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

V. V. Lehtola, R. P. Linna, K. Kaski

Research output: Contribution to journalArticleAcademicpeer-review

45 Citations (Scopus)

Abstract

n forced polymer translocation, the average translocation time τ scales with respect to pore force f and polymer length N as τ∼f−1Nβ. We demonstrate that an artifact in the Metropolis Monte Carlo method resulting in breakage of the force scaling with large f may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent β⩽1+ν is not universal, but depends on f. Moreover, we show that forced translocation can be described by a relatively simple force balance argument and β to arise solely from the initial polymer configuration.
Original languageEnglish
Article number061803
Pages (from-to)1-8
Number of pages8
JournalPhysical Review E
Volume78
DOIs
Publication statusPublished - 29 Dec 2008
Externally publishedYes

Keywords

  • biomembrane transport
  • differential equations
  • molecular biophysics
  • Monte Carlo methods
  • nonlinear dynamical systems
  • polymers
  • stochastic processes
  • ITC-ISI-JOURNAL-ARTICLE

Cite this

@article{57dc762c90dd421dad0e5cddff009266,
title = "Critical evaluation of the computational methods used in the forced polymer translocation",
abstract = "n forced polymer translocation, the average translocation time τ scales with respect to pore force f and polymer length N as τ∼f−1Nβ. We demonstrate that an artifact in the Metropolis Monte Carlo method resulting in breakage of the force scaling with large f may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent β⩽1+ν is not universal, but depends on f. Moreover, we show that forced translocation can be described by a relatively simple force balance argument and β to arise solely from the initial polymer configuration.",
keywords = "biomembrane transport, differential equations, molecular biophysics, Monte Carlo methods, nonlinear dynamical systems, polymers, stochastic processes, ITC-ISI-JOURNAL-ARTICLE",
author = "Lehtola, {V. V.} and Linna, {R. P.} and K. Kaski",
year = "2008",
month = "12",
day = "29",
doi = "10.1103/PhysRevE.78.061803",
language = "English",
volume = "78",
pages = "1--8",
journal = "Physical review E: covering statistical, nonlinear, biological, and soft matter physics",
issn = "2470-0045",
publisher = "American Physical Society",

}

Critical evaluation of the computational methods used in the forced polymer translocation. / Lehtola, V. V.; Linna, R. P.; Kaski, K.

In: Physical Review E, Vol. 78, 061803, 29.12.2008, p. 1-8.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Critical evaluation of the computational methods used in the forced polymer translocation

AU - Lehtola, V. V.

AU - Linna, R. P.

AU - Kaski, K.

PY - 2008/12/29

Y1 - 2008/12/29

N2 - n forced polymer translocation, the average translocation time τ scales with respect to pore force f and polymer length N as τ∼f−1Nβ. We demonstrate that an artifact in the Metropolis Monte Carlo method resulting in breakage of the force scaling with large f may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent β⩽1+ν is not universal, but depends on f. Moreover, we show that forced translocation can be described by a relatively simple force balance argument and β to arise solely from the initial polymer configuration.

AB - n forced polymer translocation, the average translocation time τ scales with respect to pore force f and polymer length N as τ∼f−1Nβ. We demonstrate that an artifact in the Metropolis Monte Carlo method resulting in breakage of the force scaling with large f may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent β⩽1+ν is not universal, but depends on f. Moreover, we show that forced translocation can be described by a relatively simple force balance argument and β to arise solely from the initial polymer configuration.

KW - biomembrane transport

KW - differential equations

KW - molecular biophysics

KW - Monte Carlo methods

KW - nonlinear dynamical systems

KW - polymers

KW - stochastic processes

KW - ITC-ISI-JOURNAL-ARTICLE

UR - https://ezproxy2.utwente.nl/login?url=https://doi.org/10.1103/PhysRevE.78.061803

UR - https://ezproxy2.utwente.nl/login?url=https://library.itc.utwente.nl/login/2008/isi/lehtola_cri.pdf

U2 - 10.1103/PhysRevE.78.061803

DO - 10.1103/PhysRevE.78.061803

M3 - Article

VL - 78

SP - 1

EP - 8

JO - Physical review E: covering statistical, nonlinear, biological, and soft matter physics

JF - Physical review E: covering statistical, nonlinear, biological, and soft matter physics

SN - 2470-0045

M1 - 061803

ER -