Simulated Scanning Tunneling Microscopy Research Articles

Electronic structure of the InP(111) $$A - \left( {\sqrt 3 \times \sqrt 3 } \right)$$ semiconductor surface

We present a first-principles theoretical study of the relative formation energies and the electronic states of the \(InP\left( {111} \right)A - \left( {\sqrt 3 \times \sqrt 3 } \right)\) surface. The energetically most favorable reconstruction has a T4-site P trimer on the surface, which exhibits a metallic band character and does not obey the electron counting rule (ECR). The stability of this structure is attributed to the balance between the ECR and the minimization of local distortion in the surface region. Our results for the simulated scanning tunneling microscopy images confirm the experimental interpretation of bright protrusions on the P trimers.

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 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.

Electronic properties of self-assembled trimesic acid monolayer on graphene.

The adsorption of trimesic acid (TMA) on a graphene surface has been studied with density functional theory. By considering the adsorption of a single TMA molecule on different sites on graphene, we have been able to perform a detailed analysis of the equilibrium geometry, charge transfer, electronic properties in terms of density of states and band structure, and finally scanning tunneling microscopy simulations on those simple systems. The results for isolated adsorption were then compared to the behavior of the TMA unit within two different self-assembled monolayers. Our results indicate that structural deformations of TMA may significantly contribute to the magnitude of p-doping and band gap opening in graphene. The formation of a hydrogen bonding network within the assembly improves the stability of the adlayer, but its adhesion on graphene is significantly reduced. The magnitude of p-doping in graphene per TMA unit remains nearly constant from the isolated to the assembled systems, but the magnitude of the band gap opening appears to be strongly correlated with the breaking of symmetry of π-states of graphene by the TMA patterning on the surface. Our results suggest that polymorphism in self-assembled adlayers could be used to tune and control the electronic properties of graphene.

Three-dimensional simulation of scanning tunneling microscopy for semiconductor carrier and impurity profiling

Scanning tunneling microscopy for semiconductor carrier profiling is simulated in three dimensions. By solving the tunnel currents between a probe tip and a sample consistently with the current continuity equations, current–voltage characteristics in good agreement with measurements are obtained. Critical differences from potential-based calculations are observed under depletion and inversion conditions. By preparing a current–concentration table from samples with uniform concentrations, the carrier profile in p-n junction samples can be extracted by estimating the concentrations at each position. It is revealed that the tunnel current is spread around the depletion region of a p-n junction, which affects the results dramatically. When a proposed simulation is iteratively used with measurements, impurity profile extraction is possible even in the depletion region.

Atomic imaging and modeling of H2O2(g) surface passivation, functionalization, and atomic layer deposition nucleation on the Ge(100) surface.

Passivation, functionalization, and atomic layer deposition nucleation via H2O2(g) and trimethylaluminum (TMA) dosing was studied on the clean Ge(100) surface at the atomic level using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). Chemical analysis of the surface was performed using x-ray photoelectron spectroscopy, while the bonding of the precursors to the substrate was modeled with density functional theory (DFT). At room temperature, a saturation dose of H2O2(g) produces a monolayer of a mixture of -OH or -O species bonded to the surface. STS confirms that H2O2(g) dosing eliminates half-filled dangling bonds on the clean Ge(100) surface. Saturation of the H2O2(g) dosed Ge(100) surface with TMA followed by a 200 °C anneal produces an ordered monolayer of thermally stable Ge-O-Al bonds. DFT models and STM simulations provide a consistent model of the bonding configuration of the H2O2(g) and TMA dosed surfaces. STS verifies the TMA/H2O2/Ge surface has an unpinned Fermi level with no states in the bandgap demonstrating the ability of a Ge-O-Al monolayer to serve as an ideal template for further high-k deposition.

Efficient Method for Fast Simulation of Scanning Tunneling Microscopy with a Tip Effect

On the basis of Bardeen's perturbation theory on electron tunneling and inspired by Paz et al.'s study, a new expression for the tunneling current between the scanning tunneling microscopy (STM) tip and sample has been obtained, and it provides us with an efficient method to simulate STM images. The method can be implemented in any code of first-principles computing software, which offers the wave functions of the tip and sample, calculated independently at the same footing, as input. By calculating the integral with fast Fourier transform (FFT), simulating the STM image of a given sample surface by a database of different tips on a PC turns out to be not a time-consuming work. Compared with Paz et al.'s method, our method abandons the application of the vacuum Green function and possesses better computing efficiency, fewer parameters, and more reasonable simulated results especially at lower computing cost. Simple tip-sample systems, such as H-H and Pd2-Ag2, are taken as benchmarks to test our method. The topographic images of a CO molecule adsorbed on a Cu(111) surface obtained by using a tungsten tip and a CO-terminated tip are also simulated, and the simulated results are in good agreement with the experimental ones.

