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Atomic-scale intrinsic defects play a key role in controlling functional electronic properties of two-dimensional (2D) materials. Here, we present a low-temperature scanning–tunneling microscopy and spectroscopy investigation of a common point-defect in monolayer molybdenum disulfide (MoS2). We employ a sample preparation method in which the film surface is never exposed to air so that the native dangling bonds surrounding the defects in the film are preserved. Molybdenum vacancies are identified by their three characteristic in-gap resonances by combining scanning–tunneling measurements with parallel Green’s function-based theoretical modeling. The relative energy shifts between the various in-gap states allow us to identify a relative charge difference between two of the observed vacancies. The role of the substrate on the band structure of the defective MoS2 monolayer is unveiled. Our study highlights the effects of the substrate on the in-gap states of common defects found in MoS2 providing a pathway in designing and optimizing 2D materials for electronic applications.

Heterostructures of graphite/MoS2 display a wide range of lattice registry due to rotational alignment and/or lattice mismatch. Using high resolution scanning tunneling microscopy and spectroscopy (STM/STS) we investigated electronic properties of these heterostructures and observed changes in the bandgap as a function of the twist angle between the layers. Green's function based electronic structure calculations were carried out in order to shed light on the mechanism underlying the observed bandgap changes. Indirect coupling between the pz orbitals of the substrate Carbon atoms and the dz2 orbitals of the MoS2 layers (mediated by the pz orbitals of the bottom S layers) is found to be responsible for changes in the valence-band edge. Simple stacking of van der Waals materials with diverse properties have the potential to enable the fabrication of novel materials and device structures with tailored electronic properties. acceptedVersion

Silicene is a graphene-like material with relatively strong spin-orbit coupling exhibiting gapless topologically protected edge states. In addition, it has a buckled structure, and hence, it stands as a feasible candidate for spintronic applications, where spin-polarized channels could be controlled with external electric fields realized with voltage gates attached to a Silicene sheet. Breaking the periodicity in 2D-materials with spin-orbit coupling produces one-dimensional edge and interface nanostructures that may give rise to an intrinsic locking of spin-polarization to electron momentum. We consider field induced and chemical ways to create interfaces to give way to spin polarized states for both zigzag and armchair alignments. While the spin polarization of a field induced interface channel can be feasibly tuned, a chemical interface is less flexibly tunable. However, controlling Fermi-level, e.g. with a gate voltage, might serve as a spin valve along the interface. acceptedVersion

Motivated by the recent experiments indicating superconductivity in metal-decorated graphene sheets, we investigate their quasi-particle structure within the framework of an effective tight-binding Hamiltonian augmented by appropriate BCS-like pairing terms for p-type order parameter. The normal state band structure of graphene is modified not only through interaction with adsorbed metal atoms, but also due to the folding of bands at Brillouin zone boundaries resulting from a $\sqrt{3}\times\sqrt{3}R30^{\circ}$ reconstruction. Several different types of pairing symmetries are analyzed utilizing Nambu-Gorkov Green's function techniques to show that $p+ip$-symmetric nearest-neighbor pairing yields the most enhanced superconducting gap. The character of the order parameter depends on the nature of the atomic orbitals involved in the pairing process and exhibits interesting angular and radial asymmetries. Finally, we suggest a method to distinguish between singlet and triplet type superconductivity in the presence of magnetic substitutional impurities using scanning tunneling spectroscopy., Preprint, 15 pages, 4+1 figures

Electrons confined within a two-dimensional (2D) honeycomb potential can host localized electronic states at their edges. These edge states exhibit distinctive electronic properties relative to the bulk and may result in spin polarization or topologically protected conduction. However, the synthesis and characterization of well-defined 2D structures which host such edge states remain challenging. Here, we confirm the presence of a two-dimensional electron gas (2DEG) and find evidence for unique edge states in the Ag-induced honeycomb surface reconstruction of silicon nanosheets (SiNSs) grown on Ag(111). Atomic-scale scanning tunneling microscopy and computational modeling confirm that the electronic properties of the SiNS surface are determined by the honeycomb surface reconstruction. This surface presents ordered edge terminations with distinct spectroscopic signatures associated with the edge orientation, and calculations suggest that Rashba-type spin-orbit coupling may result in spin-polarized conduction along certain edge orientations. This quantification of the electronic structure of edge states in SiNS 2DEGs will address ongoing efforts to engineer quantum effects in silicon-based nanostructures. acceptedVersion

