Theory of the scanning tunneling microscope: Xe on Ni and Al

Microstructure investigation of plant architecture with X-ray microscopy

In recent years, the plant morphology has been well studied by multiple approaches at cellular and subcellular levels. Two-dimensional (2D) microscopy techniques offer imaging of plant structures on a wide range of magnifications for researchers. However, subcellular imaging is still challenging in plant tissues like roots and seeds. Here we use a three-dimensional (3D) imaging technology based on the X-ray microscope (XRM) and analyze several plant tissues from different plant species. The XRM provides new insights into plant structures using non-destructive imaging at high-resolution and high contrast. We also utilized a workflow aiming to acquire accurate and high-quality images in the context of the whole specimen. Multiple plant samples including rice, tobacco, Arabidopsis and maize were used to display the differences of phenotypes. Our work indicates that the XRM is a powerful tool to investigate plant microstructure in high-resolution scale. Our work also provides evidence that evaluate and quantify tissue specific differences for a range of plant species. We also characterize novel plant tissue phenotypes by the XRM, such as seeds in Arabidopsis, and utilize them for novel observation measurement. Our work represents an evaluated spatial and temporal resolution solution on seed observation and screening.

2D vertical field-effect transistor

Within the framework of 2D materials, we present four theoretical models of a vertical field-effect transistor (FET) composed of simple alternate graphene and MoS₂ layers. The electronic transport properties at a specific graphene/MoS₂ interface in each configuration are investigated by focusing in particular on the current as a function of the gate voltage. The gate voltage, simulated with a shift of the bands of a specific layer, allows us to tune the current at the interface and the charge transfer between the planes. This analysis of the charge transfer as a function of the gate voltage reveals a strong connection with the transport characteristics as the slope of the current curve. The analysis of physical phenomena at the graphene/MoS₂ interface can further improve the 2D vertical FET performance and contribute to the development of new 2D nanotechnology.

Weakly Trapped, Charged, and Free Excitons in Single-Layer MoS2 in the Presence of Defects, Strain, and Charged Impurities

Few- and single-layer MoS₂ host substantial densities of defects. They are thought to influence the doping level, the crystal structure, and the binding of electron-hole pairs. We disentangle the concomitant spectroscopic expression of all three effects and identify to what extent they are intrinsic to the material or extrinsic to it, i.e., related to its local environment. We do so by using different sources of MoS₂-a natural one and one prepared at high pressure and high temperature-and different substrates bringing varying amounts of charged impurities and by separating the contributions of internal strain and doping in Raman spectra. Photoluminescence unveils various optically active excitonic complexes. We discover a defect-bound state having a low binding energy of 20 meV that does not appear sensitive to strain and doping, unlike charged excitons. Conversely, the defect does not significantly dope or strain MoS₂. Scanning tunneling microscopy and density functional theory simulations point to substitutional atoms, presumably individual nitrogen atoms at the sulfur site. Our work shows the way to a systematic understanding of the effect of external and internal fields on the optical properties of two-dimensional materials.

High resolution SPM imaging of organic molecules with functionalized tips

One of the most remarkable and exciting achievements in the field of scanning probe microscopy (SPM) in the last years is the unprecedented sub-molecular resolution of both atomic and electronic structures of single molecules deposited on solid state surfaces. Despite its youth, the technique has already brought many new possibilities to perform different kinds of measurements, which cannot be accomplished by other techniques. This opens new perspectives in advanced characterization of physical and chemical processes and properties of molecular structures on surfaces. Here, we discuss the history and recent progress of the high resolution imaging with a functionalized probe by means of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and inelastic electron tunneling spectroscopy (IETS). We describe the mechanisms responsible for the high-resolution AFM, STM and IETS-STM contrast. The complexity of this technique requires new theoretical approaches, where a relaxation of the functionalized probe is considered. We emphasise the similarities of the mechanism driving high-resolution SPM with other imaging methods. We also summarise briefly significant achievements and progress in different branches. Finally we provide brief perspectives and remaining challenges of the further refinement of these high-resolution methods.

