Multi-scale modeling of 2D GaSe FETs with strained channels.

Electronic devices based on bidimensional materials (2DMs) are the subject of an intense experimental research, that demands a tantamount theoretical activity. The latter must be hold up by a varied set of tools able to rationalize, explain and predict the operation principles of the devices. However, in the broad context of multi-scale computational nanoelectronics, there is currently a lack of simulation tools connecting atomistic descriptions with semi-classical mesoscopic device-level simulations and able to properly explain the performance of many state-of-the-art devices. To contribute to filling this gap we present a multi-scale approach that combines fine-level material calculations with a semi-classical drift-diffusion transport model. Its use is exemplified by assessing 2DM field effect transistors with strained channels, showing excellent capabilities to capture the changes in the crystal structure and their impact into the device performance. Interestingly, we verify the capacity of strain in monolayer GaSe to enhance the conduction of one type of carrier, enabling the possibility to mimic the effect of chemical doping on 2D materials. These results illustrate the great potential of the proposed approach to bridge levels of abstraction rarely connected before and thus contribute to the theoretical modeling of state-of-the-art 2DM-based devices.

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 electrons and holes coexisting in space. The localized single-particle states are calculated in the envelope function approximation based on a three-band k·p Hamiltonian obtained from density-functional-theory 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.

Laser-Beam-Patterned Topological Insulating States on Thin Semiconducting MoS_{2}.

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 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 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.

Graphene flakes obtained by local electro-exfoliation of graphite with a STM tip.

Graphite surfaces can be manipulated by several methods to create graphene structures of different shapes and sizes. Scanning tunneling microscopy (STM) can be used to create these structures either through mechanical contact between the tip and the surface or through electro-exfoliation. In the latter, the mechanisms involved in the process of exfoliation at an applied voltage are not fully understood. Here, we show how a graphite surface can be locally exfoliated in a systematic manner by applying an electrostatic force with a STM tip at the edge of a terrace, forming triangular flakes several nanometers in length. We demonstrate, through experiments and simulations, how these flakes are created by a two-step process: first a voltage ramp must be applied at the edge of the terrace, and then the tip must be scanned perpendicular to the edge. Ab initio electrostatic calculations reveal that the presence of charges on the graphite surface weakens the interaction between layers allowing for exfoliation at voltages in the same range as those used experimentally. Molecular dynamics simulations show that a force applied locally on the edge of a step produces triangular flakes such as those observed under STM. Our results provide new insights into surface modification that can be extended to other layered materials.

Topologically protected quantum transport in locally exfoliated bismuth at room temperature.

We report electrical conductance measurements of Bi nanocontacts created by repeated tip-surface indentation using a scanning tunneling microscope at temperatures of 4 and 300 K. As a function of the elongation of the nanocontact, we measure robust, tens of nanometers long plateaus of conductance G0 = 2e2/h at room temperature. This observation can be accounted for by the mechanical exfoliation of a Bi(111) bilayer, a predicted quantum spin Hall (QSH) insulator, in the retracing process following a tip-surface contact. The formation of the bilayer is further supported by the additional observation of conductance steps below G0 before breakup at both temperatures. Our finding provides the first experimental evidence of the possibility of mechanical exfoliation of Bi bilayers, the existence of the QSH phase in a two-dimensional crystal, and, most importantly, the observation of the QSH phase at room temperature.

Nonequilibrium Magneto-Conductance as a Manifestation of Spin Filtering in Chiral Nanojunctions.

It is generally accepted that spin-dependent electron transmission may appear in chiral systems, even without magnetic components, as long as significant spin-orbit coupling is present in some of its elements. However, how this chirality-induced spin selectivity (CISS) manifests in experiments, where the system is taken out of equilibrium, is still debated. Aided by group theoretical considerations and nonequilibrium DFT-based quantum transport calculations, here we show that when spatial symmetries that forbid a finite spin polarization in equilibrium are broken, a net spin accumulation appears at finite bias in an arbitrary two-terminal nanojunction. Furthermore, when a suitably magnetized detector is introduced into 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, hence establishing an interconnection between these quantities.

Shift Current with Gaussian Basis Sets and 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-wave 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 us to reduce computation time and unveiling the complete symmetry properties of the conductivity tensor under general light polarization.

