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The link between changes in the material crystal structure and its mechanical, electronic, magnetic, and optical functionalities - known as the structure-property relationship - is the cornerstone of the contemporary materials science research. The recent advances in scanning transmission electron and scanning probe microscopies (STEM and SPM) have opened an unprecedented path towards examining the materials structure-property relationships on the single-impurity and atomic-configuration levels. Lacking, however, are the statistics-based approaches for cross-correlation of structure and property variables obtained in different information channels of the STEM and SPM experiments. Here we have designed an approach based on a combination of sliding window fast Fourier transform, Pearson correlation matrix, and linear and kernel canonical correlation, to study a relationship between lattice distortions and electron scattering from SPM data on graphene with defects. Our analysis revealed that the strength of coupling to strain is altered between different scattering channels, which can explain coexistence of several quasiparticle interference patterns in nanoscale regions of interest. In addition, the application of kernel functions allowed us to extract a non-linear component of the relationship between the lattice strain and scattering intensity in graphene. The outlined approach can be further utilized towards analyzing correlations in various multi-modal imaging techniques where the information of interest is spatially distributed and generally has a complex multidimensional nature.

Electron correlation effects caused by the topological zero mode of a hydrogenated graphene vacancy, $V_{111}$, with three adsorbed hydrogen atoms is discussed theoretically. A Kondo model is derived from the multi-reference representation of the density functional theory, where exchange scattering processes between the zero mode and low-energy modes in the Dirac cones are estimated. Even when the Dirac cone is slightly off from the charge neutral point, a finite on-site correlation energy, $U_0$, for the zero mode of an isolated $V_{111}$ allows the half-filling of the localized level giving a spin $s=1/2$. The anti-ferromagnetic Kondo screening mediated by higher order scattering processes becomes dominant in the dilute limit of the vacancies. Our estimation of relevant two body interactions certifies appearance of the Kondo effect at low temperatures., Comment: 17 pages, 10 figures

Understanding how foreign chemical species bond to atomic vacancies in graphene layers can advance our ability to tailor the electronic and magnetic properties of defective graphenic materials. Here we use ultra-high vacuum scanning tunneling microscopy (UHV-STM) and density functional theory to identify the precise structure of hydrogenated single atomic vacancies in a topmost graphene layer of graphite and establish a connection between the details of hydrogen passivation and the electronic properties of a single atomic vacancy. Monovacancy-hydrogen complexes are prepared by sputtering of the graphite surface layer with low energy ions and then exposing it briefly to an atomic hydrogen environment. High-resolution experimental UHV-STM imaging allows us to determine unambiguously the positions of single missing atoms in the defective graphene lattice and, in combination with the ab initio calculations, provides detailed information about the distribution of low-energy electronic states on the periphery of the monovacancy-hydrogen complexes. We found that a single atomic vacancy where each sigma-dangling bond is passivated with one hydrogen atom shows a well-defined signal from the non-bonding pi-state which penetrates into the bulk with a (\sqrt 3 \times \sqrt 3)R30^ \circ periodicity. However, a single atomic vacancy with full hydrogen termination of sigma-dangling bonds and additional hydrogen passivation of the extended pi-state at one of the vacancy's monohydrogenated carbon atoms is characterized by complete quenching of low-energy localized states. In addition, we discuss the migration of hydrogen atoms at the periphery of the monovacancy-hydrogen complexes which dramatically change the vacancy's low-energy electronic properties, as observed in our low-bias high-resolution STM imaging., Comment: Accepted for publication in Physical Review B

We investigate the chemisorptions of oxygen molecules on bilayer graphene (BLG) and its electrically modified charge-doping effect using conductivity measurement of the field effect transistor channeled with BLG. We demonstrate that the change of the Fermi level by manipulating the gate electric field significantly affects not only the rate of molecular adsorption but also the carrier-scattering strength of adsorbed molecules. Exploration of the charge transfer kinetics reveals the electrochemical nature of the oxygen adsorption on BLG. [This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Nano Letters, {\copyright} American Chemical Society after peer review. To access the final edited and published work see http://dx.doi.org/10.1021/nl202002p.], Comment: 10 pages, 6 figures

The electronic structure of nanographene in pristine and fluorinated activated carbon fibers (ACFs) have been investigated with near-edge x-ray absorption fine structure (NEXAFS) and compared with magnetic properties we reported on previously. In pristine ACFs in which magnetic properties are governed by non-bonding edge states of the \pi-electron, a pre-peak assigned to the edge state was observed below the conduction electron {\pi}* peak close to the Fermi level in NEXAFS. Via the fluorination of the ACFs, an extra peak, which was assigned to the \sigma-dangling bond state, was observed between the pre-peak of the edge state and the {\pi}* peak in the NEXAFS profile. The intensities of the extra peak correlate closely with the spin concentration created upon fluorination. The combination of the NEXAFS and magnetic measurement results confirms the coexistence of the magnetic edge states of \pi-electrons and dangling bond states of \sigma-electrons on fluorinated nanographene sheets., Comment: 4 figures, to appear in Phys. Rev. B