Theoretical characterisation of point defects on a MoS2 monolayer by scanning tunnelling microscopy

Different S and Mo vacancies as well as their corresponding antisite defects in a free-standing MoS2 monolayer are analysed by means of scanning tunnelling microscopy (STM) simulations. Our theoretical methodology, based on the Keldysh nonequilibrium Green function formalism within the density functional theory (DFT) approach, is applied to simulate STM images for different voltages and tip heights. Combining the geometrical and electronic effects, all features of the different STM images can be explained, providing a valuable guide for future experiments. Our results confirm previous reports on S atom imaging, but also reveal a strong dependence on the applied bias for vacancies and antisite defects that include extra S atoms. By contrast, when additional Mo atoms cover the S vacancies, the MoS2 gap vanishes and a bias-independent bright protrusion is obtained in the STM image. Finally, we show that the inclusion of these point defects promotes the emergence of reactive dangling bonds that may act as efficient adsorption sites for external adsorbates.

Theoretical study of carbon-based tips for scanning tunnelling microscopy

Motivated by recent experiments, we present here a detailed theoretical analysis of the use of carbon-based conductive tips in scanning tunnelling microscopy. In particular, we employ ab initio methods based on density functional theory to explore a graphitic, an amorphous carbon and two diamond-like tips for imaging with a scanning tunnelling microscope (STM), and we compare them with standard metallic tips made of gold and tungsten. We investigate the performance of these tips in terms of the corrugation of the STM images acquired when scanning a single graphene sheet. Moreover, we analyse the impact of the tip-sample distance and show that it plays a fundamental role in the resolution and symmetry of the STM images. We also explore in depth how the adsorption of single atoms and molecules in the tip apexes modifies the STM images and demonstrate that, in general, it leads to an improved image resolution. The ensemble of our results provides strong evidence that carbon-based tips can significantly improve the resolution of STM images, as compared to more standard metallic tips, which may open a new line of research in scanning tunnelling microscopy.

Submolecular Imaging by Noncontact Atomic Force Microscopy with an Oxygen Atom Rigidly Connected to a Metallic Probe

In scanning probe microscopy, the imaging characteristics in the various interaction channels crucially depend on the chemical termination of the probe tip. Here we analyze the contrast signatures of an oxygen-terminated copper tip with a tetrahedral configuration of the covalently bound terminal O atom. Supported by first-principles calculations we show how this tip termination can be identified by contrast analysis in noncontact atomic force and scanning tunneling microscopy (NC-AFM, STM) on a partially oxidized Cu(110) surface. After controlled tip functionalization by soft indentations of only a few angstroms in an oxide nanodomain, we demonstrate that this tip allows imaging an organic molecule adsorbed on Cu(110) by constant-height NC-AFM in the repulsive force regime, revealing its internal bond structure. In established tip functionalization approaches where, for example, CO or Xe is deliberately picked up from a surface, these probe particles are only weakly bound to the metallic tip, leading to lateral deflections during scanning. Therefore, the contrast mechanism is subject to image distortions, artifacts, and related controversies. In contrast, our simulations for the O-terminated Cu tip show that lateral deflections of the terminating O atom are negligible. This allows a detailed discussion of the fundamental imaging mechanisms in high-resolution NC-AFM experiments. With its structural rigidity, its chemically passivated state, and a high electron density at the apex, we identify the main characteristics of the O-terminated Cu tip, making it a highly attractive complementary probe for the characterization of organic nanostructures on surfaces.