Atomic structure and electronic properties of the In/Si(111)2×2 surface

The Si(111)2$\ifmmode\times\else\texttimes\fi{}$2-In reconstruction can be considered as a precursor phase for the formation of the metallic $\sqrt{7}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$ phases of In overlayers on a Si(111) surface. Using the ab initio random structure searching method, comparison of simulated and experimental scanning tunneling microscopy images, and resemblance of the calculated band structure to the experimental angle-resolved photoelectron spectra, we examined various 2$\phantom{\rule{0.16em}{0ex}}\ifmmode\times\else\texttimes\fi{}\phantom{\rule{0.16em}{0ex}}$2 structure models with 0.5, 0.75, 1.0, and 1.25 monolayer In coverage. The only model which fits well all the requirements is the one-monolayer model, where three In atoms in the ${T}_{4}$ sites form a trimer centered in the ${H}_{3}$ site and the fourth In atom occupies the on-top (${T}_{1}$) site.

Unveiling the mechanism of water partial dissociation on Ru(0001).

We have studied the mechanism of the partial dissociation of water on Ru(0001) by high resolution scanning tunneling microscopy (STM). The thermal evolution of water at submonolayer coverage has been tracked in the 110-145K temperature range to identify the precursor structures for the partial dissociation. These were found to consist of hexagons arranged in thin stripes aligned along the close packed Ru [21¯1¯0] directions. The partially dissociated phase, on the other hand, contains a mixture of H2O and OH hexagons arranged into wider stripes and rotated by 30° with respect to the intact water stripes. The atomic structure of both types of stripes is determined with the aid of density functional theory and STM simulations, providing insights into the partial dissociation reaction path. The reaction is found to be exothermic by around 0.4eV and initiating at the edges of the intact water stripes. Hydrogen atoms, from water dissociation or already present at the surface, are found to play an important role in the kinetics of the reactions.

Origin of symmetric STM images for the asymmetric atomic configuration on GaAs(001)–c(4 × 4)α surfaces

The empty-state scanning tunneling microscopy (STM) images of GaAs-c(4×4)α show symmetric features at positive biases, contrary to the naive prediction based on electron counting model. In this paper, we report that STM simulations based on first-principles electronic structure calculations successfully demonstrate symmetric images consistent with the STM observations. Furthermore, simple analysis has revealed that the origin of the symmetric images is the combined local electron density of multiple orbitals, and is essentially different from those on GaAs–c(4×4)β surfaces.

Bismuth-containing c(4 × 4) surface structure of the GaAs(1 0 0) studied by synchrotron-radiation photoelectron spectroscopy and ab initio calculations

Bismuth (Bi) induced c(4×4) surface structure of the GaAs(100) substrate, i.e., the GaAs(100)c(4×4)-Bi surface has been studied with synchrotron-radiation photoelectron spectroscopy and ab initio calculations. The surface was prepared by combining molecular beam epitaxy and in situ electron diffraction methods, and then the sample was transferred to a photoemission chamber without breaking ultrahigh vacuum conditions. Calculations show that the c(4×4)β type unit cells, which consist of Bi-Bi and Bi-As dimers, are energetically favored on the surface and that Bi atoms occupy only the topmost atomic sites bonding to the As layer below. The presence of the c(4×4)β structure is supported by the comparison of measured and calculated core-level shifts of the GaAs(100)c(4×4)-Bi surface. Simulated scanning-tunneling-microscopy (STM) images, based on the suggested models, are presented for the comparison with future STM measurements.

Topological domain walls and quantum valley Hall effects in silicene

Silicene is a two-dimensional honeycomb lattice made of silicon atoms, which is considered to be a new Dirac fermion system. Based on first-principles calculations, we examine the possibility of the formation of solitonlike topological domain walls (DWs) in silicene. We show that the DWs between regions of distinct ground states of the buckled geometry should bind electrons when a uniform electric field is applied in the perpendicular direction to the sheet. The topological origin of the electron confinement is demonstrated based on numerical calculations of the valley-specific Hall conductivities, and possible experimental signatures of the quantum valley Hall effects are discussed using simulated scanning tunneling microscopy images. Our results strongly suggest that silicene could be an ideal host for the quantum valley Hall effect, thus providing a pathway to the valleytronics in silicon-based technology.

Predicting the stability of surface phases of molybdenum selenides

The selenization of molybdenum might become an important step in the production of nanostructures based on the layered compound MoSe2. It is already technologically relevant for the production of thin film chalcopyrite solar cells. However, the control of the process is still very poor, due to the lack of basic knowledge of the surface thermodynamics of the system. Here, we present a theoretical study on the stability of surface adlayers of Se on the Mo(110) surface, predicting surface patterns and their stability range in terms of temperature and selenium partial pressure. Our results, based on density functional theory, show that the attainable Se coverages range from 1/4 to 3/4 of a monolayer for systems in equilibrium with a gas formed of Se molecules. We provide simulated scanning tunneling microscopy images to help the experimental characterization of adsorbed surface patterns.

