Modular implementation of the linear- and cubic-scaling orbital minimization methods in electronic structure codes using atomic orbitals.

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 distributed block compressed sparse row (DBCSR) and scalable linear algebra package (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.

A pre-time-zero spatiotemporal microscopy technique for the ultrasensitive determination of the thermal diffusivity of thin films.

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. The particular advantage of this technique is that it enables quantifying thermal transport without requiring any material input parameters or strong heating. We demonstrate the direct determination of the thermal diffusivities of films with a thickness of around 15 nm, consisting of the layered materials MoSe2 (0.18 cm2/s), WSe2 (0.20 cm2/s), MoS2 (0.35 cm2/s), and WS2 (0.59 cm2/s). This technique paves the way for observing nanoscale thermal transport phenomena and tracking diffusion of a broad range of species.

Atomically Sharp Lateral Superlattice Heterojunctions Built-In Nitrogen-Doped Nanoporous Graphene.

Nanometer scale lateral heterostructures with atomically sharp band discontinuities can be conceived as the 2D analogues of vertical Van der Waals heterostructures, where pristine properties of each component coexist with interfacial phenomena that result in a variety of exotic quantum phenomena. However, despite considerable advances in the fabrication of lateral heterostructures, controlling their covalent interfaces and band discontinuities with atomic precision, scaling down components and producing periodic, lattice-coherent superlattices still represent major challenges. Here, a synthetic strategy to fabricate nanometer scale, coherent lateral superlattice heterojunctions with atomically sharp band discontinuity is reported. By merging interdigitated arrays of different types of graphene nanoribbons by means of a novel on-surface reaction, superlattices of 1D, and chemically heterogeneous nanoporous junctions are obtained. The latter host subnanometer quantum dipoles and tunneling in-gap states, altogether expected to promote interfacial phenomena such as interribbon excitons or selective photocatalysis.

Unraveling Heat Transport and Dissipation in Suspended MoSe2 from Bulk to Monolayer.

Understanding heat flow in layered transition metal dichalcogenide (TMD) crystals is crucial for applications exploiting these materials. Despite significant efforts, several basic thermal transport properties of TMDs are currently not well understood, in particular how transport is affected by material thickness and the material's environment. This combined experimental-theoretical study establishes a unifying physical picture of the intrinsic lattice thermal conductivity of the representative TMD MoSe2 . Thermal conductivity measurements using Raman thermometry on a large set of clean, crystalline, suspended crystals with systematically varied thickness are combined with ab initio simulations with phonons at finite temperature. The results show that phonon dispersions and lifetimes change strongly with thickness, yet the thinnest TMD films exhibit an in-plane thermal conductivity that is only marginally smaller than that of bulk crystals. This is the result of compensating phonon contributions, in particular heat-carrying modes around ≈0.1 THz in (sub)nanometer thin films, with a surprisingly long mean free path of several micrometers. This behavior arises directly from the layered nature of the material. Furthermore, out-of-plane heat dissipation to air molecules is remarkably efficient, in particular for the thinnest crystals, increasing the apparent thermal conductivity of monolayer MoSe2 by an order of magnitude. These results are crucial for the design of (flexible) TMD-based (opto-)electronic applications.

Magnetic properties of coordination clusters with {Mn4} and {Co4} antiferromagnetic cores.

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 atomic magnetic moments and strength of the intra-molecular magnetic couplings. In particular, the dependence of the magnetization versus field of the two molecules switches with temperature: at low temperature the magnetization is smaller in {Mn4} than in Co4, 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 {Mn4} with respect to {Co4}. Moreover {Co4} 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 together with electronic correlation effects for a reliable description of these compounds.

Basic aspects of the charge density wave instability of transition metal trichalcogenides NbSe3and monoclinic-TaS3.

NbSe3and monoclinic-TaS3(m-TaS3) are quasi-1D metals containing three different types of chains and undergoing two different charge density wave Peierls transitions atTP1andTP2associated with type III and type I chains, respectively. The nature of these transitions is discussed on the basis of first-principles DFT calculation of their Fermi surface (FS) and electron-hole response function. Because of the stronger inter-chain interactions, the FS and electron-hole response function are considerably more complex for NbSe3thanm-TaS3; 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 electron-hole response for NbSe3are found with the (0a*, 0c*) and (1/2a*, 1/2c*) transverse components atTP1andTP2, respectively, whereas the second maximum is not observed form-TaS3atTP2. Analysis of the different inter-chain coupling mechanisms leads to the conclusion that FS nesting effects are only relevant to set the transversea*components in NbSe3. The strongest inter-chain Coulomb coupling mechanism must be taken into account for the transverse coupling alongc*in NbSe3and along botha*andc*form-TaS3. Phonon spectrum calculations reveal the formation of a giant 2kFKohn anomaly form-TaS3. All these results support a weak coupling scenario for the Peierls transition of transition metal trichalcogenides.

