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This article introduces a groundbreaking analytical workflow designed for the holistic characterisation, modelling and physical simulation of device heterostructures. Our innovative workflow autonomously, comprehensively and locally characterises the crystallographic information and 3D orientation of the crystal phases, the elemental composition, and the strain maps of devices from (scanning) transmission electron microscopy data. It converts a manual characterisation process that traditionally takes days into an automatic routine completed in minutes. This is achieved through a physics-guided artificial intelligence model that combines unsupervised and supervised machine learning in a modular way to provide a representative 3D description of the devices, materials structures, or samples under analysis. To culminate the process, we integrate the extracted knowledge to automate the generation of both 3D finite element and atomic models of millions of atoms acting as digital twins, enabling simulations that yield essential physical and chemical insights crucial for understanding the device's behaviour in practical applications. We prove this end-to-end workflow with a state-of-the-art materials platform based on SiGe planar heterostructures for hosting coherent and scalable spin qubits. Our workflow connects representative digital twins of the experimental devices with their theoretical properties to reveal the true impact that every atom in the structure has on their electronic properties, and eventually, into their functional quantum performance. Notably, the versatility of our workflow is demonstrated through its successful application to a wide array of materials systems, device configurations and sample morphologies.

We present SIESTA-BdG, an implementation of the simultaneous solution of the Bogoliubov-de Gennes (BdG) and Density Functional Theory (DFT) problem in SIESTA, a first-principles method and code for material simulations which uses pseudopotentials and a localized basis set. This unified approach describes both conventional and unconventional superconducting states, and enables a description of inhomogeneous superconductors and heterostructures. We demonstrate the validity, accuracy, and efficiency of SIESTA-BdG by computing physically relevant quantities (superconducting charge density, band structure, superconducting gap features, density of states) for conventional singlet (Nb, Pb) and unconventional (FeSe) superconductors. We find excellent agreement with experiments and results obtained within the KKR-BdG computational framework. SIESTA-BdG forms the basis for modelling quantum transport in superconducting devices and including - in an approximate fashion - the superconducting DFT potential of Oliveira, Gross, and Kohn.

Diffusion is one of the most ubiquitous transport phenomena in nature. Experimentally, it can be tracked by following point spreading in space and time. Here, we introduce a spatiotemporal pump-probe microscopy technique that exploits the residual spatial temperature profile obtained through the transient reflectivity when probe pulses arrive before pump pulses. This corresponds to an effective pump-probe time delay of 13 ns, determined by the repetition rate of our laser system (76 MHz). This pre-time-zero technique enables probing the diffusion of long-lived excitations created by previous pump pulses with nanometer accuracy, and is particularly powerful for following in-plane heat diffusion in thin films. In contrast to existing techniques for quantifying thermal transport it does not require any material input parameters or strong heating. We demonstrate the direct determination of the thermal diffusivities of the layered materials MoSe$_2$ (0.18 cm$^2$/s), WSe$_2$ (0.20 cm$^2$/s), MoS$_2$ (0.35 cm$^2$/s), and WS$_2$ (0.59 cm$^2$/s). This technique paves the way for observing novel nanoscale thermal transport phenomena and tracking diffusion of a broad range of species.

We evidence the possibility for coherent electrical manipulation of the spin orientation of topologically protected edge states in a low-symmetry quantum spin Hall insulator. By using a combination of ab-initio simulations, symmetry-based modeling, and large-scale calculations of the spin Hall conductivity, it is shown that small electric fields can efficiently vary the spin textures of edge currents in monolayer 1T'-WTe2 by up to a 90-degree spin rotation, without jeopardizing their topological character. These findings suggest a new kind of gate-controllable spin-based device, topologically protected against disorder and of relevance for the development of topological spintronics.

We present a code modularization approach to design efficient and massively parallel cubic and linear-scaling solvers for electronic structure calculations using atomic orbitals. The modular implementation of the orbital minimization method, in which linear algebra and parallelization issues are handled via external libraries, is demonstrated in the SIESTA code. The DBCSR and ScaLAPACK libraries are used for algebraic operations with sparse and dense matrices, respectively. The MatrixSwitch and libOMM libraries, recently developed within the Electronic Structure Library, facilitate switching between different matrix formats and implement the energy minimization. We show results comparing the performance of several cubic-scaling algorithms, and also demonstrate the parallel performance of the linear-scaling solvers, and their supremacy over the cubic-scaling solvers for insulating systems with sizes of several hundreds of atoms., Comment: 13 pages, 10 figures

Diamond is one of the most studied materials because of its unique combination of remarkable electrical, mechanical, thermal and optical properties. Using a fully self-consistent ab initio theory of coupled electron-phonon transport, we reveal another striking behavior: a huge drag enhancement of the thermopower of lightly doped diamond. Thermopower values of around 100,000 microvolts per Kelvin are found at 100 K, significantly exceeding the highest previously measured value in the correlated metal FeSb2, and occurring at much higher temperatures. The enormous thermopower in diamond arises primarily from exceptionally weak anharmonic phonon decay around and below 100 K that facilitates efficient momentum exchange between charge carriers and phonons through electron-phonon interactions. Exceedingly large thermoelectric power factors are also identified. This work gives insights into the physics of the coupled electron-phonon system in solids and advances our understanding of thermoelectric transport in the regime of strong drag.

