arXiv subjects

J. J. Palacios

Publications and source records attributed to J. J. Palacios.

At least 19 recordsLinked to original sources

arXiv2026

ANT:UI: An interactive 3D tool for preparing ANT.Gaussian molecular junction geometries

ANT.UI is a Python graphical interface that automates the construction of molecular-junction geometries for NEGF-DFT quantum transport calculations. Through a real-time 3D viewer, users interactively position electrodes and molecules and generate complete, ready-to-run input files for Gaussian and ANT.Gaussian without manual scripting. Dedicated Pull, Grid, and Rotation assistants further automate electrode-pulling sequences, surface scans, and step-wise rotation studies, with optional geometry-optimisation chaining across each sequence. By replacing a process that previously demanded days of custom scripting with a point-and-click workflow, ANT.UI accelerates research in theoretical molecular electronics and lowers the barrier to entry for new users. The software also exports all constructed geometries in standard XYZ format, allowing direct reuse in molecular dynamics codes or third-party visualization tools without manual reformatting.

cond-mat.mes-hall↗

arXiv2026

Microscopic screening theory for excitons in two-dimensional materials: A bridge between effective models and ab initio descriptions

We present a computational approach for exciton calculations in two-dimensional (2D) materials within the Bethe-Salpeter equation (BSE) framework, employing an atomistic description with point-like orbitals. Unlike widespread efficient calculations that rely on classical or effective interaction models, such as the Rytova-Keldysh model, our method incorporates quantum screened interactions. By explicitly computing the 2D dielectric function at the random-phase approximation level, we capture screening effects beyond such approximations with an accuracy akin to first-principles methods. Consequently, we can realistically estimate excitonic binding energies with a bearable computational cost. A detailed account of the various convergence parameters sheds light on a possible cause of the large dispersion of binding energies reported in the literature using first-principles GW/BSE implementations. This work thus provides an alternative pathway towards efficient and faithful dielectric screening and exciton computations in low-dimensional materials.

cond-mat.mes-hall↗

arXiv2026

Extreme-ultraviolet optical response of atomically-thin molybdenum disulfide

We report multi-angle reflectivity measurements in the extreme-ultraviolet (XUV) range for mono- and bilayer MoS$_2$ on a Si$_3$N$_4$ substrate. Using a single-sheet 2D conductivity model, we extract the complex optical response of the MoS$_2$ bilayer between 25 and 90 eV and derive an effective refractive index by introducing a thickness equal to the interlayer spacing. The MoS$_2$ monolayer response is consistently reproduced either by halving the 2D conductivity or the effective thickness, indicating a robust scaling with layer number. The resulting optical constants display a broad resonance at the Mo N$_{2,3}$ edge with no signatures of sharp core-exciton features despite the reduced dimensionality. First-principles calculations reproduce the experimental results and show that local-field (Hartree) effects dominate the XUV response, while screened-exchange (SEX) contributions remain weak and mainly induce spectral shifts. Our analysis demonstrates that excitonic effects play a minor role in the XUV optical response of atomically thin MoS$_2$, highlighting key differences with respect to the visible and infrared regimes, and calling for a reassessment of the use of Mo-based transition metal dichalcogenides in attosecond spectroscopy and XUV excitonics.

physics.optics↗

arXiv2025

Building unconventional magnetic phases on graphene by H atom manipulation: From altermagnets to Lieb ferrimagnets

Engineering all fundamental magnetic phases within a single material platform would mark a significant milestone in materials science and spintronics, reducing complexity and costs in device fabrication by eliminating the need for integrating and interfacing different materials. Here, we demonstrate that graphene can host all non-relativistic magnetic phases-namely, diamagnetism, paramagnetism, ferromagnetism, antiferromagnetism, ferrimagnetism, altermagnetism and fully compensated ferrimagnetism -- by using single hydrogen atoms as building blocks. Through precise manipulation of these atoms by scanning tunneling microscopy, we can experimentally create all such magnetic phases. Their different magnetic character is confirmed by density functional theory and mean-field Hubbard calculations. In particular, we show that the new magnetic paradigm known as altermagnetism can be realized, exhibiting directionally spin-split energy bands coexisting with zero net magnetization due to protecting spatial symmetries. It is furthermore possible to create fully compensated ferrimagnets, lacking these symmetries and therefore presenting unrestricted spin splitting of the bands, with a vanishing net magnetization which in this case is protected by Lieb's theorem. These findings put forward H-functionalized graphene as a versatile platform to design, build and study these new emergent magnetic phases at the atomic scale.