Adsorption and dissociation of oxygen molecules on Si(111)-(7×7) surface

The adsorption and dissociation of O2 molecules on Si(111)-(7×7) surface have been studied by first-principles calculations. Our results show that all the O2 molecular species adsorbed on Si(111)-(7×7) surface are unstable and dissociate into atomic species with a small energy barrier about 0.1 eV. The single O2 molecule adsorption tends to form an ins×2 or a new metastable ins×2* structure on the Si adatom sites and the further coming O2 molecules adsorb on those structures to produce an ad-ins×3 structure. The ad-ins×3 structure is indeed highly stable and kinetically limited for diving into the subsurface layer to form the ins×3-tri structure by a large barrier of 1.3 eV. Unlike the previous views, we find that all the ad-ins, ins×2, and ad-ins×3 structures show bright images, while the ins×2*, ins×3, and ins×3-tri structures show dark images. The proposed oxidation pathways and simulated scanning tunneling microscope images account well for the experimental results and resolve the long-standing confusion and issue about the adsorption and reaction of O2 molecules on Si(111) surface.

Electronic and structural properties of nitrogen adsorbed Nb(100) surfaces: An ab initio study

We have performed an ab initio total energy investigation of the electronic and structural properties of nitrogen adsorbed Nb(100) surface, N/Nb(100). We find an energetic preference for the nitrogen adsorption on the hollow sites of the Nb(100) surface. Upon the presence of N adatoms, there is a reduction of the electronic density of states near the Fermi level. However, the metallic character of the Nb(100) surface has been maintained. The (occupied) electronic states of N adatoms are resonant within the valence band of Nb(100), mostly lying at 4 eV below the Fermi level. Further investigations reveal the formation of energetically stable N/Nb(100)–(n × 1) phase, being the (2 × 1), (5 × 1), and (10 × 1) the most likely ones. Those (n × 1) structures are composed by NbN stripes separated by N vacancy lines. Our scanning tunneling microscopy simulations indicate the formation of bright lines lying on the Nb atoms neighboring the (dark) N vacancy lines, giving rise to an anisotropic electronic structure on the N/Nb(100)–(n × 1) surface. That is, the metallic character of the surface has been strengthened along the vacancy-lines.

Structural Properties of Azobenzene Self-Assembled Monolayers by Atomistic Simulations

Azobenzene self-assembled monolayers (SAMs) are examples of optomechanical nanostructures capable of producing mechanical work through the well-known azobenzene photoisomerization process. Experimental studies have provided information on their structural properties, but an atomistic description of the SAMs in both the cis and trans forms is still lacking. In this work, a computational investigation of the SAM structures is conducted by classical molecular dynamics with a dedicated force. Experimental data on the SAM unit cell is used to set up SAM models of different molecular densities. The optimal structures are identified through the comparison with structural data from X-ray photoelectron and near-edge X-ray absorption fine structure spectroscopies. The resulting SAM atomistic models are validated by comparing simulated and experimental scanning tunneling microscopy images.

Topological insulator Bi2Se3(111) surface doped with transition metals: Anab initioinvestigation

Based on first-principles calculations, we provide a map of the energetic stability and the electronic behavior of the topologically protected surface states of the topological insulator (TI), Bi${}_{2}$Se${}_{3}$, doped with transition metals (TMs), TM/Bi${}_{2}$Se${}_{3}$(111). We find that Fe, Mn, and Cr impurities are energetically more stable at the Bi substitutional sites, whereas we may find energetically stable substitutional as well as interstitial configurations for Co and Ni impurity atoms. Through scanning tunneling microscopy simulations, we verify that each TM atomic species and its position in the Bi${}_{2}$Se${}_{3}$(111) surface can be identified. The substitutional Fe and Cr impurities exhibit an energetic preference for the out-of-plane net magnetic moment, giving rise to a small energy gap at the Dirac point (DP), whereas the in-plane magnetic moment of substitutional Mn/Bi${}_{2}$Se${}_{3}$(111) promotes a shift of the DP from the center of the surface Brillouin zone, opening up a small energy gap. For the substitutional impurities, the shapes of the metallic bands are somewhat preserved compared with the energy bands of the pristine Bi${}_{2}$Se${}_{3}$(111) surface. Interstitial Co atoms also present an in-plane net magnetic moment, where we find the formation of metallic bands, suppressing the presence of the DP. For the Ni/Bi${}_{2}$Se${}_{3}$(111) impurity there is not a net magnetic moment, and therefore, the DP is preserved. Further formation energy results indicate other plausible (meta)stable impurity configurations, giving rise to quite different scenarios for the topological properties of TM/Bi${}_{2}$Se${}_{3}$(111), even for the same TM impurity.