Some meta-stable polymorphs of bismuth monolayer (bismuthene) can host topologically nontrivial phases. However, it remains unclear if these polymorphs can become stable through interaction with a substrate, whether their topological properties are preserved, and how to design an optimal substrate to make the topological phase more robust. Using first-principles techniques we demonstrate that bismuthene polymorphs can become stable over silicon carbide (SiC), silicon (Si), silicon dioxide (SiO2) and that the proximity interaction in the heterostructures has a significant effect on the electronic structure of the monolayer, even when bonding is weak. We show that the van der Waals interactions and the breaking of the sublattice symmetry are the main factors driving changes in the electronic structure. Our work demonstrates that substrate interaction can strengthen the topological properties of bismuthene polymorphs and make them accessible for experimental investigation and technological applications.

The origin of the charge density wave in TaTe$_4$ is discussed on the basis of a first-principles DFT analysis of the Fermi surface, electron-hole response function, phonon band structure of the average structure and structural optimization of the modulated phase. Analysis of the band structure and Fermi surface of the average structure clearly proves that despite the presence of TaTe$_4$ chains in the crystal structure, TaTe$_4$ is in fact a 3D material as far as the electronic structure near the Fermi level is concerned. A Fermi surface nesting mechanism is dismissed as the origin of the 2$a\times2a\times3c$ structural modulation. The optimized 2$a$\xone2$a$\xone3$c$ structure, which is found to be the more stable modulation in agreement with the experimental observations, can be obtained directly from a soft-phonon mode computed for the undistorted structure. Our results suggest that the driving force for the distortion is the maximization of Ta-Ta metal-metal bonding subject to inducing the minimum bonding decrease in the Te sublattice.

Understanding thermal transport in layered transition metal dichalcogenide (TMD) crystals is crucial for a myriad of applications exploiting these materials. Despite significant efforts, several basic thermal transport properties of TMDs are currently not well understood. Here, we present a combined experimental-theoretical study of the intrinsic lattice thermal conductivity of the representative TMD MoSe$_2$, focusing on the effect of material thickness and the material's environment. We use Raman thermometry measurements on suspended crystals, where we identify and eliminate crucial artefacts, and perform $ab$ $initio$ simulations with phonons at finite, rather than zero, temperature. We find that phonon dispersions and lifetimes change strongly with thickness, yet (sub)nanometer thin TMD films exhibit a similar in-plane thermal conductivity ($\sim$20~Wm$^{-1}$K$^{-1}$) as bulk crystals ($\sim$40~Wm$^{-1}$K$^{-1}$). This is the result of compensating phonon contributions, in particular low-frequency modes with a surprisingly long mean free path of several micrometers that contribute significantly to thermal transport for monolayers. We furthermore demonstrate that out-of-plane heat dissipation to air is remarkably efficient, in particular for the thinnest crystals. These results are crucial for the design of TMD-based applications in thermal management, thermoelectrics and (opto)electronics.

elphbolt is a modern Fortran (2018 standard) code for efficiently solving the coupled electron-phonon Boltzmann transport equations from first principles. Using results from density functional and density functional perturbation theory as inputs, it can calculate the effect of the non-equilibrium phonons on the electronic transport (phonon drag) and non-equilibrium electrons on the phononic transport (electron drag) in a fully self-consistent manner and obeying the constraints mandated by thermodynamics. It can calculate the lattice, charge, and thermoelectric transport coefficients for the temperature gradient and electric fields, and the effect of the mutual electron-phonon drag on these transport properties. The code fully exploits the symmetries of the crystal and the transport-active window to allow the sampling of extremely fine electron and phonon wave vector meshes required for accurately capturing the drag phenomena. The coarray feature of modern Fortran, which offers native and convenient support for parallelization, is utilized. The code is compact, readable, well-documented, and extensible by design.

Interference effects in finite sections of one-dimensional moir\'e crystals are investigated using a Landauer-B\"uttiker formalism within the tight-binding approximation. We explain interlayer transport in double-wall carbon nanotubes and design a predictive model. Wave function interference is visible at the mesoscale: in the strong coupling regime, as a periodic modulation of quantum conductance and emergent localized states; in the localized-insulating regime, as a suppression of interlayer transport, and oscillations of the density of states. These results could be exploited to design quantum electronic devices.