Anion ordering transition and Fermi surface electron-hole instabilities in the (TMTSF)2ClO4 and (TMTSF)2NO3 Bechgaard salts analyzed through the first-principles Lindhard response function.

The first-principles electron-hole Lindhard response function has been calculated and analyzed in detail for two (TMTSF)2 X (X = ClO4 and NO3) Bechgaard salts undergoing different anion-ordering (AO) transitions. The calculation was carried out using the real triclinic low-temperature structures. The evolution of the electron-hole response with temperature for both relaxed and quenched salts is discussed. It is shown that the 2k F response of the quenched samples of both salts display a low temperature curved and tilted triangular continuum of maxima. This is not the case for the relaxed samples. (TMTSF)2ClO4 in the AO state exhibits a more quasi-1D response than in the non AO state and relaxed (TMTSF)2NO3 shows a sharp maximum. The curved triangular plateau of the quenched samples results from multiple nesting of the warped quasi-1D Fermi surface which implies the existence of a large q range of electron-hole fluctuations. This broad maxima region is around 1% of the Brillouin zone area for the X = ClO4 salt (and X = PF6) but only 0.1% for the X = NO3 salt. It is suggested that the strong reduction of associated SDW fluctuations could explain the non detection of the SDW-mediated superconductivity in (TMTSF)2NO3. The calculated maxima of the Lindhard response nicely account for the modulation wave vector experimentally determined by NMR in the SDW ground state of the two salts. The critical AO wave vector for both salts is located in regions where the Lindhard response is a minimum so that they are unrelated to any electron-hole instability. The present first-principles calculation reveals 3D effects in the Lindhard response of the two salts at low temperature which are considerably more difficult to model in analytical approaches.

Siesta: Recent developments and applications.

A review of the present status, recent enhancements, and applicability of the Siesta program is presented. Since its debut in the mid-1990s, Siesta's flexibility, efficiency, and free distribution have 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, density functional theory (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 modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering Siesta runs, and various post-processing 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, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure 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.

Fermi surface electron-hole instability of the (TMTSF)2PF6 Bechgaard salt revealed by the first-principles Lindhard response function.

We report the first-principles DFT calculation of the electron-hole Lindhard response function of the (TMTSF)2PF6 Bechgaard salt using the real triclinic low-temperature structure. The Lindhard response is found to change considerably with temperature. Near the 2k F spin density wave (SDW) instability it has the shape of a broad triangular plateau as a result of the multiple nesting associated with the warped quasi-one-dimensional Fermi surface. The evolution of the 2k F broad maximum as well as the effect of pressure and deuteration is calculated and analyzed. The thermal dependence of the electron-hole coherence length deduced from these calculations compares very well with the experimental thermal evolution of the 2k F bond order wave correlation length. The existence of a triangular plateau of maxima in the low-temperature electron-hole Lindhard response of (TMTSF)2PF6 should favor a substantial mixing of q-dependent fluctuations which can have important consequences in understanding the phase diagram of the 2k F SDW ground state, the mechanism of superconductivity and the magneto-transport of this paradigmatic quasi-one-dimensional material. The first-principles DFT Lindhard response provides a very accurate and unbiased approach to the low-temperature instabilities of (TMTSF)2PF6 which can take into account in a simple way 3D effects and subtle structural variations, thus providing a very valuable tool in understanding the remarkable physics of molecular conductors.

Coexistence of Elastic Modulations in the Charge Density Wave State of 2 H-NbSe2.

Bulk and single-layer 2 H-NbSe2 exhibit identical charge density wave order (CDW) with a quasi-commensurate 3 × 3 superlattice periodicity. Here we combine scanning tunnelling microscopy (STM) imaging at T = 1 K of 2 H-NbSe2 with first-principles density functional theory (DFT) calculations to investigate the structural atomic rearrangement of this CDW phase. Our calculations for single-layers reveal that six different atomic structures are compatible with the 3 × 3 CDW distortion, although all of them lie on a very narrow energy range of at most 3 meV per formula unit, suggesting the coexistence of such structures. Our atomically resolved STM images of bulk 2 H-NbSe2 unambiguously confirm this by identifying two of these structures. Remarkably, these structures differ from the X-ray crystal structure reported for the bulk 3 × 3 CDW which in fact is also one of the six DFT structures located for the single-layer. Our calculations also show that due to the minute energy difference between the different phases, the ground state of the 3 × 3 CDW could be extremely sensitive to doping, external strain or internal pressure within the crystal. The presence of multiphase CDW order in 2 H-NbSe2 may provide further understanding of its low temperature state and the competition between different instabilities.

