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Gudinas A, Moscatello J, Hollen SM. Defect identification and statistics toolbox: automated defect analysis for scanning probe microscopy images. J Phys Condens Matter 2020; 33:045901. [PMID: 33059332 DOI: 10.1088/1361-648x/abc1b2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Identifying and classifying defects in scanning probe microscopy (SPM) images is an important task that is tedious to perform by hand. In this paper we present the defect identification and statistics toolbox (DIST), an image processing toolbox for identifying and analyzing atomic defects in SPM images. DIST combines automation with user input to accurately and efficiently identify defects and automatically compute critical statistics. We describe using DIST for interactive image processing, generating contour plots for isolating extrema from an image background, and processes for identifying defects.
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Affiliation(s)
- Alana Gudinas
- University of New Hampshire, Department of Physics and Astronomy, 9 Library Way, Durham, NH 03824, United States of America
| | - Jason Moscatello
- University of New Hampshire, Department of Physics and Astronomy, 9 Library Way, Durham, NH 03824, United States of America
| | - Shawna M Hollen
- University of New Hampshire, Department of Physics and Astronomy, 9 Library Way, Durham, NH 03824, United States of America
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2
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Tikhomirova KA, Tantardini C, Sukhanova EV, Popov ZI, Evlashin SA, Tarkhov MA, Zhdanov VL, Dudin AA, Oganov AR, Kvashnin DG, Kvashnin AG. Exotic Two-Dimensional Structure: The First Case of Hexagonal NaCl. J Phys Chem Lett 2020; 11:3821-3827. [PMID: 32330050 DOI: 10.1021/acs.jpclett.0c00874] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
NaCl is one of the simplest compounds and was thought to be well-understood, and yet, unexpected complexities related to it were uncovered at high pressure and in low-dimensional states. Here, exotic hexagonal NaCl thin films on the (110) diamond surface were crystallized in the experiment following a theoretical prediction based on ab initio evolutionary algorithm USPEX. State-of-the-art calculations and experiments showed the existence of a hexagonal NaCl thin film, which is due to the strong chemical interaction of the NaCl film with the diamond substrate.
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Affiliation(s)
- Kseniya A Tikhomirova
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
| | - Christian Tantardini
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
| | - Ekaterina V Sukhanova
- Emanuel Institute of Biochemical Physics RAS, 4 Kosigina Street, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Pereulok, Dolgoprudny 141700, Russia
| | - Zakhar I Popov
- Emanuel Institute of Biochemical Physics RAS, 4 Kosigina Street, Moscow 119334, Russia
| | - Stanislav A Evlashin
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
| | - Mikhail A Tarkhov
- Institute of Nanotechnologies of Microelectronics of the Russian Academy of Sciences, 32 A Leninsky Prospekt, Moscow 119991, Russia
| | | | - Alexander A Dudin
- Institute of Nanotechnologies of Microelectronics of the Russian Academy of Sciences, 32 A Leninsky Prospekt, Moscow 119991, Russia
| | - Artem R Oganov
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Pereulok, Dolgoprudny 141700, Russia
- International Center for Materials Discovery, Northwestern Polytechnical University, Xi'an 710072, China
| | - Dmitry G Kvashnin
- Emanuel Institute of Biochemical Physics RAS, 4 Kosigina Street, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, 9 Institutsky Pereulok, Dolgoprudny 141700, Russia
| | - Alexander G Kvashnin
- Skolkovo Institute of Science and Technology, 30, bld. 1 Bolshoy Boulevard, Moscow 121205, Russia
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Kvashnin AG, Kvashnin DG, Oganov AR. Novel Unexpected Reconstructions of (100) and (111) Surfaces of NaCl: Theoretical Prediction. Sci Rep 2019; 9:14267. [PMID: 31582761 PMCID: PMC6776646 DOI: 10.1038/s41598-019-50548-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/12/2019] [Indexed: 11/09/2022] Open
Abstract
We have predicted stable reconstructions of the (100) and (111) surfaces of NaCl using the global optimization algorithm USPEX. Several new reconstructions, together with the previously reported ones, are found. For the cleaved bare (100) surface, pure Na and pure Cl are the only stable surface phases. Our study of the (111) surface shows that a newly predicted Na3Cl-(1 × 1) reconstruction is thermodynamically stable in a wide range of chlorine chemical potentials. It has a sawtooth-like profile where each facet reproduces the (100) surface of rock-salt NaCl, hinting on the preferred growth of the (100) surface. We used Bader charge analysis to explain the preferable formation of this sawtooth-like Na3Cl-(1 × 1) reconstruction of the (111) surface of NaCl. We find that at a very high chemical potential of Na, the polar (and normally absent) (111) surface becomes part of the equilibrium crystal morphology. At both very high and very low chemical potentials of Cl, we predict a large decrease of surface energy and fracture toughness (the Rehbinder effect).