Contrast stability and 'stripe' formation in scanning tunnelling microscopy imaging of highly oriented pyrolytic graphite: the role of STM-tip orientations

Highly oriented pyrolytic graphite (HOPG) is an important substrate in many technological applications and is routinely used as a standard in Scanning Tunnelling Microscopy (STM) calibration, which makes the accurate interpretation of the HOPG STM contrast of great fundamental and applicative importance. We demonstrate by STM simulations based on electronic structure obtained from first principles that the relative local orientation of the STM-tip apex with respect to the HOPG substrate has a considerable effect on the HOPG STM contrast. Importantly for experimental STM analysis of HOPG, the simulations indicate that local tip-rotations maintaining a major contribution of the d(3z(2)-r(2)) tip-apex state to the STM current affect only the secondary features of the HOPG STM contrast resulting in 'stripe' formation and leaving the primary contrast unaltered. Conversely, tip-rotations leading to enhanced contributions from m ≠ 0 tip-apex electronic states can cause a triangular-hexagonal change in the primary contrast. We also report a comparison of two STM simulation models with experiments in terms of bias-voltage-dependent STM topography brightness correlations and discuss our findings for the HOPG(0 0 0 1) surface in combination with tungsten tip models of different sharpnesses and terminations.

Understanding scanning tunneling microscopy contrast mechanisms on metal oxides: a case study

A comprehensive analysis of contrast formation mechanisms in scanning tunneling microscopy (STM) experiments on a metal oxide surface is presented with the oxygen-induced (2√2×√2)R45° missing row reconstruction of the Cu(100) surface as a model system. Density functional theory and electronic transport calculations were combined to simulate the STM imaging behavior of pure and oxygen-contaminated metal tips with structurally and chemically different apexes while systematically varying bias voltage and tip-sample distance. The resulting multiparameter database of computed images was used to conduct an extensive comparison with experimental data. Excellent agreement was attained for a large number of cases, suggesting that the assumed model tips reproduce most of the commonly encountered contrast-determining effects. Specifically, we find that depending on the bias voltage polarity, copper-terminated tips allow selective imaging of two structurally distinct surface Cu sites, while oxygen-terminated tips show complex contrasts with pronounced asymmetry and tip-sample distance dependence. Considering the structural and chemical stability of the tips reveals that the copper-terminated apexes tend to react with surface oxygen at small tip-sample distances. In contrast, oxygen-terminated tips are considerably more stable, allowing exclusive surface oxygen imaging at small tip-sample distances. Our results provide a conclusive understanding of fundamental STM imaging mechanisms, thereby providing guidelines for experimentalists to achieve chemically selective imaging by properly selecting imaging parameters.

Arbitrary tip orientation in STM simulations: 3D WKB theory and application to W(110)

We extend the orbital-dependent electron tunnelling model implemented within the three-dimensional (3D) Wentzel-Kramers-Brillouin (WKB) atom-superposition approach for simulating scanning tunnelling microscopy (STM) by including arbitrary tip orientations. The orientation of the tip is characterized by a local coordinate system centred on the tip apex atom obtained by a rotation with respect to the sample coordinate system. The rotation is described by the Euler angles. Applying our method, we highlight the role of the real-space shape of the electron orbitals involved in the tunnelling, and analyse the convergence and the orbital contributions of the tunnelling current above the W(110) surface depending on the orientation of a model tungsten tip. We also simulate STM images at constant-current condition, and find that their quality depends very much on the tip orientation. Some orientations result in protrusions on the images that do not occur above W atoms. The presence of such apparent atom positions makes it difficult to identify the exact position of surface atoms. It is suggested that this tip orientation effect should be considered in the evaluation of experimental STM images on other surfaces as well. The presented computationally efficient tunnelling model could prove to be useful for obtaining more information on the local tip geometry and orientation by comparing STM experiments to a large number of simulations with systematically varied tip orientations.

Tailoring structural and electronic properties of RuO2 nanotubes: a many-body approach and electronic transport

The electrical conduction properties of ruthenium oxide nanocables are of high interest. These cables can be built as thin shells of RuO2 surrounding an inner solid nanowire of a dielectric insulating silica material. With this motivation we have investigated the structural, electronic and transport properties of RuO2 nanotubes using the density functional formalism, and applying many-body corrections to the electronic band structure. The structures obtained for the thinnest nanotubes are of the rutile type. The structures of nanotubes with larger diameters deviate from the rutile structure and have in common the formation of dimerized Ru-Ru rows along the axial direction. The cohesive energy shows an oscillating behavior as a function of the tube diameter. With the exception of the thinnest nanotubes, there is a correlation such that the electronic band structures of tubes with high cohesive energies show small gaps at the Fermi energy, whereas the less stable nanotubes exhibit metallic behavior, with bands crossing the Fermi surface. The electronic conductance of nanotubes of finite length connected to gold electrodes has been calculated using a Green-function formalism, and correlations have been established between the electronic band structure and the conductance at zero bias.