Three-dimensional Wentzel-Kramers-Brillouin approach for the simulation of scanning tunneling microscopy and spectroscopy

We review the recently developed three-dimensional (3D) atom-superposition approach for simulating scanning tunneling microscopy (STM) and spectroscopy (STS) based on ab initio electronic structure data. In the method, contributions from individual electron tunneling transitions between the tip apex atom and each of the sample surface atoms are summed up assuming the one-dimensional (1D) Wentzel-Kramers-Brillouin (WKB) approximation in all these transitions. This 3D WKB tunneling model is extremely suitable to simulate spin-polarized STM and STS on surfaces exhibiting a complex noncollinear magnetic structure, i.e., without a global spin quantization axis, at very low computational cost. The tip electronic structure from first principles can also be incorporated into the model, that is often assumed to be constant in energy in the vast majority of the related literature, which could lead to a misinterpretation of experimental findings. Using this approach, we highlight some of the electron tunneling features on a prototype frustrated hexagonal antiferromagnetic Cr monolayer on Ag(111) surface. We obtain useful theoretical insights into the simulated quantities that is expected to help the correct evaluation of experimental results. By extending the method to incorporate a simple orbital dependent electron tunneling transmission, we reinvestigate the bias voltage- and tip-dependent contrast inversion effect on the W(110) surface. STM images calculated using this orbital dependent model agree reasonably well with Tersoff-Hamann and Bardeen results. The computational efficiency of the model is remarkable as the k-point samplings of the surface and tip Brillouin zones do not affect the computational time, in contrast to the Bardeen method. In a certain case we obtain a relative computational time gain of 8500 compared to the Bardeen calculation, without the loss of quality. We discuss the advantages and limitations of the 3D WKB method, and show further ways to improve and extend it.

Electronic structure and transport properties of N2AA-doped armchair and zigzag graphene nanoribbons

Substitutional doping in graphene nanoribbons (GNRs) promises to enable specific tuning of their electronic properties. Recent work by Lv et al (2012 Nature Sci. Rep. 2 586) on large sheets of nitrogen-doped graphene determined that a highly predominant amount of nitrogen dopants (80%) are present in pairs of neighbouring atoms of the same sublattice A, denoted as N2AA dopants, following the notation of Lv et al. Here, we explore the electronic and transport properties of armchair (aGNR) and zigzag (zGNR) graphene nanoribbons under different orientations of the N2AA dopants with respect to the ribbon growth direction. For all dopant configurations of zGNRs and aGNRs, we find a substantial decrease in conductance, with new conductance gaps opening in some cases, and spatially localized states induced around the dopant sites. We also provide simulated scanning tunnelling microscopy images that will aid in the experimental identification of the presence of these structures in N-doped GNR samples.

Size-selective self-assembly of magnetic Mn nanoclusters on Si(111)

We show by first-principles calculations two types of magnetic magic Mn clusters on the Si(111)-(7 × 7) surface. The first is a small triangular Mn7 cluster stabilized by the solid-centered Mn-Si3 bonds on the top layer, and the second is a large hexagonal Mn13 cluster favored by the confining potential wells of the faulted half unit cells on the Si(111) surface. These two structural models are distinct from that of the planar group-III clusters on Si(111) and produce simulated scanning tunneling microscopy images in reasonable agreement with recent experimental observations. These results offer key insights for understanding the complex energetic landscape on the Si(111)-(7 × 7) surface, which is critical to precisely controlled growth of Mn nanocluster arrays with specific size, magnetic moment, and good uniformity.

Interaction of Graphene-on-Al(111) Composite with d-Glucopyranose and Its Application in Biodetection

Carbohydrates play a key role in biology, medicine, nanotechnology, and energy storage. However, the physics underlying the interaction between nanomaterials and carbohydrates is still unclear. In this study, we analyzed the interaction of the graphene-on-Al(111) composite with d-glucopyranose. It was observed that the d-glucopyranose molecule can be steadily adsorbed on the surface of the graphene-on-Al(111) composite. The mechanism of this stable adsorption was revealed by the local charges in the graphene induced by the polar group in d-glucopyranose when they are close to each other. Simulated scanning tunneling microscopy (STM) images of d-glucopyranose on the surface of the graphene-on-Al(111) composite, as application of this nanomaterial, show that the gg conformations of d-glucopyranose can be distinguished from the other conformations via the STM technique as a result of the interaction of the graphene-on-Al(111) composite with d-glucopyranose. Therefore, the graphene-on-Al(111) composite is exp...