@phdthesis{Mohn2012,
   abstract = {In this thesis work, a combination of low-temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM) was used to study single atoms and molecules on thin insulating films. We show that noncontact-AFM can yield important additional information for these systems, which had previously been studied only with STM.},
   author = {Fabian Mohn},
   doi = {10.5283/epub.25245},
   school = {University of Regensburg},
   journal = {epub.uni-regensburg.de},
   pages = {130},
   title = {Probing electronic and structural properties of single molecules on the atomic scale.},
   url = {https://epub.uni-regensburg.de/25245/},
   year = {2012}
}
@phdthesis{Stirling2014,
   abstract = {The class of instruments considered in this thesis, scanning probe microscopes (SPM), raster scan a sensory probe over a surface to form both high resolution images and quantitative interaction measurements. Understanding and extracting information from SPM data has been considered extensively in the three decades since the first SPM. Major developments tend to be greeted with their own theory and data analysis techniques. The more gradual evolution of equipment has not, however, attracted the same level of theoretical consideration. In this thesis we consider the SPM from an instrumentation perspective, concentrating on two specific types of microscope: the scanning tunnelling microscope (STM) and the atomic force microscope (AFM). Both of these microscopes rely on a sensory probe or sensor to induce and measure the desired interaction. We have carefully considered a range of experiments from a ‘sensor-eye-view’, both theoretically and experimentally. We first consider the effect of the geometry of AFM sensors on quantitative force measurements, identifying that the length of tips that the length of tips can induce an unwanted coupling of lateral and normal forces. We go further by developing methods to experimentally correct these force measurements along with designing a sensor which exploits symmetry to separate lateral and normal forces. We also consider the ways to automatically optimise the apex of the sensory probe of an STM to give the desired imaging resolution using a combination of prescribed routines and genetic algorithms. Image analysis techniques developed for this work have been developed into an open source toolbox to automatically process and analyse SPM images. Finally, we use control theory to analyse the feedback controlling the SPM probe. We find that the methods used in the literature do not fully consider the method with which the control loop is implemented in SPM. We employ a modified approach which results in more realistic simulated SPM operation.},
   author = {Julian Stirling},
   school = {University of Nottingham},
   pages = {215},
   title = {Scanning Probe Microscopy from the Perspective of the Sensor.},
   url = {http://eprints.nottingham.ac.uk/14000/1/Thesis.pdf},
   year = {2014}
}
@book{Voigtlander2007,
   author = {Bert Voigtländer},
   city = {Berlin, Heidelberg},
   doi = {10.1002/9783527612451.ch3},
   isbn = {9783527612451},
   journal = {Surface Characterization: A User's Sourcebook},
   keywords = {Atomic force microscope,Scanning probe microscopes,Scanning probe microscopy,Scanning tunnelling microscope,Visualization of surface microtopography},
   pages = {77-81},
   publisher = {Springer Berlin Heidelberg},
   title = {Scanning probe microscopy},
   url = {http://link.springer.com/10.1007/978-3-662-45240-0},
   year = {2007}
}
@article{Eigler1990,
   abstract = {SINCE its invention in the early 1980s by Binnig and Rohrer1,2, the scanning tunnelling microscope (STM) has provided images of surfaces and adsorbed atoms and molecules with unprecedented resolution. The STM has also been used to modify surfaces, for example by locally pinning molecules to a surface3 and by transfer of an atom from the STM tip to the surface4. Here we report the use of the STM at low temperatures (4 K) to position individual xenon atoms on a single-crystal nickel surface with atomic pre-cision. This capacity has allowed us to fabricate rudimentary structures of our own design, atom by atom. The processes we describe are in principle applicable to molecules also. In view of the device-like characteristics reported for single atoms on surfaces5,6, the possibilities for perhaps the ultimate in device miniaturization are evident. © 1990 Nature Publishing Group.},
   author = {D. M. Eigler and E. K. Schweizer},
   doi = {10.1038/344524a0},
   issn = {00280836},
   issue = {6266},
   journal = {Nature},
   keywords = {Humanities and Social Sciences,Science,multidisciplinary},
   pages = {524-526},
   publisher = {Nature Publishing Group},
   title = {Positioning single atoms with a scanning tunnelling microscope},
   volume = {344},
   url = {https://www.nature.com/articles/344524a0},
   year = {1990}
}
@article{Morgenstern2013,
   author = {Karina Morgenstern and Nicolas Lorente and Karl-Heinz Rieder},
   issue = {9},
   journal = {Phys. Status Solidi B},
   pages = {1671-1751},
   title = {Controlled manipulation of single atoms and small molecules using the scanning tunnelling microscope},
   volume = {250},
   url = {http://onlinelibrary.wiley.com/doi/10.1002/pssb.201248392/full papers2://publication/doi/10.1002/pssb.201248392},
   year = {2013}
}
@article{Avouris1995,
   author = {Phaedon Avouris},
   doi = {10.1021/ar00051a002},
   issn = {15204898},
   issue = {3},
   journal = {Accounts of Chemical Research},
   pages = {95-102},
   title = {Manipulation of Matter at the Atomic and Molecular Levels},
   volume = {28},
   url = {https://pubs.acs.org/doi/abs/10.1021/ar00051a002},
   year = {1995}
}
@article{Otte2016,
   abstract = {The advent of devices based on single dopants, such as the single-atom transistor, the single-spin magnetometer and the single-atom memory, has motivated the quest for strategies that permit the control of matter with atomic precision. Manipulation of individual atoms by lowerature scanning tunnelling microscopy provides ways to store data in atoms, encoded either into their charge state, magnetization state or lattice position. A clear challenge now is the controlled integration of these individual functional atoms into extended, scalable atomic circuits. Here, we present a robust digital atomic-scale memory of up to 1kilobyte (8,000bits) using an array of individual surface vacancies in a chlorine-terminated Cu(100) surface. The memory can be read and rewritten automatically by means of atomic-scale markers and offers an areal density of 502terabits per square inch, outperforming state-of-the-art hard disk drives by three orders of magnitude. Furthermore, the chlorine vacancies are found to be stable at temperatures up to 77K, offering the potential for expanding large-scale atomic assembly towards ambient conditions.},
   author = {F. E. Kalff and M. P. Rebergen and E. Fahrenfort and J. Girovsky and R. Toskovic and J. L. Lado and J. Fernández-Rossier and A. F. Otte},
   doi = {10.1038/nnano.2016.131},
   issn = {17483395},
   issue = {11},
   journal = {Nature Nanotechnology},
   keywords = {Scanning probe microscopy,Structural properties,Surface patterning,Surfaces,interfaces and thin films},
   pages = {926-929},
   pmid = {27428273},
   publisher = {Nature Publishing Group},
   title = {A kilobyte rewritable atomic memory},
   volume = {11},
   url = {www.nature.com/naturenanotechnology},
   year = {2016}
}
@article{Crommie1993,
   abstract = {A method for confining electrons to artificial structures at the nanometer lengthscale is presented. Surface state electrons on a copper(111) surface were confined to closed structures (corrals) defined by barriers built from iron adatoms. The barriers were assembled by individually positioning iron adatoms with the tip of a 4-kelvin scanning tunneling microscope (STM). A circular corral of radius 71.3 Å was constructed in this way out of 48 iron adatoms. Tunneling spectroscopy performed inside of the corral revealed a series of discrete resonances, providing evidence for size quantization. STM images show that the corral's interior local density of states is dominated by the eigenstate density expected for an electron trapped in a round two-dimensional box.},
   author = {M. F. Crommie and C. P. Lutz and D. M. Eigler},
   doi = {10.1126/science.262.5131.218},
   issn = {00368075},
   issue = {5131},
   journal = {Science},
   pages = {218-220},
   pmid = {17841867},
   publisher = {American Association for the Advancement of Science},
   title = {Confinement of electrons to quantum corrals on a metal surface},
   volume = {262},
   url = {http://science.sciencemag.org/},
   year = {1993}
}
@article{Rashidi2018,
   abstract = {Atomic scale characterization and manipulation with scanning probe microscopy rely upon the use of an atomically sharp probe. Here we present automated methods based on machine learning to automatically detect and recondition the quality of the probe of a scanning tunneling microscope. As a model system, we employ these techniques on the technologically relevant hydrogen-terminated silicon surface, training the network to recognize abnormalities in the appearance of surface dangling bonds. Of the machine learning methods tested, a convolutional neural network yielded the greatest accuracy, achieving a positive identification of degraded tips in 97\% of the test cases. By using multiple points of comparison and majority voting, the accuracy of the method is improved beyond 99\%. The methods described here can easily be generalized to other material systems and nanoscale imaging techniques.},
   author = {Mohammad Rashidi and Robert A. Wolkow},
   doi = {10.1021/acsnano.8b02208},
   issn = {1936-0851},
   issue = {6},
   journal = {ACS Nano},
   keywords = {1,11,atoms using scanning probe,convolutional neural network,he ability to directly,hydrogen terminated silicon,in situ tip conditioning,machine learning,microscopy,scanning probe microscopy,spm,surface dangling bonds,visualize and manipulate individual},
   pages = {5185-5189},
   title = {Autonomous Scanning Probe Microscopy in-situ Tip Conditioning through Machine Learning},
   volume = {12},
   url = {http://arxiv.org/abs/1803.07059},
   year = {2018}
}
@article{Celotta2014,
   abstract = {A major goal of nanotechnology is to develop the capability to arrange matter at will by placing individual atoms at desired locations in a predetermined configuration to build a nanostructure with specific properties or function. The scanning tunneling microscope has demonstrated the ability to arrange the basic building blocks of matter, single atoms, in two-dimensional configurations. An array of various nanostructures has been assembled, which display the quantum mechanics of quantum confined geometries. The level of human interaction needed to physically locate the atom and bring it to the desired location limits this atom assembly technology. Here we report the use of autonomous atom assembly via path planning technology; this allows atomically perfect nanostructures to be assembled without the need for human intervention, resulting in precise constructions in shorter times. We demonstrate autonomous assembly by assembling various quantum confinement geometries using atoms and molecules and describe the benefits of this approach.},
   author = {Robert J. Celotta and Stephen B. Balakirsky and Aaron P. Fein and Frank M. Hess and Gregory M. Rutter and Joseph A. Stroscio},
   doi = {10.1063/1.4902536},
   issn = {10897623},
   issue = {12},
   journal = {Review of Scientific Instruments},
   pmid = {25554264},