Spin-electronic devices are poised to become part of mainstream microelectronic technology .Downsizing them, however, faces the intrinsic difficulty that as ferromagnets become smaller, it becomes more difficult to stabilize their magnetic moment. Antiferromagnets are much more stable, and thus research on antiferromagnetic spintronics has developed into a fast-growing field. Here, we provide proof of concept data that allows us to expand the area of antiferromagnetic spintronics to the hitherto elusive level of individual molecules. In contrast to all previous work on molecular spintronics, our detection scheme of the molecule's spin state does not rely on a magnetic moment. Instead, we use field-effect transistor devices constituting of an isolated, contacted single-wall carbon nanotube covalently bound to a limited number of molecular antiferromagnets incorporating four Mn(II) or Co(II) ions. Time-dependent quantum transport measurement along the functionalized nanotube show step-like transitions between several distinct current levels, which we attribute to transitions between different antiferromagnetic states of individual molecular complexes grafted on the nanotube. A statistical analysis of the switching events using factorial cumulants indicates that the cobalt complexes switch independently from each other, while a coherent superposition of the antiferromagnetic spin states of the molecules along the nanotube is observed for the manganese complexes. The long coherence time (several seconds at 100 mK) is made possible by the absence of spin and orbital momentum in the relevant states of the manganese complex, while the cobalt complex includes a significant orbital momentum contribution due to the pseudo-octahedral d$^7$ metal centers., Comment: including supplementary information

We present a joint experimental and theoretical characterization of the magnetic properties of coordination clusters with an antiferromagnetic core of four magnetic ions. Two different compounds are analyzed, with Co and Mn ions in the core. While both molecules are antiferromagnetic, they display different sensitivities to external magnetic field, according to the different strength of the intra-molecular magnetic coupling. In particular, the dependence of the magnetization versus field of the two molecules switches with temperatures: at low temperature the magnetization is smaller in \{Mn$_4$\}, while the opposite happens at high temperature. Through a detailed analysis of the electronic and magnetic properties of the two compounds we identify a stronger magnetic interaction between the magnetic ions in \{Mn$_4$\} with respect to \{Co$_4$\}. Moreover \{Co$_4$\} displays not negligible spin-orbit related effects that could affect the spin lifetime in future antiferromagnetic spintronic applications. We highlight the necessity to account for these spin-orbit effects for a reliable description of these compounds., Comment: 8 pages, 5 figures + supplementary Information

NbSe$_3$ and monoclinic-TaS$_3$ ($m$-TaS$_3$) are quasi-1D metals containing three different types of chains and undergoing two different charge density wave (CDW) Peierls transitions at T$_{P_1}$ and T$_{P_2}$. The nature of these transitions is discussed on the basis of first-principles DFT calculation of their electron-hole Lindhard response function. As a result of stronger inter-chain interactions the Fermi surface (FS) and Lindhard function of NbSe$_3$ are considerably more complex than those for $m$-TaS$_3$; however a common scenario can be put forward to rationalize the results. The intra-chain inter-band nesting processes dominate the strongest response for both type I and type III chains of the two compounds. Two well-defined maxima of the Lindhard response for NbSe$_3$ are found with the (0$a$*, 0$c$*) and (1/2$a$*, 1/2$c$*) transverse components at T$_{P_1}$ and T$_{P_2}$, respectively, whereas the second maximum is not observed for $m$-TaS$_3$ at T$_{P2}$. Analysis of the different inter-chain coupling mechanisms leads to the conclusion that FS nesting effects are only relevant to set the transverse $a$* components in NbSe$_3$. For the transverse coupling along $c$* in NbSe$_3$ and along both $a$* and $c$* for $m$-TaS$_3$, one must take into account the strongest inter-chain Coulomb coupling mechanism. Phonon spectrum calculations show the formation of a giant 2$k_F$ Kohn anomaly in $m$-TaS$_3$. All these results support the weak coupling scenario for the Peierls transition of transition metal trichalcogenides.

Proximity effects are one of the pillars of exotic phenomena and technological applications of two dimensional materials. However, the interactions nature depends strongly on the materials involved, their crystalline symmetries, and interfacial properties. Here we used large-scale first-principle calculations to demonstrate that strain and twist-angle are efficient knobs to tailor the spin-orbit coupling in graphene transition metal dichalcogenide heterobilayers. We found that by choosing a twist-angle of 30 degrees, the spin relaxation times increase by two orders of magnitude, opening a path to improve these heterostructures spin transport capability. Moreover, we demonstrate that strain and twist angle will modify the relative values of valley-Zeeman and Rashba spin-orbit coupling, allowing to tune the system into an ideal Dirac-Rashba regime. These results enable us to envision an answer for the variability of spin-orbit coupling found in different experiments and have significant consequences for applications that depend on polycrystallinity, where grains form at different orientations.

