arXiv subjects

Ralph H. Scheicher

Publications and source records attributed to Ralph H. Scheicher.

18 recordsLinked to original sources

arXiv2024

The influence of hydrogen on the electronic structure in transition metallic glasses

We investigate the influence of hydrogen on the electronic structure of a binary transition metallic glass of V$_{80}$Zr$_{20}$. We examine the hybridization between the hydrogen and metal atoms with the aid of hard x-ray photoelectron spectroscopy. Combined with ab initio density functional theory, we are able to show and predict the formation of $s$-$d$ hybridized energy states. With optical transmission and resistivity measurements, we investigate the emergent electronic properties formed out of those altered energy states, and together with the theoretical calculations of the frequency-dependent conductivity tensor, we qualitatively support the observed strong wavelength-dependency of the hydrogen-induced changes on the optical absorption and a positive parabolic change in resistivity with hydrogen concentration.

cond-mat.mtrl-sci↗

arXiv2017

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.

cond-mat.mes-hall↗

arXiv2017

A zero-depth nanopore capillary for the analysis of translocating biomolecules

High-fidelity analysis of translocating biomolecules through nanopores demands shortening the nanocapillary length to a minimal value. Existing nanopores and capillaries, however, inherit a finite length from the parent membranes. Here, we form nanocapillaries of zero depth by dissolving two superimposed and crossing metallic nanorods, thereby opening two overlapping nanofluidic channels molded in a polymeric resin. In an electrolyte, the interface shared by the crossing fluidic channels is mathematically of zero thickness and defines the narrowest constriction in the stream of ions through the nanopore device. This novel architecture provides the possibility to design nanopore fluidic channels, particularly with a robust 3D architecture maintaining the ultimate zero thickness geometry independently of the thickness of the fluidic channels. With orders of magnitude reduced biomolecule translocation speed, and lowered electronic and ionic noise compared to nanopores in 2D materials, our findings establish interfacial nanopores as a scalable platform for realizing nanofluidic systems, capable of single-molecule detection.

physics.bio-ph↗

arXiv2016

Interface of graphene nanopore and hexagonal boron nitride as a sensing device

The atomically-precise controlled synthesis of graphene stripes embedded in hexagonal boron nitride opens up new possibilities for the construction of nanodevices with applications in sensing. Here, we explore properties related to electronic structure and quantum transport of a graphene nanoroad embedded in hexagonal boron nitride, using a combination of density functional theory and the non-equilibrium Green's functions method to calculate the electric conductance. We find that the graphene nanoribbon signature is preserved in the transmission spectra and that the local current is mainly confined to the graphene domain. When a properly sized nanopore is created in the graphene part of the system, the electronic current becomes restricted to a carbon chain running along the border with hexagonal boron nitride. This circumstance could allow the hypothetical nanodevice to become highly sensitive to the electronic nature of molecules passing through the nanopore, thus opening up ways for the detection of gas molecules, amino acids, or even DNA sequences based on a measurement of the real-time conductance modulation in the graphene nanoroad.

cond-mat.mtrl-sci↗

arXiv2015

Contrasting interedge superexchange interactions of graphene nanoribbons embedded in h-BN and graphane

Based on first-principles density-functional theory calculations, we present a comparative study of the elec- tronic structures of ultranarrow zigzag graphene nanoribbons (ZGNRs) embedded in hexagonal boron nitride (BN) sheet and fully hydrogenated graphene (graphane) as a function of their width N (the number of zigzag C chains composing the ZGNRs). We find that ZGNRs/BN have the nonmagnetic ground state except at N = 5 and 6 with a weakly stabilized half-semimetallic state, whereas ZGNRs/graphane with N >= 2 exhibit a strong antiferromagnetic coupling between ferromagnetically ordered edge states on each edge. It is revealed that the disparate magnetic properties of the two classes of ZGNRs are attributed to the contrasting interedge superexchange interactions arising from different interface structures: i.e., the asymmetric interface structure of ZGNRs/BN gives a relatively short-range and weak superexchange interaction between the two inequivalent edge states, while the symmetric interface structure of ZGNRs/graphane gives a long-range, strong interedge superexchange interaction.