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Affiliation(s)
- Alexander G Kvashnin
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, 3 Nobel Street, Moscow, 121205, Russia.,Moscow Institute of Physics and Technology, 9 Institutsky Pereulok, Dolgoprudny, 141700, Russia
| | - Dmitry G Kvashnin
- Emanuel Institute of Biochemical Physics RAS, 4 Kosigina Street, Moscow, 119334, Russia. .,National University of Science and Technology MISIS, 4 Leninskiy Prospekt, Moscow, 119049, Russia.
| | - Artem R Oganov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, 3 Nobel Street, Moscow, 121205, Russia.,Moscow Institute of Physics and Technology, 9 Institutsky Pereulok, Dolgoprudny, 141700, Russia.,International Center for Materials Discovery, Northwestern Polytechnical University, Xi'an, 710072, China
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Wagner M, Negreiros FR, Sementa L, Barcaro G, Surnev S, Fortunelli A, Netzer FP. Nanostripe pattern of NaCl layers on Cu(110). Phys Rev Lett 2013; 110:216101. [PMID: 23745897 DOI: 10.1103/physrevlett.110.216101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Indexed: 06/02/2023]
Abstract
A sodium chloride monolayer on a Cu(110) surface gives rise to a highly corrugated periodic nanostripe pattern of the (100) lattice as observed by scanning tunneling microscopy and low-energy electron diffraction. As revealed by density-functional calculations, this pattern is a consequence of the frustration of the overlayer-substrate chemical bonding produced by epitaxial mismatch. The coexistence of regions of strong Cu-Cl covalent and weak nonbonding interactions leads to a chemically induced topographic modulation here realized in a two-dimensional dielectric. The carpetlike growth of the NaCl layer across Cu step edges induces a distinct contrast inversion in the stripe pattern as a result of the change in epitaxial relationship due to the stacking sequence of the (110) Cu layers. It is demonstrated that the competition between local substrate-overlayer and intraoverlayer interactions can support a well-defined heteroepitaxial relationship of a ionic dielectric film and a metal surface, with important consequences for the nanoscale morphology and related properties.
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Affiliation(s)
- M Wagner
- Surface and Interface Physics, Institute of Physics, Karl-Franzens University Graz, A-8010 Graz, Austria
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Senanayake SD, Sadowski JT, Evans J, Kundu S, Agnoli S, Yang F, Stacchiola D, Flege JI, Hrbek J, Rodriguez JA. Nanopattering in CeOx/Cu(111): A New Type of Surface Reconstruction and Enhancement of Catalytic Activity. J Phys Chem Lett 2012; 3:839-843. [PMID: 26286407 DOI: 10.1021/jz300159p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Our results indicate that small amounts of an oxide deposited on a stable metal surface can trigger a massive surface reconstruction under reaction conditions. In low-energy electron microscopy (LEEM) experiments, no reconstruction of Cu(111) is observed after chemisorbing oxygen or after reducing O/Cu(111) in a CO atmosphere. On the other hand, LEEM images taken in situ during the reduction of CeO2/CuO1-x/Cu(111) show a complex nonuniform transformation of the surface morphology. Ceria particles act as nucleation sites for the growth of copper microterraces once CuO1-x is reduced. Can this reconstructed surface be used to enhance the catalytic activity of inverse oxide/metal catalysts? Indeed, CeOx on reconstructed Cu(111) is an extremely active catalyst for the water-gas shift process (CO + H2O → H2 + CO2), with the Cu microterraces providing very efficient sites for the dissociation of water and subsequent reaction with CO.