   title = {Autonomous assembly of atomically perfect nanostructures using a scanning tunneling microscope},
   volume = {85},
   year = {2014}
}
@techReport{Xu2018,
   abstract = {Adaptive immunity is analogous to machine learning as the immune system learns about dangerous pathogens and discriminates them from safe self-molecules. Each immune cell has a unique receptor for specific immunological recognition. The binding affinity between the receptors and antigenic peptides mainly determines immunological recognition followed by subsequent responses. Is the integrated binding affinity sufficient to probe the digital information of peptide sequences? To answer this fundamental question, we examined whether the affinity-based discrimination of peptide sequences is learnable and generalizable by artificial neural networks (ANNs) that process the digital information of receptors and peptides. We made use of large scale high-throughput data of T-cell receptors (TCRs) and open-source peptides amino acid sequences as the input layer data, and computationally examined the success and failure of immune recognition based on the pairwise binding energy of their amino acid sequences as output layer data. Machine learning successfully captured the relevant information of molecular interactions and discriminated between strong and weak affinity pairs. This suggests the potential applicability of artificial neural networks to predict the immune responsiveness of certain antigenic peptides once their sequence information is provided. In addition, we used two methods to describe amino acids: with and without considering the amino acid strength. The sequences with heterogeneous strengths of amino acids diminished TCR "reading" of the exact information of each amino acid site on the peptides for the immune response. This may be why natural TCRs have moderate amino acid compositions after thymic selection. 3},
   author = {Jin Xu and Junghyo Jo},
   journal = {undefined},
   title = {Artificial neural networks for immunological recognition},
   year = {2018}
}
@article{Tordeux2018,
   abstract = {Pedestrian behaviours tend to depend on the type of facility. Therefore accurate predictions of pedestrians movements in complex geometries (including corridor, bottleneck or intersection) are difficult to achieve for classical models with few parameters. Artificial neural networks have multiple parameters and are able to identify various types of patterns. They could be a suitable alternative for forecasts. We aim in this paper to present first steps testing this approach. We compare estimations of pedestrian speed with a classical model and a neural network for combinations of corridor and bottleneck experiments. The results show that the neural network is able to differentiate the two geometries and to improve the estimation of pedestrian speeds when the geometries are mixed.},
   author = {Antoine Tordeux and Mohcine Chraibi and Armin Seyfried and Andreas Schadschneider},
   journal = {Traffic and Granular Flow '17},
   pages = {327-335},
   publisher = {Springer International Publishing},
   title = {Prediction of Pedestrian Speed with Artificial Neural Networks},
   url = {http://arxiv.org/abs/1801.09782},
   year = {2018}
}
@inproceedings{Bimbraw2015,
   abstract = {The field of autonomous automation is of interest to researchers, and much has been accomplished in this area, of which this paper presents a detailed chronology. This paper can help one understand the trends in autonomous vehicle technology for the past, present, and future. We see a drastic change in autonomous vehicle technology since 1920s, when the first radio controlled vehicles were designed. In the subsequent decades, we see fairly autonomous electric cars powered by embedded circuits in the roads. By 1960s, autonomous cars having similar electronic guide systems came into picture. 1980s saw vision guided autonomous vehicles, which was a major milestone in technology and till date we use similar or modified forms of vision and radio guided technologies. Various semi-autonomous features introduced in modern cars such as lane keeping, automatic braking and adaptive cruise control are based on such systems. Extensive network guided systems in conjunction with vision guided features is the future of autonomous vehicles. It is predicted that most companies will launch fully autonomous vehicles by the advent of next decade. The future of autonomous vehicles is an ambitious era of safe and comfortable transportation.},
   author = {Keshav Bimbraw},
   doi = {10.5220/0005540501910198},
   isbn = {9789897581229},
   booktitle = {ICINCO 2015 - 12th International Conference on Informatics in Control, Automation and Robotics, Proceedings},
   keywords = {Automation,Autonomous cars,Autonomous vehicles,Cars,Intelligent transportation technologies and system,Mechatronics systems},
   pages = {191-198},
   publisher = {SciTePress},
   title = {Autonomous cars: Past, present and future: A review of the developments in the last century, the present scenario and the expected future of autonomous vehicle technology},
   volume = {1},
   year = {2015}
}
@article{Giaever1960,
   author = {Ivar Giaever},
   doi = {10.1103/PhysRevLett.5.147},
   issn = {00319007},
   issue = {4},
   journal = {Physical Review Letters},
   pages = {147-148},
   title = {Energy gap in superconductors measured by electron tunneling},
   volume = {5},
   url = {https://link.aps.org/doi/10.1103/PhysRevLett.5.147},
   year = {1960}
}
@article{Schlier1959,
   abstract = {Diffraction patterns obtained from atomically clean germanium surfaces contained half-integral order beams in (110) azimuths for both (100) and (110) surfaces and in all azimuths for the (111) surface. These results are considered to be due to displacements of surface atoms from their normal bulk lattice positions in the surface plane. Adsorption of oxygen on all of these surfaces extinguished all of the diffraction beams which were not integral order. In addition to the normal surface lattice spacings of clean (111) and (100) surfaces of silicon, there were surface structures with larger spacings, most of which depended on the conditions of ion bombardment and/or subsequent heat treatment. Two such structures have been observed for the (100) surface of silicon; one is a double-spaced lattice in the (110) azimuth, similar to that for germanium, and the other has a spacing about 8% greater than that of normal silicon and was obtained only after radiation quenching of the crystal from 1000°C. Two large-spaced structures were observed for the (111) surface. All of these structures were extinguished by exposure to oxygen. Evidence is presented which indicates that these structures were not due to contamination but to the silicon itself. The method of determining the kinetics of gas adsorption from the low-energy electron diffraction beams is outlined and the calculations of the fractional coverage and sticking probability are presented for oxygen. For silicon crystals, the calculations of surface coverages and sticking coefficients for oxygen were found to depend on the preceding treatments of the crystals. The rate of adsorption of oxygen was proportional to the pressure, at least for pressures below 10-6 mm Hg, and depended on the preceding treatments of the crystals. After oxygen adsorption, the clean germanium surface could be regenerated by heating at 500°C for 30 min and for silicon it was regenerated by heating at 900°C for a few minutes. A comparison with results of other observers is given.},
   author = {R. E. Schlier and H. E. Farnsworth},
   doi = {10.1063/1.1730126},
   issn = {00219606},
   issue = {4},
   journal = {The Journal of Chemical Physics},
   pages = {917-926},
   title = {Structure and adsorption characteristics of clean surfaces of germanium and silicon},
   volume = {30},
   url = {http://aip.scitation.org/doi/10.1063/1.1730126},
   year = {1959}
}
@article{Binnig1983,
   abstract = {The 7 × 7 reconstruction on Si(111) was observed in real space by scanning tunneling microscopy. The experiment strongly favors a modified adatom model with 12 adatoms per unit cell and an inhomogeneously relaxed underlying top layer. © 1983 The American Physical Society.},
   author = {G. Binnig and H. Rohrer and Ch Gerber and E. Weibel},
   doi = {10.1103/PhysRevLett.50.120},
   issn = {00319007},
   issue = {2},
   journal = {Physical Review Letters},
   pages = {120-123},
   title = {7 × 7 Reconstruction on Si(111) Resolved in Real Space},
   volume = {50},
   url = {https://link.aps.org/doi/10.1103/PhysRevLett.50.120},
   year = {1983}
}
@article{Giessibl2000,
   abstract = {The atomic force microscope images surfaces by sensing the forces between a sharp tip and a sample. If the tip-sample interaction is dominated by short- range forces due to the formation of covalent bonds, the image of an individual atom should reflect the angular symmetry of the interaction. Here, we report on a distinct substructure in the images of individual adatoms on silicon (111)- (7x7), two crescents with a spherical envelope. The crescents are interpreted as images of two atomic orbitals of the front atom of the tip. Key for the observation of these subatomic features is a force-detection scheme with superior noise performance and enhanced sensitivity to short-range forces.},
   author = {Franz J. Giessibl and S. Hembacher and H. Bielefeldt and J. Mannhart},
   doi = {10.1126/science.289.5478.422},
   issn = {00368075},
   issue = {5478},
   journal = {Science},
   pages = {422-425},
   title = {Subatomic features on the silicon (111)-(7x7) surface observed by atomic force microscopy},
   volume = {289},
   url = {www.sciencemag.org},
   year = {2000}
}
@article{Takayanagi1985,
   abstract = {Structural analysis of the surface reconstructions investigated by ultrahigh vacuum (UHV) transmission electron microscopy(TEM) and diffraction (TED) is shown. By TED intensity analysis a new structural model of Si(111)‐7×7 is derived. The model basically consists of 12 adatoms arranged locally in the 2×2 structure, nine dimers on the sides of the triangular subunits of the 7×7 unit cell and a stacking fault layer. UHV–HREM of Si (111)‐7×7 surface is commented.},
   author = {K. Takayanagi and Y. Tanishiro and M. Takahashi and S. Takahashi},
   doi = {10.1116/1.573160},
   issn = {0734-2101},
   issue = {3},
   journal = {Journal of Vacuum Science \& Technology A: Vacuum, Surfaces, and Films},
   pages = {1502-1506},
   publisher = {American Vacuum Society},
   title = {Structural analysis of Si(111)‐7×7 by UHV‐transmission electron diffraction and microscopy},
   volume = {3},
   url = {http://avs.scitation.org/doi/10.1116/1.573160},
   year = {1985}
}
@article{Giessibl1995,
   abstract = {Achieving high resolution under ultrahigh-vacuum conditions with the force microscope can be difficult for reactive surfaces, where the interaction forces between the tip and the samples can be relatively large. A force detection scheme that makes use of a modified cantilever beam and senses the force gradient through frequency modulation is described. The reconstructed silicon (111)-(7x7) surface was imaged in a noncontact mode by force microscopy with atomic resolution (6 angstroms lateral, 0.1 angstrom vertical).},
   author = {Franz J. Giessibl},
   doi = {10.1126/science.267.5194.68},
   issn = {00368075},
   issue = {5194},
   journal = {Science},
   pages = {68-71},
   pmid = {17840059},
   publisher = {American Association for the Advancement of Science},
   title = {Atomic resolution of the silicon (111)-(7x7) surface by atomic force microscopy},
   volume = {267},
