Anton Grigoriev

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 nonequilibrium Greens 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 magnitude, a distinction between the four DNA bases appears possible, thus ranking the approach promising for rapid whole-genome sequencing applications.

Enhanced DNA Sequencing Performance Through Edge-Hydrogenation of Graphene Electrodes

The use of graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing is proposed, and molecular dynamics simulations in conjunction with electronic transport calculations are performed to explore the potential merits of this idea. The results of the 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. Furthermore, the effect of the distance between opposing electrodes is investigated and two regimes identified: 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, it is concluded 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.

Functionalized Nanopore-Embedded Electrodes for Rapid DNA Sequencing

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.

Theoretical Study of Electronic Transport through DNA Nucleotides in a Double-Functionalized Graphene Nanogap

Graphene nanogaps and nanopores show potential for the purp ose of electrical DNA sequencing, in particular because single-base resolution ap pears to be readily achievable. Here, we evaluated from first principles the advantages of a nanoga p 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 cond uctance properties of the four nucleotides occurring in DNA when located between the opposin g fu ctionalized graphene electrodes. In particular, we determined the electrical tunnel i g current variation as a function of To whom correspondence should be addressed †Uppsala University ‡Nakhon Phanom University ¶Royal Institute of Technology 1 the applied bias and the associated differential conductan ce t a voltage which appears suitable to distinguish between the four nucleotides. Intriguingly , we observe for one of the nucleotides a negative differential resistance effect.

DNA sequencing with nanopores from an ab initio perspective

Advances in materials research means that we find ourselves at the verge of constructing nano-scale devices capable of electrically addressing individual molecules in order to identify or utilize their electrical or electromechanical properties. An important application in life sciences would be electromechanical translocation of a DNA molecule through a nanopore, between nano-scale electrodes, allowing to electrically read out the base sequence (genome). This approach promises to drastically lower the cost per genome, allowing for extensive application in medical diagnostics. Owing to the involved extremely small dimensions which require nanometer-resolution in the fabrication, atomistic modeling plays a crucial role in testing hypothetical device architectures for their performance in nucleobase distinction. First-principles simulations are ideally suited to explore the interactions involved in such scenarios and lay the foundation for electronic transport calculations. This role of computations is even more important here, since it is experimentally not possible to observe directly the kinetics occurring during translocation of a DNA molecule through a nanopore. Here, we provide a brief review of the state of the field, focusing on ab initio studies of nanopore-based DNA sequencing, in particular on the promising recent development regarding graphene nanopores and nanogaps.

Cumulene molecular wire conductance from first principles

We present first principles calculations of current-voltage characteristics (IVC) and conductance of Au(111):S-2-cumulene-S-2:Au(111) molecular wire junctions with realistic contacts. The transport properties are calculated using full self-consistent ab initio nonequilibrium Greens function density-functional theory methods under external bias. The conductance of the cumulene wires shows oscillatory behavior depending on the number of carbon atoms (double bonds). Among all conjugated oligomers, we find that cumulene wires with odd number of carbon atoms yield the highest conductance with metalliclike ballistic transport behavior. The reason is the high density of states in broad lowest unoccupied molecular orbital levels spanning the Fermi level of the electrodes. The transmission spectrum and the conductance depend only weakly on applied bias, and the IVC is nearly linear over a bias region of +/- 1 V. Cumulene wires are therefore potential candidates for metallic connections in nanoelectronic applications.

Double-functionalized nanopore-embedded gold electrodes for rapid DNA sequencing

We have studied the effect of double-functionalization on gold electrodes for improving nanopore-based DNA sequencing. The functionalizing molecular probes are, respectively, capable of temporarily forming hydrogen bonds with both the nucleobase part and the phosphate group of the target DNA, thus potentially minimizing the structural fluctuations of a single-stranded DNA molecule passing between the gold electrodes. The results of our first-principles study indicate that the proposed setup yields current signals that differ by at least 1 order of magnitude for the four different nucleic acid bases, thus offering the possibility to electrically distinguish them.

Assessment of a nanoparticle bridge platform for molecular electronics measurements

A combination of electron beam lithography, photolithography and focused ion beam milling was used to create a nanogap platform, which was bridged by gold nanoparticles in order to make electrical measurements and assess the platform under ambient conditions. Non-functionalized electrodes were tested to determine the intrinsic response of the platform and it was found that creating devices in ambient conditions requires careful cleaning and awareness of the contributions contaminants may make to measurements. The platform was then used to make measurements on octanethiol (OT) and biphenyldithiol (BPDT) molecules by functionalizing the nanoelectrodes with the molecules prior to bridging the nanogap with nanoparticles. Measurements on OT show that it is possible to make measurements on relatively small numbers of molecules, but that a large variation in response can be expected when one of the metal-molecule junctions is physisorbed, which was partially explained by attachment of OT molecules to different sites on the surface of the Au electrode using a density functional theory calculation. On the other hand, when dealing with BPDT, high yields for device creation are very difficult to achieve under ambient conditions. Significant hysteresis in the I-V curves of BPDT was also observed, which was attributed primarily to voltage induced changes at the interface between the molecule and the metal.

Effective masses and electronic structure of diamond including electron correlation effects in first principles calculations using the GW-approximation

We present calculated interband transitions and effective masses for diamond from first principles including electron correlation effects via the GW-approximation. Our findings are in agreement with experiments, already the first iteration of the GW-scheme gives a direct gap at the gamma-point of 7.38 eV and a indirect gap of 5.75 eV close to experimental values. For deeper bands a quasiparticle self-consistent method is necessary to accurately reproduce the valence band width to 23.1 eV. We also obtain effective hole masses along different symmetry axes and electron conduction masses, ml = 1.1m0 and mt = 0.22m0

Configuration- and Conformation-Dependent Electronic-Structure Variations in 1,4-Disubstituted Cyclohexanes Enabled by a Carbon-to-Silicon Exchange

Cyclohexane, with its well-defined conformers, could be an ideal force-controlled molecular switch if it were to display substantial differences in electronic and optical properties between its conformers. We utilize σ conjugation in heavier analogues of cyclohexanes (i.e. cyclohexasilanes) and show that 1,4-disubstituted cyclohexasilanes display configuration- and conformation-dependent variations in these properties. Cis- and trans-1,4-bis(trimethylsilylethynyl)cyclohexasilanes display a 0.11 V difference in their oxidation potentials (computed 0.11 V) and a 0.34 eV difference in their lowest UV absorption (computed difference between first excitations 0.07 eV). This is in stark contrast to differences in the corresponding properties of analogous all-carbon cyclohexanes (computed 0.02 V and 0.03 eV, respectively). Moreover, the two chair conformers of the cyclohexasilane trans isomer display large differences in electronic-structure-related properties. This enables computational design of a mechanically force-controlled conductance switch with a calculated single-molecule ON/OFF ratio of 213 at zero-bias voltage.