Numerical simulation of the electrophoretic transport of a biopolymer through a synthetic nano-pore

Alapati, Suresh; Fernandes, Dolfred Vijay; Suh, Yong Kweon

doi:10.1080/08927022.2011.553229

Cited by 9 publications

(14 citation statements)

References 37 publications

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“…We use LBE to include the effect of HI between the polymer and the fluid. This work is the extension of our earlier work [19,20]. The main aim of this study is to know the effect of nanopore length on the polymer’s translocation speed inside the pore and to find the reason for the decrease of the translocation velocity within the elongated nanopore.…”

Section: Introductionmentioning

confidence: 79%

“…For this purpose, we use a four-point interpolation function, which is given by [10]

w false(r false) = {\begin{matrix} \frac{1}{8} (3 - 2 | r | + \sqrt{1 + 4 | r | - 4 r^{2}}) & 0 \leq | r | \leq 1 \\ \frac{1}{8} (5 - 2 | r | - \sqrt{- 7 + 12 | r | - 4 r^{2}}) & 1 \leq | r | \leq 2 \\ 0 & 2 \leq | r | \end{matrix}

where r is the distance from the bead position to a surrounding grid point. Note that Γ bare in Equation (3) is different from the actual friction coefficient Γ (see Reference [19] for more details) and when there is no HI effect, we just set u i = 0 and Γ bare = Γ in Equation (3).…”

Section: Methods Of Numerical Simulationmentioning

confidence: 99%

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Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study

2013

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Abstract:In this study, we simulate the electrophoretic motion of a bio-polymer through a synthetic nanopore in the presence of an external bias voltage by considering the hydrodynamic interactions between the polymer and the fluid explicitly. The motion of the polymer is simulated by 3D Langevin dynamics technique by modeling the polymer as a worm-like-chain, while the hydrodynamic interactions are incorporated by the lattice Boltzmann equation. We report the simulation results for three different lengths of the nanopore. The translocation time increases with the pore length even though the electrophoretic force on the polymer is the same irrespective of the pore length. This is attributed to the fact that the translocation velocity of each bead inside the nanopore decreases with the pore length due to the increased fluid resistance force caused by the increase in the straightened portion of the polymer. We confirmed this using a theoretical formula.

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Section: Introductionmentioning

confidence: 79%

“…For this purpose, we use a four-point interpolation function, which is given by [10]

w false(r false) = {\begin{matrix} \frac{1}{8} (3 - 2 | r | + \sqrt{1 + 4 | r | - 4 r^{2}}) & 0 \leq | r | \leq 1 \\ \frac{1}{8} (5 - 2 | r | - \sqrt{- 7 + 12 | r | - 4 r^{2}}) & 1 \leq | r | \leq 2 \\ 0 & 2 \leq | r | \end{matrix}

Section: Methods Of Numerical Simulationmentioning

confidence: 99%

Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study

2013

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“…Here, x cut = 2 1/6 σ is the cut-off distance, which ensures that only a repulsive interaction takes place when two beads are closer than x cut . The bond-stretching potential, which restores the link length l to the equilibrium link length l 0 is given by [13] V bond (…”

Section: Cilia Motionmentioning

confidence: 99%

“…The bending potential, which restores the angle between neighboring links θ to the equilibrium angle θ 0 = π, is calculated from [13] V bond (θ) =…”

Section: Cilia Motionmentioning

confidence: 99%

Simulation by using the lattice Boltzmann method of microscopic particle motion induced by artificial cilia

Alapati

Seong

Mannoor

et al. 2016

Journal of the Korean Physical Society

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In this paper, we present the results obtained from the simulation of particle motion induced by the fluid flow driven by an array of beating artificial cilia inside a micro-channel. A worm-like-chain model is used to simulate the elastic cilia, and the lattice Boltzmann equation is used to compute the fluid flow. We employ a harmonic force at the extreme tip of each cilium to actuate it. Our simulation methods are first validated by applying them to the motion of a single cilium and a freely falling sphere. After validation, we simulate the fluid flow generated by an array of beating cilia and find that a maximum flow rate is achieved at an optimum sperm number. Next, we simulate the motion of a neutrally buoyant spherical particle at this optimum sperm number by tracking the particle motion with a smoothed profile method. We address the effect of the following parameters on the particle velocity: the gap between cilia and particle, the particle size, the cilia density, and the presence of an array of intermediate particles.

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“…For further details about these potentials and the values of the corresponding parameters, one can refer to Ref. 22. F drag,i , F ran,i , and F elec,i represent the drag force, random force, and the electrophoretic force, respectively, acting on each bead.…”

Section: A Polymer Modelmentioning

confidence: 99%

Numerical and theoretical study on the mechanism of biopolymer translocation process through a nano-pore

Alapati

Fernandes

Suh

2011

The Journal of Chemical Physics

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We conducted a numerical study on the translocation of a biopolymer from the cis side to the trans side of a membrane through a synthetic nano-pore driven by an external electric field in the presence of hydrodynamic interactions (HIs). The motion of the polymer is simulated by 3D Langevin dynamics technique using a worm-like chain model of N identical beads, while HI between the polymer and fluid are incorporated by the lattice Boltzmann equation. The translocation process is induced by electrophoretic force, which sequentially straightens out the folds of the initial random configuration of the polymer chain on the cis side. Our simulation results on translocation time and velocity are in good quantitative agreement with the corresponding experimental ones when the surface charge on the nano-pore and the HI effect are considered explicitly. We found that the translocation velocity of each bead inside the nano-pore mainly depends upon the length of the straightened portion of the polymer in forced motion near the pore. We confirmed this by a theoretical formula. After performing simulations with different pore lengths, we observed that translocation velocity mainly depends upon the applied potential difference rather than upon the electric field inside the nano-pore.

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Numerical simulation of the electrophoretic transport of a biopolymer through a synthetic nano-pore

Cited by 9 publications

References 37 publications

Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study

Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study

Simulation by using the lattice Boltzmann method of microscopic particle motion induced by artificial cilia

Numerical and theoretical study on the mechanism of biopolymer translocation process through a nano-pore

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