We uncover the electronic structure of molecular graphene produced by adsorbed CO molecules on a copper (111) surface by means of first-principles calculations. Our results show that the band structure is fundamentally different from that of conventional graphene, and the unique features of the electronic states arise from coexisting honeycomb and Kagome symmetries. Furthermore, the Dirac cone does not appear at the K-point but at the Γ-point in the reciprocal space and is accompanied by a third, almost flat band. Calculations of the surface structure with Kekule distortion show a gap opening at the Dirac point in agreement with experiments. Simple tight-binding models are used to support the first-principles results and to explain the physical characteristics behind the electronic band structures.

We stand at the threshold of a new ‘golden age’ of spectroscopic studies of materials for unraveling how charge, spin, orbital and lattice degrees of freedom interact to produce emergent phenomena and exotic states of matter. In this connection, the need for proper modeling of various highly resolved spectroscopies is becoming of critical importance in providing discriminating tests of competing theoretical models and as a rational basis for future experimentation. Here we present an overview of our modeling efforts aimed at obtaining a realistic description of various highly resolved spectroscopies in complex materials with illustrative examples drawn from angle-resolved photoemission studies of the cuprate high-temperature superconductors.

We discuss a comprehensive scheme for modeling various highly resolved spectroscopies of the cuprates where effects of matrix element, crystal structure, strong electron correlations, and superconductivity are included realistically in material-specific detail. A number of illustrative examples drawn from our recent work are presented. Specific issues in the cuprate physics considered are: (i) Origin of high-energy kink or the waterfall effect; (ii) Dichroic effects in angle-resolved photoemission spectrum; (iii) Asymmetry of the scanning tunneling spectrum between the processes of electron extraction and injection; (iv) Persistence of ‘Mott’ like high-energy features with doping in optical spectra; (v) Magnetic excitations in electron and hole doped cuprates.

In an effort to develop and implement techniques for making direct contact between the electronic spectra and various spectroscopies resolved highly in energy, momentum or real-space position, we present highlights of our recent work aimed at understanding angle-resolved photoemission (ARPES), resonant inelastic X-ray scattering (RIXS) and scanning tunneling microscopy/spectroscopy (STM/STS) spectra in the cuprates.

In this paper we simulate STM and STS experiments for CO monomers and dimers on Cu(1 1 1) surface. We show that the contrast of STM images can be attributed to interference effects between tunneling channels, and suggest that functionalizing the microscope tip improves the channel selectivity of STM. Furthermore, we show that voltage and position dependent tunneling spectra also reflect the same interference effects, but adds the energy resolution to the channel analysis. Especially in the case of nonresonant tunneling, STS measures local density of states only indirectly. The present study suggests that STS in constant height mode can be used in investigating the phase and energy sensitivity of tunneling channels in adsorbate molecules and nanostructures.

The electronic structure of GaAs(1 1 0) surface is analyzed using Density Functional Theory (DFT-GGA) in atomic orbital basis (LCAO). The surface orbitals and the corresponding local density of electronic states (LDOS) are calculated for purposes of interpreting STM images. We show how local atomic orbitals of surface atoms are related to tunneling channels for electrons in STM imaging. A destructive interference between orbitals of two neighbouring atoms increases the contrast between the two atoms, and this is reflected in directionality of STM patterns of GaAs(1 1 0) surfaces. We also discuss how the basic formalism of Tersoff–Hamann approach to STM simulation can be reformulated to reveal the role of phase difference between tunneling channels.

In a recent scanning tunneling microscopy (STM) experiment [Appl. Phys. Lett. 71 (1997) 213], CO molecules have been distinguished from another adsorbate species on Cu(1 1 1) surface using a controlled transfer of a CO molecule to the microscope tip. With a clean tip, both adsorbates are seen as dark depressions in the STM image. Functionalizing the tip with a CO molecule inverts the contrast of the adsorbed CO, but the images of the other species remain dark. In this Letter, we calculate STM images of CO for both the tip conditions, and reproduce the contrast inversion. Interference effects between different tunneling channels explain this behaviour: the contrast inversion takes place because the currents through both the adsorbate and the tip molecule are of the same order of magnitude as the current through vacuum, but they are in an opposite phase to through vacuum tunneling.