A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-nineties, SIESTA's flexibility, efficiency and free distribution has given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here we describe the more recent implementations on top of that core scheme, which include: full spin-orbit interaction, non-repeated and multiple-contact ballistic electron transport, DFT+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient Van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as Wannier90 and the second-principles modelling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various postprocessing utilities. SIESTA has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low level libraries, as well as data standards and support for them, in particular the PSML definition and library for transferable pseudopotentials, and the interface to the ELSI library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments., Comment: 29 pages, 23 figures

Enhancing the spin-orbit interaction in graphene, via proximity effects with topological insulators, could create a novel 2D system that combines nontrivial spin textures with high electron mobility. In order to engineer practical spintronics applications with such graphene/topological insulator (Gr/TI) heterostructures, an understanding of the hybrid spin-dependent properties is essential. {However to date, despite the large number of experimental studies on Gr/TI heterostructures reporting a great variety of remarkable (spin) transport phenomena, little is known about the true nature of the spin texture of the interface states as well as their role on the measured properties. Here we use {\it ab initio} simulations and tight-binding models to determine the precise spin texture of electronic states in graphene interfaced with a Bi$_2$Se$_3$ topological insulator. Our calculations predict the emergence of a giant spin lifetime anisotropy in the graphene layer, which should be a measurable hallmark of spin transport in Gr/TI heterostructures, and suggest novel types of spin devices

Analysis of the band structure of TiS$_3$ single-layers suggests the possibility of changing their physical behaviour by injecting electron carriers. The anisotropy of the valence and conduction bands is explained in terms of their complex orbital composition. The nature of the Fermi surface and Lindhard response function for different doping concentrations is studied by means of first-principles DFT calculations. It is suggested that for electron doping levels $x$ (number of electrons per unit cell) $\sim$ 0.18-0.30$e^-$ the system could exhibit incommensurate charge or spin modulations which, however, would keep the metallic state whereas systems doped with smaller $x$ would be 2D metals without any electronic instability. The effect of spin-orbit coupling in the band dispersion is analysed. The DFT effective masses are used to study the plasmon spectrum from an effective low energy model. We find that this material supports highly anisotropic plasmons, with opposite anisotropy for the electron and hole bands., Comment: Accepted for publication in 2D Materials

A density functional theory study of NbSe$_2$ single-layers in the normal non-modulated and the $3\times3$ CDW states is reported. We show that, in the single layer, the CDW barely affects the Fermi surface of the system, thus ruling out a nesting mechanism as the driving force for the modulation. The CDW stabilizes levels lying around 1.5 eV below the Fermi level within the Se-based valence band but having a substantial Nb-Nb bonding character. The absence of interlayer interactions leads to the suppression of the pancake-like portion of the bulk Fermi surface in the single-layer. We perform scanning tunneling microscopy simulations and find that the images noticeably change with the sign and magnitude of the voltage bias. The atomic corrugation of the Se sublayer induced by the modulation plays a primary role in leading to these images, but the electronic reorganization also has an important contribution. The analysis of the variation of these images with the bias voltage does not support a Fermi surface nesting mechanism for the CDW. It is also shown that underlying graphene layers (present in some of the recent experimental work) do not modify the conduction band, but do affect the shape of the valence band of NbSe$_2$ single-layers. The relevance of these results in understanding recent physical measurements for NbSe$_2$ single-layers is discussed.

Single- and few-layer transition metal dichalcogenides have recently emerged as a new family of layered crystals with great interest, not only from the fundamental point of view, but also because of their potential application in ultrathin devices. Here we review the electronic properties of semiconducting $MX_2$, where $M=$Mo or W and $X=$ S or Se. Based on of density functional theory calculations, which include the effect of spin-orbit interaction, we discuss the band structure of single-layer, bilayer and bulk compounds. The band structure of these compounds is highly sensitive to elastic deformations, and we review how strain engineering can be used to manipulate and tune the electronic and optical properties of those materials. We further discuss the effect of disorder and imperfections in the lattice structure and their effect on the optical and transport properties of $MX_2$. The superconducting transition in these compounds, which has been observed experimentally, is analyzed, as well as the different mechanisms proposed so far to explain the pairing. Finally, we include a discussion on the excitonic effects which are present in these systems., Comment: 9 pages, 4 figures. Short review article for special issue of Ann. Phys. on "Two-dimensional materials"