The wavefunction of a massless fermion consists of two chiralities, left-handed and right-handed, which are eigenstates of the chiral operator. The theory of weak interactions of elementally particle physics is not symmetric about the two chiralities, and such a symmetry breaking theory is referred to as a chiral gauge theory. The chiral gauge theory can be applied to the massless Dirac particles of graphene. In this paper we show within the framework of the chiral gauge theory for graphene that a topological soliton exists near the boundary of a graphene nanoribbon in the presence of a strain. This soliton is a zero-energy state connecting two chiralities and is an elementally excitation transporting a pseudospin. The soliton should be observable by means of a scanning tunneling microscopy experiment., Comment: 7 pages, 4 figures

Standing waves near the zigzag and armchair edges, and their Berry's phases are investigated. It is suggested that the Berry's phase for the standing wave near the zigzag edge is trivial, while that near the armchair edge is non-trivial. A non-trivial Berry's phase implies the presence of a singularity in parameter space. We have confirmed that the Dirac singularity is absent (present) in the parameter space for the standing wave near the zigzag (armchair) edge. The absence of the Dirac singularity has a direct consequence in the local density of states near the zigzag edge. The transport properties of graphene nanoribbons observed by recent numerical simulations and experiments are discussed from the point of view of the Berry's phases for the standing waves., Comment: 6 pages, 4 figures

The quantum corrections to the energies of the $\Gamma$ point optical phonon modes (Kohn anomalies) in graphene nanoribbons are investigated. We show theoretically that the longitudinal optical modes undergo a Kohn anomaly effect, while the transverse optical modes do not. In relation to Raman spectroscopy, we show that the longitudinal modes are not Raman active near the zigzag edge, while the transverse optical modes are not Raman active near the armchair edge. These results are useful for identifying the orientation of the edge of graphene nanoribbons by G band Raman spectroscopy, as is demonstrated experimentally. The differences in the Kohn anomalies for nanoribbons and for metallic single wall nanotubes are pointed out, and our results are explained in terms of pseudospin effects., Comment: 11 pages, 6 figures

The edge states that emerge at hydrogen-terminated zigzag edges embedded in dominant armchair edges of graphite are carefully investigated by ultrahigh-vacuum scanning tunneling microscopy (STM) measurements. The edge states at the zigzag edges have different spatial distributions dependent on the $\alpha$- or $\beta$-site edge carbon atoms. In the case that the defects consist of a short zigzag (or a short Klein) edge, the edge state is present also near the defects. The amplitude of the edge state distributing around the defects in an armchair edge often has a prominent hump in a direction determined by detailed local atomic structure of the edge. The tight binding calculation based on the atomic arrangements observed by STM reproduces the observed spatial distributions of the local density of states., Comment: 9 pages, 11 figures, accepted for Physical Review B

The presence of structure-dependent edge states of graphite is revealed by both ambient- and ultra-highvacuum- (UHV) scanning tunneling microscopy (STM) / scanning tunneling spectroscopy (STS) observations. On a hydrogenated zigzag (armchair) edge, bright spots are (are not) observed together with (SQRT(3) by SQRT(3))R30 superlattice near the Fermi level (V_S = −30 mV for a peak of the local density of states (LDOS)) under UHV, demonstrating that a zigzag edge is responsible for the edge states, although there is no appreciable difference between as-prepared zigzag and armchair edges in air. Even in hydrogenated armchair edge, however, bright spots are observed at defect points, at which partial zigzag edges are created in the armchair edge., Comment: 4 pages, 4 figures, contents for experimental/theoretical reseachers, accepted as an issue of Physical Review B (PRB)

Superperiodic patterns near a step edge were observed by STM on several-layer-thick graphite sheets on a highly oriented pyrolitic graphite substrate, where a dislocation network is generated at the interface between the graphite overlayer and the substrate. Triangular- and rhombic-shaped periodic patterns whose periodicities are around 100 nm were observed on the upper terrace near the step edge. In contrast, only outlines of the patterns similar to those on the upper terrace were observed on the lower terrace. On the upper terrace, their geometrical patterns gradually disappeared and became similar to those on the lower terrace without any changes of their periodicity in increasing a bias voltage. By assuming a periodic scattering potential at the interface due to dislocations, the varying corrugation amplitudes of the patterns can be understood as changes in LDOS as a result of the beat of perturbed and unperturbed waves, i.e. the interference in an overlayer. The observed changes in the image depending on an overlayer height and a bias voltage can be explained by the electronic wave interference in the ultra-thin overlayer distorted under the influence of dislocation-network structures., Comment: 8 pages; 6 figures; Paper which a part of cond-mat/0311068 is disscussed in detail