cond-mat.mtrl-sci↗

arXiv2024

First Principles Excitons in Periodic Systems with Gaussian Density Fitting and Ewald Potential Functions

Excitons, namely neutral excitations in a system of electrons arising from the electron-hole interaction, are often essential to explain optical measurements in materials. They are governed by the Bethe-Salpeter equation, which can be cast into a matrix form that is formally analogous to the one for electrons at the mean-field level. However, constructing the corresponding excitonic Hamiltonian in practice is challenging, specially from a computational perspective if one wishes to surpass effective models. Methods that enable such calculations from the different density-functional theory frameworks currently available are, therefore, convenient. In this work we present an approach to solve the BSE employing Gaussian basis functions starting from a self-consistent, possibly hybrid calculation in any non-metallic solid. It is based on the Gaussian density fitting or resolution of the identity approximation to reduce the initial quartic scaling in the basis dimension, in combination with the use of Ewald-type potential functions to automatically sum the conditionally convergent lattice series. As an illustration of the computational implementation, we provide examples of exciton spectra and optical absorption in some paradigmatic 2D and 3D materials where the single-particle approximation fails qualitatively.

cond-mat.str-el↗

arXiv2024

Amorphization-induced topological and insulator-metal transitions in bidimensional Bi$_x$Sb$_{1-x}$ alloys

Bismuth has been shown to be topological in its different allotropes and compounds, with one of the most notable examples being the Bi-Sb alloy, the first 3D topological insulator ever discovered. In this paper we explore two-dimensional alloys of Bi and Sb, both crystalline and amorphous, to determine the critical concentrations that render the alloys topological. For the amorphous alloy, we determine the effect of structural disorder on its topological properties, remarkably observing a trivial to topological transition as disorder increases. The alloys are modelled using a Slater-Koster tight-binding model and the topological behaviour is assessed through the entanglement spectrum together with artificial neural networks. Additionally, we perform electronic transport calculations with results compatible with those of the entanglement spectrum, which, furthermore, reveal an insulator to metal transition in the highly disordered regime.

cond-mat.dis-nn↗

arXiv2024

Excitons in nonlinear optical responses: shift current in MoS$_2$ and GeS monolayers

It is well-known that exciton effects are determinant to understand the optical absorption spectrum of low-dimensional materials. However, the role of excitons in nonlinear optical responses has been much less investigated at an experimental level. Additionally, computational methods to calculate nonlinear conductivities in real materials are still not widespread, particularly taking into account excitonic interactions. We present a methodology to calculate the excitonic second-order optical responses in 2D materials relying on: (i) ab initio tight-binding Hamiltonians obtained by Wannier interpolation and (ii) the Bethe-Salpeter equation with effective electron-hole interactions. Here, in particular, we explore the role of excitons in the shift current of monolayer materials. Focusing on MoS$_2$ and GeS monolayer systems, our results show that $2p$-like excitons, which are dark in the linear response regime, yield a contribution to the photocurrent comparable to that of $1s$-like excitons. Under radiation with intensity $\sim 10^{4} $W/cm$^2$, the excitonic theory predicts in-gap photogalvanic currents of almost $\sim 10$ nA in sufficiently clean samples, which is typically one order of magnitude higher than the value predicted by independent-particle theory near the band edge.

cond-mat.mes-hall↗

arXiv2023

Shift current with Gaussian basis sets $\&$ general prescription for maximally-symmetric summations in the irreducible Brillouin zone

The bulk photovoltaic effect is an experimentally verified phenomenon by which a direct charge current is induced within a non-centrosymmetric material by light illumination. Calculations of its intrinsic contribution, the shift current, are nowadays amenable from first-principles employing plane-waves bases. In this work we present a general method for evaluating the shift conductivity in the framework of localized Gaussian basis sets that can be employed in both the length and velocity gauges, carrying the idiosyncrasies of the quantum-chemistry approach. The (possibly magnetic) symmetry of the system is exploited in order to fold the reciprocal space summations to the representation domain, allowing to reduce computation time and unveiling the complete symmetry properties of the conductivity tensor under general light polarization.

cond-mat.mtrl-sci↗

arXiv2023

Non-equilibrium spin accumulation and magneto-conductance in chiral nanojunctions from density-functional $\&$ group theory