One of the main characteristics of the new family of two-dimensional crystals of semiconducting transition metal dichalcogenides (TMD) is the strong spin-orbit interaction, which makes them very promising for future applications in spintronics and valleytronics devices. Here we present a detailed study of the effect of spin-orbit coupling (SOC) on the band structure of single-layer and bulk TMDs, including explicitly the role of the chalcogen orbitals and their hybridization with the transition metal atoms. To this aim, we combine density functional theory (DFT) calculations with a Slater-Koster tight-binding model. Whereas most of the previous tight-binding models have been restricted to the K and K' points of the Brillouin zone (BZ), here we consider the effect of SOC in the whole BZ, and the results are compared to the band structure obtained by DFT methods. The tight-binding model is used to analyze the effect of SOC in the band structure, considering separately the contributions from the transition metal and the chalcogen atoms. Finally, we present a scenario where, in the case of strong SOC, the spin/orbital/valley entanglement at the minimum of the conduction band at Q can be probed and be of experimental interest in the most common cases of electron-doping reported for this family of compounds., Comment: 12 pages, 6 figures

In this paper we present a paradigmatic tight-binding model for single-layer as well as for multi-layered semiconducting MoS$_2$ and similar transition metal dichalcogenides. We show that the electronic properties of multilayer systems can be reproduced in terms of a tight-binding modelling of the single-layer hopping terms by simply adding the proper interlayer hoppings ruled by the chalcogenide atoms. We show that such tight-binding model permits to understand and control in a natural way the transition between a direct-gap band structure, in single-layer systems, to an indirect gap in multilayer compounds in terms of a momentum/orbital selective interlayer splitting of the relevant valence and conduction bands. The model represents also a suitable playground to investigate in an analytical way strain and finite-size effects.

We investigate the charge transport properties of planar amorphous graphene that is fully topologically disordered, in the form of sp2 three-fold coordinated networks consisting of hexagonal rings, but also including many pentagons and heptagons distributed in a random fashion. Using the Kubo transport methodology and the Lanczos method, the density of states, mean free paths and semiclassical conductivities of such amorphous graphene membranes are computed. Despite a large increase in the density of states close to the charge neutrality point, all electronic properties are dramatically degraded, evidencing an Anderson insulating state caused by topological disorder alone. These results are supported by Landauer-Buttiker conductance calculations, which show a localization length as short as 5 nanometers

We develop a first-principles computational method for investigating the dielectric screening in extended systems using the self-consistent Sternheimer equation and localized non-orthogonal basis sets. Our approach does not require the explicit calculation of unoccupied electronic states, only uses two-center integrals, and has a theoretical scaling of order O(N^3). We demonstrate this method by comparing our calculations for silicon, germanium, diamond, and LiCl with reference planewaves calculations. We show that accuracy comparable to planewaves calculations can be achieved via a systematic optimization of the basis set., Comment: 6 pages, 3 figures

We present a systematic study of the performance of numerical pseudo-atomic orbital basis sets in the calculation of dielectric matrices of extended systems using the self-consistent Sternheimer approach of [F. Giustino et al., Phys. Rev. B 81 (11), 115105 (2010)]. In order to cover a range of systems, from more insulating to more metallic character, we discuss results for the three semiconductors diamond, silicon, and germanium. Dielectric matrices calculated using our method fall within 1-3% of reference planewaves calculations, demonstrating that this method is promising. We find that polarization orbitals are critical for achieving good agreement with planewaves calculations, and that only a few additional \zeta 's are required for obtaining converged results, provided the split norm is properly optimized. Our present work establishes the validity of local orbital basis sets and the self-consistent Sternheimer approach for the calculation of dielectric matrices in extended systems, and prepares the ground for future studies of electronic excitations using these methods., Comment: 10 pages, 8 figures

An efficient computational methodology is used to explore charge transport properties in chemically-modified (and randomly disordered) graphene-based materials. The Hamiltonians of various complex forms of graphene are constructed using tight-binding models enriched by first-principles calculations. These atomistic models are further implemented into a real-space order-N Kubo-Greenwood approach, giving access to the main transport length scales (mean free paths, localization lengths) as a function of defect density and charge carrier energy. An extensive investigation is performed for epoxide impurities with specific discussions on both the existence of a minimum semi-classical conductivity and a crossover between weak to strong localization regime. The 2D generalization of the Thouless relationship linking transport length scales is here illustrated based on a realistic disorder model., Comment: 14 pages, 18 figures, submitted

Spin-dependent features in the conductivity of graphene, chemically modified by a random distribution of hydrogen adatoms, are explored theoretically. The spin effects are taken into account using a mean-field self-consistent Hubbard model derived from first-principles calculations. A Kubo-Greenwood transport methodology is used to compute the spin-dependent transport fingerprints of weakly hydrogenated graphene-based systems with realistic sizes. Conductivity responses are obtained for paramagnetic, antiferromagnetic, or ferromagnetic macroscopic states, constructed from the mean-field solutions obtained for small graphene supercells. Magnetoresistance signals up to $\sim 7%$ are calculated for hydrogen densities around 0.25%. These theoretical results could serve as guidance for experimental observation of induced magnetism in graphene., Comment: 4 pages, 4 figures

