Star-shaped polymer translocation into a nanochannel: Langevin dynamics simulations

Tilahun, Mesay; Tatek, Yergou B.

doi:10.1088/1402-4896/acafad

Cited by 4 publications

(1 citation statement)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This constitutes a traditional framework to tackle innumerous problems, particularly those whose physical parameters depend non-trivially on space. As illustrations we mention the modeling of: transport processes [59,60], organic semiconductors [61], star-shaped polymer translocation into a nanochannel [62], periodic porous material [63], and turbulent two-particle diffusion in configuration space [64][65][66][67][68]. Further, in the case of drifts with time-dependent coefficients (even if implicitly), the Fokker-Planck equation approach helps to understand unusual dynamics, as the asymptotics of continuous time random walk models [69][70][71], logarithmic oscillations for moments of physical variables [72] and dynamical diversity for systems driven by colored noise [73][74][75][76][77][78][79][80][81][82].…”

Section: Introductionmentioning

confidence: 99%

Asymmetric space-dependent systems: partial stabilization through the addition of noise and exact solutions for the corresponding nonlinear Langevin equations

Fa,

Ho,

Matos

et al. 2023

Phys. Scr.

View full text Add to dashboard Cite

In many instances, the dynamical richness and complexity observed in natural phenomena can be related to stochastic drives influencing their temporal evolution. For example, random noise allied to spatial asymmetries may induce stabilization of otherwise diverging trajectories in dynamical systems. However, to identify how exactly this takes place in actual processes usually is not a simple task. Here we unveil a few trends leading to dynamical stabilization and diversity of behavior by introducing Gaussian white noise to a class of exactly solvable non-linear deterministic models displaying space-dependent drifts. For the resulting nonlinear Langevin equations, the associated Fokker-Planck equations can be solved through the similarity method or the Fourier transform technique. By comparing the cases with and without noise, we discuss the changes in the systems dynamical characteristics. Simple examples of drift and diffusion coefficients are explicitly analyzed and comparisons with some other models in the literature are made. Our study illustrates the rich phenomenology originated from spatially heterogeneous dynamical systems under the influence of white noise.

show abstract

Section: Introductionmentioning

confidence: 99%

Asymmetric space-dependent systems: partial stabilization through the addition of noise and exact solutions for the corresponding nonlinear Langevin equations

Fa,

Ho,

Matos

et al. 2023

Phys. Scr.

View full text Add to dashboard Cite

show abstract

Transport of a comb-like polymer across a nanochannel subject to a pulling force

Adane,

Tatek,

Tilahun

2024

J. Phys.: Condens. Matter

View full text Add to dashboard Cite

We investigate the dynamics of comb-like polymer translocation through a nanochannel using three-dimensional Langevin dynamics simulations based on a coarse-grained chain model. A comprehensive set of simulations are performed to examine the effects of system parameters such as the grafting density $\rho$ of the side chains, the polymer chain length, the nanochannel dimensions, and the magnitude of the pulling force on the translocation dynamics. For a given polymer chain length, keeping the backbone length is constant while varying $\rho$, we have found that the dependence of the mean translocation time $\left\langle \tau\right\rangle $ on $\rho$ is non-monotonic, with a maximum translocation time for a specific $\rho$ at which the translocation is the slowest.The simulation results also show that $\left\langle \tau\right\rangle $ is not significantly affected by the channel width above a certain radius, while the comb-like polymer translocation is hindered by a narrower channel due to increased interactions between the chain monomers and the channel. In addition, $\left\langle \tau\right\rangle $ increases linearly with the nanochannel length.A linear scaling relationship between the mean translocation time $\left\langle \tau\right\rangle$ and the chain length $N$ of polymer is obtained, $\left\langle \tau\right\rangle \sim N$. Similarly, the dependence of $\left\langle \tau\right\rangle$ on the backbone chain size $N_{bb}$ has a quasi-linear dependence, $\left\langle \tau\right\rangle \sim N_{bb}$. On the other hand, the translocation velocity $v$ follows a power-law relationship with the polymer chain length $N$ as $v \sim N^{-1}$. The mean translocation time also shows an inverse linear relationship with the magnitude of the pulling force $F$, $\left\langle \tau\right\rangle \sim F^{-1}$. The power-law relationships discovered in this study contribute to the fundamental understanding of the comb polymer translocation dynamics and to establishing a framework for further investigations in this field.

show abstract

A Monte Carlo study on a 3-dimensional comb polymer translocation through a nanopore driven by an electric field

Bruh,

Tatek

2024

Modelling Simul. Mater. Sci. Eng.

View full text Add to dashboard Cite

A lattice Monte Carlo simulation study of the translocation of comb polymers through a nanopore subjected to an electric field is presented. The translocation dynamics was extensively studied in terms of the applied electric field strength, the pore size, and the comb polymer topology. The variations of the most probable translocation time $\tau_p$ and the mean translocation time \mt\ as a function of the applied electric field strength show distinct features, the latter exhibiting a nonmonotonic dependence on the electric field. We were able to show the existence of a critical field strength $\delta \epsilon_c$ defined by the narrowest distribution of the translocation time, which is closely related to the size of the nanopore. In addition, we have found that the critical field strength also defines a transition point between two regimes of translocation: a smooth translocation for a field strength below $\delta \epsilon_c$ and a chaotic translocation for a field strength above $\delta \epsilon_c$. Moreover, for the smallest pore size ($r_p = 1$), monomers can only cross the nanopore in a single file, while for larger pores different modes of polymer translocation are identified. Finally, the dependence of the mean translocation time on the backbone length is governed by a power law relationship $\left < \tau \right > \sim {N_B}^{\alpha}$, where the scaling exponent $\alpha$ is found to be in the range of 1.3--1.7 for the set of side chain lengths and nanopore sizes investigated. As for the side chain length $N_S$, the mean translocation time is found to follow a linear dependence $\left < \tau \right > \sim {N_S}$.

show abstract

Star-shaped polymer translocation into a nanochannel: Langevin dynamics simulations

Cited by 4 publications

References 67 publications

Asymmetric space-dependent systems: partial stabilization through the addition of noise and exact solutions for the corresponding nonlinear Langevin equations

Asymmetric space-dependent systems: partial stabilization through the addition of noise and exact solutions for the corresponding nonlinear Langevin equations

Transport of a comb-like polymer across a nanochannel subject to a pulling force

A Monte Carlo study on a 3-dimensional comb polymer translocation through a nanopore driven by an electric field

Contact Info

Product

Resources

About