   url = {https://www.sciencemag.org/lookup/doi/10.1126/science.267.5194.68},
   year = {1995}
}
@article{Chiutu2012,
   abstract = {We show that the precise orientation of a C60 molecule which terminates the tip of a scanning probe microscope can be determined with atomic precision from submolecular contrast images of the fullerene cage. A comparison of experimental scanning tunneling microscopy data with images simulated using computationally inexpensive Hückel theory provides a robust method of identifying molecular rotation and tilt at the end of the probe microscope tip. Noncontact atomic force microscopy resolves the atoms of the C60 cage closest to the surface for a range of molecular orientations at tip-sample separations where the molecule-substrate interaction potential is weakly attractive. Measurements of the C60C60 pair potential acquired using a fullerene-terminated tip are in excellent agreement with theoretical predictions based on a pairwise summation of the van der Waals interactions between C atoms in each cage, i.e., the Girifalco potential [L. Girifalco, J. Phys. Chem. 95, 5370 (1991)].},
   author = {C. Chiutu and A. M. Sweetman and A. J. Lakin and A. Stannard and S. Jarvis and L. Kantorovich and J. L. Dunn and P. Moriarty},
   doi = {10.1103/PhysRevLett.108.268302},
   isbn = {0031-9007\n1079-7114},
   issn = {00319007},
   issue = {26},
   journal = {Physical Review Letters},
   pages = {268302},
   pmid = {23005019},
   title = {Precise orientation of a single C 60 molecule on the tip of a scanning probe microscope},
   volume = {108},
   url = {https://link.aps.org/doi/10.1103/PhysRevLett.108.268302},
   year = {2012}
}
@article{Davey1925,
   abstract = {The lattice constant a has been determined within 0.1 percent (.03 percent for W) for aluminum, iron, nickel, copper, molybdenum, palladium, silver, tungsten, platinum, gold, lead and bismuth, by direct comparison with NaCl, a(NaCl)=2.814A. As pure samples as could be obtained were used, from 99.55 percent for Ni to 99.9995 percent for tungsten, and in many cases commercially pure samples were also measured for comparison. The results for the purest samples are summarized in Table XIII. The density from the x-ray data is in each case (except Al and Ag) greater than the density of the bulk metal as given in the literature, the difference being rather large for Mo (10.21 vs 9.1), for Pd (12.25 vs 11.9) and W (19.32 vs 18.77). For pure W remarkably sharp lines were obtained. For Bi a piece of a single artificial crystal was used. © 1925 The American Physical Society.},
   author = {Wheeler P. Davey},
   doi = {10.1103/PhysRev.25.753},
   issn = {0031899X},
   issue = {6},
   journal = {Physical Review},
   pages = {753-761},
   title = {Precision measurements of the lattice constants of twelve common metals},
   volume = {25},
   url = {https://link.aps.org/doi/10.1103/PhysRev.25.753},
   year = {1925}
}
@article{Yothers2017,
   abstract = {We have developed a real-space method to correct distortion due to thermal drift and piezoelectric actuator nonlinearities on scanning tunneling microscope images using Matlab. The method uses the known structures typically present in high-resolution atomic and molecularly-resolved images as an internal standard. Each image feature (atom or molecule) is first identified in the image. The locations of each feature's nearest neighbors (NNs) are used to measure the local distortion at that location. The local distortion map across the image is simultaneously fit to our distortion model, which includes thermal drift in addition to piezoelectric actuator hysteresis and creep. The image coordinates of the features and image pixels are corrected using an inverse transform from the distortion model. We call this technique the thermal-drift, hysteresis, and creep transform (DHCT). Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional real-space image analyses are now possible with these corrected images. Using graphite(0001) as model system, we show lattice fitting to the corrected image, averaged unit cell images, and symmetry-averaged unit cell images. Statistical analysis of the distribution of the image features around their best-fit lattice sites measures the aggregate noise in the image, which can be expressed as feature confidence ellipsoids.},
   author = {Mitchell P Yothers and Aaron E Browder and Lloyd A Bumm},
   doi = {10.1063/1.4974271},
   journal = {Review of Scientific Instruments},
   pages = {013708},
   title = {Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images},
   volume = {88},
   url = {https://doi.org/10.1063/1.4974271},
   year = {2017}
}
@article{Gordon2020,
   abstract = {Currently, researchers spend significant time manually searching through large volumes of data produced during scanning probe imaging to identify specific patterns and motifs formed via self-assembly and self-organization. Here, we use a combination of Monte Carlo simulations, general statistics, and machine learning to automatically distinguish several spatially correlated patterns in a mixed, highly varied data set of real AFM images of self-organized nanoparticles. We do this regardless of feature-scale and without the need for manually labeled training data. Provided that the structures of interest can be simulated, the strategy and protocols we describe can be easily adapted to other self-organized systems and data sets. This article has not yet been cited by other publications.},
   author = {Oliver M. Gordon and Jo E. A. Hodgkinson and Steff M. Farley and Eugénie L. Hunsicker and Philip J. Moriarty},
   doi = {10.1021/acs.nanolett.0c03213},
   issn = {1530-6984},
   issue = {10},
   journal = {Nano Letters},
   keywords = {Atomic Force Microscopy,Dewetting,File Search,Machine Learning,Monte Carlo,Nanoparticle},
   pages = {7688-7693},
   publisher = {American Chemical Society (ACS)},
   title = {Automated Searching and Identification of Self-Organized Nanostructures},
   volume = {20},
   url = {https://dx.doi.org/10.1021/acs.nanolett.0c03213},
   year = {2020}
}
@article{Carleo2019,
   abstract = {Machine learning encompasses a broad range of algorithms and modeling tools used for a vast array of data processing tasks, which has entered most scientific disciplines in recent years. We review in a selective way the recent research on the interface between machine learning and physical sciences. This includes conceptual developments in machine learning (ML) motivated by physical insights, applications of machine learning techniques to several domains in physics, and cross-fertilization between the two fields. After giving basic notion of machine learning methods and principles, we describe examples of how statistical physics is used to understand methods in ML. We then move to describe applications of ML methods in particle physics and cosmology, quantum many body physics, quantum computing, and chemical and material physics. We also highlight research and development into novel computing architectures aimed at accelerating ML. In each of the sections we describe recent successes as well as domain-specific methodology and challenges.},
   author = {Giuseppe Carleo and Ignacio Cirac and Kyle Cranmer and Laurent Daudet and Maria Schuld and Naftali Tishby and Leslie Vogt-Maranto and Lenka Zdeborová},
   doi = {10.1103/RevModPhys.91.045002},
   issue = {4},
   journal = {Reviews of Modern Physics},
   pages = {045002},
   title = {Machine learning and the physical sciences},
   volume = {91},
   url = {http://arxiv.org/abs/1903.10563 http://dx.doi.org/10.1103/RevModPhys.91.045002 https://link.aps.org/doi/10.1103/RevModPhys.91.045002},
   year = {2019}
}
@article{Mehta2018,
   abstract = {Machine Learning (ML) is one of the most exciting and dynamic areas of modern research and application. The purpose of this review is to provide an introduction to the core concepts and tools of machine learning in a manner easily understood and intuitive to physicists. The review begins by covering fundamental concepts in ML and modern statistics such as the bias-variance tradeoff, overfitting, regularization, generalization, and gradient descent before moving on to more advanced topics in both supervised and unsupervised learning. Topics covered in the review include ensemble models, deep learning and neural networks, clustering and data visualization, energy-based models (including MaxEnt models and Restricted Boltzmann Machines), and variational methods. Throughout, we emphasize the many natural connections between ML and statistical physics. A notable aspect of the review is the use of Python Jupyter notebooks to introduce modern ML/statistical packages to readers using physics-inspired datasets (the Ising Model and Monte-Carlo simulations of supersymmetric decays of proton-proton collisions). We conclude with an extended outlook discussing possible uses of machine learning for furthering our understanding of the physical world as well as open problems in ML where physicists may be able to contribute. (Notebooks are available at https://physics.bu.edu/~pankajm/MLnotebooks.html )},
   author = {Pankaj Mehta and Marin Bukov and Ching-Hao Wang and Alexandre G. R. Day and Clint Richardson and Charles K. Fisher and David J. Schwab},
   doi = {10.1016/j.physrep.2019.03.001},
   journal = {Physics Reports},
   pages = {1-124},
   publisher = {Elsevier B.V.},
   title = {A high-bias, low-variance introduction to Machine Learning for physicists},
   volume = {810},
   url = {http://arxiv.org/abs/1803.08823 http://dx.doi.org/10.1016/j.physrep.2019.03.001},
   year = {2018}
}
@article{Zdeborova2017,
   abstract = {A recent burst of activity in applying machine learning to tackle fundamental questions in physics suggests that associated techniques may soon become as common in physics as numerical simulations or calculus.},
   author = {Lenka Zdeborová},
   doi = {10.1038/nphys4053},
   issue = {5},
   journal = {Nature Physics},
   pages = {420-421},
   title = {New tool in the box},
   volume = {13},
   url = {https://doi.org/10.1038/nphys4053},
   year = {2017}
}
@misc{Si_a,
   title = {CODATA Value: lattice parameter of silicon},
   url = {https://physics.nist.gov/cgi-bin/cuu/Value?asil}
}
@article{Du2010,
   abstract = {The adsorption properties of individual fullerene molecules at room-temperature have been investigated by scanning tunneling microscopy. Statistical analysis of the images demonstrates that fullerene molecules prefer to adsorb on five specific sites: corner hole, the middle of the faulted and unfaulted parts, and the top of the rest atoms within the faulted and unfaulted parts. High-resolution images of individual fullerene molecules on each of the adsorption sites show distinct intramolecular structures. By combining these internal fine structures with theoretical simulations, the molecular orientations at each of the adsorption sites can be unambiguously determined. © 2010 American Institute of Physics.},
   author = {Xinli Du and Feng Chen and Xiu Chen and Xianxin Wu and Yingxiang Cai and Xiaoqing Liu and Li Wang},
   doi = {10.1063/1.3529446},
   issn = {00036951},
   issue = {25},
   journal = {Applied Physics Letters},
   title = {Adsorption geometry of individual fullerene on Si surface at room-temperature},
   volume = {97},
   year = {2010}
}
@article{Kroto1991,
   author = {H W Kroto and A W Allaf and S P Balm},
   isbn = {1959632124},
   journal = {Chem. Rev},
   pages = {1213-1235},
   title = {C60: Buckminsterfullerene},
   volume = {91},
   url = {https://pubs.acs.org/sharingguidelines},
   year = {1991}
}
@article{Rashidi2019,