A Group-Theoretic Approach to the Origin of Chirality-Induced Spin-Selectivity in Nonmagnetic Molecular Junctions.

Spin-orbit coupling gives rise to a range of spin-charge interconversion phenomena in nonmagnetic 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 nonmagnetic 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 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.

Reversible change of the spin state in a manganese phthalocyanine by coordination of CO molecule.

We show that the magnetic state of individual manganese phthalocyanine (MnPc) molecules on a Bi(110) surface is modified when the Mn2+ center coordinates to CO molecules adsorbed on top. Using scanning tunneling spectroscopy we identified this change in magnetic properties from the broadening of a Kondo-related zero-bias anomaly when the CO-MnPc complex is formed. The original magnetic state can be recovered by selective desorption of individual CO molecules. First principles calculations show that the CO molecule reduces the spin of the adsorbed MnPc from S=1 to S=1/2 and strongly modifies the respective screening channels, driving a transition from an underscreened Kondo state to a state of mixed valence.

Mechanical annealing of metallic electrodes at the atomic scale.

The process of creating an atomically defined and robust metallic tip is described and quantified using measurements of contact conductance between gold electrodes and numerical simulations. Our experiments show how the same conductance behavior can be obtained for hundreds of cycles of formation and rupture of the nanocontact by limiting the indentation depth between the two electrodes up to a conductance value of approximately 5G0 in the case of gold. This phenomenon is rationalized using molecular dynamics simulations together with density functional theory transport calculations which show how, after repeated indentations (mechanical annealing), the two metallic electrodes are shaped into tips of reproducible structure. These results provide a crucial insight into fundamental aspects relevant to nanotribology or scanning probe microscopies.

Critical comparison of electrode models in density functional theory based quantum transport calculations.

We study the performance of two different electrode models in quantum transport calculations based on density functional theory: parametrized Bethe lattices and quasi-one-dimensional wires or nanowires. A detailed account of implementation details in both the cases is given. From the systematic study of nanocontacts made of representative metallic elements, we can conclude that the parametrized electrode models represent an excellent compromise between computational cost and electronic structure definition as long as the aim is to compare with experiments where the precise atomic structure of the electrodes is not relevant or defined with precision. The results obtained using parametrized Bethe lattices are essentially similar to the ones obtained with quasi-one-dimensional electrodes for large enough cross-sections of these, adding a natural smearing to the transmission curves that mimics the true nature of polycrystalline electrodes. The latter are more demanding from the computational point of view, but present the advantage of expanding the range of applicability of transport calculations to situations where the electrodes have a well-defined atomic structure, as is the case for carbon nanotubes, graphene nanoribbons, or semiconducting nanowires. All the analysis is done with the help of codes developed by the authors which can be found in the quantum transport toolbox ALACANT and are publicly available.

Spin-transfer torque on a single magnetic adatom.

We theoretically show how the spin orientation of a single magnetic adatom can be controlled by spin polarized electrons in a scanning tunneling microscope configuration. The underlying physical mechanism is spin assisted inelastic tunneling. By changing the direction of the applied current, the orientation of the magnetic adatom can be completely reversed on a time scale that ranges from a few nanoseconds to microseconds, depending on bias and temperature. The changes in the adatom magnetization direction are, in turn, reflected in the tunneling conductance.

[Traumatic spondyloptosis C7-T1 without neurologic deficit]. / Espondiloptosis traumática C7-T1 sin compromiso neurológico.

Traumatic spondyloptosis is a serious injury usually caused by high-energy trauma; It consists of the anterior or posterior dislocation of 100% or more of the underlying vertebral body, which can become a total injury of the spinal cord, producing a neurological deficit; this type of injury represents stage 4 and 5 of Allen-Ferguson. Clinical case: A 50-year-old man who suffers a car accident, he receive frontal impact when he was a driver, colliding with the retaining wall, referred from another hospital to emergency room, managed with C7 hemicorpectomy, c7-t1 discectomy, spondylodesis with anterior plate (C6-T1), and posterior approach + Fascetectomies of C7-T1, facet joint screws C6 and transpedicular fixation of T1. Discussion: Subaxial cervical spondyloptosis is relatively rare clinical entity, a complete clinical examination is important in diagnosis, taking in considerations the injury mechanism. For treatment we have a multiple options, at this case anterior-posterior (360 degrees) treatment it was the better option for Us; however, must be personalized and consider the early rehabilitation of patient.

