Complex band structure with non-orthogonal basis set: analytical properties and implementation in the SIESTA code.

The complex band structure (CBS), although not directly observable, determines many properties of a material where the periodicity is broken, such at surfaces, interfaces and defects. Furthermore, its knowledge helps in the interpretation of electronic transport calculations and in the study of topological materials. Here we extend the transfer matrix method, often used to compute the complex bands, to electronic structures constructed using an atomic non-orthogonal basis set. We demonstrate that when the overlap matrix is not the identity, the non-orthogonal case, spurious features appear in the analytic continuation of the band structure to the complex plane. The properties of these are studied both numerically and analytically and discussed in the context of existing literature. Finally, a numerical implementation to extract the CBS from periodic calculations carried out with the density functional theory codesiestais presented. This is constructed as a simple post-processing tool, and it is therefore amenable to high-throughput studies of insulators and semiconductors.

Unveiling phonons in a molecular qubit with four-dimensional inelastic neutron scattering and density functional theory.

Phonons are the main source of relaxation in molecular nanomagnets, and different mechanisms have been proposed in order to explain the wealth of experimental findings. However, very limited experimental investigations on phonons in these systems have been performed so far, yielding no information about their dispersions. Here we exploit state-of-the-art single-crystal inelastic neutron scattering to directly measure for the first time phonon dispersions in a prototypical molecular qubit. Both acoustic and optical branches are detected in crystals of [VO(acac)[Formula: see text]] along different directions in the reciprocal space. Using energies and polarisation vectors calculated with state-of-the-art Density Functional Theory, we reproduce important qualitative features of [VO(acac)[Formula: see text]] phonon modes, such as the presence of low-lying optical branches. Moreover, we evidence phonon anti-crossings involving acoustic and optical branches, yielding significant transfers of the spin-phonon coupling strength between the different modes.

Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history.

A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we combined genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to evaluate the consequences of commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong signatures of recent population declines. Bottleneck strength is associated with breeding habitat and mating system variation, and together with global abundance explains much of the variation in genetic diversity across species. Overall, bottleneck intensity is unrelated to IUCN status, although the three most heavily bottlenecked species are endangered. Our study reveals an unforeseen interplay between human exploitation, animal biology, demographic declines and genetic diversity.

Theoretical Evaluation of [VIV(α-C3S5)3]2- as Nuclear-Spin-Sensitive Single-Molecule Spin Transistor.

In a straightforward application of molecular nanospintronics to quantum computing, single-molecule spin transistors can be used to measure nuclear spin qubits. Conductance jumps accompany electronic spin flips at the so-called anticrossings between energy levels, which take place only at specific magnetic fields determined by the nuclear spin state. To date, the only molecular hardware employed for this technique has been the terbium(III) bis(phthalocyaninato) complex. Here we explore theoretically whether a similar behavior is expected for a highly stable molecular spin qubit, the vanadium tris-dithiolate complex [VIV(α-C3S5)3]2-. We consider such a molecule between two gold electrodes and determine the spin-dependent conductance. We verify that the transport channel in experimental conditions does not overlap with the occupied spin orbitals, indicating that the spin states may survive in the conduction regime. We validate the robustness of the theoretical methodology by studying two chemically related vanadium complexes and offer some criteria to guide the experiments.

Charge and spin transport in single and packed ruthenium-terpyridine molecular devices: Insight from first-principles calculations.

Using first-principles calculations, we study the electronic and transport properties of rutheniumterpyridine molecules sandwiched between two Au(111) electrodes. We analyse both single and packed molecular devices, more amenable to scaling and realistic integration approaches. The devices display all together robust negative differential resistance features at low bias voltages. Remarkably, the electrical control of the spin transport in the studied systems implies a subtle distribution of the magnetisation density within the biased devices and highlights the key role of the Au(111) electrical contacts.

Current-induced changes of migration energy barriers in graphene and carbon nanotubes.