cond-mat.mes-hall↗

arXiv2014

Effect of uniaxial strain on the site occupancy of hydrogen in vanadium from density-functional calculations

We investigate the influence of uniaxial strain on site occupancy of hydrogen vanadium, using density functional theory. The site occupancy is found to be strongly influenced by the strain state of the lattice. The results provide the conceptual framework of the atomistic description of the observed hysteresis in the alpha to beta phase transition in bulk, as well as the preferred octahedral occupancy of hydrogen in strained V layers.

cond-mat.mtrl-sci↗

arXiv2014

Silicene as a new ultrafast DNA sequencing device

Silicene, a hexagonal buckled 2-D allotrope of silicon, shows potential as a platform for numerous new applications, and may allow for easier integration with existing silicon-based microelectronics than graphene. Here, we show that silicene could function as an ultrafast electrical DNA sequencing device. We investigated the stability of this novel nano-bio system, its electronic properties and the pronounced effects on the transverse electronic transport, i.e., changes in the transmission and the conductance caused by adsorption of each nucleobase, explored by us through the non-equilibrium Green's function method. Intriguingly, despite the relatively weak interaction between nucleobases and silicene, significant changes in the transmittance at zero bias are predicted by us, in particular for the two nucleobases cytosine and guanine. Our findings suggest that silicene could be utilized as an integrated-circuit biosensor as part of a lab-on-a-chip device for DNA sequencing.

cond-mat.mes-hall↗

arXiv2013

Physisorption of DNA nucleobases on h-BN and graphene: vdW-corrected DFT calculations

We present a comparative study of DNA nucleobases [guanine (G), adenine (A), thymine (T), and cytosine (C)] adsorbed on hexagonal boron nitride (\textit{h}-BN) sheet and graphene, using local, semilocal, and van der Waals (vdW) energy-corrected density-functional theory (DFT) calculations. Intriguingly, despite the very different electronic properties of BN sheet and graphene, we find rather similar binding energies for the various nucleobase molecules when adsorbed on the two types of sheets. The calculated binding energies of the four nucleobases using the local, semilocal, and DFT+vdW schemes are in the range of 0.54 ${\sim}$ 0.75 eV, 0.06 ${\sim}$ 0.15 eV, and 0.93 ${\sim}$ 1.18 eV, respectively. In particular, the DFT+vdW scheme predicts not only a binding energy predominantly determined by vdW interactions between the base molecules and their substrates decreasing in the order of G$>$A$>$T$>$C, but also a very weak hybridization between the molecular levels of the nucleobases and the $π$-states of the BN sheet or graphene. This physisorption of G, A, T, and C on the BN sheet (graphene) induces a small interfacial dipole, giving rise to an energy shift in the work function by 0.11 (0.22), 0.09 (0.15), $-$0.05 (0.01), and 0.06 (0.13) eV, respectively.

cond-mat.mes-hall↗

arXiv2012

Bilayer Graphene Lateral Contacts for DNA Sequencing

Translocation of DNA through a nanopore with embedded electrodes is at the centre of new rapid inexpensive sequencing methods which allow distinguishing the four nucleobases by their different electronic structure. However, the subnanometer separation between nucleotides in DNA requires ultra-sharp probes. Here, we propose a device architecture consisting of a nanopore formed in bilayer graphene, with the two layers acting as separate electrical contacts. The 0.34 nm interlayer distance of graphene is ideally suited for electrical coupling to a single nucleobase, avoiding the difficulty of fabricating probes with subnanometer precision. The top and bottom graphene electrodes contact the target molecule from the same lateral side, removing the orders-of-magnitude tunneling current variations between smaller pyrimidine bases and larger purine bases. We demonstrate that incorporating techniques for molecular manipulation enables the proposed device to sequence single-stranded DNA and that it offers even the prospect of sequencing double-stranded DNA.

cond-mat.mes-hall↗

arXiv2012

Transverse Electronic Transport through DNA Nucleotides with Functionalized Graphene Electrodes