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Affiliation(s)
| | | | - Jaime Evans
- §Facultad de Ciencias, Universidad Central de Venezuela, Caracas, 1020-A Venezuela
| | | | | | | | | | - Jan I Flege
- ∥Institute of Solid State Physics, University of Bremen, Bremen, Germany
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Rasool HI, Song EB, Allen MJ, Wassei JK, Kaner RB, Wang KL, Weiller BH, Gimzewski JK. Continuity of graphene on polycrystalline copper. Nano Lett 2011; 11:251-256. [PMID: 21117698 DOI: 10.1021/nl1036403] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The atomic structure of graphene on polycrystalline copper substrates has been studied using scanning tunneling microscopy. The graphene overlayer maintains a continuous pristine atomic structure over atomically flat planes, monatomic steps, edges, and vertices of the copper surface. We find that facets of different identities are overgrown with graphene's perfect carbon honeycomb lattice. Our observations suggest that growth models including a stagnant catalytic surface do not apply to graphene growth on copper. Contrary to current expectations, these results reveal that the growth of macroscopic pristine graphene is not limited by the underlying copper structure.
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Affiliation(s)
- Haider I Rasool
- Deparment of Chemistry and Biochemistry and California NanoSystems Institute, University of California at Los Angeles, Los Angeles, California 90095, United States.
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Swart I, Gross L, Liljeroth P. Single-molecule chemistry and physics explored by low-temperature scanning probe microscopy. Chem Commun (Camb) 2011; 47:9011-23. [DOI: 10.1039/c1cc11404b] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Repp J, Meyer G. STM Manipulation of Single Atoms and Molecules on Insulating Films. Atomic and Molecular Manipulation. Elsevier; 2011. pp. 17-49. [DOI: 10.1016/b978-0-08-096355-6.00002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Corso M, Schiller F, Fernández L, Cordón J, Ortega JE. Electronic states in faceted Au(111) studied with curved crystal surfaces. J Phys Condens Matter 2009; 21:353001. [PMID: 21828621 DOI: 10.1088/0953-8984/21/35/353001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Vicinal Au(111) surfaces exhibit periodic faceting within a wide range of miscut angles. There, the system segregates two alternating phases with different step lattice constants d(w) and d(n). Using a curved crystal surface that allows a smooth variation of the surface orientation, we have studied, as a function of the miscut angle, the evolution of Au(111) faceted structures by scanning tunneling microscopy, and their electronic surface states by angle-resolved photoemission. We observe that surface bands reflect the two-phase character of the faceted system, i.e. we find d(w)- and d(n)-like states that evolve accordingly to the faceted structure. Using a photoemission calculation we prove that the apparently complex topology hides relatively simple physics, i.e. the same free-electron-like dispersion and repulsive step scattering that feature surface bands in stepped noble metal surfaces. On the grounds of such simulations, we discuss the possible interference of the electronic energy in the delicate free energy balance that determines the critical size of reconstructed (d(w)) and unreconstructed (d(n)) terraces during Au faceting.
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Affiliation(s)
- M Corso
- DIPC, Manuel Lardizábal 4, E-20018 San Sebastián, Spain
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De Padova P, Quaresima C, Perfetti P, Olivieri B, Leandri C, Aufray B, Vizzini S, Lay GL. Growth of straight, atomically perfect, highly metallic silicon nanowires with chiral asymmetry. Nano Lett 2008; 8:271-275. [PMID: 18092826 DOI: 10.1021/nl072591y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In the quest of nano-objects for future electronics, silicon nanowires could possibly take over carbon nanotubes. Here we show the growth by self-organization of straight, massively parallel silicon nanowires having a width of 1.6 nm, which are atomically perfect and highly metallic conductors. Surprisingly, these silicon nanowires display a strong symmetry breaking across their widths with two chiral species that self-assemble in large left-handed and right-handed magnetic-like domains.
