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The identification of the surface atomic structure having a large unit cell remains a major challenge, while this surface structure is the starting point for templated growth on it. The atomic structure of the carbon-induced R(15 × 3)-W(110) is investigated by scanning tunneling microscopy (STM) operated around 80 K in near-contact mode, combined with the first-principles calculations. It is shown that the R(15 × 3) reconstruction results from the moire pattern, which a W-C bilayer of α-W2C(0001) forms with the W(110) substrate, confirming an earlier prediction by Bauer et al. Besides the moire pattern, the present structure contains the surface lattice deformation, the main ingredient of the other model, and provides a comprehensive picture, well reconciling the two previous models.

The introduction of ferromagnetic order in topological insulators in general breaks the time-reversal symmetry and a gap is opened in topological surface bands. Various studies have focused on gap-opened magnetic topological insulators, because such modified band structures provide a promising platform for observing exotic quantum physics. However, the role of antiferromagnetic order in topological insulators is still controversial. In this report, we demonstrate that it is possible to restore the topological surface states by effectively reducing the antiferromagnetic ordering in Gd-substituted Bi2Te3. We successfully control the magnetic impurities via thermal treatments in ultra-high vacuum condition and observe apparent restoration of topological surface band dispersions. The microscopic mechanism of atomic rearrangements and the restoration process of topological surface states are unraveled by the combination of scanning tunneling microscopy measurements and density functional theory calculations. This work provides an effective way to control the magnetic impurities which is strongly correlated with topological surface states.

The adsorption of acetonitrile (CH3CN) on Si(111)-(7 × 7) at a room temperature has been investigated using scanning tunneling microscopy (STM) and first-principles calculations. The site-specific ...

Adsorption of CO molecules on Si(111)-(7×7) is investigated by using scanning tunneling microscopy (STM) and density-functional theory calculations. The most reactive site on the Si(111)-(7×7) surface is the corner adatom in the faulted half unit (FHU), followed by the center adatom in the FHU. The initial sticking probability of CO molecules on Si(111)-(7×7) at room temperature (RT) is estimated to be ∼ 4 × 10 10 molecules/( cm 2 ·Langmuir), which is comparable with that on Si(001)-(2×1). From the experiments and theoretical calculations, the adsorption of CO molecules are found to occur on Si adatoms either in the upright on-top configuration or in the back-bond inserted configuration, while the adsorption on the rest and the corner hole atoms (which are theoretically probable) are not observable using STM due to their low-lying geometries. Though the sticking probability is very low, every surface dangling bond on the surface can bind strongly with the C atom of a CO molecule even at temperatures higher than RT.

Recent studies on a quasi-one-dimensional (quasi-1D) charge-density-wave (CDW) system, In atomic wires on Si(111), have brought intriguing issues on topological solitons in quasi-1D systems: the existence of few-atom-sized solitons, chirality of solitons, and the realization of logic exploiting the chirality switching. Using scanning tunneling microscopy and first-principles calculations, we show that the previously reported ``short'' phase-flip defects are In adatoms and thus have nonsolitonic nature, resolving the controversy over the existence of highly localized solitons. The observed ``long'' phase-flip and phase-slip defects are genuine solitons with and without chirality, respectively. While achiral solitons (phase-slip defects) can exist on the pristine CDW ($8\ifmmode\times\else\texttimes\fi{}2$) surface, chiral solitons (phase-flip defects) cannot due to their breakage of $8\ifmmode\times\else\texttimes\fi{}2$ ordering. The chiral solitons can exist only when they are trapped by In adatoms and constitute a part of a closed-loop domain wall. The intertwinement of chiral solitons and In adatoms implies the limitations of the previously proposed logic utilizing soliton chirality, but it provides an opportunity to realize this by controlling the In-adatom defect.