Graphene nanogaps and nanopores show potential for the purpose of electrical DNA sequencing, in particular because single-base resolution appears to be readily achievable. Here, we evaluated from first principles the advantages of a nanogap setup with functionalized graphene edges. To this end, we employed density functional theory and the non-equilibrium Green's function method to investigate the transverse conductance properties of the four nucleotides occurring in DNA when located between the opposing functionalized graphene electrodes. In particular, we determined the electrical tunneling current variation as a function of the applied bias and the associated differential conductance at a voltage which appears suitable to distinguish between the four nucleotides. Intriguingly, we observe for one of the nucleotides a negative differential resistance effect.

cond-mat.mes-hall↗

arXiv2011

Predicted formation of superconducting platinum-hydride crystals under pressure in the presence of molecular hydrogen

Noble metals adopt close-packed structures at ambient pressure and rarely undergo structural transformation at high pressures. Platinum (Pt), in particular, is normally considered to be unreactive and is therefore not expected to form hydrides under pressure. We predict that platinum hydride (PtH) has a lower enthalpy than its constituents solid Pt and molecular hydrogen at pressures above 21.5 GPa. We have calculated structural phase transitions from tetragonal to hexagonal close-packed or face-centered cubic (fcc) PtH between 70 and 80 GPa. Linear response calculations indicate that PtH is a superconductor at these pressures with a critical temperature of about 10--25 K. These findings help to shed light on recent observations of pressure-induced metallization and superconductivity in hydrogen-rich materials. We show that formation of fcc metal hydrides under pressure is common among noble metal hydrides and examine the possibility of superconductivity in these materials.

cond-mat.supr-con↗

arXiv2011

Theoretical study of C60 as catalyst for dehydrogenation in LiBH4

Complex light metal hydrides possess many properties which make them attractive as a storage medium for hydrogen, but typically, catalysts are required to lower the hydrogen desorption temperature and to facilitate hydrogen uptake in the form of a reversible reaction. The overwhelming focus in the search for catalysing agents has been on compounds containing titanium, but the precise mechanism of their actions remains somewhat obscure. A recent experiment has now shown that fullerenes (C$_{60}$) can also act as catalyst for both hydrogen uptake and release in lithium borohydride (LiBH$_4$). In an effort to understand the involved mechanism, we have employed density functional theory to carry out a detailed study of the interaction between this complex metal hydride and the carbon nanomaterial. Considering a stepwise reduction of the hydrogen content in LiBH$_4$, we find that the presence of C$_{60}$ can lead to a substantial reduction of the involved H-removal energies. This effect is explained as a consequence of the interaction between the BH$_x^-$ complex and the C$_{60}$ entity.

cond-mat.mtrl-sci↗

arXiv2011

Transverse conductance of DNA nucleotides in a graphene nanogap from first principles

The fabrication of nanopores in atomically-thin graphene has recently been achieved and translocation of DNA has been demonstrated. Taken together with an earlier proposal to use graphene nanogaps for the purpose of DNA sequencing, this approach can resolve the technical problem of achieving single-base resolution in electronic nucleobase detection. We have theoretically evaluated the performance of a graphene nanogap setup for the purpose of whole-genome sequencing, by employing density functional theory and the non-equilibrium Green's function method to investigate the transverse conductance properties of nucleotides inside the gap. In particular, we determined the electrical tunneling current variation at finite bias due to changes in the nucleotides orientation and lateral position. Although the resulting tunneling current is found to fluctuate over several orders of magnitudes, a distinction between the four DNA bases appears possible, thus ranking the approach promising for rapid whole-genome sequencing applications.

physics.ins-det↗

arXiv2010

Enhanced DNA sequencing performance through edge-hydrogenation of graphene electrodes

