Driven translocation dynamics of polynucleotides through a nanopore: off-lattice Monte-Carlo simulations

Chen, C.-M.

doi:10.1016/j.physa.2004.11.026

Cited by 21 publications

(12 citation statements)

References 24 publications

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“…Other studies have used off-lattice MC to study translocation driven by an external or adsorption force [194][195][196]. Finally, one approach has mapped the translocation onto a 1-D diffusion process and then employed an exact numerical technique to obtain results [122,197].…”

Section: Nanopore Translocationmentioning

confidence: 99%

Modeling the separation of macromolecules: A review of current computer simulation methods

et al. 2009

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Theory and numerical simulations play a major role in the development of improved and novel separation methods. In some cases, computer simulations predict counterintuitive effects that must be taken into account in order to properly optimize a device. In other cases, simulations allow the scientist to focus on a subset of important system parameters. Occasionally, simulations even generate entirely new separation ideas! In this article, we review the main simulation methods that are currently being used to model separation techniques of interest to the readers of Electrophoresis. In the first part of the article, we provide a brief description of the numerical models themselves, starting with molecular methods and then moving towards more efficient coarse-grained approaches. In the second part, we briefly examine nine separation problems and some of the methods used to model them. We conclude with a short discussion of some notoriously hard-to-model separation problems and a description of some of the available simulation software packages.

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Section: Nanopore Translocationmentioning

confidence: 99%

Modeling the separation of macromolecules: A review of current computer simulation methods

et al. 2009

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“…Approaches to a DNA sequencing using synthetic nanopores have been recently reviewed (Rhee and Burns, 2006, 2007; Branton et al 2008). Nanopores can be an effective tool for confinement of a DNA (Aksimentiev et al, 2004a; Aksimentiev et al, 2004b; Chen, 2005; Fredlake et al , 2006; Healy, 2007; Kricka et al , 2005; Nakane et al , 2003; Ryan et al , 2007, Zhao et al 2007, Payne et al 2008), while the translocating DNA efficiently mask ionic current through the pore, specific of a nucleotide instantaneously in the pore (Kasianowicz et al, 1996; Howorka et al, 2001). Alternatively, a tunneling current measured across the pore transversally to the translocating DNA varies with a base passing the pore (Zikic et al, 2006, Zhang et al, 2006, Lagerqvist et al , 2006).…”

Section: Introductionmentioning

confidence: 99%

A long DNA segment in a linear nanoscale Paul trap

et al. 2009

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We study the dynamics of a linear distributed line charge such as a single stranded DNA in a nanoscale, linear 2D Paul trap in vacuum. Using molecular dynamics simulations we show that a line charge can be trapped effectively in the trap within well defined range of stability parameters. We investigated (i) a flexible bounded string of charged beads, and (ii) a ssDNA polymer of variable length, for various trap parameters. A line charge undergoes oscillations or rotations as it moves depending on its initial angle, position of the center-of-mass and velocity. The stability region for a strongly bonded line of charged beads is similar to that of a single ion with the same charge over mass ratio. A single stranded DNA, as long as 40nm, does not fold or curl in the Paul trap, but could undergo rotations about the center of mass. To prevent the rotations, we show that a stretching field in the axial direction can effectively prevent the rotations and increase the confinement stability.

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“…The attraction FENE force derives from U F ENE potential and the repulsive LJ force derives from U LJ potential. The supplementary forces also acting on the monomers such as the viscous friction force F = 6πη and the external force F=qE due to the electric field action are [12]. As a parenthesis, we remember that translocation time was defined by Chuang et al using the restriction that the first monomer cannot back out of the pore [13].…”

Section: Resultsmentioning

confidence: 99%

Two-dimensional diffusion model for the biopolymers dynamics at nanometer scale

Pãun

2009

Open Physics

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Abstract:In this paper the driven transport of linear polymers through a nanopore is presented. Biopolymer physical behavior in an external electric field is modeled and its motion is simulated using the Langevin impulse integrator method. Within fairly large limits, the polymer translocation time is inversely proportional with the electric field intensity and directly proportional with the polymer chain length.

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Driven translocation dynamics of polynucleotides through a nanopore: off-lattice Monte-Carlo simulations

Cited by 21 publications

References 24 publications

Modeling the separation of macromolecules: A review of current computer simulation methods

Modeling the separation of macromolecules: A review of current computer simulation methods

A long DNA segment in a linear nanoscale Paul trap

Two-dimensional diffusion model for the biopolymers dynamics at nanometer scale

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