We report density functional theory calculations on the vacancy-induced magnetic properties of the wurzite GaN $$(10\bar 10)$$ surface. Among various intrinsic vacancies on the surface, we focus on the monatomic Ga and N vacancies. We have found two stable geometries of a surface Ga vacancy and one stable geometry of a surface N vacancy. Two stable surface Ga vacancy structures are shown to have magnetic moments of 3 μ B , which is the same as for the bulk Ga vacancy. Differently from the bulk N vacancy carrying null magnetic moment, the monatomic surface N vacancy has a finite magnetic moment of 1 μ B . These results support the experimental claim that the roomtemperature ferromagnetism observed in inorganic nanoparticles is due to surface vacancies and their complexes. We also present simulated scanning tunneling microscope images for comparison with those obtained in future experimental studies.

Incorporation of carbon (C) atoms in the Si(111)-(7 × 7) surface is investigated by using scanning tunneling microscopy and density-functional theory calculations. C atoms are supplied through thermal dissociation of CO molecules adsorbed on the Si(111)-(7 × 7) surface. One C atom can be incorporated substitutionally below the Si adatoms of the (7 × 7) structure. However, the stable (7 × 7) surface can accommodate only a very small amount of C atoms and the surplus C atoms are swept away to the step edges in the form of silicon-carbon clusters, restoring the clean Si(111)-(7 × 7) structure on the flat terrace. In contrast to the B-induced 3 × 3 reconstruction, high density C atoms do not induce a single crystalline 3 × 3 reconstruction over a wide area of Si(111).

We perform spin-polarized density functional theory calculations for a Zn vacancy on the ZnO(10 $\bar 1$ 0) surface. Two stable configurations of the surface Zn vacancy are found, and the activation energy barrier is estimated to be ∼0.01 eV. The lower energy configuration has a newly formed surface Zn-O bond to restore the bulk-like structure on the surface. Due to the newly formed bond, the vacancy state in the band gap is characterized by a complicated hybridization of neighboring surface and subsurface atoms and by a more extended electron density. Despite such a hybridization, the surface Zn vacancy is found to have a robust magnetic moment of 1 μ B , implying that surface Zn vacancies may be responsible for the ferromagnetism observed in ZnO thin films and nanoparticles. Simulated scanning tunneling microscope images show that the two structures of the surface Zn vacancy can be distinguished in the filled-state images.

The initial adsorption of oxygen molecules on Si(001) is investigated at room temperature. The scanning tunneling microscopy images reveal a unique bright O2-induced feature. The very initial sticking coefficient of O2 below 0.04 Langmuir is measured to be ∼0.16. Upon thermal annealing at 250–600 °C, the bright O2-induced feature is destroyed, and the Si(001) surface is covered with dark depressions that seem to be oxidized structures with -Si-O-Si- bonds. This suggests that the observed bright O2-induced feature is an intermediate precursor state that may be either a silanone species or a molecular adsorption structure.

The Cl-saturated Si(001) surface is investigated by employing density functional theory calculations. From the electronic density of states, the low- and the high-bias filled-state images and the empty-state images are found to originate from Cl(3p) states directed in-plane, in parallel with the Si dimer row, and perpendicular to the surface (z), respectively. The bright triplet, which is a characteristic scanning tunneling microscopy (STM) feature of an unchlorinated bare Si dimer, is attributed to an occupied dangling bond state of the bare Si dimer that is hybridized with the neighboring Cl(3pz) orbital. The previously observed split-dimer feature is confirmed to be the dimer-bond oxidized structure. Finally, we suggest that the initial back-bond oxidation does not occur on the chlorinated Si(001) surface because it is energetically not favored compared with dimer-bond oxidation and because its STM simulation does not match experimental images.

The dissociative adsorption of water molecules on Si(001) was studied up to 850 K by scanning tunneling microscopy. Water molecules dissociate into OH and H fragments to form on-dimer (OD) and interdimer (ID) configurations, and the population ratio nID/nOD is measured to change from ∼5 at room temperature to the saturation value of ∼0.6 above 500 K, contradicting to the prediction from the static transition-state theory. The sticking coefficient also shows an abnormal temperature dependence. The temperature dependence in the H dissociation and in the molecular adsorption can be elucidated only by taking into account the flip-flop motion of Si dimers.