   abstract = {As the development of atom scale devices transitions from novel, proof-of-concept demonstrations to state-of-the-art commercial applications, automated assembly of such devices must be implemented. Here we present an automation method for the identification of defects prior to atomic fabrication via hydrogen lithography using deep learning. We trained a convolutional neural network to locate and differentiate between surface features of the technologically relevant hydrogen-terminated silicon surface imaged using a scanning tunneling microscope. Once the positions and types of surface features are determined, the predefined atomic structures are patterned in a defect-free area. By training the network to differentiate between common defects we are able to avoid charged defects as well as edges of the patterning terraces. Augmentation with previously developed autonomous tip shaping and patterning modules allows for atomic scale lithography with minimal user intervention.},
   author = {Mohammad Rashidi and Jeremiah Croshaw and Kieran Mastel and Marcus Tamura and Hedieh Hosseinzadeh and Robert A. Wolkow},
   doi = {10.1088/2632-2153/ab6d5e},
   issn = {2632-2153},
   issue = {2},
   journal = {Machine Learning: Science and Technology},
   keywords = {Automated fabrication,Convolutional neural network,Hydrogen terminated silicon,Scanning probe microscopy,Surface dangling bonds},
   pages = {025001},
   publisher = {arXiv},
   title = {Deep learning-guided surface characterization for autonomous hydrogen lithography},
   volume = {1},
   url = {https://doi.org/10.1088/2632-2153/ab6d5e},
   year = {2019}
}
@article{Gordon2019,
   abstract = {One of the largest obstacles facing scanning probe microscopy is the constant need to correct flaws in the scanning probe in situ. This is currently a manual, time-consuming process that would benefit greatly from automation. Here we introduce a convolutional neural network protocol that enables automated recognition of a variety of desirable and undesirable scanning probe tip states on both metal and non-metal surfaces. By combining the best performing models into majority voting ensembles, we find that the desirable states of H:Si(100) can be distinguished with a mean precision of 0.89 and an average receiver-operator-characteristic curve area of 0.95. More generally, high and low-quality tips can be distinguished with a mean precision of 0.96 and near perfect area-under-curve of 0.98. With trivial modifications, we also successfully automatically identify undesirable, non-surface-specific states on surfaces of Au(111) and Cu(111). In these cases we find mean precisions of 0.95 and 0.75 and area-under-curves of 0.98 and 0.94, respectively.},
   author = {O. Gordon and P. D'Hondt and L. Knijff and S. Freeney and F. Junqueira and P. Moriarty and I. Swart},
   doi = {10.1063/1.5099590},
   issue = {111},
   journal = {Review of Scientific Instruments},
   pages = {103704},
   title = {Scanning Probe State Recognition With Multi-Class Neural Network Ensembles},
   volume = {90},
   url = {http://arxiv.org/abs/1903.09101},
   year = {2019}
}
@article{Giessibl2003,
   abstract = {This article reviews the progress of atomic force microscopy in ultrahigh vacuum, starting with its invention and covering most of the recent developments. Today, dynamic force microscopy allows us to image surfaces of conductors and insulators in vacuum with atomic resolution. The most widely used technique for atomic-resolution force microscopy in vacuum is frequency-modulation atomic force microscopy (FM-AFM). This technique, as well as other dynamic methods, is explained in detail in this article. In the last few years many groups have expanded the empirical knowledge and deepened our theoretical understanding of frequency-modulation atomic force microscopy. Consequently spatial resolution and ease of use have been increased dramatically. Vacuum atomic force microscopy opens up new classes of experiments, ranging from imaging of insulators with true atomic resolution to the measurement of forces between individual atoms.},
   author = {Franz J Giessibl},
   doi = {10.1103/RevModPhys.75.949},
   issue = {3},
   journal = {Reviews of Modern Physics},
   pages = {949-983},
   title = {Advances in atomic force microscopy},
   volume = {75},
   url = {https://link.aps.org/doi/10.1103/RevModPhys.75.949},
   year = {2003}
}
@article{Sweetman2016,
   abstract = {It is generally accepted that the exposed surfaces of silicon crystals are highly reactive due to the dangling bonds which protrude into the vacuum. However, surface reconstruction not only modifies the reactivity of bulk silicon crystals, but also plays a key role in determining the properties of silicon nanocrystals. In this study we probe the reactivity of silicon clusters at the end of a scanning probe tip by examining their interaction with closed-shell fullerene molecules. Counter to intuitive expectations, many silicon clusters do not react strongly with the fullerene cage, and we find that only specific highly oriented clusters have sufficient reactivity to break open the existing carbon-carbon bonds.},
   author = {Adam Sweetman and Julian Stirling and Samuel Paul Jarvis and Philipp Rahe and Philip Moriarty},
   doi = {10.1103/PhysRevB.94.115440},
   journal = {PHYSICAL REVIEW B},
   pages = {115440},
   title = {Measuring the reactivity of a silicon-terminated probe},
   volume = {94},
   year = {2016}
}
@article{Samuel1959,
   abstract = {Two machine-learning procedures have been investigated in some detail using the game of checkers. Enough work has been done to verify the fact that a computer can be programmed so that it will learn to play a better game of checkers than can be played by the person who wrote the program. Furthermore, it can learn to do this in a remarkably short period of time (8 or 10 hours of machine-playing time) when given only the rules of the game, a sense of direction, and a redundant and incomplete list of parameters which are thought to have something to do with the game, but whose correct signs and relative weights are unknown and unspecified. The principles of machine learning verified by these experiments are, of course, applicable to many other situations.},
   author = {A. L. Samuel},
   doi = {10.1147/rd.33.0210},
   issn = {0018-8646},
   issue = {3},
   journal = {IBM Journal of Research and Development},
   pages = {210-229},
   title = {Some Studies in Machine Learning Using the Game of Checkers},
   volume = {3},
   url = {http://ieeexplore.ieee.org/document/5392560/},
   year = {1959}
}
@article{Woolley2011,
   abstract = {We describe the development and application of an imaging protocol, which evolves a scanning probe's atomic structure in parallel with automated optimization of the scan parameters. Our protocol coerces the system into a state that produces a specific atomic resolution image type without human involvement. © 2011 American Institute of Physics.},
   author = {Richard A.J. Woolley and Julian Stirling and Adrian Radocea and Natalio Krasnogor and Philip Moriarty},
   doi = {10.1063/1.3600662},
   issn = {00036951},
   issue = {25},
   journal = {Applied Physics Letters},
   keywords = {automation,genetic algorithms,graphite,optimisation,scanning probe microscopy},
   pages = {253104},
   publisher = {American Institute of PhysicsAIP},
   title = {Automated probe microscopy via evolutionary optimization at the atomic scale},
   volume = {98},
   url = {http://aip.scitation.org/doi/10.1063/1.3600662},
   year = {2011}
}
@book{Bai2000,
   author = {Chunli. Bai},
   city = {Berlin},
   isbn = {3540657150},
   journal = {Scanning tunneling microscopy and its applications},
   keywords = {Scanning tunneling microscopy},
   pages = {368},
   publisher = {Springer},
   title = {Scanning tunneling microscopy and its applications},
   year = {2000}
}
@article{Seo2017,
   abstract = {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 ∼4×1010 molecules/(cm2·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.},
   author = {Eonmi Seo and Daejin Eom and Jung Min Hyun and Hanchul Kim and Ja Yong Koo},
   doi = {10.1016/j.susc.2016.09.007},
   issn = {00396028},
   journal = {Surface Science},
   keywords = {Ab initio calculation,Adsorption configuration,CO,Scanning tunneling microscopy,Si(111)-(7×7) surface},
   pages = {33-38},
   publisher = {Elsevier B.V.},
   title = {Adsorption of CO molecules on the Si(111)-(7×7) surface},
   volume = {656},
   year = {2017}
}
@article{Siahaan2015,
   abstract = {We introduce an alternative type of probe for scanning tunneling microscopy (STM). Instead of using a needle-like tip made from a piece of metallic wire, a sharp-edged cleaved insulating substrate, which is initially covered by a thin conductive film, is used. The sharp tip is formed at the intersection of the two cleaved sides. Using this approach a variety of materials for STM probes can be used, and functionalization of STM probes is possible. The working principle of different probes made of metallic (Pt, Co, and CoB), indium-tin oxide, as well as Cu/Pt and Co/Pt multilayer films are demonstrated by STM imaging of clean Cu(001) and Cu(111) surfaces as well as the epitaxial Co clusters on Cu(111).},
   author = {T. Siahaan and O. Kurnosikov and B. Barcones and H. J.M. Swagten and B. Koopmans},
   doi = {10.1088/0957-4484/27/3/03LT01},
   issn = {13616528},
   issue = {3},
   journal = {Nanotechnology},
   keywords = {probes fabrication,probes functionalization,scanning tuneling microscopy,stm probe},
   pages = {03LT01},
   publisher = {Institute of Physics Publishing},
   title = {Cleaved thin-film probes for scanning tunneling microscopy},
   volume = {27},
   year = {2015}
}
@article{Wu2005,
   abstract = {A systematic comparison is reported on the dynamics and clustering behaviors of alkali metals (Li, Na, K, Cs), by using scanning tunneling microscopy, work-function measurements and first-principles calculations, to reveal their adsorption behavior differences. At room temperature, Li forms magic clusters whose number density increase linearly with the Li coverage, while both Na and K form two-dimensional(2D) gases at coverage < 0.08 ML, and magic clusters at coverage > 0.08 ML. K atoms diffuse faster in the 2D gas phase, with stronger charge transfer to the Si substrate than Na atoms. Cs behaves somewhat similarly, i.e., from 2D gas to clusters depending on the coverage, although the Cs clusters appears rather irregular. The clustering behaviors of Li, Na, K, and Cs are very different. In the K cluster case there is no intermixing between K and Si atoms, and the K clusters are very mobile inside the half(7×7) unit cell, whereas Na clusters are unmovable due to the site-exchange between Na atoms and the adatoms. © 2005 THE PHYSICAL SOCIETY OF THE REPUBLIC OF CHINA.},
   author = {Ke Hui Wu and Y. Fujikawa and Y. Takamura and T. Sakurai},
   doi = {10.1116/1.585546},
   issn = {05779073},
   issue = {1 II},
   journal = {Chinese Journal of Physics},
   pages = {197-211},
   title = {Alkali metal adsorption on the Si(111)-(7×7) surface},
   volume = {43},
   year = {2005}
}
@article{Larsson2008,