La espondiloptosis traumática es una lesión muy rara y grave generalmente causada por traumatismos de alta energía. Consiste en la dislocación anterior o posterior de 100% o más al cuerpo vertebral subyacente, lo que puede generar compresión y lesión total de la médula espinal, produciendo déficit neurológico; este tipo de lesión representa la etapa 4 y 5 de Allen. Caso clínico: Masculino de 50 años quien sufre accidente automovilístico al colisionar contra muro de contención, generándose lesión de tipo hiperextensión-compresión cervicotorácica, manejado con hemicorpectomía C7, discectomía C7-T1, espondilodesis con placa anterior (C6-C7, C7-T1), toma y aplicación de injerto, abordaje posterior + fascetectomías de C7 + fijación transfacetaria C6 y transpedicular de T1. Discusión: Encontramos que la estabilización temprana con pinza de Gardner más el abordaje anterior y posterior brindan adecuados resultados en cuanto a integridad sensitiva y motora del paciente así como una pronta rehabilitación.

Simple STM tip functionalization for rapid DNA sequencing: an Ab initio Green's function study.

An ab initio nonequilibrium Green's function study of the electron-transport properties of the adenine, thymine, cytosine, and guanine DNA bases located between gold electrodes has been performed. One-electron transmission spectra were calculated for both gold and sulfur-modified gold electrodes, which are model conditions of scanning tunneling microscopy (STM) experiments with the different tips. It is shown that the nature of chemical bonding between molecules and metal electrodes plays the most significant role in the overall conductance of the systems. The distance between electrodes and the size of molecules are less important, at least when both sides of the molecule form chemical contact with the electrodes. On the basis of the obtained results, a simple two-pass DNA sequencing scheme is suggested.

An implementation of spin-orbit coupling for band structure calculations with Gaussian basis sets: Two-dimensional topological crystals of Sb and Bi.

We present an implementation of spin-orbit coupling (SOC) for density functional theory band structure calculations that makes use of Gaussian basis sets. It is based on the explicit evaluation of SOC matrix elements, both the radial and angular parts. For all-electron basis sets, where the full nodal structure is present in the basis elements, the results are in good agreement with well-established implementations such as VASP. For more practical pseudopotential basis sets, which lack nodal structure, an ad-hoc increase of the effective nuclear potential helps to capture all relevant band structure variations induced by SOC. In this work, the non-relativistic or scalar-relativistic Kohn-Sham Hamiltonian is obtained from the CRYSTAL code and the SOC term is added a posteriori. As an example, we apply this method to the Bi(111) monolayer, a paradigmatic 2D topological insulator, and to mono- and multilayer Sb(111) (also known as antimonene), the former being a trivial semiconductor and the latter a topological semimetal featuring topologically protected surface states.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry.

BACKGROUND: The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS. AIMS: The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results. SOURCES: Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed. CONTENT: Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided. IMPLICATIONS: Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner.

Franckeite as a naturally occurring van der Waals heterostructure.

The fabrication of van der Waals heterostructures, artificial materials assembled by individual stacking of 2D layers, is among the most promising directions in 2D materials research. Until now, the most widespread approach to stack 2D layers relies on deterministic placement methods, which are cumbersome and tend to suffer from poor control over the lattice orientations and the presence of unwanted interlayer adsorbates. Here, we present a different approach to fabricate ultrathin heterostructures by exfoliation of bulk franckeite which is a naturally occurring and air stable van der Waals heterostructure (composed of alternating SnS2-like and PbS-like layers stacked on top of each other). Presenting both an attractive narrow bandgap (<0.7 eV) and p-type doping, we find that the material can be exfoliated both mechanically and chemically down to few-layer thicknesses. We present extensive theoretical and experimental characterizations of the material's electronic properties and crystal structure, and explore applications for near-infrared photodetectors.

Diagnostic accuracy of the Xpert® MTB/RIF cycle threshold level to predict smear positivity: a meta-analysis.