Scanning tunneling microscopy was used to study the adsorption behaviors of NH 3 molecules across Si dimer rows on a Si(0 0 1)-2 × 1 surface, taking into account the existence of both the on-dimer (OD) and inter-dimer (ID) adsorption configurations. In the OD configuration, the dissociated NH 2 and H form bonds with two Si atoms of a dimer. On the other hand, in the ID configuration, they adsorb at two Si atoms on the same side of two adjacent dimers along the dimer row. The OD configurations on the neighboring dimer rows were preferentially aligned perpendicular to the dimer rows, indicating a strong attractive interaction across the dimer rows, whereas the NH 3 molecules adsorbed in the ID configuration rarely showed ordering behavior.

We have performed total-energy calculations to study theoretical scanning tunneling microscopy (STM) images of the Si(1 1 1)3 × 2 surfaces induced by the adsorption of alkaline-earth metals (AEMs). Previously, in a series of works on Ba/Si(1 1 1) system, we have found that the observed Si(1 1 1)3 × 1–Ba LEED phase indeed has a 3 × 2 periodicity with a Ba coverage of 1/6 ML and the HCC substrate structure. Based on results of the Ba case, we proposed that the HCC structure is also adopted for other AEM atoms, which was confirmed by our recent work. In this paper, we mainly report the STM simulations for different AEM systems to compare with existing experimental data. We discuss the difference in the detailed STM images for different AEM adsorbates. Especially, the difference in filled-state images between Mg and other AEM atoms is attributed to the strong Mg–Si interaction.

We have performed total-energy density-functional calculations using ab initio pseudopotentials to investigate the atomic geometry and scanning tunneling microscopy (STM) of K adsorbed on the InAs(110) surface. We have identified the most favorable adsorption geometry formed by K adatoms occupying two almost degenerate adsorption sites. Based on this structure, we have simulated the STM images showing asymmetric and zigzag chain along the [ 1 1 ¯ 0 ] direction for both negative and positive sample biases. The calculated STM images agree with the recent STM observation.

New evidence of the paired end-bridge configuration in the room-temperature adsorption geometries of C 2 H 2 molecules on Si(0 0 1) is presented by scanning tunneling microscopy (STM) and ab initio pseudopotential calculations. The distinct four-leaved feature occupying two adjacent Si dimer sites in the experimental empty-state STM images are well reproduced by simulations of the paired end-bridge adsorption configuration. Calculated energetics suggests that the Si(0 0 1) surface is covered by paired end-bridge structures at the saturation coverage of 1 ML, in agreement with the existing experiments.

We report the formation of atomically flat Si(0 0 1) surfaces with C incorporation using thermal dissociation of C 2 H 2 molecules. The resulting surface phases are investigated by scanning tunneling microscopy and found to contain C atoms as much as 0.2 monolayer (ML) without roughening. At low C concentrations, C-induced vacancy line defects are generated on the surface, forming a 2× n superstructure. As the C concentration increases, a new phase with a c(4×4) structure starts to appear and coexists with the 2× n phase, eventually covering the whole surface at about 0.2 ML. The C atoms in the 2× n superstructure are thought to occupy substitutional sites in a subsurface layer and constitute a δ-like distribution.

Acetylene molecules adsorbed on the Si(0 0 1) surface are studied by scanning tunneling microscope and ab initio pseudopotential calculations. In case of room-temperature adsorption, there are basically two different kinds of di-σ bonding geometries at low coverage: (i) on-top and (ii) end-bridge di-σ configurations. The tetra-σ configurations are not found. Theoretical calculations show that the paired end-bridge configuration is dominant at high coverage. Based on these findings, we discuss the results at saturation coverage in the existing literature consistently. Subsequent annealing of the C 2 H 2 /Si(0 0 1) surface induces different C-induced surface structures depending on the acetylene coverage. At low coverage, parallel lines of dimer vacancies are observed. As the amount of the adsorbed acetylene increases, the c(4×4) ordered phase replaces the dimer vacancy line phase. Near saturation, clusters are formed and the surface becomes rough.