Relation between the chemical force and the tunnelling current in atomic point contacts: a simple model

The relation between the tunnelling current I(t) and the interaction energy/force E in an atomic-scale contact is discussed in the framework of a theoretical model established here. According to our model, we predict the existence of two characteristic scaling regimes, where the tunnelling current is either proportional to the interaction energy, I(t) ~ E, or to the square of the interaction energy, I(t) ~ E(2). We show that the existence of a given regime is basically controlled by two parameters: (i) the energy degeneracy Δ and (ii) the hopping t between electronic levels involved in the interaction process. In addition, we discuss the validity of the Bardeen method to determine the tunnelling current in the short tip-sample distances.

Reversal of atomic contrast in scanning probe microscopy on (111) metal surfaces

We study the origin of atomic contrast on Cu(111) and Pt(111) surfaces probed by a non-contact atomic force microscope and scanning tunnelling microscope. First-principles simulations of the interaction between the atoms of the scanning tip and those of the probed surface show a dependence of the resulting contrast on the tip-sample distance and reveal a close relation between contrast changes and relaxation of atomic positions in both the tip and the sample. Contrast reversion around the distance where the short-range attractive atomic force reaches its maximum is predicted for both types of microscopies. We also demonstrate a relation between the maximal attractive force in a F-z atomic force spectroscopy and the chemical identity of the apex atom on the imaging tip.

Understanding atomic-resolved STM images on TiO2(110)-(1 x 1) surface by DFT calculations

We present a combination of experimental STM images and DFT calculations to understand the atomic scale contrast of features found in high-resolution STM images. Simulating different plausible structural models for the tip, we have been able to reproduce various characteristics previously reported in experimental images on TiO(2)(110)-(1 x 1) under controlled UHV conditions. Our results allow us to determine the influence of different chemical and morphological tip terminations on the atomic-resolution STM images of the TiO(2)(110)-(1 x 1) surface. The commonest images have been properly explained using standard models for a W tip, either clean or with a single O atom located at the apex. Furthermore, a double transfer of oxygen atoms can account for different types of bizarre atomic-resolution features occasionally seen, and not conclusively interpreted before. Importantly, we discuss how typical point-defects are imaged on this surface by different tips, namely bridging O vacancies and adsorbed OH groups.

Theoretical study of electronic and transport properties of PPy-Pt(111) and PPy-C(111):H interfaces

We present a first-principles study of promising hybrid organic-inorganic interface systems consisting of a polypyrrole (PPy) chain sandwiched between metallic Pt(111) or hydrogen-terminated diamond C(111):H electrodes. We combine ab initio density-functional-theory total energy calculations, Green's function approach and the complex band-structure method in order to determine electronic and transport properties of those organic-semiconductor/metal (semiconductor) interfaces. We analyze one- and multi-bond nanocontact formation including structural modification (H desorption) as well as PPy length dependence. For selected ground state configurations of the considered interface systems we study their energetics and structural properties. Through the analysis of the local density of states, in particular isosurfaces of the charge density, the mechanism of the charge transfer and the charge neutrality levels are determined. The voltage dependence of the electrical conductance and the I-V characteristics are compared to the transport properties based on the complex band-structure method. The obtained results support recent experiments, where PPy nanowires are formed via electrochemical synthesis and placed between platinum or diamond microelectrodes.