An electron current can move atoms in a nanoscale device with important consequences for the device operation and breakdown. We perform first principles calculations aimed at evaluating the possibility of changing the energy barriers for atom migration in carbon-based systems. In particular, we consider the migration of adatoms and defects in graphene and carbon nanotubes. Although the current-induced forces are large for both the systems, in graphene the force component along the migration path is small and therefore the barrier height is little affected by the current flow. In contrast, the same barrier is significantly reduced in carbon nanotubes as the current increases. Our work also provides a real-system numerical demonstration that current-induced forces within density functional theory are non-conservative.

The image charge effect and vibron-assisted processes in Coulomb blockade transport: a first principles approach.

We present a combination of density functional theory and of both non-equilibrium Green's function formalism and a Master equation approach to accurately describe quantum transport in molecular junctions in the Coulomb blockade regime. We apply this effective first-principles approach to reproduce the experimental results of Perrin et al., [Nat. Nanotechnol., 2013, 8, 282] for the transport properties of a Au-(Zn)porphyrin-Au molecular junction. We demonstrate that energy level renormalization due to the image charge effect is crucial to the prediction of the current onset in the current-voltage, I-V, curves as a function of electrode separation. Furthermore, we show that for voltages beyond that setting the current onset, the slope of the I-V characteristics is determined by the interaction of the charge carriers with molecular vibrations. This corresponds to current-induced local heating, which may also lead to an effective reduced electronic coupling. Overall our scheme provides a fully ab initio description of quantum transport in the Coulomb blockade regime in the presence of electron-vibron coupling.

Tailoring highly conductive graphene nanoribbons from small polycyclic aromatic hydrocarbons: a computational study.

Pyrene, the smallest two-dimensional mesh of aromatic rings, with various terminal thiol substitutions, has been considered as a potential molecular interconnect. Charge transport through two terminal devices has been modeled using density functional theory (with and without self interaction correction) and the non-equilibrium Green's function method. A tetra-substituted pyrene, with dual thiol terminal groups at opposite ends, has been identified as an excellent candidate, owing to its high conductance, virtually independent of bias voltage. The two possible extensions of its motif generate two series of graphene nanoribbons, with zigzag and armchair edges and with semimetallic and semiconducting electron band structure, respectively. The effects related to the wire length and the bias voltage on the charge transport have been investigated for both sets. The conductance of the nanoribbons with a zigzag edge does not show either length or voltage dependence, owing to an almost perfect electron transmission with a continuum of conducting channels. In contrast, for the armchair nanoribbons a slow exponential attenuation of the conductance with the length has been found, due to their semiconducting nature.

Time-dependent electron transport through a strongly correlated quantum dot: multiple-probe open-boundary conditions approach.

We present a time-dependent study of electron transport through a strongly correlated quantum dot, which combines adiabatic lattice density functional theory in the Bethe ansatz local-density approximation (BALDA) to the Hubbard model, with the multiple-probe battery method for open-boundary simulations in the time domain. In agreement with the recently proposed dynamical picture of Coulomb blockade, a characteristic driven regime, defined by regular current oscillations, is demonstrated for a certain range of bias voltages. We further investigate the effects of systematically improving the approximation for the electron-electron interaction at the dot site (going from non-interacting, through Hartree-only to adiabatic BALDA) on the transmission spectrum and the I-V characteristics. In particular, a negative differential conductance is obtained at large bias voltages and large Coulomb interaction strengths. This is attributed to the combined effect of the electron-electron interaction at the dot and the finite bandwidth of the electrodes.

Assessment of density functional theory for iron(II) molecules across the spin-crossover transition.

