| 1. |
- Feliciano, Gustavo T., et al.
(författare)
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Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems : A QM/MM-NEGF Approach
- 2018
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 122:2, s. 485-492
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Tidskriftsartikel (refereegranskat)abstract
- The effects of the environment in nanoscopic materials can play a crucial role in device design. Particularly in biosensors, where the system is usually embedded in a solution, water and ions have to be taken into consideration in atomistic simulations of electronic transport for a realistic description of the system. In this work, we present a methodology that combines quantum mechanics/molecular mechanics methods (QM/MM) with the nonequilibrium Green’s function framework to simulate the electronic transport properties of nanoscopic devices in the presence of solvents. As a case in point, we present further results for DNA translocation through a graphene nanopore. In particular, we take a closer look into general assumptions in a previous work. For this sake, we consider larger QM regions that include the first two solvation shells and investigate the effects of adding extra k-points to the NEGF calculations. The transverse conductance is then calculated in a prototype sequencing device in order to highlight the effects of the solvent.
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| 2. |
- Feliciano, Gustavo T., et al.
(författare)
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Capacitive DNA Detection Driven by Electronic Charge Fluctuations in a Graphene Nanopore
- 2015
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Ingår i: Physical Review Applied. - 2331-7019. ; 3:3
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Tidskriftsartikel (refereegranskat)abstract
- The advent of parallelized automated methods for rapid whole-genome analysis has led to an exponential drop in costs, thus greatly accelerating biomedical research and discovery. Third-generation sequencing techniques, which would utilize the characteristic electrical conductance of the four different nucleotides, could facilitate longer base read lengths and an even lower price per genome. In this work, we propose and apply a quantum-classical hybrid methodology to quantitatively determine the influence of the solvent on the dynamics of DNA and the resulting electron transport properties of a prototypic sequencing device utilizing a graphene nanopore through which the nucleic-acid chain is threaded. Our results show that charge fluctuations in the nucleotides are responsible for characteristic conductance modulations in this system, which can be regarded as a field-effect transistor tuned by the dynamic aqueous environment.
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| 3. |
- He, Haiying, et al.
(författare)
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Functionalized Nanopore-Embedded Electrodes for Rapid DNA Sequencing
- 2008
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 112:10, s. 3456-3459
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Tidskriftsartikel (refereegranskat)abstract
- With the aim of improving nanopore-based DNA sequencing, we explored the effects of functionalizing the embedded gold electrodes with purine and pyrimidine molecules. Hydrogen bonds formed between the molecular probe and target bases stabilize the scanned DNA unit against thermal fluctuations and thus greatly reduce noise in the current signal. The results of our first-principles study indicate that this proposed scheme could allow DNA sequencing with a robust and reliable yield, producing current signals that differ by at least 1 order of magnitude for the different bases.
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| 4. |
- Martins, Ernane de Freitas, et al.
(författare)
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A multiscale approach for electronic transport simulation of carbon nanostructures in aqueous solvent
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 24:39, s. 24404-24412
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Tidskriftsartikel (refereegranskat)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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| 5. |
- Martins, Ernane de Freitas, et al.
(författare)
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Simulating DNA Chip Design Using All-Electronic Graphene-Based Substrates
- 2019
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Ingår i: Molecules. - : MDPI. - 1431-5157 .- 1420-3049. ; 24:5
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Tidskriftsartikel (refereegranskat)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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| 6. |
- Martins, Ernane de Freitas, et al.
(författare)
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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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Ingår i: Carbon. - : Elsevier BV. - 0008-6223 .- 1873-3891. ; 158, s. 314-319
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Tidskriftsartikel (refereegranskat)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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