We study tip-adsorbate–substrate interactions in scanning tunneling microscopy (STM) manipulation and imaging, and the influence of impurities on the images. Thence, we perform molecular dynamics simulations and calculate qualitative STM images for oxygen on Pt(1 1 1) surface. The adsorption site of the oxygen molecule is found to be in accordance with ab initio calculations. The calculated STM image has a good resemblance to the experimental ones. The contamination of the tip by oxygen or water alters the STM image strongly. Molecular dynamics simulations on manipulations of oxygen on the surface reveal several mechanisms of how molecular oxygen can be either produced or decomposed with STM tip. Finally, we find out that transfer of oxygen from the surface to an STM tip is not very probable.

The highest temperature superconductors are electronically inhomogeneous at the nanoscale, suggesting the existence of a local variable which could be harnessed to enhance the superconducting pairing. Here we report the relationship between local doping and local strain in the cuprate superconductor Bi$_2$Sr$_2$CaCu$_2$O$_{8+x}$. We use scanning tunneling microscopy to discover that the crucial oxygen dopants are periodically distributed, in correlation with local strain. Our picoscale investigation of the intra-unit-cell positions of all oxygen dopants provides essential structural input for a complete microscopic theory.

Molecular dynamics simulations are performed to study adsorption of methane on Pd(1 1 0). The direct dissociation is found to take place due to transfer of incident translational energy into vibrational modes of the molecule. The deformation modes of the molecule appear to be the most susceptive to this energy transfer. At high incident translational energies the molecules tend to dissociate directly, while at intermediate energies the molecules are bounced off the surface. At low energies, the molecules are trapped into a physisorption state, which may be a gateway to thermally assisted dissociation within a longer time.

Dissociative adsorption of methane has been investigated on Pd {1 1 0} by using molecular beam surface scattering. The initial sticking probability has been determined in the translational energy range of 7–95 kJ/mol and at selected vibrational energies from 300 to 700 K. The measured initial sticking probability is found to increase strongly with both translational and vibrational energy of CH4 molecules. The activation of the dissociative chemisorption of CH4 induced by the vibrational energy is shown to depend on the translational energy and is attributed to the excitation of the bending modes of the incident molecule. We have also performed molecular dynamics simulations to investigate the dissociation mechanism theoretically. The simulations clearly demonstrate that an efficient energy transfer occurs upon adsorption between the translational and vibrational energies of the incident CH4 molecule, which thereby facilitates the deformation of the molecular structure of CH4 resulting in dissociation.

The free-energy contribution of phonons to surface reconstruction of Pd 110 is studied by Green's function methods. The adsorbate is modelled as a local perturbation to the dynamical matrix, the effect of which is solved from Dyson's equation. The phonons have a high entropy at the reconstructed surface, thus easing the reconstruction as the temperature increases. Adding an impurity atom with a low Debye temperature further enhances the entropy effect in favour of reconstruction.

Through relativistic photoemission calculations for the Au(111) surface state at the Fermi level, we study the photon energy dependence of circular dichroism. The dichromatic signal (${D}_{S}$) pattern changes 23 times with photon energies between 7 and 100 eV, and we have found 13 different patterns in the ${k}_{\ensuremath{\parallel}}$ map at the Fermi level for the ${D}_{S}$ from the Au(111) surface state with normal incidence light. We show that the photon energy dependence of ${D}_{S}$ is very complex even in the simplest case. The sign change in the circular dichroism as a function of photon energy is related to the relative phases of the complex expansion coefficients of different outgoing partial waves in a time-reversed low-energy electron diffraction state. With off-normal incidence, the $z$ component of the incoming photon field is dominant, and the fine structure seen in the ${D}_{S}$ in the normal incidence case is lost very rapidly, moving from a normal to an off-normal incidence. We also report that the Rashba split surface state of Au(111) has a significant component of $d$-type orbital due to relativistic effects and the computational setup used.