Spin Proximity Effects in Graphene/Topological Insulator Heterostructures.

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. 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 ab initio simulations and tight-binding models to determine the precise spin texture of electronic states in graphene interfaced with a Bi2Se3 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.

Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach.

The effects of the environment in nanoscopic materials can play a crucial role in device design. Particularly in biosensors, where the system is usually embedded in a solution, water and ions have to be taken into consideration in atomistic simulations of electronic transport for a realistic description of the system. In this work, we present a methodology that combines quantum mechanics/molecular mechanics methods (QM/MM) with the nonequilibrium Green's function framework to simulate the electronic transport properties of nanoscopic devices in the presence of solvents. As a case in point, we present further results for DNA translocation through a graphene nanopore. In particular, we take a closer look into general assumptions in a previous work. For this sake, we consider larger QM regions that include the first two solvation shells and investigate the effects of adding extra k-points to the NEGF calculations. The transverse conductance is then calculated in a prototype sequencing device in order to highlight the effects of the solvent.

Nanotexturing To Enhance Photoluminescent Response of Atomically Thin Indium Selenide with Highly Tunable Band Gap.

Manipulating properties of matter at the nanoscale is the essence of nanotechnology, which has enabled the realization of quantum dots, nanotubes, metamaterials, and two-dimensional materials with tailored electronic and optical properties. Two-dimensional semiconductors have revealed promising perspectives in nanotechnology. However, the tunability of their physical properties is challenging for semiconductors studied until now. Here we show the ability of morphological manipulation strategies, such as nanotexturing or, at the limit, important surface roughness, to enhance light absorption and the luminescent response of atomically thin indium selenide nanosheets. Besides, quantum-size confinement effects make this two-dimensional semiconductor to exhibit one of the largest band gap tunability ranges observed in a two-dimensional semiconductor: from infrared, in bulk material, to visible wavelengths, at the single layer. These results are relevant for the design of new optoelectronic devices, including heterostructures of two-dimensional materials with optimized band gap functionalities and in-plane heterojunctions with minimal junction defect density.

Carbon nanotubes as substrates for molecular spiropyran-based switches.

We present a joint theory-experiment study investigating the excitonic absorption of spiropyran-functionalized carbon nanotubes. The functionalization is promising for engineering switches on a molecular level, since spiropyrans can be reversibly switched between two different conformations, inducing a distinguishable and measurable change of optical transition energies in the substrate nanotube. Here, we address the question of whether an optical read-out of such a molecular switch is possible. Combining density matrix and density functional theory, we first calculate the excitonic absorption of pristine and functionalized nanotubes. Depending on the switching state of the attached molecule, we observe a red-shift of transition energies by about 15 meV due to the coupling of excitons with the molecular dipole moment. Then we perform experiments measuring the absorption spectrum of functionalized carbon nanotubes for both conformations of the spiropyran molecule. We find good qualitative agreement between the theoretically predicted and experimentally measured red-shift, confirming the possibility for an optical read-out of the nanotube-based molecular switch.

Y:BaZrO3 perovskite compounds I: DFT study on the unprotonated and protonated local structures.

Y-doped BaZrO(3) derivatives were studied by density functional theory (DFT) to investigate the local arrangements of the octahedral sites in Pm3m cubic frameworks. Single- and double substitution of zirconium by yttrium were considered, including in the presence of a nearby oxygen vacancy. Although the structural symmetry of undoped barium zirconate was not modified after yttrium doping, the presence of yttrium induced several differences in the oxygen sites around it, according to the local geometrical arrangement of yttrium in the host matrix. As an example, the differences between such oxygen sites were shown in the presence of a proton. In this case, different stabilization energies characterized the protonated fragments. Only in those structures, in which two yttrium atoms were neighbors (i.e., formed Y-O-Y moieties), were the relative energy differences between the corresponding proton stable sites in agreement with the order of magnitude of the experimental proton-hopping activation energies. The distribution of such energy differences suggested a grouping of the oxygen atoms into three sets, which had peculiar structural features that weren't easily deducible from their topologies. The existence of proton traps was also discussed on the basis of the energy-difference distributions.

Electroresistance effect in ferroelectric tunnel junctions with symmetric electrodes.

