Detection of defective DNA in carbon nanotubes by combined molecular dynamics/tight-binding technique

Xu, Yang; Mi, Xiao-Bing; Aluru, N. R.

doi:10.1063/1.3231922

Cited by 6 publications

(4 citation statements)

References 25 publications

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“…Note that recent molecular dynamics work has seen significant advancement with methods and energy potentials progressing much beyond the standard L - J potentials used in this paper. The use of more realistic materials and the incorporation of more advanced model approaches can be seen in work by Narayan Aluru [52,53] at University of Illinois and in work by Harvey Zambrano [54,55] at University of Concepcion in Chile.…”

Section: Mathematical Modelmentioning

confidence: 99%

Role of Solid Wall Properties in the Interface Slip of Liquid in Nanochannels

et al. 2018

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A two-dimensional molecular dynamics model of the liquid flow inside rough nanochannels is developed to investigate the effect of a solid wall on the interface slip of liquid in nanochannels with a surface roughness constructed by rectangular protrusions. The liquid structure, velocity profile, and confined scale on the boundary slip in a rough nanochannel are investigated, and the comparison of those with a smooth nanochannel are presented. The influence of solid wall properties, including the solid wall density, wall-fluid coupling strength, roughness height and spacing, on the interfacial velocity slip are all analyzed and discussed. It is indicated that the rough surface induces a smaller magnitude of the density oscillations and extra energy losses compared with the smooth solid surface, which reduce the interfacial slip of liquid in a nanochannel. In addition, once the roughness spacing is very small, the near-surface liquid flow dominates the momentum transfer at the interface between liquid and solid wall, causing the role of both the corrugation of wall potential and wall-fluid coupling strength to be less obvious. In particular, the slip length increases with increasing confined scales and shows no dependence on the confined scale once the confined scale reaches a critical value. The critical confined scale for the rough channel is larger than that of the smooth scale.

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Section: Mathematical Modelmentioning

confidence: 99%

Role of Solid Wall Properties in the Interface Slip of Liquid in Nanochannels

et al. 2018

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“…They were examined using deoxyribonucleic acid (DNA) primers to determine if the model can assist in the determination of DNA hybridization. DNA is a double-stranded biological molecule that has instruction about genes for the biological development of all cellular forms of life [12,13]. Hybridization is the process where one strand of the DNA (F-DNA) bonds together with the other complementary strands (R-DNA) to form a double helical DNA structure.…”

Section: Sensing and Detection With The Sensormentioning

confidence: 99%

Intermediate Frequency AC Signal Analysis for Bionanosensor

Desai

Sanisetty

Steber

et al. 2011

Journal of Nanotechnology

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Nanobiosensors are devices which incorporate nanomaterials to detect miniscule quantities of biological and chemical agents. The authors have already developed a novel bionanosensor (BNS) for quick, efficient, and precise detection of bacterial pathogens using the principles of CNT-DNA interaction and DNA hybridization. The detection ability of the (BNS) was observed to be independent of the device resistance. Two new methods (low-pass filter (LPF) and curve fitting (CF)) were developed for better analysis of the BNS. These methods successfully model the BNS. Evidence is provided to elucidate the success of the model, which can explain the DNA hybridization on the sensor surface. These models successfully demonstrated the detection of DNA hybridization versus nonhybridization. Thus, the models can not only help in better and efficient design and operation of the BNS, but can also be used to analyze other similar nanoscale devices.

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“…Within such 0small confinement, the behaviors of water molecules and ions are sensitive to slight variation of their interactions with the CNT inner surface [32][33][34] . Of particular relevance to the current work, the transport of DNA through CNT has also been studied by both experiment and simulation [34][35][36][37][38] , along with many other nanopore systems 12, 16, 39-44 . However, there are still limited simulation studies about how the DNA distribution within the CNT and the concomitant ion transport depend on the DNA sequence. In recent experimental work of our colleagues 30 , the nanopore was constructed by embedding ultra-short single-walled CNTs (SWCNTs) into a lipid bilayer.…”

Section: Introductionmentioning

confidence: 99%

“…Because of its unique properties, such as well-defined structure and controllable pore size, carbon nanotubes (CNTs) constitute a promising class of nanopore materials. The transport of water and ions through CNTs has been studied extensively. − Within such a small confinement, the behaviors of water molecules and ions are sensitive to slight variation of their interactions with the CNT inner surface. − Of particular relevance to the current work, the transport of DNA through CNT has also been studied by both experiment and simulation, − along with many other nanopore systems. ,,− However, there are still limited simulation studies about how the DNA distribution within the CNT and the concomitant ion transport depend upon the DNA sequence. In recent experimental work of our colleagues, the nanopore was constructed by embedding ultra-short single-walled carbon nanotubes (SWCNTs) into a lipid bilayer.…”

Section: Introductionmentioning

confidence: 99%

Sensitive Detection of a Modified Base in Single-Stranded DNA by a Single-Walled Carbon Nanotube

et al. 2015

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In this work, we use molecular dynamics simulations to study the responses of the configuration of single-strand DNA (ssDNA) within a carbon nanotube (CNT) and the concomitant ion flow to a single modified base, i.e., benzoimidazole (Bzim)-modified 5-hydroxymethyl cytosine (5hmC). Our simulation results show the Bzim-modified 5hmC can considerably increase the ion flow through a single-walled carbon nanotube (SWCNT), despite its larger size, which is consistent with prior experimental results. This phenomenon is attributed to enhanced adsorption of DNA to the interior wall of the CNT driven by the Bzim-modified 5hmC, leading to a reduced steric effect on ion transport through the CNT. As revealed in this work, the distribution of ssDNA can be affected by limited change in the interactions with the CNT surface. Such behavior of ssDNA within small-sized CNTs can be exploited to further improve the sensitivity of nanopore detection.

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Detection of defective DNA in carbon nanotubes by combined molecular dynamics/tight-binding technique

Cited by 6 publications

References 25 publications

Role of Solid Wall Properties in the Interface Slip of Liquid in Nanochannels

Role of Solid Wall Properties in the Interface Slip of Liquid in Nanochannels

Intermediate Frequency AC Signal Analysis for Bionanosensor

Sensitive Detection of a Modified Base in Single-Stranded DNA by a Single-Walled Carbon Nanotube

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