Topological Line Defects around Graphene Nanopores for DNA Sequencing

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 QM/MM and non-equilibrium Green's functions 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.Comment: 6 figures and 6 page

Hyperfine magnetic field in ferromagnetic graphite

Information on atomic-scale features is required for a better understanding of the mechanisms leading to magnetism in non-metallic, carbon-based materials. This work reports a direct evaluation of the hyperfine magnetic field produced at 13C nuclei in ferromagnetic graphite by nuclear magnetic resonance (NMR). The experimental investigation was made possible by the results of first-principles calculations carried out in model systems, including graphene sheets with atomic vacancies and graphite nanoribbons with edge sites partially passivated by oxygen. A similar range of maximum hyperfine magnetic field values (18-21T) was found for all systems, setting the frequency span to be investigated in the NMR experiments; accordingly, a significant 13C NMR signal was detected close to this range without any external applied magnetic field in ferromagnetic graphite

Atomistic Study of Water Confined in Silica.

In this work, we have used a combined of atomistic simulation methods to explore the effects of confinement of water molecules between silica surfaces. Firstly, the mechanical properties of water severe confined (~3A) between two silica alpha-quartz was determined based on first principles calculations within the density functional theory (DFT). Simulated annealing methods were employed due to the complex potential energry surface, and the difficulties to avoid local minima. Our results suggest that much of the stiffness of the material (46%) remains, even after the insertion of a water monolayer in the silica. Secondly, in order to access typical time scales for confined systems, classical molecular dynamics was used to determine the dynamical properties of water confined in silica cylindrical pores, with diameters varying from 10 to 40A. in this case we have varied the passivation of the silica surface, from 13% to 100% of SiOH, and the other terminations being SiOH2 and SiOH3, the distribution of the different terminations was obtained with a Monte Carlo simulation. The simulations indicates a lowering of the diffusion coefficientes as the diameter decreases, due to the structuration of hydrogen bonds of water molecules; we have also obtained the density profiles of the confined water and the interfacial tension

Bridging Borophene and Metal Surfaces: Structural, Electronic, and Electron Transport Properties

Currently, solid interfaces composed of two-dimensional materials (2D) in contact with metal surfaces (m-surf) have been the subject of intense research, where the borophene bilayer (BBL) has been considered a prominent material for the development of electronic devices based on 2D platforms. In this work, we present a theoretical study of the energetic, structural, and electronic properties of the BBL/m-surf interface, with m-surf = Ag, Au, and Al (111) surfaces, and the electronic transport properties of BBL channels connected to the BBL/m-surf top contacts. We find that the bottom-most BBL layer becomes metalized, due to the orbital hybridization with the metal surface states, resulting in BBL/m-surf ohmic contacts, meanwhile, the inner and top-most boron layers kept their semiconducting character. The net charge transfers reveal that BBL has become $n$-type ($p$-type) doped for m-surf = Ag, and Al (= Au). A thorough structural characterization of the BBL/m-surf interface, using a series of simulations of the X-ray photoelectron spectra, shows that the formation of BBL/m-surf interface is characterized by a redshift of the B-$1s$ spectra. Further electronic transport results revealed the emergence of a Schottky barrier between 0.1 and 0.2\,eV between the BBL/m-surf contact and the BBL channels. We believe that our findings are timely, bringing important contributions to the applicability of borophene bilayers for developing 2D electronic devices

Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/h-BN nanopore

The feasibility of synthesizing unnatural DNA/RNA has recently been demonstrated, giving rise to new perspectives and challenges in the emerging field of synthetic biology, DNA data storage, and even the search for extraterrestrial life in the universe. In line with this outstanding potential, solid-state nanopores have been extensively explored as promising candidates to pave the way for the next generation of label-free, fast, and low-cost DNA sequencing. In this work, we explore the sensitivity and selectivity of a graphene/h-BN based nanopore architecture towards detection and distinction of synthetic Hachimoji nucleobases. The study is based on a combination of density functional theory and the non-equilibrium Green's function formalism. Our findings show that the artificial nucleobases are weakly binding to the device, indicating a short residence time in the nanopore during translocation. Significant changes in the electron transmission properties of the device are noted depending on which artificial nucleobase resides in the nanopore, leading to a sensitivity in distinction of up to 80%. Our results thus indicate that the proposed nanopore device setup can qualitatively discriminate synthetic nucleobases, thereby opening up the feasibility of sequencing even unnatural DNA/RNA.All authors contributed equally to this work</p