The In/Si(111)4$\ifmmode\times\else\texttimes\fi{}1$ surface with In wires is a prototypical one-dimensional electron system showing a temperature-induced structural phase transition. While most impurities are known to decrease the transition temperature $({T}_{c})$, oxygen was reported to increase the ${T}_{c}$. In order to understand the exceptional influence of oxygen, we have examined the initial stages of oxygen adsorption on the surface by scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. Oxygen molecules were found to dissociate and adsorb as atoms on the surface. STM revealed three distinct O adsorption features as well as occasional transformations from one to another. The high-resolution images showed that all three adsorbed O features were located at the center of the In trimer at both edges of the In wire. This registry is in contradiction with the previous theoretical predictions [S. Wippermann et al., Phys. Rev. Lett. 100, 106802 (2008)]. The present DFT calculations identified two of the features as O atoms incorporated in the interstitial region between the In wire and subsurface Si layer.

The isolated As vacancy on the GaAs (110) surface is investigated using ab initio pseudopotentials. The relaxed atomic structure reveals an inward relaxation of the neighboring surface Ga atoms regardless of the vacancy charge state. The stable charge state is determined to be (+1) in p-type material from the formation energies. Three vacancy states, two located within the band gap, are identified. The character of the vacancy wavefunctions is described in detail and discussed in connection with the charge-state dependent relaxation. Despite the inward relaxation of surface Ga neighbors, the theoretical scanning tunneling microscopy topography shows enhanced tunneling into these sites, which is in agreement with existing experiments. The origin of this apparent contradiction is attributed to the nature of the wavefunction for one of the unoccupied vacancy states.

Point defects on a $\mathrm{Si}(001)\ensuremath{-}(2\ifmmode\times\else\texttimes\fi{}1)$ surface were examined by scanning tunneling microscopy and ab initio pseudopotential calculations. The residual water molecules in the ultrahigh vacuum chamber are found to be the sole origin of the type-$C$ defects. Most of the apparent dimer vacancies in the filled-state images were found to show a distinct $U$-shaped triple-dimer footprint in the empty-state images, which also originate from water adsorption. These two defects were identified as a single dissociated water molecule forming Si-OH and Si-H bonds in the interdimer (type-$C$ defect) and the on-dimer (dimer-vacancy-like or $U$-shape defect) configurations.

Impurities interact with a charge density wave (CDW) and affect the phase transitions in low-dimensional systems. By using scanning tunneling microscopy, we visualize the interaction between oxygen impurities and the CDW in indium atomic wires on Si(111), a prototypical one-dimensional electronic system, and unveil the microscopic mechanism of the intriguing O-induced increase of the transition temperature (Tc). Driven by the fluctuating CDW, the O atoms adopt an asymmetric structure. By adjusting the asymmetry, a pair of O impurities in close distance can pin the one-dimensional CDW, which develops into the two-dimensional domains. First-principles calculations showed that the asymmetric interstitially-incorporated O defects induce shear strains, which assists the formation of hexagon structure of the CDW phase. The cooperative interplay between the O impurities and the CDW is responsible for the enhancement of the CDW condensation and the consequent increase in Tc.

Initial adsorption configurations of $\mathrm{N}{\mathrm{H}}_{3}$ molecules on the Si(001) surface are studied by using scanning tunneling microscopy (STM) and ab initio pseudopotential calculations. In contrast to the previous consensus of single configuration, we demonstrate that there exist two distinct STM features. One is found to be the existing model of on-dimer configuration, that is characterized by the previously unreported ``U-shape'' empty-state feature. The other is identified to be $\mathrm{N}{\mathrm{H}}_{2}$ and H adsorbed at the same side of two adjacent dimers along the dimer row. The identification of all the adsorption configurations would be useful for the quantitative analysis of Si nitridation.

