Monte Carlo simulation on polymer translocation in crowded environment

Cao, Wei-Ping; Sun, Li‐Zhen; Wang, Chao; Luo, Meng‐Bo

doi:10.1063/1.3658047

Cited by 43 publications

(48 citation statements)

References 52 publications

(87 reference statements)

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“…In addition to the EV effect of NPs, polymer-NP attraction would also change the free-energy landscape of polymer translocation, and thus it affects the translocation property of polymers [40][41][42][43]. Both the dynamic Monte Carlo (MC) simulation and the Langevin dynamics (LD) simulation showed that the polymer-NP attraction could obviously change the translocation time of polymers.…”

Section: Introductionmentioning

confidence: 99%

“…Both the dynamic Monte Carlo (MC) simulation and the Langevin dynamics (LD) simulation showed that the polymer-NP attraction could obviously change the translocation time of polymers. The attractive NPs at the trans side could draw the polymer through the pore by lowering the energy, and thus decrease the translocation time [40]. However, the diffusion rate of polymers was slowed down at strong polymer-NP attraction because the polymers were adsorbed on NPs, thus the translocation time was significantly increased at strong polymer-NP attraction.…”

Section: Introductionmentioning

confidence: 99%

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Translocation of polymers into crowded media with dynamic attractive nanoparticles

2015

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The translocation of polymers through a small pore into crowded media with dynamic attractive nanoparticles is simulated. Results show that the nanoparticles at the trans side can affect the translocation by influencing the free-energy landscape and the diffusion of polymers. Thus the translocation time τ is dependent on the polymer-nanoparticle attraction strength ɛ and the mobility of nanoparticles V. We observe a power-law relation of τ with V, but the exponent is dependent on ɛ and nanoparticle concentration. In addition, we find that the effect of attractive dynamic nanoparticles on the dynamics of polymers is dependent on the time scale. At a short time scale, subnormal diffusion is observed at strong attraction and the diffusion is slowed down by the dynamic nanoparticles. However, the diffusion of polymers is normal at a long time scale and the diffusion constant increases with the increase in V.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Translocation of polymers into crowded media with dynamic attractive nanoparticles

2015

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“…In the first regime R G0 > D > σ f , normal diffusion < Δr 2 > ∝t is always observed at long time scale, even at large ε fp . Such behavior is different from the subnormal diffusion of a polymer in a crowding environment with random fillers (12). At strong polymer-filler interactions, although the diffusion of the polymer is slow, the normal diffusion survives at a long time scale after In the second regime D > R G0~σf , normal diffusion < Δr 2 > ∝t is only observed at small ε fp before the adsorption.…”

Section: Resultsmentioning

confidence: 97%

“…Experiments found that the thermal and mechanical properties of polymethyl methacrylate/carbon nanofibers were significantly enhanced when compared to polymethyl methacrylate with no carbon nanofibers (11). Moreover, it was found that a normal diffusion of polymer in dilute solution will change to a sub-diffusion in media with random distributed fillers (12). In addition, the translocation of the polymer was dependent on the properties of fillers (12,13).…”

Section: Introductionmentioning

confidence: 98%

“…Moreover, it was found that a normal diffusion of polymer in dilute solution will change to a sub-diffusion in media with random distributed fillers (12). In addition, the translocation of the polymer was dependent on the properties of fillers (12,13). Fillers like dendrimers may play important roles in the delivery of DNA or drug in biological systems (14).…”

Section: Introductionmentioning

confidence: 98%

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Size and diffusion of polymer in media filled with periodic fillers

Zhang

Huang

et al. 2014

E-Polymers

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The effect of nanosized fillers on the equilibrium and dynamic properties of a single polymer chain has been studied by using off-lattice Monte Carlo (MC) simulation. Fillers of identical size are arranged periodically in the system and the Lennard-Jones (LJ) interaction is considered between the polymer and fillers. Our results show that the statistical size and dynamic diffusion properties of the polymer are not only dependent on the size of the polymer relative to the size of fillers and the distance between fillers, but also dependent on the interaction between the polymer and filler. The statistical size of the polymer can increase or decrease. Normal diffusion is always observed for long polymers and small fillers, whereas a transition from a desorbed state to an adsorbed state is observed for short polymers and large fillers. Finally, the size and diffusion of the polymer on an infinitely large surface are studied for comparison.

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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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Monte Carlo simulation on polymer translocation in crowded environment

Cited by 43 publications

References 52 publications

Translocation of polymers into crowded media with dynamic attractive nanoparticles

Translocation of polymers into crowded media with dynamic attractive nanoparticles

Size and diffusion of polymer in media filled with periodic fillers

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

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