It is theoretically well established that a spin-dependent electron transmission generally appears in chiral systems, even without magnetic components, as long as a strong spin-orbit coupling is present in some of its elements. However, how this translates into the so-called chirality-induced spin selectivity in experiments, where the system is taken out of equilibrium, is still debated. Aided by non-equilibrium DFT-based quantum transport calculations, here we show that, when spatial symmetries that forbid a finite spin polarization in equilibrium are broken, a \textit{net} spin accumulation appears at finite bias in an arbitrary two-terminal nanojunction. Furthermore, when a suitably magnetized detector is introduced in the system, the net spin accumulation, in turn, translates into a finite magneto-conductance. The symmetry prerequisites are mostly analogous to those for the spin polarization at any bias, with the vectorial nature given by the direction of magnetization.

cond-mat.mes-hall↗

arXiv2023

A group-theoretic approach to the origin of chirality-induced spin selectivity in non-magnetic molecular junctions

Spin-orbit coupling gives rise to a range of spin-charge interconversion phenomena in non-magnetic systems where certain spatial symmetries are reduced or absent. Chirality-induced spin selectivity (CISS), a term that generically refers to a spin-dependent electron transfer in non-magnetic chiral systems, is one such case, appearing in a variety of seemingly unrelated situations ranging from inorganic materials to molecular devices. In particular, the origin of CISS in molecular junctions is a matter of an intense current debate. Here we derive a set of geometrical conditions for this effect to appear, hinting at the fundamental role of symmetries beyond otherwise relevant quantitative issues. Our approach, which draws on the use of point-group symmetries within the scattering formalism for transport, shows that electrode symmetries are as important as those of the molecule when it comes to the emergence of a spin-polarization and, by extension, to the possible appearance of CISS. It turns out that standalone metallic nanocontacts can exhibit spin-polarization when relative rotations which reduce the symmetry are introduced. As a corollary, molecular junctions with $\textbf{achiral}$ molecules can also exhibit spin-polarization along the direction of transport, provided that the whole junction is chiral in a specific way. This formalism also allows the prediction of qualitative changes of the spin-polarization upon substitution of a chiral molecule in the junction with its enantiomeric partner. Quantum transport calculations based on density functional theory corroborate all of our predictions and provide further quantitative insight within the single-particle framework.

cond-mat.mes-hall↗

arXiv2022

Dynamic bonding influenced by the proximity of adatoms to one-atom high step edges

Low-temperature scanning tunneling microscopy is used here to study dynamic bonding of gold atoms on surfaces under low coordination conditions. In the experiments, using an atomically-sharp gold tip, a gold adatom is deposited onto a gold surface with atomic precision either on the first hollow site near a step edge, or far away from it. Classical molecular dynamics simulations at 4.2 K and density functional theory calculations serve to elucidate the difference in the bonding behavior between these two different placements, while also providing information on the crystalline classification of the STM tips based on their experimental performance.

cond-mat.mtrl-sci↗

arXiv2022

A comprehensive study of the velocity, momentum and position matrix elements for Bloch states using a local orbital basis

We present a comprehensive study of the velocity operator, $\hat{\boldsymbol{v}}=\frac{i}{\hbar} [\hat{H},\hat{\boldsymbol{r}}]$, when used in crystalline solids calculations. The velocity operator is key to the evaluation of a number of physical properties and its computation, both from a practical and fundamental perspective, has been a long-standing debate for decades. Our work summarizes the different approaches found in the literature, connecting them and filling the gaps in the sometimes non-rigorous derivations. In particular we focus on the use of local orbital basis sets where the velocity operator cannot be approximated by the $k$-derivative of the Bloch Hamiltonian matrix. Among other things, we show how the correct expression can be found without unequivocal mathematical steps, how the Berry connection makes its way in this expression, and how to properly deal with the two popular gauge choices that coexist in the literature. Finally, we explore its use in density functional theory calculations by comparing with its real-space evaluation through the identification with the canonical momentum operator. This comparison offers us, in addition, a glimpse of the importance of non-local corrections, which may invalidate the naive momentum-velocity correspondence.

cond-mat.mes-hall↗

arXiv2020

Atomic-scale control of graphene magnetism using hydrogen atoms

Isolated hydrogen atoms absorbed on graphene are predicted to induce magnetic moments. Here we demonstrate that the adsorption of a single hydrogen atom on graphene induces a magnetic moment characterized by a ~20 meV spin-split state at the Fermi energy. Our scanning tunneling microscopy (STM) experiments, complemented by first-principles calculations, show that such a spin-polarized state is essentially localized on the carbon sublattice complementary to the one where the H atom is chemisorbed. This atomically modulated spin-texture, which extends several nanometers away from the H atom, drives the direct coupling between the magnetic moments at unusually long distances. Using the STM tip to manipulate H atoms with atomic precision, we demonstrate the possibility to tailor the magnetism of selected graphene regions.

