introductionmentioning

confidence: 99%

Theoretical Modeling of Polymer Translocation: From the Electrohydrodynamics of Short Polymers to the Fluctuating Long Polymers

2019

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The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer fluctuations. In this review, we discuss the modeling of polymer translocation in the distinct regimes of short and long polymers where these two effects decouple. For the case of short polymers where polymer fluctuations are negligible, we present a stiff polymer model including the details of the electrohydrodynamic forces on the translocating molecule. We first show that the electrohydrodynamic theory can accurately characterize the hydrostatic pressure dependence of the polymer translocation velocity and time in pressure-voltage-driven polymer trapping experiments. Then, we discuss the electrostatic correlation mechanisms responsible for the experimentally observed DNA mobility inversion by added multivalent cations in solid-state pores, and the rapid growth of polymer capture rates by added monovalent salt in α -Hemolysin pores. In the opposite regime of long polymers where polymer fluctuations prevail, we review the iso-flux tension propagation (IFTP) theory, which can characterize the translocation dynamics at the level of single segments. The IFTP theory is valid for a variety of polymer translocation and pulling scenarios. We discuss the predictions of the theory for fully flexible and rodlike pore-driven and end-pulled translocation scenarios, where exact analytic results can be derived for the scaling of the translocation time with chain length and driving force.

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“…Previous theoretical approaches to understand the translocation of a polymer chain can be categorized into two broad categories: (i) phenomenological or scaling-based theories (27)(28)(29)(30)(31)(32) and (ii) microscopic or free energy-based theories (33)(34)(35)(36)(37)(38)(39)(40)(41). In many of the phenomenological theories, translocation proceeds due to tension propagation along the chain.…”

Section: Introductionmentioning

confidence: 99%

“…In many of the phenomenological theories, translocation proceeds due to tension propagation along the chain. Furthermore, polymer statistics are incorporated through the so-called tension blobs (27,(29)(30)(31)(32). While this and other related approaches have some qualitative agreement with experiments, direct quantitative comparisons are difficult due to undetermined prefactors in scaling relations.…”

Section: Introductionmentioning

confidence: 99%

Macromolecule Translocation in a Nanopore: Center of Mass Drift–Diffusion over an Entropic Barrier

Dell¹,

Muthukumar²

2019

Preprint

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Many fundamental biological processes involve moving macromolecules across membranes, through nanopores, in a process called translocation. Such motion is necessary for gene expression and regulation, tissue formation, and viral infection. Furthermore, in recent years nanopore technologies have been developed for single molecule detection of biological and synthetic macromolecules, which have been most notably employed in next generation DNA sequencing devices. Many successful theories have been established, which calculate the entropic barrier required to elongate a chain during translocation. However, these theories are at the level of the translocation coordinate (number of forward steps) and thus lack a clear connection to experiments and simulations. Furthermore, the proper diffusion coefficient for such a coordinate is unclear. In order to address these issues, we propose a center of mass (CM) theory for translocation. We start with the entropic barrier approach and show that the translocation coordinate is equivalent to the center of mass of the chain, providing a direct interpretation of previous theoretical studies. We thus recognize that the appropriate dynamics is given by CM diffusion, and calculate the appropriate diffusion constant (Rouse or Zimm) as the chain translocates. We illustrate our theoretical approach with a planar nanopore geometry and calculate some characteristic dynamical predictions. Our main result is the connection between the translocation coordinate and the chain CM, however, we also find that the translocation time is sped up by 1-2 orders of magnitude if hydrodynamic interactions are present. Our approach can be extended to include the details included in previous translocation theories. Most importantly this work provides a direct connection between theoretical approaches and experiments or simulations. SIGNIFICANCE Macromolecule motion through nanopores is critical for many biological processes, and has been recently employed for nucleic acid sequencing. Despite this, direct theoretical understandings of translocation are difficult to evaluate due to the introduction of the translocation coordinate. In this manuscript, we propose a theory for translocation written at the center of mass level of the polymer chain. This theoretical approach is more easily compared to experimental and simulation results, and additionally allows one to accurately account for hydrodynamic interactions on the macromolecule dynamics.

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Dynamics of Polymer Translocation: A Short Review with an Introduction of Weakly-Driven Regime

Cited by 42 publications

References 34 publications

Dynamics of driven translocation of semiflexible polymers

Dynamics of driven translocation of semiflexible polymers

Theoretical Modeling of Polymer Translocation: From the Electrohydrodynamics of Short Polymers to the Fluctuating Long Polymers

Macromolecule Translocation in a Nanopore: Center of Mass Drift–Diffusion over an Entropic Barrier

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