Instability and translocation through nanopores of DNA interacting with single-layer materials

Alshehri, Mansoor H.; Duraihem, Faisal Z.; Oud, Mohammed A. Aba

doi:10.1039/d0ra06359b

Cited by 4 publications

(3 citation statements)

References 34 publications

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“…Therefore, we used mathematical modeling techniques that are necessary to formulate explicit analytical criteria and ideal model behaviour to complement the efforts of experimentalists. The interactions between various nanostructured materials have been widely determined using mathematical modeling [ 20 , 21 , 22 , 23 , 24 ]. The standard method for this modeling is to employ the Lennard–Jones potential together with the continuous approximation; which is assumed that the atoms are uniformly distributed over the surface of the molecules [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Investigation of Interaction of Noble Metals (Cu, Ag, Au, Pt and Ir) with Nanosheets

Alshehri

2021

Micromachines

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Two-dimensional nanomaterials, such as graphene and hexagonal boron nitride nanosheets, have attracted tremendous interest in the research community and as a starting point for the development of nanotechnology. Using classical applied mathematical modeling, we derive explicit analytical expressions to determine the binding energies of noble metals, including copper, silver, gold, platinum and iridium (Cu, Ag, Au, Pt and Ir) atoms, on graphene and hexagonal boron nitride nanosheets. We adopt the 6–12 Lennard–Jones potential function, together with the continuous approach, to determine the preferred minimum energy position of an offset metal atom above the surface of the graphene and hexagonal boron nitride nanosheets. The main results of this study are analytical expressions of the interaction energies, which we then utilize to report the mechanism of adsorption of the metal atoms on graphene and hexagonal boron nitride surfaces. The results show that the minimum binding energy occured when Cu, Ag, Au, Pt and Ir were set at perpendicular distances in the region from 3.302 Å to 3.683 Å above the nanosheet surface, which correspond to adsorption energies in the region ranging from 0.842 to 2.978 (kcal/mol). Our results might assist in providing information on the interaction energies between the metal atoms and the two-dimensional nanomaterials.

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Section: Introductionmentioning

confidence: 99%

Investigation of Interaction of Noble Metals (Cu, Ag, Au, Pt and Ir) with Nanosheets

Alshehri

2021

Micromachines

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“…Mathematical modelling may also be used to accurately predict the ideal configurations and the main physical parameters. Mathematical modelling has been widely used to obtain the interaction energies between various nanostructured materials [15,[21][22][23][24]. The usual method of modelling in this area is to apply the Lennard-Jones function with the continuous approximation, which assumes that the atoms are uniformly distributed over the volume or surface of the molecules [21].…”

Section: Introductionmentioning

confidence: 99%

Computational Study on the Interaction and Moving of ssDNA through Nanosheets

Alshehri

2021

Crystals

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The adsorption characteristics and moving through nanopores of a single-stranded deoxyribonucleic acid (ssDNA) molecule on monolayers, such ashexagonal boron nitride and graphene nanosheets, were studied using the continuous approach with the 6–12 Lennard–Jones potential function. The ssDNA molecule is assumed to be at a distance l above the sheet, and the relation between the minimum energy location and the perpendicular distance of the ssDNA molecule from the nanosheet surface is found. In addition, by assuming that there is a hole in the surface of the nanosheet as a pore, the interaction energies for the ssDNA molecule moving through the pore in the surface of the nanosheet (used to calculate the radius p of the hole) are obtained, which provides the minimum energies. Furthermore, a comparative study with graphene was performed in order to compare with hexagonal boron nitride nanosheets. Our results indicate that the binding energies of the ssDNA onto graphene and hexagonal boron nitride nanosheets are approximately 15.488 and 17.582 (kcal/mol), corresponding to perpendicular distances of l=20.271 and l=20.231 Å, respectively. In addition, we observe that the ssDNA molecule passes through graphene and hexagonal boron nitride nanopores when the gap radius p>7.5 Å. Our results provide critical insights to understand and develop the interactions and translocation of DNA molecules with and through nanosheets.

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“…Although BNNTs and CNTs have structural similarities, the two nanotubes differ in some properties, which cause different behaviors for each. For example, the bond lengths of C-C bonds and B-N bonds are approximately 1.42 and 1.45 Å, respectively [9,10].…”

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Continuum modeling for lithium storage inside nanotubes

Alsaud,

Alshehri

2023

Front. Phys.

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Lithium storage and capture are of particular importance for the development of new technology in electric vehicles and portable electronics. Nanotubes (NTs) are among many porous nanomaterials offered as potential candidates for lithium storage. In this paper, we adopt a continuum approach together with the Lennard–Jones function to determine the minimum interaction energies for lithium atoms in boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs). By minimizing the interaction energies, we may obtain the preferred type and size of the nanotubes to encapsulate the lithium atoms. The results showed that BNNTs and CNTs are attractive candidates for lithium atom encapsulation, and the optimal nanotube to enclose lithium is the BNNT with a radius equal to 3.4 Å, and corresponding (5, 5) armchair nanotubes and (9, 0) zigzag nanotubes, where the minimum energy is obtained. The present computations observed that both nanotubes are promising candidates for lithium intercalation materials suitable for battery applications.

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Instability and translocation through nanopores of DNA interacting with single-layer materials

Abstract: Using classical applied mathematical modelling to employ the 6–12 Lennard-Jones potential function along with the continuous approximation to investigate the interaction energy between dsDNA and 2D-nanomaterials, namely GRA, h-BN, MoS2 and WS2 sheets.

Cited by 4 publications

References 34 publications

Investigation of Interaction of Noble Metals (Cu, Ag, Au, Pt and Ir) with Nanosheets

Investigation of Interaction of Noble Metals (Cu, Ag, Au, Pt and Ir) with Nanosheets

Computational Study on the Interaction and Moving of ssDNA through Nanosheets

Continuum modeling for lithium storage inside nanotubes

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