cond-mat.mes-hall↗

arXiv2020

Consistency between ARPES and STM measurements on SmB$_6$

Strongly correlated topological surface states are promising platforms for next-generation quantum applications, but they remain elusive in real materials. The correlated Kondo insulator SmB$_6$ is one of the most promising candidates, with theoretically predicted heavy Dirac surface states supported by transport and scanning tunneling microscopy (STM) experiments. However, a puzzling discrepancy appears between STM and angle-resolved photoemission (ARPES) experiments on SmB$_6$. Although ARPES detects spin-textured surface states, their velocity is an order of magnitude higher than expected, while the Dirac point -- the hallmark of any topological system -- can only be inferred deep within the bulk valence band. A significant challenge is that SmB$_6$ lacks a natural cleavage plane, resulting in ordered surface domains limited to 10s of nanometers. Here we use STM to show that surface band bending can shift energy features by 10s of meV between domains. Starting from our STM spectra, we simulate the full spectral function as an average over multiple domains with different surface potentials. Our simulation shows excellent agreement with ARPES data, and thus resolves the apparent discrepancy between large-area measurements that average over multiple band-shifted domains and atomically-resolved measurements within a single domain.

cond-mat.str-el↗

arXiv2019

Surface-dominated Conductivity of Few-layered Antimonene

We present a theoretical study of the phase-coherent DC conductivity of few-layered antimonene in the presence of surface disorder. It is well known that while a single layer is a trivial semiconductor, multiple layers (typically a minimum of $\approx$ 7) turn into a semi-metal with a nontrivial topological invariant featuring protected and decoupled surface states. We employ the finite-size Kubo formalism based on density functional theory calculations to show that the conductivity is amply dominated by the topological surface states even without bulk disorder. More importantly, the conductivity of the surface states does not show traces of a metal-insulator transition while the bulk ones can be driven towards an insulating phase in presence of only surface disorder. These results suggest that few-layered antimonene, despite not being insulating in the bulk, can present many of the advantages attributed to topological insulators under very general experimental conditions.

cond-mat.mes-hall↗

arXiv2019

Laser-beam patterned topological insulating states on thin semiconducting MoS2

Identifying the two-dimensional (2D) topological insulating (TI) state in new materials and its control are crucial aspects towards the development of voltage-controlled spintronic devices with low power dissipation. Members of the 2D transition metal dichalcogenides (TMDCs) have been recently predicted and experimentally reported as a new class of 2D TI materials, but in most cases edge conduction seems fragile and limited to the monolayer phase fabricated on specified substrates. Here, we realize the controlled patterning of the 1T'-phase embedded into the 2H-phase of thin semiconducting molybdenum-disulfide (MoS2) by laser beam irradiation. Integer fractions of the quantum of resistance, the dependence on laser-irradiation conditions, magnetic field, and temperature, as well as the bulk gap observation by scanning tunneling spectroscopy and theoretical calculations indicate the presence of the quantum spin Hall phase in our patterned 1T' phases.

cond-mat.mes-hall↗

arXiv2019

Directional bonding explains high conductance values of atomic contacts in bcc metals

Atomic-sized junctions of iron, created by controlled rupture, present unusually high values of conductance compared to other metals. This result is counter-intuitive since, at the nanoscale, body-centered cubic metals are expected to exhibit lower coordination than face-centered cubic metals. In this work, classical molecular dynamics simulations of contact rupture, using an interatomic potential that accounts for directional bonding, yield highly-coordinated stable structures before rupture, unlike an isotropic bonding potential, which results in the expected stable single-atom contacts. Density functional theory electronic transport calculations show that conductance values of these highly coordinated and highly stable structures, can explain the experimentally measured values for conductance of body-centered cubic atomic contacts, thus revealing the important role of directional bonding in these metals.

cond-mat.mes-hall↗

arXiv2019

Quenching of exciton recombination in strained two-dimensional monochalcogenides

We predict that long-lived excitons with very large binding energies can also exist in a single or few layers of monochalcogenides such as GaSe. Our theoretical study shows that excitons confined by a radial local strain field are unable to recombine despite of electrons and holes co-existing in space. The localized single-particle states are calculated in the envelope function approximation based on a three-band $\boldsymbol{k}\cdot \boldsymbol{p}$ Hamiltonian obtained from DFT calculations. The binding energy and the decay rate of the exciton ground state are computed after including correlations in the basis of electron-hole pairs. The interplay between the localized strain and the caldera-type valence band, characteristic of few-layered monochalcogenides, creates localized electron and hole states with very different quantum numbers which hinders the recombination even for singlet excitons.

cond-mat.mes-hall↗