Octahedral Fe(2+) molecules are particularly interesting as they often exhibit a spin-crossover transition. In spite of the many efforts aimed at assessing the performances of density functional theory for such systems, an exchange-correlation functional able to account accurately for the energetic of the various possible spin-states has not been identified yet. Here, we critically discuss the issues related to the theoretical description of this class of molecules from first principles. In particular, we present a comparison between different density functionals for four ions, namely, [Fe(H(2)O)(6)](2+), [Fe(NH(3))(6)](2+), [Fe(NCH)(6)](2+), and [Fe(CO)(6)](2+). These are characterized by different ligand-field splittings and ground state spin multiplicities. Since no experimental data are available for the gas phase, the density functional theory results are benchmarked against those obtained with diffusion Monte Carlo, one of the most accurate methods available to compute ground state total energies of quantum systems. On the one hand, we show that most of the functionals considered provide a good description of the geometry and of the shape of the potential energy surfaces. On the other hand, the same functionals fail badly in predicting the energy differences between the various spin states. In the case of [Fe(H(2)O)(6)](2+), [Fe(NH(3))(6)](2+), [Fe(NCH)(6)](2+), this failure is related to the drastic underestimation of the exchange energy. Therefore, quite accurate results can be achieved with hybrid functionals including about 50% of Hartree-Fock exchange. In contrast, in the case of [Fe(CO)(6)](2+), the failure is likely to be caused by the multiconfigurational character of the ground state wave-function and no suitable exchange and correlation functional has been identified.

Giant resistance change across the phase transition in spin-crossover molecules.

The electronic origin of a large resistance change in nanoscale junctions incorporating spin-crossover molecules is demonstrated theoretically by using a combination of density functional theory and the nonequilibrium Green's function method for quantum transport. At the spin-crossover phase transition, there is a drastic change in the electronic gap between the frontier molecular orbitals. As a consequence, when the molecule is incorporated in a two-terminal device, the current increases by up to 4 orders of magnitude in response to the spin change. This is equivalent to a magnetoresistance effect in excess of 3000%. Since the typical phase transition critical temperature for spin-crossover compounds can be extended to well above room temperature, spin-crossover molecules appear as the ideal candidate for implementing spin devices at the molecular level.

Persistent current and Drude weight for the one-dimensional Hubbard model from current lattice density functional theory.

The Bethe ansatz local density approximation (LDA) to lattice density functional theory (LDFT) for the one-dimensional repulsive Hubbard model is extended to current-LDFT (CLDFT). The transport properties of mesoscopic Hubbard rings threaded by a magnetic flux are then systematically investigated by this scheme. In particular we present calculations of ground state energies, persistent currents and Drude weights for both a repulsive homogeneous and a single impurity Hubbard model. Our results for the ground state energies in the metallic phase compare favorably well with those obtained with numerically accurate many-body techniques. Also the dependence of the persistent currents on the Coulomb and the impurity interaction strength, and on the ring size are all well captured by LDA-CLDFT. Our study demonstrates the value of CLDFT in describing the transport properties of one-dimensional correlated electron systems. As its computational overheads are rather modest, we propose this method as a tool for studying problems where both disorder and interaction are present.

Electric field control of valence tautomeric interconversion in cobalt dioxolene.

We demonstrate that the critical temperature for valence tautomeric interconversion in cobalt dioxolene complexes can be significantly changed when a static electric field is applied to the molecule. This is achieved by effectively manipulating the redox potential of the metallic acceptor forming the molecule. Importantly, our accurate density functional theory calculations demonstrate that already a field of 0.1 V/nm, achievable in Stark spectroscopy experiments, can produce a change in the critical temperature for the interconversion of 20 K. Our results indicate a new way for switching on and off the magnetism in a magnetic molecule. This offers the unique chance of controlling magnetism at the atomic scale by electrical means.

The search for a spin crossover transition in small sized π-conjugated molecules: a Monte Carlo study.

The spin crossover transition in π-conjugated polymers is a complex phenomenon involving a balance between Coulomb interaction and collective lattice distortions. We explore such a transition with a minimal electronic model comprising a Hubbard-U on-site repulsive potential and both electron-phonon and hyperfine interactions. The model is then solved numerically for small molecules at finite temperature by Monte Carlo methods in the search for the spin crossover. This is done at the mean field level in the Hubbard-U interaction at half filling. We demonstrate that for a certain region of the parameter space there is a spin crossover, where the system transits from a low-spin to a high-spin state as the temperature increases. In close analogy to standard spin crossover in divalent magnetic molecules such a transition is entropy driven, with both the spin and the vibrational contributions to the entropy being relevant. Such a transition is practically unaffected by the hyperfine interaction, which only plays a minor role in determining the electronic properties.