We determine the conditions in which negative differential resistance (NDR) appears in the C$_{60}$-based molecular device of [Phys. Rev. Lett. {\bf 100}, 036807 (2008)] by means of ab-initio electron-transport simulations. Our calculations grant access to bias-dependent intrinsic properties of the molecular device, such as electronic levels and their partial widths. We show that these quantities depend on the molecule-molecule and molecule-electrode interactions of the device. Hence, NDR can be tuned by modifying the bias behavior of levels and widths using both types of interactions., Comment: 4 pages 4 figures

We have adapted the maximally-localized Wannier function approach of [I. Souza, N. Marzari and D. Vanderbilt, Phys. Rev. B 65, 035109 (2002)] to the density functional theory based Siesta method [J. M. Soler et al., J. Phys.: Cond. Mat. 14, 2745 (2002)] and applied it to the study of Co substitutional impurities in bulk copper as well as to the Cu (111) surface. In the Co impurity case, we have reduced the problem to the Co d-electrons and the Cu sp-band, permitting us to obtain an Anderson-like Hamiltonian from well defined density functional parameters in a fully orthonormal basis set. In order to test the quality of the Wannier approach to surfaces, we have studied the electronic structure of the Cu (111) surface by again transforming the density functional problem into the Wannier representation. An excellent description of the Shockley surface state is attained, permitting us to be confident in the application of this method to future studies of magnetic adsorbates in the presence of an extended surface state.

We study the mechanism leading to the metallization of the $\beta$-SiC(001) Si-rich surface induced by hydrogen adsorption. We analyze the effects of band bending and demonstrate the existence of a quasi-2D electron gas, which originates from the donation of electrons from adsorbed hydrogen to bulk conduction states. We also provide a simple model that captures the main features of the results of first-principles calculations, and uncovers the basic physics of the process., Comment: accepted for publication in physica status solidi - Rapid Research Letters

This paper has been withdrawn by the authors (see text)., Comment: This paper has been withdrawn

We investigate, by means of first-principles calculations, structural and transport properties of junctions made of symmetric dithiolated molecules placed between Au electrodes. As the electrodes are pulled apart, we find that it becomes energetically favorable that Au atoms migrate to positions between the electrode surface and thiol terminations, with junction structures alternating between symmetric and asymmetric. As a result, the calculated $\emph{IV}$ curves alternate between rectifying and non-rectifying behaviors as the electrodes are pulled apart, which is consistent with recent experimental results.

The experimental STM images for the CDW phase of the blue bronze RbMoO3 have been successfully explained on the basis of first-principles DFT calculations. Although the density of states near the Fermi level strongly concentrates in two of the three types of Mo atoms Mo-II and Mo-III, the STM measurement mostly probes the contribution of the uppermost O atoms of the surface, associated with the Mo-IO6 octahedra. In addition, it is found that the surface concentration of Rb atoms plays a key role in determining the surface nesting vector and hence the periodicity of the CDW modulation. Significant experimental inhomogeneities of the b* surface component of the wavevector of the modulation, probed by STM, are reported. The calculated changes in the surface nesting vector are consistent with the observed experimental inhomogeneities., Comment: 4 pages 5 Figures

We show by ab initio calculations that the electron-phonon coupling matrix element M of the radial breathing mode in single-walled carbon nanotubes depends strongly on tube chirality. For nanotubes of the same diameter the coupling strength |M|^2 is up to one order of magnitude stronger for zig-zag than for armchair tubes. For (n,m) tubes M depends on the value of (n-m) mod 3, which allows to discriminate semiconducting nano tubes with similar diameter by their Raman scattering intensity. We show measured resonance Raman profiles of the radial breathing mode which support our theoretical predictions.

We investigate the electronic structure of gap and band tail states in amorphous silicon. Starting with two 216-atom models of amorphous silicon with defect concentration close to the experiments, we systematically study the dependence of electron localization on basis set, density functional and spin polarization using the first principles density functional code Siesta. We briefly compare three different schemes for characterizing localization: information entropy, inverse participation ratio and spatial variance. Our results show that to accurately describe defect structures within self consistent density functional theory, a rich basis set is necessary. Our study revealed that the localization of the wave function associated with the defect states decreases with larger basis sets and there is some enhancement of localization from GGA relative to LDA. Spin localization results obtained via LSDA calculations, are in reasonable agreement with experiment and with previous LSDA calculations on a-Si:H models., Comment: 16 pages, 11 Postscript figures, To appear in Phys. Rev. B