   abstract = {Density functional theory (DFT) and low-temperature scanning tunneling microscopy (STM) have been combined to examine the bonding of individual C60 molecules on Cu(111). Energy-resolved differential-conductance maps have been measured for individual C60 molecules adsorbed on a Cu(111) surface by means of low-temperature STM, which are compared to and complemented by theoretically computed spectral images. It has been found that C60 chemisorbs with a six-membered ring parallel to the surface at two different Cu(111) binding sites that constitute two exclusive hexagonal sublattices. On each sublattice, C60 is bonded in one particular rotational conformer, i.e., C60 molecules bind to the Cu(111) surface in two different azimuthal orientations differing by 60°depending on which sublattice the binding site belongs to. The binding conformation of C60 and its orientation with regard to the copper surface can be deduced by this joint experimental-theoretical approach. Six possible pairs of C60 configurations on three different Cu surface binding sites have been identified that fulfil the requirements of the two sublattices and are consistent with all experimental and theoretical data. Theory proposes that two of these configuration pairs are most likely. We have found that DFT does not get the binding energy between rotational conformers in the correct order. We also report two different C60 monolayers on Cu(111): one with alternating orientations of neighboring molecules at low temperature and the other with (4×4) structure after annealing above room temperature. © 2008 The American Physical Society.},
   author = {J. Andreas Larsson and Simon D. Elliott and James C. Greer and Jascha Repp and Gerhard Meyer and Rolf Allenspach},
   doi = {10.1103/PhysRevB.77.115434},
   issn = {10980121},
   issue = {11},
   journal = {Physical Review B - Condensed Matter and Materials Physics},
   pages = {1-9},
   title = {Orientation of individual C60 molecules adsorbed on Cu(111): Low-temperature scanning tunneling microscopy and density functional calculations},
   volume = {77},
   year = {2008}
}
@article{Becker1982,
   abstract = {From crystal to crystal comparison, the d<inf>220</inf> lattice spacing in PERFX and WASO silicon crystals used in the only two existing absolute measurements have been found to be equal within ±2×10<sup>-7</sup>d<inf>220</inf>. This demonstrates that generic variabilities of the two crystals account only for a small part of the 1.8×10<sup>-6</sup>d<inf>220</inf> difference in the two absolute measurements. In a new series of 336 single measurements, our d<inf>220</inf> value reported recently has been confirmed within ±2×10<sup>-8</sup>d<inf>220</inf>. From these results we derive the following lattice parameter for highly pure silicon single crystals:a<inf>0</inf>=(543 102.018±0.034) fm (at 22.5°C, in vacuum). © 1982 Springer-Verlag.},
   author = {P. Becker and P. Scyfried and H. Siegert},
   doi = {10.1007/BF02026423},
   issn = {14346036},
   issue = {1},
   journal = {Zeitschrift für Physik B Condensed Matter},
   keywords = {Condensed Matter Physics,Engineering,Inorganic Chemistry,general},
   pages = {17-21},
   publisher = {Springer-Verlag},
   title = {The lattice parameter of highly pure silicon single crystals},
   volume = {48},
   url = {https://link.springer.com/article/10.1007/BF02026423},
   year = {1982}
}
@article{Sugimoto2010,
   abstract = {We perform simultaneous atomic force microscopy (AFM) and scanning tunneling microscopy (STM) measurements on the Si(111)-(7×7) surface. AFM/STM constant height images are obtained at various tip-surface distances. Force/current distance spectroscopy using the same tip apex allows us to estimate the relative tip-surface distance for each image as well as the short/long-range force and the tunneling current. We demonstrate that the tunneling current at tip-surface distances where AFM clearly resolves atoms is much larger than the typical values in conventional STM. In addition, at the tip-surface distances for conventional STM, the short-range force is too small to provide atomic contrast in AFM. We show that the differences in the signal-to-noise ratio of the constant height images between AFM and STM produce different optimal imaging distances. In addition, we note that the different imaging distance also influences images obtained using double tips.},
   author = {Yoshiaki Sugimoto and Yuuki Nakajima and Daisuke Sawada and Ken-ichi Morita and Masayuki Abe and Seizo Morita},
   doi = {10.1103/PhysRevB.81.245322},
   issue = {24},
   journal = {Physical Review B},
   pages = {245322},
   title = {Simultaneous AFM and STM measurements on the Si(111)-(7×7) surface},
   volume = {81},
   url = {http://link.aps.org/doi/10.1103/PhysRevB.81.245322 http://prb.aps.org/abstract/PRB/v81/i24/e245322 papers2://publication/doi/10.1103/PhysRevB.81.245322},
   year = {2010}
}
@article{Bartels1997,
   abstract = {A reliable procedure for controlled vertical transfer of single CO molecules between a Cu(111) surface and a scanning tunneling microscope tip and vice versa is demonstrated. It is shown that with a tip having a single CO molecule at its apex, chemical contrast is achieved allowing distinction of adsorbed CO molecules and oxgen atoms, which look very similar to the bare metal tip. © 1997 American Institute of Physics.},
   author = {L. Bartels and G. Meyer and K. H. Rieder},
   doi = {10.1063/1.119503},
   issn = {00036951},
   issue = {2},
   journal = {Applied Physics Letters},
   keywords = {carbon compounds,scanning tunnelling microscopy},
   pages = {213-215},
   publisher = {American Institute of Physics Inc.},
   title = {Controlled vertical manipulation of single CO molecules with the scanning tunneling microscope: A route to chemical contrast},
   volume = {71},
   url = {http://aip.scitation.org/doi/10.1063/1.119503},
   year = {1997}
}
@article{Toth2015,
   abstract = {Focused electron beam induced processing (FEBIP) is a suite of direct-write, high resolution techniques that enable fabrication and editing of nanostructured materials inside scanning electron microscopes and other focused electron beam (FEB) systems. Here we detail continuum techniques that are used to model FEBIP, and release software that can be used to simulate a wide range of processes reported in the FEBIP literature. These include: (i) etching and deposition performed using precursors that interact with a surface through physisorption and activated chemisorption, (ii) gas mixtures used to perform simultaneous focused electron beam induced etching and deposition (FEBIE and FEBID), and (iii) etch processes that proceed through multiple reaction pathways and generate a number of reaction products at the substrate surface. We also review and release software for Monte Carlo modeling of the precursor gas flux which is needed as an input parameter for continuum FEBIP models.},
   author = {Milos Toth and Charlene Lobo and Vinzenz Friedli and Aleksandra Szkudlarek and Ivo Utke},
   doi = {10.3762/bjnano.6.157},
   issn = {21904286},
   issue = {1},
   journal = {Beilstein Journal of Nanotechnology},
   keywords = {Continuum model,Deposition,Electron beam processing,Etching,Gas injection system},
   pages = {1518-1540},
   publisher = {Beilstein-Institut Zur Forderung der Chemischen Wissenschaften},
   title = {Continuum models of focused electron beam induced processing},
   volume = {6},
   year = {2015}
}
@article{Kawai2016,
   abstract = {The state of vanishing friction known as superlubricity has important applications for energy saving and increasing the lifetime of devices. Superlubricity, as detected with atomic force microscopy, appears when sliding large graphite flakes or gold nanoclusters across surfaces, for example. However, the origin of the behavior is poorly understood because of the lack of a controllable nanocontact. We demonstrated the superlubricity of graphene nanoribbons when sliding on gold with a joint experimental and computational approach. The atomically well-defined contact allows us to trace the origin of superlubricity, unraveling the role played by ribbon size and elasticity, as well as by surface reconstruction. Our results pave the way to the scale-up of superlubricity and thus to the realization of frictionless coatings.},
   author = {Shigeki Kawai and Andrea Benassi and Enrico Gnecco and Hajo Söde and Rémy Pawlak and Xinliang Feng and Klaus Müllen and Daniele Passerone and Carlo A. Pignedoli and Pascal Ruffieux and Roman Fasel and Ernst Meyer},
   doi = {10.1126/science.aad3569},
   issn = {10959203},
   issue = {6276},
   journal = {Science},
   pages = {957-961},
   publisher = {American Association for the Advancement of Science},
   title = {Superlubricity of graphene nanoribbons on gold surfaces},
   volume = {351},
   url = {www.sciencemag.org/content/351/6276/953/suppl/DC1},
   year = {2016}
}
@article{Lawrence2020,
   abstract = {Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces.},
   author = {James Lawrence and Gabriele C Sosso and Luka Đorđević and Harry Pinfold and Davide Bonifazi and Giovanni Costantini},
   doi = {10.1038/s41467-020-15898-2},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications},
   pages = {2103},
   title = {Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding},
   volume = {11},
   url = {https://doi.org/10.1038/s41467-020-15898-2 https://www.nature.com/articles/s41467-020-15898-2},
   year = {2020}
}
@article{Wagner2021,
   abstract = {The state of deprotonation/protonation of surfaces has far-ranging implications in chemistry, from acid–base catalysis1 and the electrocatalytic and photocatalytic splitting of water2, to the behaviour of minerals3 and biochemistry4. An entity’s acidity is described by its proton affinity and its acid dissociation constant pKa (the negative logarithm of the equilibrium constant of the proton transfer reaction in solution). The acidity of individual sites is difficult to assess for solids, compared with molecules. For mineral surfaces, the acidity is estimated by semi-empirical concepts, such as bond-order valence sums5, and increasingly modelled with first-principles molecular dynamics simulations6,7. At present, such predictions cannot be tested—experimental measures, such as the point of zero charge8, integrate over the whole surface or, in some cases, individual crystal facets9. Here we assess the acidity of individual hydroxyl groups on In2O3(111)—a model oxide with four different types of surface oxygen atom. We probe the strength of their hydrogen bonds with the tip of a non-contact atomic force microscope and find quantitative agreement with density functional theory calculations. By relating the results to known proton affinities of gas-phase molecules, we determine the proton affinity of the different surface sites of In2O3 with atomic precision. Measurements on hydroxylated titanium dioxide and zirconium oxide extend our method to other oxides. Non-contact atomic force microscopy measurements are used to probe the hydrogen bond strength of individual surface hydroxyl groups and determine their acidity with atomic precision.},
   author = {Margareta Wagner and Bernd Meyer and Martin Setvin and Michael Schmid and Ulrike Diebold},
   doi = {10.1038/s41586-021-03432-3},
   issn = {0028-0836},
   issue = {7856},
   journal = {Nature},
   keywords = {Chemical physics,Scanning probe microscopy},
   pages = {722-725},
   publisher = {Nature Publishing Group},
   title = {Direct assessment of the acidity of individual surface hydroxyls},
   volume = {592},
   url = {http://www.nature.com/articles/s41586-021-03432-3},
   year = {2021}
}
@inproceedings{Skeini2006,
   abstract = {An automation scheme for atom/molecule manipulations with the scanning tunneling microscope tip is developed. The program recognizes the type of particles to be manipulated such as atoms, molecules, or nanoparticles based on their sizes and shapes. It also determines the obstacles to be avoided during manipulation such as defects, steps, and clusters. The shortest manipulation paths are then computed by the program and finally, the manipulations are performed according to the computed paths. This method allows automated construction of nanostructures using single atoms or molecules as basic building blocks. © 2006 IEEE.},