The C amount and the structure of the $\mathrm{S}\mathrm{i}(001)\mathrm{\text{\ensuremath{-}}}c(4\ifmmode\times\else\texttimes\fi{}4)$ surface is studied using scanning tunneling microscopy (STM) and ab initio calculations. The $c(4\ifmmode\times\else\texttimes\fi{}4)$ phase is found to contain $1/8$ monolayer C (1 C atom in each primitive unit cell). From the C amount and the symmetry of high-resolution STM images, it is inferred that the C atoms substitute the fourth-layer site below the dimer row. We construct a structure model relying on ab initio energetics and STM simulations. Each C atom induces an on-site dimer vacancy and two adjacent rotated dimers on the same dimer row. The $c(4\ifmmode\times\else\texttimes\fi{}4)$ phase constitutes the subsurface ${\mathrm{S}\mathrm{i}}_{0.875}{\mathrm{C}}_{0.125}$ $\ensuremath{\delta}$ layer with two-dimensionally ordered C atoms.

We study the atomic structure of the $\mathrm{Si}(111)3\ifmmode\times\else\texttimes\fi{}2\ensuremath{-}\mathrm{Ba}$ surface using low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), and ab initio calculations. A $3\ifmmode\times\else\texttimes\fi{}2$ periodicity is observed not only in STM but also in LEED. From dual-bias STM imaging and total-energy calculations, the recently proposed honeycomb chain-channel (HCC) structure [G. Lee et al., Phys. Rev. Lett. 87, 056104 (2001)] is confirmed to be the most favorable among various candidate structures. Calculations varying Ba-Ba distance in the channel show that the Ba atoms interact repulsively. Diffusion of Ba atoms along the channel, occurring in a concerted manner, is found to be unlikely at room temperature. This is consistent with the STM observation that the Ba atoms occupy specific sites. However, some static disorder in site occupation is observed and shown to be energetically probable. We suggest that the Si(111) surface has a tendency towards the $3\ifmmode\times\else\texttimes\fi{}1\ensuremath{-}\mathrm{HCC}$ reconstruction when one electron per $3\ifmmode\times\else\texttimes\fi{}1$ unit are supplied and fully saturate the Si dangling bonds.

The initial formation of the samarium/silicon interface is studied by combining scanning tunneling microscopy (STM), low-energy electron diffraction, and ab initio pseudopotential calculations. A $\mathrm{Si}(111)3\ifmmode\times\else\texttimes\fi{}2$-Sm reconstruction is formed at a Sm coverage of 1/6 monolayer. High-resolution STM images reveal a strong bias-voltage dependence for the $3\ifmmode\times\else\texttimes\fi{}2$ reconstruction. In the empty-state STM images, the rows with a $\ifmmode\times\else\texttimes\fi{}2$ periodicity are shown at high bias voltages, and attributed to Sm atoms. At low bias voltage, an additional double row feature with a $\ifmmode\times\else\texttimes\fi{}1$ periodicity appears and dominates the empty-state image as the bias voltage decreases. The paired protrusions with the $\ifmmode\times\else\texttimes\fi{}1$ periodicity in the double rows in the empty-state image are attributed to Si atoms. In the filled-state STM images, double rows of protrusions forming zigzag chains with a $3\ifmmode\times\else\texttimes\fi{}1$ structure are observed and assigned to Si atoms. We propose a honeycomb chain-channel model for the $3\ifmmode\times\else\texttimes\fi{}2$ phase, common to alkali metals and alkaline-earth metals on Si(111). Simulated STM images based on this model are in excellent agreement with experiment.