We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of this idea. The results of our investigation show that, compared to the unhydrogenated system, edge-hydrogenated graphene electrodes facilitate the temporary formation of H-bonds with suitable atomic sites in the translocating DNA molecule. As a consequence, the average conductivity is drastically raised by about 3 orders of magnitude while exhibiting significantly reduced statistical variance. We have furthermore investigated how these results are affected when the distance between opposing electrodes is varied and have identified two regimes: for narrow electrode separation, the mere hindrance due to the presence of protruding hydrogen atoms in the nanopore is deemed more important, while for wider electrode separation, the formation of H-bonds becomes the dominant effect. Based on these findings, we conclude that hydrogenation of graphene electrode edges represents a promising approach to reduce the translocation speed of DNA through the nanopore and substantially improve the accuracy of the measurement process for whole-genome sequencing.

physics.bio-ph↗

arXiv2010

Theoretical Study of Physisorption of Nucleobases on Boron Nitride Nanotubes: A New Class of Hybrid Nano-Bio Materials

We investigate the adsorption of the nucleic acid bases, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) on the outer wall of a high curvature semiconducting single-walled boron nitride nanotube (BNNT) by first principles density functional theory calculations. The calculated binding energy shows the order: G>A\approxC\approxT\approxU implying that the interaction strength of the (high-curvature) BNNT with the nucleobases, G being an exception, is nearly the same. A higher binding energy for the G-BNNT conjugate appears to result from a stronger hybridization of the molecular orbitals of G and BNNT, since the charge transfer involved in the physisorption process is insignificant. A smaller energy gap predicted for the G-BNNT conjugate relative to that of the pristine BNNT may be useful in application of this class of biofunctional materials to the design of the next generation sensing devices.

physics.bio-ph↗

arXiv2007

First-principles Study of Physisorption of Nucleic Acid Bases on Small-Diameter Carbon Nanotube

We report the results of our first-principles study based on density functional theory on the interaction of the nucleic acid base molecules adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U), with a single-walled carbon nanotube (CNT). Specifically, the focus is on the physisorption of base molecules on the outer wall of a (5,0) metallic CNT possessing one of the smallest diameters possible. Compared to CNTs with large diameters, the physisorption energy is found to be reduced in the high-curvature case. The base molecules exhibit significantly different interaction strengths, and the calculated binding energies follow the hierarchy G > A > T > C > U, which appears to be independent of the tube curvature. The stabilizing factor in the interaction between the base molecule and CNT is dominated by the molecular polarizability that allows a weakly attractive dispersion force to be induced between them. The present study provides an improved understanding of the role of the base sequence in deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) on their interactions with carbon nanotubes of varying diameters.

cond-mat.soft↗

arXiv2007

Functionalized nanopore-embedded electrodes for rapid DNA sequencing

The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form of data analysis [7]. Here we propose a new approach that relies on functionalized nanopore-embedded electrodes to achieve an unambiguous distinction of the four nucleic acid bases in the DNA sequencing process. This represents a significant improvement over previously studied designs [8,9] which cannot reliably distinguish all four bases of DNA. The transport properties of the setup investigated by us, employing state-of-the-art density functional theory together with the non-equilibrium Green's Function method, leads to current responses that differ by at least one order of magnitude for different bases and can thus provide a much more robust read-out of the base sequence. The implementation of our proposed setup could thus lead to a viable protocol for rapid DNA sequencing with significant consequences for the future of genome related research in particular and health care in general.

physics.bio-ph↗

arXiv2007

Physisorption of Nucleobases on Graphene

We report the results of our first-principles investigation on the interaction of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) with graphene, carried out within the density functional theory framework, with additional calculations utilizing Hartree--Fock plus second-order Moeller-Plesset perturbation theory. The calculated binding energy of the nucleobases shows the following hierarchy: G > T ~ C ~ A > U, with the equilibrium configuration being very similar for all five of them. Our results clearly demonstrate that the nucleobases exhibit significantly different interaction strengths when physisorbed on graphene. The stabilizing factor in the interaction between the base molecule and graphene sheet is dominated by the molecular polarizability that allows a weakly attractive dispersion force to be induced between them. The present study represents a significant step towards a first-principles understanding of how the base sequence of DNA can affect its interaction with carbon nanotubes, as observed experimentally.

cond-mat.mtrl-sci↗