   author = {Timur Skeini and James F. Steiner and Saw W. Hla},
   doi = {10.1109/nano.2006.247727},
   isbn = {1424400783},
   booktitle = {2006 6th IEEE Conference on Nanotechnology, IEEE-NANO 2006},
   keywords = {Atomic precision,Automated system,Low temperature,Metallic surface engineering,Scanning tunneling microscope,Ultra high vacuum},
   pages = {610-612},
   publisher = {Institute of Electrical and Electronics Engineers Inc.},
   title = {Automated atomicscale construction},
   volume = {2},
   year = {2006}
}
@article{Wang2021,
   abstract = {Scanning tunneling spectroscopy (STS), a technique that records the change in the tunneling current as a function of the bias (dI/dV) across the gap between a tip and the sample, is a powerful tool to characterize the electronic structure of single molecules and nanomaterials. While performing STS, the structure and condition of the scanning probe microscopy (SPM) tips are critical for reliably obtaining high quality point spectra. Here, we present an automated program based on machine learning models that can identify the Au(111) Shockley surface state in dI/dV point spectra and perform tip conditioning on clean or sparsely covered gold surfaces with minimal user intervention. We employed a straightforward height-based segmentation algorithm to analyze STM topographic images to identify tip conditioning positions and used 1789 archived dI/dV spectra to train machine learning models that can ascertain the condition of the tip by evaluating the quality of the spectroscopic data. Decision tree based ensemble and boosting models and deep neural networks (DNNs) have been shown to reliably identify tips in suitable conditions for STS. We expect the automated program to reduce operational costs and time, increase reproducibility in surface science studies, and accelerate the discovery and characterization of novel nanomaterials by STM. The strategies presented in this paper can readily be adapted to STM tip conditioning on a wide variety of other common substrates.},
   author = {Shenkai Wang and Junmian Zhu and Raymond Blackwell and Felix R. Fischer},
   doi = {10.1021/acs.jpca.0c10731},
   issn = {15205215},
   issue = {6},
   journal = {Journal of Physical Chemistry A},
   pages = {1384-1390},
   pmid = {33560124},
   publisher = {American Chemical Society},
   title = {Automated tip conditioning for scanning tunneling spectroscopy},
   volume = {125},
   url = {https://pubs.acs.org/doi/abs/10.1021/acs.jpca.0c10731},
   year = {2021}
}
@article{Randall2012,
   abstract = {Analysis of Scanning Tunneling Microscope (STM) images [1] is being pursued, in our case to enable the identification of atomic terraces, Si dimers, dangling bonds, vacancies, and surface contamination on Si (100) 2 × 1 H passivated surfaces. This analytical technique is a critical component of Atomically Precise Manufacturing, aiding in the automation of H depassivation lithography [2,3] and patterned Si atomic layer epitaxy (ALE) [4] where it is necessary to register, in an automated process, each lithography step to the desired pattern with atomic precision. We have previously presented work [5] showing that after least squares plane fitting histogram analysis could provide a quantitative measure of image quality and that simple thresholds could be used to identify some dimers and vacancies if the image resolution was high enough. That work was done with a series of image analysis techniques selected manually and required high image quality with a single atomic terrace preferred. © 2012 Elsevier B.V. All rights reserved.},
   author = {J. N. Randall and J. R. Von Ehr and J. B. Ballard and J. H.G. Owen and E. Fuchs},
   doi = {10.1016/j.mee.2012.07.021},
   issn = {01679317},
   journal = {Microelectronic Engineering},
   keywords = {Image analysis,Lithography,Scanning Tunneling Microscope,Si surface},
   pages = {214-217},
   publisher = {Elsevier},
   title = {Automated scanning tunneling microscope image analysis of Si (100):H 2 × 1 surfaces},
   volume = {98},
   year = {2012}
}
@article{Straton2015,
   abstract = {Crystallographic image processing (CIP) techniques may be utilized in scanning probe microscopy (SPM) to glean information that has been obscured by signals from multiple probe tips. This may be of particular importance for scanning tunneling microscopy (STM) and requires images from samples that are periodic in two dimensions (2D). The image-forming current for double-tips in STM is derived with a slight modification of the independent-orbital approximation (IOA) to allow for two or more tips. Our analysis clarifies why crystallographic averaging works well in removing the effects of a blunt STM tip (that consists of multiple mini-tips) from recorded 2D periodic images and also outlines the limitations of this image-processing technique for certain spatial separations of STM double-tips. Simulations of multiple mini-tip effects in STM images (that ignore electron interference effects) may be understood as modeling multiple mini-tip (or tip shape) effects in images that were recorded with other types of SPMs as long as the lateral sample feature sizes to be imaged are much larger than the effective scanning probe tip sizes.},
   author = {Jack C. Straton and Bill Moon and Taylor T. Bilyeu and Peter Moeck},
   doi = {10.1186/s40679-015-0014-6},
   issn = {21980926},
   issue = {1},
   journal = {Advanced Structural and Chemical Imaging},
   keywords = {Crystallographic image processing,Scanning probe microscopy,Scanning tunneling microscopy},
   pages = {14},
   publisher = {Springer},
   title = {Removal of multiple-tip artifacts from scanning tunneling microscope images by crystallographic averaging},
   volume = {1},
   url = {http://www.stackoverflow.com/questions/5825149/},
   year = {2015}
}
@article{Ziatdinov2017,
   abstract = {Recent advances in scanning transmission electron and scanning probe microscopies have opened exciting opportunities in probing the materials structural parameters and various functional properties in real space with angstrom-level precision. This progress has been accompanied by an exponential increase in the size and quality of data sets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large data sets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent. Here we demonstrate an application of deep neural networks to extract information from atomically resolved images including location of the atomic species and type of defects. We develop a "weakly supervised" approach that uses information on the coordinates of all atomic species in the image, extracted via a deep neural network, to identify a rich variety of defects that are not part of an initial training set. We further apply our approach to interpret complex atomic and defect transformation, including switching between different coordination of silicon dopants in graphene as a function of time, formation of peculiar silicon dimer with mixed 3-fold and 4-fold coordination, and the motion of molecular "rotor". This deep learning-based approach resembles logic of a human operator, but can be scaled leading to significant shift in the way of extracting and analyzing information from raw experimental data.},
   author = {Maxim Ziatdinov and Ondrej Dyck and Artem Maksov and Xufan Li and Xiahan Sang and Kai Xiao and Raymond R. Unocic and Rama Vasudevan and Stephen Jesse and Sergei V. Kalinin},
   doi = {10.1021/acsnano.7b07504},
   issn = {1936086X},
   issue = {12},
   journal = {ACS Nano},
   keywords = {graphene,neural networks,scanning transmission electron microscopy (STEM),transition-metal dichalcogenide (TMDC),weakly supervised learning},
   pages = {12742-12752},
   pmid = {29215876},
   publisher = {American Chemical Society},
   title = {Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations},
   volume = {11},
   url = {https://pubs.acs.org/doi/abs/10.1021/acsnano.7b07504},
   year = {2017}
}
@misc{Vasudevan2019,
   abstract = {The use of statistical/machine learning (ML) approaches to materials science is experiencing explosive growth. Here, we review recent work focusing on the generation and application of libraries from both experiment and theoretical tools. The library data enables classical correlative ML and also opens the pathway for exploration of underlying causative physical behaviors. We highlight key advances facilitated by this approach and illustrate how modeling, macroscopic experiments, and imaging can be combined to accelerate the understanding and development of new materials systems. These developments point toward a data-driven future wherein knowledge can be aggregated and synthesized, accelerating the advancement of materials science.},
   author = {Rama K. Vasudevan and Kamal Choudhary and Apurva Mehta and Ryan Smith and Gilad Kusne and Francesca Tavazza and Lukas Vlcek and Maxim Ziatdinov and Sergei V. Kalinin and Jason Hattrick-Simpers},
   doi = {10.1557/mrc.2019.95},
   issn = {21596867},
   issue = {3},
   journal = {MRS Communications},
   pages = {821-838},
   publisher = {Cambridge University Press},
   title = {Materials science in the artificial intelligence age: High-throughput library generation, machine learning, and a pathway from correlations to the underpinning physics},
   volume = {9},
   url = {https://doi.org/10.1557/mrc.2019.95},
   year = {2019}
}
@article{Gordon2020b,
   abstract = {We discuss the exciting prospects for a step change in our ability to map and modify matter at the atomic/molecular level by embedding machine learning algorithms in scanning probe microscopy (with a particular focus on scanning tunnelling microscopy, STM). This nano-AI hybrid approach has the far-reaching potential to realise a technology capable of the automated analysis, actuation, and assembly of matter with a precision down to the single chemical bond limit.},
   author = {Oliver M Gordon and Philip J Moriarty},
   doi = {10.1088/2632-2153/ab7d2f},
   issue = {2},
   journal = {Machine Learning: Science and Technology},
   pages = {023001},
   publisher = {IOP Publishing},
   title = {Machine learning at the (sub)atomic scale: next generation scanning probe microscopy},
   volume = {1},
   url = {https://doi.org/10.1088/2632-2153/ab7d2f},
   year = {2020}
}
@article{Sotres2021,
   abstract = {Scanning probe microscopies allow investigating surfaces at the nanoscale\{,\} in real space and with unparalleled signal-to-noise ratio. However\{,\} these microscopies are not used as much as it would be expected considering their potential. The main limitations preventing a broader use are the need of experienced users\{,\} the difficulty in data analysis and the time-consuming nature of experiments that require continuous user supervision. In this work\{,\} we addressed the latter and developed an algorithm that controlled the operation of an Atomic Force Microscope (AFM) that\{,\} without the need of user intervention\{,\} allowed acquiring multiple high-resolution images of different molecules. We used DNA on mica as a model sample to test our control algorithm\{,\} which made use of two deep learning techniques that so far have not been used for real time SPM automation. One was an object detector\{,\} YOLOv3\{,\} which provided the location of molecules in the captured images. The second was a Siamese network that could identify the same molecule in different images. This allowed both performing a series of images on selected molecules while incrementing the resolution\{,\} as well as keeping track of molecules already imaged at high resolution\{,\} avoiding loops where the same molecule would be imaged an unlimited number of times. Overall\{,\} our implementation of deep learning techniques brings SPM a step closer to full autonomous operation.},