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Abstract
Surface structures on wide band gap insulators and their use as templates for the growth of adsorbates are reviewed. Surface structures include evaporation structures, vicinal surfaces, facetted surfaces, epitaxial structures, or structures transferred to or induced by the growth of thin films. Most structures have been realized so far on Al(2)O(3) and on alkali halide crystals. The guided growth of adsorbates is discussed, considering the examples of metallic clusters or wires and ordered films of organic molecules.
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Affiliation(s)
- Roland Bennewitz
- Physics Department, McGill University, 3600 rue University, Montréal, Quebec H3A 2T8, Canada
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BRAUN KF, MORESCO F, MORGENSTERN K, FÖLSCH S, REPP J, HLA SW, MEYER G, RIEDER KH. MANIPULATION OF ATOMS AND MOLECULES FOR CONSTRUCTION OF NANOSYSTEMS: THE SCANNING TUNNELING MICROSCOPE AS AN OPERATIVE TOOL. Int J Nanosci 2003. [DOI: 10.1142/s0219581x03001218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Controlled manipulations with scanning tunneling microscope (STM) down to the scale of small molecules and single atoms allow to build molecular and atomic nanosystems, leading to the fascinating possibility of creating manmade structures on atomic scale. Here we present a short review on investigations based on atomic scale manipulation. Upon soft lateral manipulation of adsorbed species, in which only tip/particle forces are used, three different manipulation modes can be discerned: pushing, pulling and sliding. Even the manipulation of strongly bound native substrate atoms is possible. We demonstrate applications as local analytic and synthetic chemistry tools, with important consequences on surface structure research. Vertical manipulation of Xe and CO leads to improved imaging with functionalized tips. With CO deliberately transferred to the tip, we have also succeeded to perform vibrational spectroscopy on single molecules. Furthermore, we describe how we have reproduced a full chemical reaction with single molecules, whereby all basic steps, namely preparation of the reactants, diffusion and association, are induced with the STM tip. Here also field and electron current effects are employed. Finally, we have extended the manipulation techniques to large specially designed molecules by performing lateral manipulation in constant height and realizing the principle of a conformational molecular switch. Artificial nanoscale structures built in atom by atom fashion can serve as quantum laboratories for investigations of various physical properties.
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Affiliation(s)
- K.-F. BRAUN
- Institute for Experimental Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - F. MORESCO
- Institute for Experimental Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - K. MORGENSTERN
- Institute for Experimental Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - S. FÖLSCH
- Institute for Experimental Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - J. REPP
- Institute for Experimental Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - S. W. HLA
- Institute for Experimental Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - G. MEYER
- Institute for Experimental Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - K. H. RIEDER
- Institute for Experimental Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany
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Gross L, Moresco F, Alemani M, Tang H, Gourdon A, Joachim C, Rieder KH. Lander on Cu(2 1 1) – selective adsorption and surface restructuring by a molecular wire. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00366-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Repp J, Fölsch S, Meyer G, Rieder KH. Ionic films on vicinal metal surfaces: enhanced binding due to charge modulation. Phys Rev Lett 2001; 86:252-255. [PMID: 11177804 DOI: 10.1103/physrevlett.86.252] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2000] [Indexed: 05/23/2023]
Abstract
NaCl films on Cu(311) exhibit a remarkably strong and localized binding between adlayer and substrate. The binding sites of the ions in the NaCl film with respect to the Cu surface are determined from atomically resolved scanning tunneling microscopy images. A new model is proposed in which the binding mechanism is controlled by the charge modulation of a regularly stepped surface due to the Smoluchowski effect. This model can be extended to explain the growth of ionic adlayers on regularly stepped and kinked metal surfaces in general.
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Affiliation(s)
- J Repp
- Institut für Experimentalphysik, Freie Universität Berlin, Germany
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