We present realistic multiband calculations of scanning tunneling spectra in Bi${}_{2}$Sr${}_{2}$CaCu${}_{2}$O${}_{8+\ensuremath{\delta}}$ over a wide doping range. Our modeling incorporates effects of a competing pseudogap and pairing gap as well as effects of strong electronic correlations, which are included by introducing self-energy corrections in the one-particle propagators. The calculations provide a good description of the two-gap features seen in experiments at low energies and the evolution of the van Hove singularity (VHS) with doping, and suggest a possible quantum critical point near the point where the VHS crosses the Fermi level.

We discuss how variations in the scanning tunneling microscope (STM) tip, whether unintentional or intentional, can lead to changes in topographic images and $dI/dV$ spectra. We consider the possibility of utilizing functionalized tips in order to improve the sensitivity of STM experiments to local irregularities at the surface or hidden below the surface layers. The change in the tip symmetry can radically alter the contrast of the topographic image due to changes in tip-surface overlap. The $dI/dV$ curves change their shape according to which sample bands the tip orbital tends to overlap. In addition, relative phases between competing tunneling channels can be inverted by changing the tip symmetry, which could help reveal the origin of a local irregularity in the tunneling spectrum.

We analyze how the coherence peaks observed in scanning tunneling spectroscopy (STS) of cuprate high-temperature superconductors are transferred from the cuprate layer to the oxide layers adjacent to the STS microscope tip. For this purpose, we have carried out a realistic multiband calculation for the superconducting state of Bi${}_{2}$Sr${}_{2}$CaCu${}_{2}$O${}_{8+\ensuremath{\delta}}$ (Bi2212) assuming a short-range $d$-wave pairing interaction confined to the nearest-neighbor Cu ${d}_{{x}^{2}\ensuremath{-}{y}^{2}}$ orbitals. The resulting anomalous matrix elements of the Green's function allow us to monitor how pairing is then induced not only within the cuprate bilayer but also within and across other layers and sites. The symmetry properties of the various anomalous matrix elements and the related selection rules are delineated.

In this work we present a method for simulating the electron-vibration coupling in adsorbate molecules using a tight-binding formalism for the electronic degrees of freedom and a real-space description of the molecular vibrations. First, we derive a formalism which is very transparent in recognizing the effect of a local vibrational perturbation on the local electronic structure at any location. Second, we apply the method to nonresonant inelastic electron-tunneling spectroscopy (IETS) of two sample molecules on generic model substrates as typically accessible within a scanning tunneling microscopy (STM) experiment. The foremost observation is that the intensity of the STM-IETS signal is not necessarily strongest in the spatial vicinity of the vibrational perturbation. Instead, it is dependent on the delocalization of the molecular orbitals, which may lead to a strong intensity quite far from the vibration. Since this is an effect of the electronic structure and not related to the transfer of the vibrational motion itself, the molecular orbitals can be treated as ``carrier waves'' of the signal from a vibrational perturbation. This effect may be important in determining the orientation of an adsorbed molecule on a substrate surface or in manipulating adsorbed molecules with an STM tip.

Molecular dynamics simulations of frictional sliding of a tip over a flat substrate in the presence of a lubricating solid film of one or two atomic layers thickness are presented. The role of adhesion in promoting wear is discussed by reference to earlier simulations of frictional sliding in the absence of a lubricating layer. Two conditions for lubrication are identified. First, the shear strength of the interface between the tip and the film must be lower than the shear strength of the tip or the underlying substrate. Secondly, the film must have a sufficient strength in compression to prevent penetration of the film by the tip. The importance of lubrication in obtaining images from the frictional force microscope is also discussed.

We present a Green's function-based framework for modeling the scanning tunneling spectrum from the normal as well as the superconducting state of complex materials where the nature of the tunneling process---i.e., the effect of the tunneling ``matrix element,'' is properly taken into account. The formalism is applied to the case of optimally doped ${\text{Bi}}_{2}{\text{Sr}}_{2}{\text{CaCu}}_{2}{\text{O}}_{8+\ensuremath{\delta}}$ (Bi2212) high-${T}_{\text{c}}$ superconductor using a large tight-binding basis set of electron and hole orbitals. The results show clearly that the spectrum is modified strongly by the effects of the tunneling matrix element and that it is not a simple replica of the local density of states of the $\text{Cu}\text{ }{d}_{{x}^{2}\ensuremath{-}{y}^{2}}$ orbitals with other orbitals playing a key role in shaping the spectra. We show how the spectrum can be decomposed usefully in terms of tunneling ``channels'' or paths through which the current flows from various orbitals in the system to the scanning tip. Such an analysis reveals symmetry-forbidden and symmetry-enhanced paths between the tip and the cuprate layers. Significant contributions arise from not only the ${\text{CuO}}_{2}$ layer closest to the tip but also from the second ${\text{CuO}}_{2}$ layer. The spectrum also contains a longer range background reflecting the nonlocal nature of the underlying Bloch states. In the superconducting state, coherence peaks are found to be dominated by the anomalous components of Green's function.