   author = {Javier Sotres and Hannah Boyd and Juan F. Gonzalez-Martinez},
   doi = {10.1039/D1NR01109J},
   issn = {2040-3364},
   issue = {20},
   journal = {Nanoscale},
   pages = {9193-9203},
   publisher = {Royal Society of Chemistry},
   title = {Enabling autonomous scanning probe microscopy imaging of single molecules with deep learning},
   volume = {13},
   url = {http://xlink.rsc.org/?DOI=D1NR01109J},
   year = {2021}
}
@article{Krull2020,
   abstract = {Scanning probe microscopy (SPM) has revolutionized the fields of materials, nano-science, chemistry, and biology, by enabling mapping of surface properties and surface manipulation with atomic precision. However, these achievements require constant human supervision; fully automated SPM has not been accomplished yet. Here we demonstrate an artificial intelligence framework based on machine learning for autonomous SPM operation (DeepSPM). DeepSPM includes an algorithmic search of good sample regions, a convolutional neural network to assess the quality of acquired images, and a deep reinforcement learning agent to reliably condition the state of the probe. DeepSPM is able to acquire and classify data continuously in multi-day scanning tunneling microscopy experiments, managing the probe quality in response to varying experimental conditions. Our approach paves the way for advanced methods hardly feasible by human operation (e.g., large dataset acquisition and SPM-based nanolithography). DeepSPM can be generalized to most SPM techniques, with the source code publicly available.},
   author = {A. Krull and P. Hirsch and C. Rother and A. Schiffrin and C. Krull},
   doi = {10.1038/s42005-020-0317-3},
   issn = {23993650},
   issue = {1},
   journal = {Communications Physics},
   keywords = {Nanoscale materials,Scanning probe microscopy},
   pages = {1-8},
   publisher = {Nature Research},
   title = {Artificial-intelligence-driven scanning probe microscopy},
   volume = {3},
   url = {https://doi.org/10.1038/s42005-020-0317-3},
   year = {2020}
}
@article{Gordon2020a,
   abstract = {Scanning probe microscopists generally do not rely on complete images to assess the quality of data acquired during a scan. Instead, assessments of the state of the tip apex, which not only determines the resolution in any scanning probe technique but can also generate a wide array of frustrating artefacts, are carried out in real time on the basis of a few lines of an image (and, typically, their associated line profiles.) The very small number of machine learning approaches to probe microscopy published to date, however, involve classifications based on full images. Given that data acquisition is the most time-consuming task during routine tip conditioning, automated methods are thus currently extremely slow in comparison to the tried-and-trusted strategies and heuristics used routinely by probe microscopists. Here, we explore various strategies by which different STM image classes (arising from changes in the tip state) can be correctly identified from partial scans. By employing a secondary temporal network and a rolling window of a small group of individual scanlines, we find that tip assessment is possible with a small fraction of a complete image. We achieve this with little-to-no performance penalty -- or, indeed, markedly improved performance in some cases -- and introduce a protocol to detect the state of the tip apex in real time.},
   author = {O. Gordon and F. Junqueira and P. Moriarty},
   doi = {10.1088/2632-2153/ab42ec},
   issue = {1},
   journal = {Machine Learning: Science and Technology},
   pages = {015001},
   publisher = {IOP Publishing},
   title = {Embedding Human Heuristics in Machine-Learning-Enabled Probe Microscopy},
   volume = {1},
   url = {http://arxiv.org/abs/1907.13401 http://dx.doi.org/10.1088/2632-2153/ab42ec},
   year = {2020}
}
@article{Huang2018,
   abstract = {Artificial intelligence (AI) and machine learning have promised to revolutionize the way we live and work, and one of the particularly promising areas for AI is image analysis. Nevertheless, many current AI applications focus on the post-processing of data, while in both materials sciences and medicine, it is often critical to respond to the data acquired on the fly. Here we demonstrate an artificial intelligence atomic force microscope (AI-AFM) that is capable of not only pattern recognition and feature identification in ferroelectric materials and electrochemical systems, but can also respond to classification via adaptive experimentation with additional probing at critical domain walls and grain boundaries, all in real time on the fly without human interference. Key to our success is a highly efficient machine learning strategy based on a support vector machine (SVM) algorithm capable of high fidelity pixel-by-pixel recognition instead of relying on the data from full mapping, making real time classification and control possible during scanning, with which complex electromechanical couplings at the nanoscale in different material systems can be resolved by AI. For AFM experiments that are often tedious, elusive, and heavily rely on human insight for execution and analysis, this is a major disruption in methodology, and we believe that such a strategy empowered by machine learning is applicable to a wide range of instrumentations and broader physical machineries.},
   author = {Boyuan Huang and Zhenghao Li and Jiangyu Li},
   doi = {10.1039/c8nr06734a},
   issn = {20403372},
   issue = {45},
   journal = {Nanoscale},
   pages = {21320-21326},
   pmid = {30422134},
   publisher = {Royal Society of Chemistry},
   title = {An artificial intelligence atomic force microscope enabled by machine learning},
   volume = {10},
   url = {https://pubs.rsc.org/en/content/articlehtml/2018/nr/c8nr06734a https://pubs.rsc.org/en/content/articlelanding/2018/nr/c8nr06734a},
   year = {2018}
}
@article{Moller2017,
   abstract = {The atomistic structure of the tip apex plays a crucial role in performing reliable atomic-scale surface and adsorbate manipulation using scanning probe techniques. We have developed an automated extraction routine for controlled removal of single hydrogen atoms from the H:Si(100) surface. The set of atomic extraction protocols detect a variety of desorption events during scanning tunneling microscope (STM)-induced modification of the hydrogen-passivated surface. The influence of the tip state on the probability for hydrogen removal was examined by comparing the desorption efficiency for various classifications of STM topographs (rows, dimers, atoms, etc). We find that dimer-row-resolving tip apices extract hydrogen atoms most readily and reliably (and with least spurious desorption), while tip states which provide atomic resolution counter-intuitively have a lower probability for single H atom removal.},
   author = {Morten Møller and Samuel P. Jarvis and Laurent Guérinet and Peter Sharp and Richard Woolley and Philipp Rahe and Philip Moriarty},
   doi = {10.1088/1361-6528/28/7/075302},
   issn = {13616528},
   issue = {7},
   journal = {Nanotechnology},
   keywords = {STM,atomic manipulation,hydrogen desorption,scanning probe microscopy,tip state},
   pages = {075302},
   pmid = {28074783},
   publisher = {Institute of Physics Publishing},
   title = {Automated extraction of single H atoms with STM: Tip state dependency},
   volume = {28},
   url = {https://iopscience.iop.org/article/10.1088/1361-6528/28/7/075302 https://iopscience.iop.org/article/10.1088/1361-6528/28/7/075302/meta},
   year = {2017}
}
@article{Ziatdinov2017a,
   abstract = {Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify ('read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function - a centerpiece in analysis of disorder-property relationship paradigm - as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.},
   author = {Maxim Ziatdinov and Artem Maksov and Sergei V. Kalinin},
   doi = {10.1038/s41524-017-0038-7},
   issn = {20573960},
   issue = {1},
   journal = {npj Computational Materials},
   keywords = {Carbon nanotubes and fullerenes,Molecular self,Scanning probe microscopy,assembly},
   pages = {31},
   publisher = {Nature Publishing Group},
   title = {Learning surface molecular structures via machine vision},
   volume = {3},
   url = {www.nature.com/npjcompumats},
   year = {2017}
}
@phdthesis{Dusch2019,
   abstract = {Scanning probe microscopy (SPM) has allowed researchers to measure materials’ structural and functional properties, such as atomic displacements and electronic properties at the nanoscale. Over the past decade, great leaps in the ability to acquire large, high resolution datasets have opened up the possibility of even deeper insights into materials. Unfortunately, these large datasets pose a problem for traditional analysis techniques (and software), necessitating the development of new techniques in order to better understand this new wealth of data. Fortunately, these developments are paralleled by the general rise of big data and the development of machine learning techniques that can help us discover and automate the process of extracting useful information from this data. My thesis research has focused on bringing these techniques to all aspects of SPM usage, from data collection through analysis. In this dissertation I present results from three of these efforts: the improvement of a vibration cancellation system developed in our group via the introduction of machine learning, the classification of SPM images using machine vision, and the creation of a new data analysis software package tailored for large, multidimensional datasets which is highly customizable and eases performance of complex analyses. Each of these results stand on their own in terms of scientific impact – for example, the machine learning approach discussed here enables a roughly factor of two to three improvement over our already uniquely successful vibration cancellation system. However, together they represent something more – a push to bring machine learning techniques into the field of SPM research, where previously only a handful of research groups have reported any attempts, and where all efforts to date have focused on analysis, rather than collection, of data. These results also represent first steps in the development of a “driverless SPM” where the SPM could, on its own, identify, collect, and begin analysis of scientifically important data.},
   author = {William Dusch},
   doi = {ISBN: 9781392318324},
   school = {The Pennsylvania State University},
   pages = {158},
   title = {DATA SCIENCE IN SCANNING PROBE MICROSCOPY: ADVANCED ANALYTICS AND MACHINE LEARNING},
   url = {https://etda.libraries.psu.edu/files/final_submissions/19104},
   year = {2019}
}
@article{Donati2016,
   abstract = {A permanent magnet retains a substantial fraction of its saturation magnetization in the absence of an external magnetic field. Realizing magnetic remanence in a single atom allows for storing and processing information in the smallest unit of matter. We show that individual holmium (Ho) atoms adsorbed on ultrathin MgO(100) layers on Ag(100) exhibit magnetic remanence up to a temperature of 30 kelvin and a relaxation time of 1500 seconds at 10 kelvin. This extraordinary stability is achieved by the realization of a symmetry-protected magnetic ground state and by decoupling the Ho spin from the underlying metal by a tunnel barrier.},
