Simulating STM transport in alkanes from first principles

Simulations of scanning tunneling microscopy measurements for molecules on surfaces are traditionally based on a perturbative approach, most typically employing the Tersoff-Hamann method. This assumes that the STM tip is far from the sample so that the two do not interact with each other. However, when the tip gets close to the molecule to perform measurements, the electrostatic interplay between the tip and substrate may generate non-trivial potential distribution, charge transfer and forces, all of which may alter the electronic and physical structure of the molecule. These effects are investigated with the ab initio quantum transport code SMEAGOL, combining non-equilibrium Green's functions formalism with density functional theory. In particular, we investigate alkanethiol molecules terminated with either CH3 or CF3 end-groups on gold surfaces, for which recent experimental data are available. We discuss the effects connected to the interaction between the STM tip and the molecule, as well as the asymmetric charge transfer between the molecule and the electrodes.Comment: 10 pages, 18 figure

Ab initio study of electron transport in dry poly(G)-poly(C) A-DNA strands

The bias-dependent transport properties of short poly(G)-poly(C) A-DNA strands attached to Au electrodes are investigated with first principles electronic transport methods. By using the non- equilibrium Green's function approach combined with self-interaction corrected density functional theory, we calculate the fully self-consistent coherent I-V curve of various double-strand polymeric DNA fragments. We show that electronic wave-function localization, induced either by the native electrical dipole and/or by the electrostatic disorder originating from the first few water solvation layers, drastically suppresses the magnitude of the elastic conductance of A-DNA oligonucleotides. We then argue that electron transport through DNA is the result of sequence-specific short-range tunneling across a few bases combined with general diffusive/inelastic processes.Comment: 15 pages, 13 figures, 1 tabl

I-V curves of Fe/MgO (001) single- and double-barrier tunnel junctions

In this work, we calculate with ab initio methods the current-voltage characteristics for ideal single- and double-barrier Fe/MgO (001) magnetic tunnel junctions. The current is calculated in the phase-coherent limit by using the recently developed SMEAGOL code, combining the nonequilibrium Green function formalism with density-functional theory. In general we find that double-barrier junctions display a larger magnetoresistance, which decays with bias at a slower pace than their single-barrier counterparts. This is explained in terms of enhanced spin filtering from the middle Fe layer sandwiched in between the two MgO barriers. In addition, for double-barrier tunnel junctions, we find a well defined peak in the magnetoresistance at a voltage of V=0.1 V. This is the signature of resonant tunneling across a majority quantum well state. Our findings are discussed in relation to recent experiments

First-principles study of high conductance DNA sequencing with carbon nanotube electrodes

Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nano-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore both reduce conformational fluctuations and significantly improve the conductance. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several $\mu$A. Below 1 V the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second-largest, cytosine the third and finally thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations. Based on these results we propose a DNA sequencing protocol combining three possible data analysis strategies.Comment: 12 pages, 17 figures, 3 table

Transmission through correlated Cun_nCoCun_n heterostructures

The effects of local electronic interactions and finite temperatures upon the transmission across the Cu$_4$CoCu$_4$ metallic heterostructure are studied in a combined density functional and dynamical mean field theory. It is shown that, as the electronic correlations are taken into account via a local but dynamic self-energy, the total transmission at the Fermi level gets reduced (predominantly in the minority spin channel), whereby the spin polarization of the transmission increases. The latter is due to a more significant $d$-electrons contribution, as compared to the non-correlated case in which the transport is dominated by $s$ and $p$ electrons.Comment: 29 pages, 7 figures, submited to PR

Ab initio study on the magneto-structural properties of MnAs

The magnetic and structural properties of MnAs are studied with ab initio methods, and by mapping total energies onto a Heisenberg model. The stability of the different phases is found to depend mainly on the volume and on the amount of magnetic order, confirming previous experimental findings and phenomenological models. It is generally found that for large lattice constants the ferromagnetic state is favored, whereas for small lattice constants different antiferromagnetic states can be stabilized. In the ferromagnetic state the structure with minimal energy is always hexagonal, whereas it becomes orthorhombically distorted if there is an antiferromagnetic component in the hexagonal plane. For the paramagnetic state the stable cell is found to be orthorhombic up to a critical lattice constant of about 3.7 Angstrom, above which it remains hexagonal. This leads to the second order structural phase transition between paramagnetic states at about 400 K, where the lattice parameter increases above this critical value with rising temperature due to the thermal expansion. For the paramagnetic state an analytic approximation for the magnitude of the orthorhombic distortion as a function of the lattice constant is given. Within the mean field approximation the dependence of the Curie temperature on the volume and on the orthorhombic distortion is calculated. For orthorhombically distorted cells the Curie temperature is much smaller than for hexagonal cells. This is mainly due to the fact that some of the exchange coupling constants in the hexagonal plane become negative for distorted cells. With these results a description of the susceptibility as function of temperature is given

Spin-orbit induced equilibrium spin currents in materials

The existence of pure spin currents in absence of any driving external field is commonly considered an exotic phenomenon appearing only in quantum materials, such as topological insulators. We demonstrate instead that equilibrium spin currents are a rather general property of materials with non-negligible spin-orbit coupling (SOC). Equilibrium spin currents can be present at the surfaces of a slab. Yet, we also propose the existence of global equilibrium spin currents, which are net bulk spin currents along specific crystallographic directions of solid-state materials. Equilibrium spin currents are allowed by symmetry in a very broad class of systems having gyrotropic point groups. The physics behind equilibrium spin currents is uncovered by making an analogy between electronic systems with SOC and non-Abelian gauge theories. The electron spin can be seen as analogous to the color degree of freedom in SU(2) gauge theories and equilibrium spin currents can then be identified with diamagnetic color currents appearing as the response to a effective non-Abelian magnetic field generated by the SOC. Equilibrium spin currents are not associated with spin transport and accumulation, but they should nonetheless be carefully taken into account when computing transport spin currents. We provide quantitative estimates of equilibrium spin currents for a number of different systems, specifically the Au(111) and Ag(111) metallic surfaces presenting Rashba-type surface states, nitride semiconducting nanostructures, and bulk materials, such as the prototypical gyrotropic medium tellurium. In doing so, we also point out the limitations of model approaches showing that first-principles calculations are needed to obtain reliable predictions. We therefore use density functional theory computing the so-called bond currents, which represent a powerful tool to deeply understand the relation between equilibrium currents, electronic structure, and crystal point group