We report a first-principles study of vacancy-induced self-diffusion in crystalline silicon. Starting form a fully relaxed configuration with a neutral vacancy, we proceed to search for local diffusion paths. The diffusion of the vacancy proceeds by hops to first nearest neighbor with an energy barrier of 0.40 eV in agreement with experimental results. Competing mechanisms are identified, like the reorientation, and the recombination of dangling bonds by Wooten-Winer-Weaire process., Comment: 10 pages, 5 figures, accepted for publication in Pysical review B

We report first-principles density-functional pseudopotential calculations on the atomic structures, electronic properties, and band offsets of BaO/BaTiO$_3$ and SrO/SrTiO$_3$ nanosized heterojunctions grown on top of a silicon substrate. The density of states at the junction does not reveal any electronic induced interface states. A dominant perovskite character is found at the interface layer. The tunability of the band offset with the strain conditions imposed by the substrate is studied. Using previously reported theoretical data available for Si/SrO, Si/BaO and BaTiO$_{3}$/SrRuO$_{3}$ interfaces we extrapolate a value for the band alignments along the whole gate stacks of technological interest: Si/SrO/SrTiO$_3$ and Si/BaO/BaTiO$_3$/SrRuO$_3$ heterostructures., Comment: 12 pages, 6 figures, submitted to Phys. Rev. B

The electronic structure of an infinite poly-guanine - poly-cytosine DNA molecule in its dry A-helix structure is studied by means of density-functional calculations. An extensive study of 30 nucleic base pairs is performed to validate the method. The electronic energy bands of DNA close to the Fermi level are then analyzed in order to clarify the electron transport properties in this particularly simple DNA realization, probably the best suited candidate for conduction. The energy scale found for the relevant band widths, as compared with the energy fluctuations of vibrational or genetic-sequence origin, makes highly implausible the coherent transport of electrons in this system. The possibility of diffusive transport with sub-nanometer mean free paths is, however, still open. Information for model Hamiltonians for conduction is provided., Comment: 8 pages, 4 figures

We address the microscopic origin of the current-induced forces by analyzing results of first principles density functional calculations of atomic gold wires connected to two gold electrodes with different electrochemical potentials. We find that current induced forces are closely related to the chemical bonding, and arise from the rearrangement of bond charge due to the current flow. We explain the current induced bond weakening/strengthening by introducing bond charges decomposed into electrode components., Comment: 4 pages, 4 figures

We have developed and implemented a self-consistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical LCAO basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need of an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory, required to minimize the energy, to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations., Comment: 22 pages, 8 figures

We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density functional theory (DFT) as implemented in the well tested Siesta approach (which uses non-local norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including selfconsistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme involving the scattering states. As an illustration, the method is applied to three systems where we are able to compare our results to earlier ab initio DFT calculations or experiments, and we point out differences between this method and existing schemes. The systems considered are: (1) single atom carbon wires connected to aluminum electrodes with extended or finite cross section, (2) single atom gold wires, and finally (3) large carbon nanotube systems with point defects., Comment: 18 pages, 23 figures

The electronic band structure of GaTe has been calculated by numerical atomic orbitals density-functional theory, in the local density approximation. In addition, the valence-band dispersion along various directions of the GaTe Brillouin zone has been determined experimentally by angle-resolved photoelectron spectroscopy. Along these directions, the calculated valence-band structure is in good concordance with the valence-band dispersion obtained by these measurements. It has been established that GaTe is a direct-gap semiconductor with the band gap located at the Z point, that is, at Brillouin zone border in the direction perpendicular to the layers. The valence-band maximum shows a marked \textit{p}-like behavior, with a pronounced anion contribution. The conduction band minimum arises from states with a comparable \textit{s}- \textit{p}-cation and \textit{p}-anion orbital contribution. Spin-orbit interaction appears to specially alter dispersion and binding energy of states of the topmost valence bands lying at $\Gamma$. By spin-orbit, it is favored hybridization of the topmost \textit{p}$_z$-valence band with deeper and flatter \textit{p$_x$}-\textit{p$_y$} bands and the valence-band minimum at $\Gamma$ is raised towards the Fermi level since it appears to be determined by the shifted up \textit{p$_x$}-\textit{p$_y$} bands., Comment: 7 text pages, 6 eps figures, submitted to PRB