Initial stages of the contact between a metallic tip and carbon nanotubes

We present an experimental and theoretical study of the interaction between a tip and single-walled carbon nanotubes (SWCNT) lying on a SiO2 surface. Adhesion and jump-to-contact forces (JC) are measured in a high vacuum system for SWCNT with diameters (D) ranging from 1.4 to 4.5 nm; we find adhesion forces approximately 3.2 nN and JC forces approximately 2.4 nN. Simulations yield adhesion forces in agreement with experiment showing that for D approximately 1.4 nm half of this force is due to tip-SWCNT and tip-SiO2 van der Waals interactions.

Mechanical and electrical properties of stretched clean and H-contaminated Pd-nanowires

We analyze theoretically the formation of stretched Pd-nanowires and their interaction with hydrogen. In our approach, we simulate the nanowire stretching process using a first-principles molecular-dynamics method to obtain realistic atomic geometries of the contact in its final stages before the nanowire breaks. The electrical conductance of the nanowire is also calculated at each point of the deformation path. For the clean Pd-nanowire in the last stages of the deformation process we find that the nanowire develops, first, a one-atom-neck and, at the end, a dimer whose bond is finally broken. For these atomic configurations, the calculated electrical conductances are in good agreement with the experimental evidence. The interaction with hydrogen is analyzed adsorbing one or two H atoms on the Pd-nanowire for different configurations along the stretching process. In the case of one H atom we obtain geometries with conductances in the range 0.8-1.4G(0), while for two H atoms we find conductance plateaus with values ∼0.5G(0) and ∼1.0G(0). These results are in excellent agreement with the experimental evidence for nanocontact breaking in an H(2) atmosphere and indicate that the conductance peak around 0.5G(0) observed experimentally is associated with nanowires where two H atoms have been adsorbed.

Scanning tunneling spectroscopy simulations of poly(3-dodecylthiophene) chains adsorbed on highly oriented pyrolytic graphite

We report on a hybrid scheme to perform efficient and accurate simulations of scanning tunneling spectroscopy (STS) of molecules weakly bonded to surfaces. Calculations are based on a tight binding (TB) technique, including a self-consistent calculation of the electronic structure of the molecule, to predict STS conductance spectra. The use of a local basis makes our model easily applicable to systems with several hundreds of atoms. We performed first-principles density-functional calculations to extract the geometrical and electronic properties of the system. In this way, we can include, in the TB scheme, the effects of structural relaxation upon adsorption on the electronic structure of the molecule. This approach is applied to the study of regioregular poly(3-dodecylthiophene) polymer chains adsorbed on highly oriented pyrolytic graphite. Results of spectroscopic calculations are discussed and compared with recently obtained experimental data.

Tuning the conductance of single-walled carbon nanotubes by ion irradiation in the Anderson localization regime

Carbon nanotubes are a good realization of one-dimensional crystals where basic science and potential nanodevice applications merge. Defects are known to modify the electrical resistance of carbon nanotubes; they can be present in as-grown carbon nanotubes, but controlling their density externally opens a path towards the tuning of the electronic characteristics of the nanotube. In this work, consecutive Ar+ irradiation doses are applied to single-walled nanotubes (SWNTs) producing a uniform density of defects. After each dose, the room-temperature resistance versus SWNT length (R(L)) along the nanotube is measured. Our data show an exponential dependence of R(L) indicating that the system is within the strong Anderson localization regime. Theoretical simulations demonstrate that mainly di-vacancies contribute to the resistance increase induced by irradiation, and that just a 0.03% of di-vacancies produces an increase of three orders of magnitude in the resistance of a SWNT of 400 nm length.

Formation of atom wires on vicinal silicon

The feasibility of creating atomic wires on vicinal silicon surfaces via pseudomorphic step-edge decoration has been analyzed for the case of Ga on Si(112). Scanning tunneling microscopy and density functional theory calculations indicate the formation of Ga zigzag chains intersected by quasiperiodic vacancy lines or "misfit dislocations." This structure strikes a balance between the system's drive towards chemical passivation and its need for strain relaxation in the atom chains. Spatially fluctuating disorder, intrinsic to the reconstruction, originates from the two symmetry-degenerate orientations of the zigzag chains on vicinal Si.