We have investigated the Li/GaAs(110) surface by combining the low-energy electron diffraction (LEED) and the ab initio pseudopotential calculations. The potential energy surface for the single atomic adsorption shows the existence of two inequivalent adsorption sites. At 0.5 monolayer coverage of Li, a well defined $1\ifmmode\times\else\texttimes\fi{}2$ LEED pattern is observed. The atomic structure at this coverage is characterized by Li zigzag chains running in the $[11\ifmmode\bar\else\textasciimacron\fi{}0]$ direction. This structure is stabilized by electron transfer from the Li adatoms to the dangling bonds of certain surface Ga atoms. The simulated scanning tunneling microscopy images show linear (asymmetric zigzag) chains along the $[11\ifmmode\bar\else\textasciimacron\fi{}0]$ direction for positive (negative) sample biases.

We report on the absolute measurement of In coverage on the Si(111)4\ifmmode\times\else\texttimes\fi{}1-In surface using medium-energy ion scattering, and present bias-dependent scanning tunneling microscopy (STM) images. The In coverage was determined to be 1 monolayer (ML). This result is in contrast to previous results of 3/4-ML In determined by semidirect measurements using Auger electron spectroscopy and STM. Our result supports a 4\ifmmode\times\else\texttimes\fi{}1-In structural model consisting of four surface In rows, which was constructed from the recent surface x-ray diffraction study and tested by subsequent theoretical calculations. The bias-dependent STM images are well reproduced by ab initio simulations based on this 1-ML-In model.

We investigate the initial stage of the C incorporation into Si(001) using thermal dissociation of ${\mathrm{C}}_{\mathrm{2}}{\mathrm{H}}_{\mathrm{2}}$. The scanning tunneling microscopy shows that C-induced dimer vacancies (DVs) with depressed adjacent dimers are generated on the surface and aligned in the dimer direction, forming the $2\ifmmode\times\else\texttimes\fi{}n$ structure. The ab initio pseudopotential calculations reveal that, with the presence of a DV in the surface, the $\ensuremath{\alpha}$ site in the fourth subsurface layer directly below the DV is the most favorable for the incorporated C atoms. The embedded C atoms align one dimensionally due to the interaction which is attractive in neighboring dimer rows but repulsive in the same dimer row.

Initial adsorption configurations of acetylene molecules on the Si(001) surface are investigated by scanning tunneling microscopy (STM) and ab initio pseudopotential calculations. Three distinctive features are observed in the STM images at low coverage. The comparison of the atomic resolution STM images with the simulation reveals that there are basically two kinds of di-$\ensuremath{\sigma}$ bonding configurations: (i) on-top over a single dimer and (ii) end-bridge between two successive dimers in the same dimer row. The third feature is identified to be a pair of end-bridge di-$\ensuremath{\sigma}$ configurations occupying the same two dimers. The tetra-$\ensuremath{\sigma}$ bonding configurations are not found. The existence of the two kinds of di-$\ensuremath{\sigma}$ bonding configurations can resolve the apparently conflicting results of the existing studies.

Scanning tunneling microscopy (STM) is one of the most successful experimental tools for probing the structure of semiconductor surfaces. However, care must be taken in interpreting the images at the atomistic limit. Often a “naive” interpretation of the STM image can yield an incorrect surface structure. We illustrate this situation via ab initio pseudopotential calculations for the STM image of the (110) GaAs surface. We will compare theoretical STM images to experimental images for the relaxed surface and for a surface with an As vacancy.

The atomic and electronic structure of an As vacancy on the GaAs(110) surface is examined using ab initio pseudopotentials. The relaxed atomic structure reveals an inward movement of the neighboring surface Ga atoms which is in disagreement with recent interpretations of the scanning tunneling microscopy (STM) images for this system. However, a careful analysis of the wave-function character of the vacancy states, and the theoretical STM image, for this geometry yields excellent agreement with the experimental STM images.

A Comment on the Letter by Hanchul Kim and James R. Chelikowsky, Phys. Rev. Lett. 77, 1063 (1996). The authors of the Letter offer a Reply.