We have developed a material specific theoretical framework for modeling scanning tunneling spectroscopy (STS) of high-temperature superconducting materials in the normal as well as the superconducting state. Results for ${\mathrm{Bi}}_{2}{\mathrm{Sr}}_{2}{\mathrm{CaCu}}_{2}{\mathrm{O}}_{8+\ensuremath{\delta}}$ (Bi2212) show clearly that the tunneling process strongly modifies the STS spectrum from the local density of states of the ${d}_{{x}^{2}\ensuremath{-}{y}^{2}}$ orbital of Cu. The dominant tunneling channel to the surface Bi involves the ${d}_{{x}^{2}\ensuremath{-}{y}^{2}}$ orbitals of the four neighboring Cu atoms. In accord with experimental observations, the computed spectrum displays a remarkable asymmetry between the processes of electron injection and extraction, which arises from contributions of Cu ${d}_{{z}^{2}}$ and other orbitals to the tunneling current.

We present a fast and efficient tight-binding (TB) method for simulating scanning tunneling microscopy (STM) imaging of adsorbate molecules on ultrathin insulating films. Due to the electronic decoupling of the molecule from the metal surface caused by the presence of the insulating overlayer, the STM images of the frontier molecular orbitals can be simulated using a very efficient scheme, which also enables the analysis of phase shifts in the STM current. Au-pentacene complex adsorbed on a NaCl bilayer on Cu substrate provides an intricate model system, which has been previously studied both experimentally and theoretically. Our calculations indicate that the complicated shape of the molecular orbitals may cause multivalued constant current surfaces -- leading to ambiguity of the STM image. The results obtained using the TB method are found to be consistent with both DFT calculations and experimental data., 19 pages, 5 figures

The wetting phenomena of thin film growth are studied with the Monte Carlo method in a lattice gas model. Results for the phase diagram are compared with earlier Mean Field, Renormalisation Group and Monte Carlo studies. Considering the thickness and smoothness of the wetting film new insight is found mainly for the layering transitions. Namely, the effect of the substrate is not directly seen in the coverage, but in the mean square deviation of the coverage. It is also found that wetting and prewetting have no profound difference in the case of the lattice gas model.

A continuous-space Monte Carlo study of wetting and layering phenomena of a generalized lattice-gas model is presented. Three bulk phases are observed, and interpreted as solid, liquid and gas phases. In the presence of a solid substrate and in the absence of lattice mismatch, dewetting transition and triple-point wetting is found to occur. Adding a lattice mismatch shifts the dewetting point towards lower temperatures, and separates one-monolayer commensurate and incommensurate solid phases one from the other.

We analyze STM images of phenyl rings and substitutional nitrobenzene in terms of molecular symmetry, local electronic structure and tunneling channels. In experimental STM images, the phenyl ring of a benzene or a substituted nitrobenzene is seen as a dark depression. In a free phenyl, the nonresonant tunneling channels through the frontier orbitals interfere in a way that makes the molecule rather transparent. In adsorption, the mixing of molecular orbitals and the surface wave functions decrease the LDOS of the system with respect to a clean surface, and this leads to low current at the molecule. Substituting one hydrogen by a nitro group leaves the STM image of the phenyl dark, but makes the substitutional group appear bright. According to our calculations the molecular orbitals of a free nitrobenzene would be also quite transparent. However, the nitro group reconstructs upon adsorption, as seen in molecular dynamics simulations. This reconstruction almost closes the energy gap between the frontier orbitals localized at the nitro group. Thus, the tunneling through the group is almost resonant and a large tunneling amplitude is obtained.