Computational modeling of a carbon nanotube-based DNA nanosensor.

During the last decade the design of biosensors, based on quantum transport in one-dimensional nanostructures, has developed as an active area of research. Here we investigate the sensing capabilities of a DNA nanosensor, designed as a semiconductor single walled carbon nanotube (SWCNT) connected to two gold electrodes and functionalized with a DNA strand acting as a bio-receptor probe. In particular, we have considered both covalent and non-covalent bonding between the DNA probe and the SWCNT. The optimized atomic structure of the sensor is computed both before and after the receptor attaches itself to the target, which consists of another DNA strand. The sensor's electrical conductance and transmission coefficients are calculated at the equilibrium geometries via the non-equilibrium Green's function scheme combined with the density functional theory in the linear response limit. We demonstrate a sensing efficiency of 70% for the covalently bonded bio-receptor probe, which drops to about 19% for the non-covalently bonded one. These results suggest that a SWCNT may be a promising candidate for a bio-molecular FET sensor.

Switching a single spin on metal surfaces by a STM Tip: Ab Initio studies.

The exchange coupling between single 3d magnetic adatoms (Cr, Mn, Fe, and Co) adsorbed on a Cu(001) surface and a Cr STM tip is studied with ab initio calculations. We demonstrate that the spin direction of single adatoms can be controlled by varying the tip-substrate distance, and the sign of the exchange energy is determined by the competition of the direct and the indirect interactions between the tip and the adatom. Based on the spin-dependent transport calculations, we find a magnetoresistance of about 70% at short tip-substrate distances.

Electronic transport calculations for rough interfaces in Al, Cu, Ag, and Au.

We present results of electronic structure and transport calculations for metallic interfaces, based on density functional theory and the non-equilibrium Green's function method. Starting from the electronic structure of smooth Al, Cu, Ag, and Au interfaces, we study the effects of different kinds of interface roughness on the transmission coefficient and the I-V characteristic. In particular, we compare prototypical interface distortions, including vacancies and metallic impurities.

Efficient atomic self-interaction correction scheme for nonequilibrium quantum transport.

Density-functional theory calculations of electronic transport based on local exchange and correlation functionals contain self-interaction errors. As a consequence, insulating molecules in weak contact with metallic electrodes erroneously form highly conducting junctions. Here we present a fully self-consistent and still computationally undemanding self-interaction correction scheme that overcomes these limitations. The method is implemented in the transport code SMEAGOL and applied to the prototypical case of benzene molecules and gold electrodes. The Kohn-Sham highest occupied molecular orbital now reproduces closely the negative of the molecular ionization potential and is moved away from the gold Fermi energy. This leads to a drastic reduction of the low-bias current in much better agreement with experiments.

Exchange parameters from approximate self-interaction correction scheme.

The approximate atomic self-interaction correction (ASIC) method to density functional theory is put to the test by calculating the exchange interaction for a number of prototypical materials, critical to local exchange and correlation functionals. ASIC total energy calculations are mapped onto a Heisenberg pairwise interaction and the exchange constants J are compared to those obtained with other methods. In general the ASIC scheme drastically improves the band structure, which for almost all the cases investigated resemble closely available photoemission data. In contrast the results for the exchange parameters are less satisfactory. Although ASIC performs reasonably well for systems where the magnetism originates from half-filled bands, it suffers from similar problems than those of local density approximation for other situations. In particular, the exchange constants are still overestimated. This reflects a subtle interplay between exchange and correlation energy, not captured by the ASIC.

Effect of the continuity of the pi conjugation on the conductance of ruthenium-octene-ruthenium molecular junctions.

The conductance of a family of ruthenium-octene-ruthenium molecular junctions with different pi conjugation are investigated using a fully self-consistent ab initio approach which combines the nonequilibrium Green's function formalism with density functional theory. Our calculations demonstrate that the continuity of the pi conjugation in the contact region as well as along the molecular backbone affects the junction conductance significantly, showing the advantage of using the ruthenium-carbon double bond as the linkage of conjugated organic molecules.