SETTING: Xpert® MTB/RIF is the most widely used molecular assay for rapid diagnosis of tuberculosis (TB). The number of polymerase chain reaction cycles after which detectable product is generated (cycle threshold value, CT) correlates with the bacillary burden.OBJECTIVE To investigate the association between Xpert CT values and smear status through a systematic review and individual-level data meta-analysis. DESIGN: Studies on the association between CT values and smear status were included in a descriptive systematic review. Authors of studies including smear, culture and Xpert results were asked for individual-level data, and receiver operating characteristic curves were calculated. RESULTS: Of 918 citations, 10 were included in the descriptive systematic review. Fifteen data sets from studies potentially relevant for individual-level data meta-analysis provided individual-level data (7511 samples from 4447 patients); 1212 patients had positive Xpert results for at least one respiratory sample (1859 samples overall). ROC analysis revealed an area under the curve (AUC) of 0.85 (95%CI 0.82-0.87). Cut-off CT values of 27.7 and 31.8 yielded sensitivities of 85% (95%CI 83-87) and 95% (95%CI 94-96) and specificities of 67% (95%CI 66-77) and 35% (95%CI 30-41) for smear-positive samples. CONCLUSION: Xpert CT values and smear status were strongly associated. However, diagnostic accuracy at set cut-off CT values of 27.7 or 31.8 would not replace smear microscopy. How CT values compare with smear microscopy in predicting infectiousness remains to be seen.

Microsatellite alterations at 5q21, 11p13, and 11p15.5 do not predict survival in non-small cell lung cancer.

We investigated the clinical implications of allelic deletions at three common sites of loss of heterozygosity (LOH) in regions 5q21, 11p15.5, and 11p13 in 86 patients with non-small cell lung cancer (NSCLC). We performed a PCR-based microsatellite polymorphism assay for detection of LOH. The microsatellite markers used were D5S82 (proximal to the APC gene), MCC (within the MCC gene), D11S904 (11p13), HRAS (within the H-ras gene), and D11S860 (11p15.5). Of the 68 informative cases at 5q21 loci, LOH was found in 14 cases (20%), whereas LOH frequency in 11p15.5 and 11p13 was 31% (19 of 61 informative cases) and 19% (12 of 63 informative cases), respectively. There was a significant correlation between 5q21 LOH and mediastinal lymph node involvement (P = 0.03). However, no differences were observed in median survival times (26 months in patients with 5q21 LOH versus 37 months in the remainder; P = 0.33) nor in patients with 11p LOH (38 months versus 32 months, respectively; P = 0.72). Cox's proportional hazards model predicted that stage was the only independent poor prognostic marker in the entire cohort of NSCLC patients. Thus, the present study revealed two important abnormalities, LOH at chromosome 5q21 and LOH at chromosome 11p, both implied in NSCLC development.

Revealing hidden clonal complexity in Mycobacterium tuberculosis infection by qualitative and quantitative improvement of sampling.

The analysis of microevolution events, its functional relevance and impact on molecular epidemiology strategies, constitutes one of the most challenging aspects of the study of clonal complexity in infection by Mycobacterium tuberculosis. In this study, we retrospectively evaluated whether two improved sampling schemes could provide access to the clonal complexity that is undetected by the current standards (analysis of one isolate from one sputum). We evaluated in 48 patients the analysis by mycobacterial interspersed repetitive unit-variable number tandem repeat of M. tuberculosis isolates cultured from bronchial aspirate (BAS) or bronchoalveolar lavage (BAL) and, in another 16 cases, the analysis of a higher number of isolates from independent sputum samples. Analysis of the isolates from BAS/BAL specimens revealed clonal complexity in a very high proportion of cases (5/48); in most of these cases, complexity was not detected when the isolates from sputum samples were analysed. Systematic analysis of isolates from multiple sputum samples also improved the detection of clonal complexity. We found coexisting clonal variants in two of 16 cases that would have gone undetected in the analysis of the isolate from a single sputum specimen. Our results suggest that analysis of isolates from BAS/BAL specimens is highly efficient for recording the true clonal composition of M. tuberculosis in the lungs. When these samples are not available, we recommend increasing the number of isolates from independent sputum specimens, because they might not harbour the same pool of bacteria. Our data suggest that the degree of clonal complexity in tuberculosis has been underestimated because of the deficiencies inherent in a simplified procedure.