The topological phase of a silicene nanoribbon holding edge states in the bulk energy gap can be easily broken by an external electric field. Here, we show through low-energy Green's function calculations that it is possible to localize conducting channels anywhere in a silicene nanoribbon by applying an inhomogeneous electric field. The spin degeneracy of these channels can also be broken in the same manner, allowing conduction of spin as well as charge. On this basis, we suggest design of a ternary logic device, which could be used in low-power circuits. Our study demonstrates that silicene and related group IV elements with honeycomb structure could provide a platform for efficient manipulation of spin currents via external electric fields, without the need to switch magnetic fields for spintronics applications.

A mean field method to study heteroepitaxial thin film growth is applied to growth, intermixing and surface reconstructions of $Au$ on $Ag(110)$. The results are in accordance with experimentally observed ``burrowing'' at submonolayer coverages and growth of elongated, $(1 \times 3)$ reconstructed, $Au$ clusters at higher coverages. At coverages of few monolayers the surface between the clusters has a high concentration of $Ag$, and ordered rows of $Au$ are formed just beneath the surface., 11 pages, 3 figures: uuencoded ps-file for the paper. mpeg simulations available at http://alpha.cc.tut.fi/~jniemine/free_ene.html To appear in Surface Science Letters

Surface reconstructions of Au film on Pd(110) substrate are studied using a local Einstein approximation to quasiharmonic theory with the Sutton-Chen interatomic potential. Temperature dependent surface free energies for different coverages and surface structures are calculated. Experimentally observed transformations from $(1\times1)$ to $(1 \times 2)$ and $(1 \times 3)$ structures can be explained in the framework of this model. Also conditions for Stranski-Krastanov growth mode are found to comply with experiments. The domain of validity of the model neglecting mixing entropy is analyzed., 7 pages, REVTeX two-column format, 3 postscript figures available on request from Jouko.Nieminen@cc.tut.fi To appear in Phys. Rev. Letters

The kinetics of ordering in the Q-state Potts model on a square lattice is studied for quenches from a high-temperature, disordered state to low temperatures below the phase-transition point. Growth laws for the average size of domains are obtained by Monte Carlo studies with Glauber dynamics for Q=3, 4, 6, and 8 for several low temperatures. In addition, the nonequilibrium structure factor is calculated for Q=8 and is shown to satisfy scaling. This study may be of some relevance to island growth in surface science, since the Potts model has been used to describe the adsorption of atoms on substrates.

The possibilities to separate different growth modes of thin films are discussed using results of Monte Carlo simulation. The growth mode can be recognized from the time evolution of the coverage, the mean square deviation of the coverage, the estimated number of clusters on the substrate and snapshots at different stages of growth. In addition to defining and verifying the criteria for layer-by-layer and island modes, we can identify the intermediate simultaneous multilayer growth.

A change in bias voltage can reverse the contrast of a scanning-tunneling microscopy (STM) image of an adsorbate molecule on a solid surface. This contrast change may take place not only in a case of tunneling in the neighborhood of a resonance level of the adsorbate, but it can also be seen in the case of a wide energy gap between highest occupied molecular-orbital and lowest unoccupied molecular-orbital levels. In order to find a unified description of contrast changes in STM images, we make comparisons between different approaches to tunneling. We especially consider the role of phase differences between possible tunneling channels. These phase differences can be related to the imaginary and real parts of the Green's function of the system which reveal whether the tunneling takes place through a resonant state or a forbidden gap. Finally, we compare experimental and calculated images of oxygen molecules on a silver surface and analyze the mechanisms of the contrast change in terms of phase shifts in different tunneling channels.

We perform a molecular dynamics (MD) study of non-dissociative adsorption of O 2 molecule on Pt{111} surface at low temperatures, and analyse the STM image of the obtained geometry. The interatomic forces for the simulation are calculated using tight-binding method in density matrix formalism with the constraint of local charge neutrality. The STM image is constructed by calculating tunneling current between a sharp metal tip and the sample. The MD simulation gives an adsorption site with a very plausible bonding behaviour. Furthermore, the corresponding STM image is similar to recent experimental images. The present simulation suggests formation of a larger complex of the oxygen molecule and two Pt atoms. It turns out that the STM image does not directly show the orientation of the O 2 molecule, and has such a complicated origin in interference of atomic orbitals of the formed complex, that an optimization of the surface structure using MD simulation, instead of intuitive considerations, is necessary.