Polymer translocation through nano-pores in vibrating thin membranes

Menais, Timothée; Mossa, Stefano; Buhot, Arnaud

doi:10.1038/srep38558

Cited by 29 publications

(21 citation statements)

References 56 publications

(101 reference statements)

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“…The contribution of the cis side friction is mainly seen in ref [29] at the begining of the translocation when the tension propagation towards the cis side is maximum. This contribution with a mean waiting time increasing slower than linearly for a large and a narrow pore (reproduced from our previous work [28]). At high pulling forces, their behaviour is similar with δ < 1 due to bonds elongation.…”

Section: A Linear Polymersupporting

confidence: 72%

“…The case of the structured polymer translocating through a narrow pore differs at low forces as we have already mentioned in previous work [28]. After a look at the mean translocation time (see Figure 6), there seems to be almost no difference at high pulling forces.…”

Section: B Structured Polymer Translocating Through Large and Narrowsupporting

confidence: 58%

“…A minimalistic model for single stranded DNA was considered incorporating three bead types [28]. The alternating phosphate (P) and sugar (S) beads form the linear polymer backbone ( Fig.…”

Section: A the Linear And Structured Polymer Modelsmentioning

confidence: 99%

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Polymer translocation under a pulling force: Scaling arguments and threshold forces

Menais

2018

Phys. Rev. E

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DNA translocation through nanopores is one of the most promising strategies for next-generation sequencing technologies. Most experimental and numerical works have focused on polymer translocation biased by electrophoresis, where a pulling force acts on the polymer within the nanopore. An alternative strategy, however, is emerging, which uses optical or magnetic tweezers. In this case, the pulling force is exerted directly at one end of the polymer, which strongly modifies the translocation process. In this paper, we report numerical simulations of both linear and structured (mimicking DNA) polymer models, simple enough to allow for a statistical treatment of the pore structure effects on the translocation time probability distributions. Based on extremely extended computer simulation data, we (i) propose scaling arguments for an extension of the predicted translocation times τ∼N^{2}F^{-1} over the moderate forces range and (ii) analyze the effect of pore size and polymer structuration on translocation times τ.

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Section: A Linear Polymersupporting

confidence: 72%

Section: B Structured Polymer Translocating Through Large and Narrowsupporting

confidence: 58%

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Polymer translocation under a pulling force: Scaling arguments and threshold forces

Menais

2018

Phys. Rev. E

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“…Drug delivery, DNA, RNA, and proteins passage through cell and/or membrane pores, as well as DNA injection and packaging by phage viruses are a few examples of a broad interesting phenomenology [1]. The passage of polymers through nanopores is also a fundamental problem in those nanotechnological studies that try to emulate the complex biological processes involved in the phenomenon [2,3], and on translocation is based the next generation of DNA sequencing technique [4][5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Force spectroscopy analysis in polymer translocation

Fiasconaro

Falo

2018

Phys. Rev. E

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This paper reports the force spectroscopy analysis of a polymer that translocates from one side of a membrane to the other side through an extended pore, pulled by a cantilever that moves with constant velocity against the damping and the potential barrier generated by the reaction of the membrane walls. The polymer is modeled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment described by a Langevin dynamics at fixed temperature. The force trajectories recorded at different velocities reveal two exponential regimes: the force increases when the first part of the chain enters the pore, and then decreases when the first monomer reaches the trans region. The spectroscopy analysis of the force values permit the estimation of the limit force to allow the translocation, related to the free energy barrier. The stall force to maintain the polymer fixed has been also calculated independently, and its value confirms the force spectroscopy outcomes.

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“…Moreover, using an alternating electric field (time-dependent driving force) in the nanopore has been implied as a source for DNA sequencing [61]. It is worth to mention an interesting results of Menais et al [64] and Fabio et al [65], where interplay between thermal fluctuations and the deformability properties of the channel play an important role in characterizing the translocation process of polymer and proteins.…”

Section: Introductionmentioning

confidence: 99%

Polymer translocation through nano-pores: influence of pore and polymer deformation

2018

Preprint

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We have simulated polymer translocation across the a α-hemolysin nano-pore via a coarse grained computational model for both the polymer and the pore. We simulate the translocation process by allowing the protein cross a free-energy barrier from a metastable state, in the presence of thermal fluctuations. The deformation in the channel, which we model by making the radius of pore change from large to small size, can be originated by the random and non-random (systematic) cellular environment, drive out the polymer out of equilibrium during the transport dynamics. We expect that in more realistic conditions, effects originating on the translocation phenomena due to the deformability of the nano-pore can either decrease or increase the transport time of biomolecule passing through the channel. Deformation in channel can occurred because the structure of αhemolysin channel is not completely immobile, hence a small pore deformation can be occurred during translocation process. We also discuss the effects of polymer deformation on the translocation process, which we achieve by varying the value of the empirical and dihedral potential constants. We investigate the dynamic and thermodynamical properties of the translocation process by revealing the statistics of translocation time as a function of the pulling inward force acting along the axis of the pore under the influence of small and large pore. We observed that a pore with small size can speed down the polymer translocation process, especially at the limit of small pulling force. A drastic increase in translocation time at the limit of low force for small pore clearly illustrate the strong interaction between the transport polymer and pore. Our results can be of fundamental importance for those experiments on DNA-RNA sorting and sequencing and drug delivery mechanism for anti-cancer therapy.

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Polymer translocation through nano-pores in vibrating thin membranes

Cited by 29 publications

References 56 publications

Polymer translocation under a pulling force: Scaling arguments and threshold forces

Polymer translocation under a pulling force: Scaling arguments and threshold forces

Force spectroscopy analysis in polymer translocation

Polymer translocation through nano-pores: influence of pore and polymer deformation

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