Understanding the effects that govern electronic transport in ferroelectric tunnel junctions (FTJs) is of vital importance to improve the efficiency of devices such as ferroelectric memories with nondestructive readout. However, our current knowledge (typically based on simple semiempirical models or first-principles calculations restricted to the limit of zero bias) remains partial, which may hinder the development of more efficient systems. For example, nowadays it is commonly believed that the tunnel electroresistance (TER) effect exploited in such devices mandatorily requires, to be sizable, the use of two different electrodes, with related potential drawbacks concerning retention time, switching, and polarization imprint. In contrast, here we demonstrate at the first-principles level that large TER values of about 200% can be achieved under finite bias in a prototypical FTJ with symmetric electrodes. Our atomistic approach allows us to quantify the contribution of different microscopic mechanisms to the electroresistance, revealing the dominant role of the inverse piezoelectric response of the ferroelectric. On the basis of our analysis, we provide a critical discussion of the semiempirical models traditionally used to describe FTJs.

Oxygen surface functionalization of graphene nanoribbons for transport gap engineering.

We numerically investigate the impact of epoxide adsorbates on the transport properties of graphene nanoribbons with width varying from a few nanometers to 15 nm. For the wider ribbons, a scaling analysis of conductance properties is performed for adsorbate density ranging from 0.1% to 0.5%. Oxygen atoms introduce a large electron-hole transport asymmetry with mean free paths changing by up to 1 order of magnitude, depending on the hole or electron nature of charge carriers. The opening of a transport gap on the electron side for GNRs as wide as 15 nm could be further exploited to control current flow and achieve larger ON/OFF ratios, despite the initially small intrinsic energy gap. The effect of the adsorbates in narrow ribbons is also investigated by full ab initio calculations to explore the limit of ultimate downsized systems. In this case, the inhomogeneous distribution of adsorbates and their interplay with the ribbon edge are found to play an important role.

Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases.

Among the distinct strategies proposed to expand the genetic alphabet, size-expanded nucleobases are promising for the development of modified DNA duplexes with improved biotechnological properties. In particular, duplexes built up by replacing canonical bases with the corresponding benzo-fused counterparts could be valuable as molecular nanowires. In this context, this study reports the results of classical molecular dynamics simulations carried out to examine the structural and dynamical features of size-expanded DNAs, including both hybrid duplexes containing mixed pairs of natural and benzo-fused bases (xDNA) and pure size-expanded (xxDNA) duplexes. Furthermore, the electronic structure of both natural and size-expanded duplexes is examined by means of density functional computations. The results confirm that the structural and flexibility properties of the canonical DNA are globally little affected by the presence of benzo-fused bases. The most relevant differences are found in the enhanced size of the grooves, and the reduction in the twist. However, the analysis also reveals subtle structural effects related to the nature and sequence of benzo-fused bases in the duplex. On the other hand, electronic structure calculations performed for xxDNAs confirm the reduction in the HOMO-LUMO gap predicted from the analysis of the natural bases and their size-expanded counterparts, which suggests that pure size-expanded DNAs can be good conductors. A more complex situation is found for xDNAs, where fluctuations in the electrostatic interaction between base pairs exerts a decisive influence on the modulation of the energy gap.

Magnetoresistance and magnetic ordering fingerprints in hydrogenated graphene.

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 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 ∼7% are calculated for hydrogen densities around 0.25%. These theoretical results could serve as guidance for experimental observation of induced magnetism in graphene.

Magnetism-dependent transport phenomena in hydrogenated graphene: from spin-splitting to localization effects.

Spin-dependent transport in hydrogenated two-dimensional graphene is explored theoretically. Adsorbed atomic hydrogen impurities can either induce a local antiferromagnetic, ferromagnetic, or nonmagnetic state depending on their density and relative distribution. To describe the various magnetic possibilities of hydrogenated graphene, a self-consistent Hubbard Hamiltonian, optimized by ab initio calculations, is first solved in the mean field approximation for small graphene cells. Then, an efficient order N Kubo transport methodology is implemented, enabling large scale simulations of functionalized graphene. Depending on the underlying intrinsic magnetic ordering of hydrogen-induced spins, remarkably different transport features are predicted for the same impurity concentration. Indeed, while the disordered nonmagnetic graphene system exhibits a transition from diffusive to localization regimes, the intrinsic ferromagnetic state exhibits unprecedented robustness toward quantum interference, maintaining, for certain resonant energies, a quasiballistic regime up to the micrometer scale. Consequently, low temperature transport measurements could unveil the presence of a magnetic state in weakly hydrogenated graphene.