Superperiodic patterns were observed by STM on two kinds of finite-sized graphene sheets. One is nanographene sheets inclined from a highly oriented pyrolitic graphite (HOPG) substrate and the other is several-layer-thick graphene sheets with dislocation-network structures against a HOPG substrate. As for the former, the in-plane periodicity increased gradually in the direction of inclination, and it is easily changed by attachment of a nanographite flake on the nanographene sheets. The oscillation pattern can be explained by the interference of electron waves confined in the inclined nanographene sheets. As for the latter, patterns and their corrugation amplitudes depended on the bias voltage and on the terrace height from the HOPG substrate. The interference effect by the perturbed and unperturbed waves in the overlayer is responsible for the patterns whose local density of states varies in space., Comment: 11 pages; 2 figures; accepted for publication in J. Phys. Chem. Solids; ISIC12

$H$-$T$ diagram of 3D diluted Ising antiferromagnet Ni$_{c}$Mg$_{1-c}$(OH)$_{2}$ with $c$ = 0.8 has been determined from measurements of SQUID DC magnetization and AC magnetic susceptibility. At $H$ = 0, this compound undergoes two magnetic phase transitions: an antiferromagnetic (AF) transition at the N\'{e}el temperature $T_{N}$ (= 20.7 K) and a reentrant spin glass (RSG) transition at $T_{RSG}$ ($\approx$ 6 K). The $H$-$T$ diagram consists of the RSG, spin glass (SG), and AF phases. These phases meet a multicritical point $P_{m}$ ($H_{m}$ = 42 kOe, $T_{m}$ = 5.6 K). The irreversibility of susceptibility defined by $\delta$ (= $\chi_{FC} - \chi_{ZFC}$) shows a negative local minimum for 10 $\leq H \leq$ 35 kOe, suggesting the existence of possible glassy phase in the AF phase. A broad peak in $\delta$ and $\chi^{\prime \prime}$ at $H \geq$ 20 kOe for $T_{N}(c=0.8,H) \leq T \leq T_{N}(c=1,H=0)$ (= 26.4 K) suggests the existence of the Griffiths phase., Comment: 11 pages, 14 figures; J. Phys. Soc. Jpn. 73 (2004) No. 1 issue, in press

Antiferromagnetism in stacked nanographite is investigated with using the Hubbard-type model. We find that the open shell electronic structure can be an origin of the decreasing magnetic moment with the decrease of the inter-graphene distance, as experiments on adsorption of molecules suggest. Next, possible charge-separated states are considered using the extended Hubbard model with nearest-neighbor interactions. The charge-polarized state could appear, when a static electric field is present in the graphene plane for example. Finally, superperiodic patterns with a long distance in a nanographene sheet observed by STM are discussed in terms of the interference of electronic wave functions with a static linear potential theoretically. In the analysis by the k-p model, the oscillation period decreases spatially in agreement with experiments., Comment: 8 pages; 6 figures; accepted for publication in J. Phys. Chem. Solids; related Web site: http://staff.aist.go.jp/k.harigaya/index_E.html

Superperiodic patterns with a long distance in a nanographene sheet observed by STM are discussed in terms of the interference of electronic wave functions. The period and the amplitude of the oscillations decrease spatially in one direction. We explain the superperiodic patterns with a static linear potential theoretically. In the k-p model, the oscillation period decreases, and agrees with experiments. The spatial difference of the static potential is estimated as 1.3 eV for 200 nm in distance, and this value seems to be reasonable in order that the potential difference remains against perturbations, for example, by phonon fluctuations and impurity scatterings. It turns out that the long-distance oscillations come from the band structure of the two-dimensional graphene sheet., Comment: Published as a LETTER in J. Phys.: Condens. Matter; 8 pages; 6 figures; Online version at http://www.iop.org/EJ/S/3/1256/0hJAmc5sCL6d.7sOO.BtLw/abstract/0953-8984/14/3 6/102

Antiferromagnetism in stacked nanographite is investigated with using the Hubbard-type models. The A-B stacking or the stacking near to that of A-B type is favorable for the hexagonal nanographite with zigzag edges, in order that magnetism appears. Next, we find that the open shell electronic structure can be an origin of the decreasing magnetic moment with the decrease of the inter-graphene distance, as experiments on adsorption of molecules suggest., Comment: 13 pages; Harigaya's Web site: http://staff.aist.go.jp/k.harigaya/welcome_E.html; Nanotech. Inst. of AIST: http://unit.aist.go.jp/nanotech/

Nanographite systems, where graphene sheets of the orders of the nanometer size are stacked, show novel magnetic properties, such as, spin-glass like behaviors, and the change of ESR line widths while gas adsorptions. Recently, it has been found that magnetic moments decrease with the decrease of the interlayer distance while water molecules are attached physically. In this paper, we consider the mechanisms of antiferromagnetism using the Hubbard-type model...

Antiferromagnetism in stacked nanographite is investigated with using the Hubbard-type model. The A-B stacking is favorable for the hexagonal nanographite with zigzag edges, in order that magnetism appears. Next, we find that the open shell electronic structures can be origins of the decreasing magnetic moment with the decrease of the inter-graphene distance, as experiments on adsorption of molecules suggest., Comment: 4 pages, 3 figures