| 1. |
- Prasongkit, Jariyanee, et al.
(author)
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Topological Line Defects Around Graphene Nanopores for DNA Sequencing
- 2018
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In: The Journal of Physical Chemistry C. - : AMER CHEMICAL SOC. - 1932-7447 .- 1932-7455. ; 122:13, s. 7094-7099
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Journal article (peer-reviewed)abstract
- Topological line defects in graphene represent an ideal way to produce highly controlled structures with reduced dimensionality that can be used in electronic devices. In this work, we propose using extended line defects in graphene to improve nucleobase selectivity in nanopore-based DNA sequencing devices. We use a combination of quantum mechanics/molecular mechanics and nonequilibrium Green's function methods to investigate the conductance modulation, fully accounting for solvent effects. By sampling over a large number of different orientations generated from molecular dynamics simulations, we theoretically demonstrate that distinguishing between the four nucleobases using line defects in a graphene-based electronic device appears possible. The changes in conductance are associated with transport across specific molecular states near the Fermi level and their coupling to the pore. Through the application of a specifically tuned gate voltage, such a device would be able to discriminate the four types of nucleobases more reliably than that of graphene sensors without topological line defects.
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| 2. |
- Martins, Ernane de Freitas, et al.
(author)
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A multiscale approach for electronic transport simulation of carbon nanostructures in aqueous solvent
- 2022
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:39, s. 24404-24412
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Journal article (peer-reviewed)abstract
- Theoretical works addressing electronic nano-devices operating in an aqueous environment often neglect solvent effects. In order to assess the role played by the polarization effects on the electronic transport properties of solvated graphene, for example in possible bio-sensing applications, we have used here a combination of polarizable force-field molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) approach, density functional theory, and non-equilibrium Green's function method. We considered different solvation conditions, the presence of defects in graphene, as well as various choices for the partitions between the quantum and classical regions in QM/MM, in which we explicitly account for polarization effects. Our results show that the polarization effects on graphene lead to changes in the structure of interfacial water molecules which are more pronounced in the vicinity of defects. The presence of water leads to increased scattering due to the long-range charge interactions with graphene. At the same time, changes in the conductance due to polarization or salt concentration are found to be small, paving the way for robust electronic nano-devices operating in aqueous environments.
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| 3. |
- Martins, Ernane de Freitas, et al.
(author)
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Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates
- 2019
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In: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 24:5
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Journal article (peer-reviewed)abstract
- In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes in the electronic transport properties of graphene interacting with DNA strands under the effect of the solvent. To investigate these systems, we applied a hybrid methodology, combining quantum and classical mechanics (QM/MM) coupled to non-equilibrium Green's functions, allowing for the calculations of electronic transport. Our results show that the proposed device has high sensitivity towards the presence of DNA, and, combined with the presence of a specific DNA probe in the form of a single-strand, it presents good selectivity towards specific nucleotide sequences.
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| 4. |
- Martins, Ernane de Freitas, et al.
(author)
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The role of water on the electronic transport in graphene nanogap devices designed for DNA sequencing
- 2020
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In: Carbon. - : Elsevier BV. - 0008-6223 .- 1873-3891. ; 158, s. 314-319
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Journal article (peer-reviewed)abstract
- Innovative methodologies for reliably and inexpensively sequencing DNA can lead to a new era of personalized medicine. In this work, we performed a theoretical investigation of a nanogap-based all electronic DNA sequencing device. To do so, we used a nitrogen-terminated nanogap on a graphene sheet with the aqueous environment fully taken into account. Our investigation is performed using a hybrid methodology combining quantum and classical mechanics coupled to non-equilibrium Green's functions for solving the electron transport across the device. The obtained results show that the DNA nucleotides can be both detected and distinguished in such a device, which indicates that it can be used as a DNA sequencing device providing very high sensitivity and selectivity. Furthermore, our results show that water plays a major role in electronic transport in nanoscopic tunneling devices, not only from an electrostatics point of view, but also by providing states that significantly increase the conductance in nanogap-based DNA sequencing devices.
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