We have developed a formulation of density functional perturbation theory for the calculation of vibrational frequencies in molecules and solids, which uses numerical atomic orbitals as a basis set for the electronic states. The (harmonic) dynamical matrix is extracted directly from the first order change in the density matrix with respect to infinitesimal atomic displacements from the equilibrium configuration. We have applied this method to study the vibrational properties of a number of hydrogen-related complexes and light impurities in silicon. The diagonalization of the dynamical matrix provides the vibrational modes and frequencies, including the local vibrational modes (LVMs) associated with the defects. In addition to tests on simple molecules, results for interstitial hydrogen, hydrogen dimers, vacancy-hydrogen and self-interstitial-hydrogen complexes, the boron-hydrogen pair, substitutional C, and several O-related defects in c-Si are presented. The average error relative to experiment for the aprox.60 predicted LVMs is about 2% with most highly harmonic modes being extremely close and the more anharmonic ones within 5-6% of the measured values., Comment: 18 pages, 1 figure

The properties of diluted Ga$_{1-x}$Mn$_x$As are calculated for a wide range of Mn concentrations within the local spin density approximation of density functional theory. M\"ulliken population analyses and orbital-resolved densities of states show that the configuration of Mn in GaAs is compatible with either 3d$^5$ or 3d$^6$, however the occupation is not integer due to the large $p$-$d$ hybridization between the Mn $d$ states and the valence band of GaAs. The spin splitting of the conduction band of GaAs has a mean field-like linear variation with the Mn concentration and indicates ferromagnetic coupling with the Mn ions. In contrast the valence band is antiferromagnetically coupled with the Mn impurities and the spin splitting is not linearly dependent on the Mn concentration. This suggests that the mean field approximation breaks down in the case of Mn-doped GaAs and corrections due to multiple scattering must be considered. We calculate these corrections within a simple free electron model and find good agreement with our {\it ab initio} results if a large exchange constant ($N\beta=-4.5$eV) is assumed., Comment: 15 pages, 14 figures

We have explored new possible phases of 3D C60-based fullerites using semiempirical potentials and ab-initio density functional methods. We have found three closely related structures - two body centered orthorhombic and one body centered cubic - having 52, 56 and 60 tetracoordinated atoms per molecule. These 3D polymers result in semiconductors with bulk moduli near 300 GPa, and shear moduli around 240 GPa, which make them good candidates for new low density superhard materials., Comment: To be published in Physical Review Letters

In this paper we report a theoretical study of the effects of the presence of boron in growing carbon nanotubes. We employ a well established Tight Binding model to describe the interactions responsible for the energetics of these systems, combined with the Molecular Dynamics simulation technique and Structural Relaxation calculations. We find, in agreement with the previous theoretical/experimental work of Blase {\em et al.} [{\em Phys. Rev. Lett.} {\bf 83}, 5078 (1999)], that boron favors (n,0) (zig-zag) tubular structures over (n,n) (arm-chair) ones by stabilizing the zig-zag edge. Furthermore, it is shown that boron has the effect of delaying the tube closure process, a fact which could explain the improved aspect ratio experimentally observed in nanotubes synthesized in the presence of boron. Our dynamical simulations lead us to propose a mechanism through which this extension of the closure time can be explained., Comment: 11 pages, 6 figures, to appear in J. Chem. Phys

We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT scheme, which is specially suited for systems with large numbers of atoms. As a first step towards the study of large DNA systems, in this work: (i) We establish the reliability of the approximations of our method (including pseudopotentials and basis sets) for the description of the hydrogen-bonded base pairs, by comparing our results with those of former calculations. We show that the interaction energies at Hartree-Fock geometries are in very good agreement with those of second order M{\o}ller-Plesset (MP2) perturbation theory (the most accurate technique that can be applied at present for system of the sizes of the base-pairs). (ii) We perform DFT structural optimizations for the 30 different DNA base-pairs, only three of which had been previously studied with DFT. Our results provide information on the effect of correlation on the structure of the other 27 base pairs, for which only Hartree-Fock geometries were formerly available., Comment: Submitted to J. Phys. Chem. B

We simulate the liquid silicon surface with first-principles molecular dynamics in a slab geometry. We find that the atom-density profile presents a pronounced layering, similar to those observed in low-temperature liquid metals like Ga and Hg. The depth-dependent pair correlation function shows that the effect originates from directional bonding of Si atoms at the surface, and propagates into the bulk. The layering has no major effects in the electronic and dynamical properties of the system, that are very similar to those of bulk liquid Si. To our knowledge, this is the first study of a liquid surface by first-principles molecular dynamics., Comment: 4 pages, 4 figures, submitted to PRL

We apply first principles calculations to study the opening of single-wall carbon nanotubes (SWNT's) by oxidation. We show that an oxygen rim can stabilize the edge of the open tube. The sublimation of CO$_2$ molecules from the rim with the subsequent closing of the tube changes from endothermic to exothermic as the tube radius increases, within the range of experimental feasible radii. We also obtain the energies for opening the tube at the cap and at the wall, the latter being significantly less favorable., Comment: 4 pages, 3 figures. Submitted to Phys. Rev. B