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

Alapati, Suresh; Seong, Woo; Suh, Yong Kweon

doi:10.3390/ma6093989

Cited by 4 publications

(3 citation statements)

References 29 publications

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“…To compute f cilia (x, t), we use a four-point interpolation function [19] that extrapolates the cilia's drag force [negative of that computed using Eq. (5)] at a particular bead's location to a specific grid point for the LBM.…”

Section: Fluid 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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Section: Fluid 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

Self Cite

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“…It was also found that the coupling of the correlated molecular motion to hydrodynamics causes significant acceleration of the translocation process [152], and wide pores can host a larger number of multiple biopolymer segments, as compared to smaller pores [221]. In addition, Alapati et al found that translocation velocity mainly depends upon the applied potential difference rather than upon the electric field inside the nanopores [222][223][224].…”

Section: Modeling Of Dna/polymer Translocation Using Lattice Boltzmanmentioning

confidence: 99%

Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs

et al. 2015

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Computational modeling has become increasingly important in biophysics, but the great challenge in numerical simulations due to the multiscale feature of biological systems limits the capability of modeling in making discoveries in biology. Innovative multiscale modeling approaches are desired to bridge different scales from nucleic acids and proteins to cells and tissues. Although all-atom molecular dynamics has been successfully applied in many microscale biological processes such as protein folding, it is still prohibitively expensive for studying macroscale problems such as biophysics of cells and tissues. On the other hand, continuum-based modeling has become a mature procedure for analysis and design in many engineering fields, but new insights for biological systems in the microscale are limited when molecular details are missing in continuum-based modeling. In this context, mesoscale modeling approaches such as Langevin dynamics, lattice Boltzmann method, and dissipative particle dynamics have become popular by simultaneously incorporating molecular interactions and long-range hydrodynamic interactions, providing insights to properties on longer time and length scales than molecular dynamics. In this review, we summarized several mesoscale simulation approaches for studying two model systems in biophysics: red blood cells (RBCs) and deoxyribonucleic acids (DNAs). The RBC is a model system for cell mechanics and biological membranes, while the DNA represents a model system for B Zhangli Peng

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“…A similar two-value behavior was predicted for δ: zero in the UB regime and 1 in the other force regimes. Simulations, on the other hand, revealed that many factors can affect the scaling behavior of polymer translocation, for example, solvent quality, , viscosity, , temperature, − pore size, − interaction between the pore and the chain, − confining geometry, − and so forth. Moreover, translocation phenomena can be mapped onto the first passage time problems .…”

Section: Introductionmentioning

confidence: 99%

Translocation of a Polyelectrolyte through a Nanopore in the Presence of Trivalent Counterions: A Comparison with the Cases in Monovalent and Divalent Salt Solutions

Hsiao

2020

ACS Omega

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A polyelectrolyte threading through a nanopore in a trivalent salt solution is investigated by means of molecular dynamics simulations under a reflective wall boundary. By varying the chain length N and the strength E of the driving electric field applied inside the pore, the translocation time is carefully calculated to get rid of the bouncing effect because of the boundary. The results are analyzed under the scaling form ⟨τ⟩ ∼ N α E –δ and four driving force regimes; namely, the unbiased, the weakly driven, the strongly driven trumpet, and the strongly driven isoflux regime, are distinguished. The exponents are calculated in each regime and compared with the cases in the monovalent and divalent salt solutions. Owing to strong condensation of counter ions, the changes of the exponents in the force regimes are found to be nontrivial. A large increase in translocation time can be, however, achieved as the driving field is weak. The variations of the chain size, the ion condensation, and the effective chain charge show that the process is proceeded in a quasi-equilibrium way in the unbiased regime and deviated to exhibit strong nonequilibrium characteristics as E increases. Several astonishing scaling behaviors of the waiting time function, the translocation velocity, and the diffusion properties are discovered in the study. The results provide deep insights into the phenomena of polyelectrolyte translocation in various salt solutions at different driving forces.

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

Cited by 4 publications

References 29 publications

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

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

Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs

Translocation of a Polyelectrolyte through a Nanopore in the Presence of Trivalent Counterions: A Comparison with the Cases in Monovalent and Divalent Salt Solutions

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