   author = {F. Donati and S. Rusponi and S. Stepanow and C. Wäckerlin and A. Singha and L. Persichetti and R. Baltic and K. Diller and F. Patthey and E. Fernandes and J. Dreiser and Šljivančanin and K. Kummer and C. Nistor and P. Gambardella and H. Brune},
   doi = {10.1126/science.aad9898},
   issn = {10959203},
   issue = {6283},
   journal = {Science},
   pages = {318-321},
   publisher = {American Association for the Advancement of Science},
   title = {Magnetic remanence in single atoms},
   volume = {352},
   url = {http://science.sciencemag.org/},
   year = {2016}
}
@article{Fuechsle2012,
   abstract = {The ability to control matter at the atomic scale and build devices with atomic precision is central to nanotechnology. The scanning tunnelling microscope can manipulate individual atoms and molecules on surfaces, but the manipulation of silicon to make atomic-scale logic circuits has been hampered by the covalent nature of its bonds. Resist-based strategies have allowed the formation of atomic-scale structures on silicon surfaces, but the fabrication of working devices - such as transistors with extremely short gate lengths, spin-based quantum computers and solitary dopant optoelectronic devices - requires the ability to position individual atoms in a silicon crystal with atomic precision. Here, we use a combination of scanning tunnelling microscopy and hydrogen-resist lithography to demonstrate a single-atom transistor in which an individual phosphorus dopant atom has been deterministically placed within an epitaxial silicon device architecture with a spatial accuracy of one lattice site. The transistor operates at liquid helium temperatures, and millikelvin electron transport measurements confirm the presence of discrete quantum levels in the energy spectrum of the phosphorus atom. We find a charging energy that is close to the bulk value, previously only observed by optical spectroscopy. © 2012 Macmillan Publishers Limited. All rights reserved.},
   author = {Martin Fuechsle and Jill A. Miwa and Suddhasatta Mahapatra and Hoon Ryu and Sunhee Lee and Oliver Warschkow and Lloyd C.L. Hollenberg and Gerhard Klimeck and Michelle Y. Simmons},
   doi = {10.1038/nnano.2012.21},
   issn = {17483395},
   issue = {4},
   journal = {Nature Nanotechnology},
   keywords = {Electronic properties and materials,Surface patterning},
   pages = {242-246},
   pmid = {22343383},
   publisher = {Nature Publishing Group},
   title = {A single-atom transistor},
   volume = {7},
   url = {www.nature.com/naturenanotechnology},
   year = {2012}
}
@article{Heinrich2002,
   abstract = {Carbon monoxide molecules were arranged in atomically precise configurations, which we call "molecule cascades," where the motion of one molecule causes the subsequent motion of another, and so on in a cascade of motion similar to a row of toppling dominoes. Isotopically pure cascades were assembled on a copper (111) surface with a low-temperature scanning tunneling microscope. The hopping rate of carbon monoxide molecules in cascades was found to be independent of temperature below 6 kelvin and to exhibit a pronounced isotope effect, hallmarks of a quantum tunneling process. At higher temperatures, we observed a thermally activated hopping rate with an anomalously low Arrhenius prefactor that we interpret as tunneling from excited vibrational states. We present a cascade-based computation scheme that has all of the devices and interconnects required for the one-time computation of an arbitrary logic function. Logic gates and other devices were implemented by engineered arrangements of molecules at the intersections of cascades. We demonstrate a three-input sorter that uses several AND gates and OR gates, as well as the crossover and fan-out units needed to connect them.},
   author = {A. J. Heinrich and C. P. Lutz and J. A. Gupta and D. M. Eigler},
   doi = {10.1126/science.1076768},
   issn = {00368075},
   issue = {5597},
   journal = {Science},
   pages = {1381-1387},
   pmid = {12399543},
   publisher = {American Association for the Advancement of Science},
   title = {Molecule cascades},
   volume = {298},
   url = {http://science.sciencemag.org/},
   year = {2002}
}
@article{Kalinin2021,
   abstract = {Machine learning and artificial intelligence (ML/AI) are rapidly becoming an indispensable part of physics research, with domain applications ranging from theory and materials prediction to high-throughput data analysis. In parallel, the recent successes in applying ML/AI methods for autonomous systems from robotics through self-driving cars to organic and inorganic synthesis are generating enthusiasm for the potential of these techniques to enable automated and autonomous experiment (AE) in imaging. Here, we aim to analyze the major pathways towards AE in imaging methods with sequential image formation mechanisms, focusing on scanning probe microscopy (SPM) and (scanning) transmission electron microscopy ((S)TEM). We argue that automated experiments should necessarily be discussed in a broader context of the general domain knowledge that both informs the experiment and is increased as the result of the experiment. As such, this analysis should explore the human and ML/AI roles prior to and during the experiment, and consider the latencies, biases, and knowledge priors of the decision-making process. Similarly, such discussion should include the limitations of the existing imaging systems, including intrinsic latencies, non-idealities and drifts comprising both correctable and stochastic components. We further pose that the role of the AE in microscopy is not the exclusion of human operators (as is the case for autonomous driving), but rather automation of routine operations such as microscope tuning, etc., prior to the experiment, and conversion of low latency decision making processes on the time scale spanning from image acquisition to human-level high-order experiment planning.},
   author = {Sergei V. Kalinin and Maxim A. Ziatdinov and Jacob Hinkle and Stephen Jesse and Ayana Ghosh and Kyle P. Kelley and Andrew R. Lupini and Bobby G. Sumpter and Rama K. Vasudevan},
   journal = {CoRR},
   title = {Automated and Autonomous Experiment in Electron and Scanning Probe Microscopy},
   volume = {abs/2103.1},
   url = {http://arxiv.org/abs/2103.12165},
   year = {2021}
}
@article{Scholkopf1998,
   abstract = {My first exposure to Support Vector Machines came this spring when heard Sue Dumais present impressive results on text categorization using this analysis technique. This issue's collection of essays should help familiarize our readers with this interesting new racehorse in the Machine Learning stable. Bernhard Scholkopf, in an introductory overview, points out that a particular advantage of SVMs over other learning algorithms is that it can be analyzed theoretically using concepts from computational learning theory, and at the same time can achieve good performance when applied to real problems. Examples of these real-world applications are provided by Sue Dumais, who describes the aforementioned text-categorization problem, yielding the best results to date on the Reuters collection, and Edgar Osuna, who presents strong results on application to face detection. Our fourth author, John Platt, gives us a practical guide and a new technique for implementing the algorithm efficiently.},
   author = {B. Hearst, M.A. and Dumais, S.T. and Osuna, E. and Platt, J. and Scholkopf},
   doi = {10.1109/5254.708428},
   issn = {10947167},
   issue = {4},
   journal = {IEEE Intelligent Systems and Their Applications},
   month = {7},
   pages = {18-21},
   title = {Support Vector Machines},
   volume = {13},
   year = {1998}
}
@article{Albrecht1988,
   abstract = {Tilt boundaries have been observed on the (0001) surface of graphite by scanning tunneling microscopy (STM). Rotation angles about the c axis of 6.5°, 8°, and 19°were found, indicating no preferential orientation of grains in the basal plane of graphite. The grain boundary region between crystallites appears disordered with a width varying between 10 and 100 Å. Moiré patterns are observed near grain boundaries when multiple tips scanning over different grains contribute to the image simultaneously. Such images support the theory that multiple isolated tips, occasionally hundreds of angstroms apart, can contribute to STM images.},
   author = {T. R. Albrecht and H. A. Mizes and J. Nogami and Sang Il Park and C. F. Quate},
   doi = {10.1063/1.99465},
   issn = {00036951},
   issue = {5},
   journal = {Applied Physics Letters},
   pages = {362-364},
   title = {Observation of tilt boundaries in graphite by scanning tunneling microscopy and associated multiple tip effects},
   volume = {52},
   year = {1988}
}
@article{Ekvall1999,
   abstract = {We have investigated methods for cleaning dc-etched polycrystalline tungsten tips for scanning tunnelling microscopy (STM). The cleaning methods include Ar-ion sputtering, heating, chemical treatments and Ne-ion self-sputtering. We correlate transmission electron microscopy images of the tip, field-emission data from the tip and images of a clean Cu(111) surface to find an optimum procedure for STM imaging. Clean and sharp tips are made by sputtering, combined with careful heating by electron bombardment. We found that optimum sputtering was obtained either by use of a 4 keV Ar-ion gun for a few seconds or by self-sputtering with Ne ions for a few seconds or until decapitation occurs.},
   author = {Inger Ekvall and Håkan Olin and Eva Olsson and Erik Wahlström and Wahlstr¨ Wahlström and Dan Claesson},
   doi = {10.1088/0957-0233/10/1/006},
   journal = {Meas. Sci. Technol},
   keywords = {STM,STM tip composition,STM tip shape,TEM,UHV,scanning tunnelling microscopy},
   pages = {11-18},
   title = {Preparation and characterization of electrochemically etched W tips for STM},
   volume = {10},
   url = {https://www.researchgate.net/publication/230989868},
   year = {1999}
}
@article{Ding2005,
   abstract = {We present an electron-beam heating device for a scanning tunneling microscopy (STM) that can be used for heating both the STM tip and the sample to 2200 K. Mounted on a linear bellows with electrical feedthroughs, the device can be readily installed into the transfer path of a vacuum load lock. We demonstrate the heating capability of the device by flash cleaning Ru(0001) and Fe(001) crystals, and W tips. The flash-cleaned W tips are coated with Fe and further used for spin-polarized imaging of the MnFe (001) system. © 2005 American Institute of Physics.},
   author = {H. F. Ding and J. E. Pearson and Dongqi Li and Ruihua Cheng and F. Y. Fradin and S. D. Bader},
   doi = {10.1063/1.2140339},
   issn = {00346748},
   issue = {12},
   journal = {Review of Scientific Instruments},
   keywords = {cleaning,electron beam applications,heating elements,iron,ruthenium,scanning tunnelling microscopy,tungsten},
   pages = {1-4},
   publisher = {American Institute of PhysicsAIP},
   title = {Electron-beam tip/sample heating device for a scanning tunneling microscopy},
   volume = {76},
   url = {https://doi.org/10.1063/1.2140339},
   year = {2005}
}
@article{Ernst2007,
   abstract = {This work deals with the preparation and characterization of tungsten tips for the use in UHV low-temperature scanning tunneling microscopy and spectroscopy (STM and STS, respectively). These specific environments require in situ facilities for tip conditioning, for further sharpening of the tips, as well as for reliable tip characterization. The implemented conditioning methods include direct resistive annealing, annealing by electron bombardment, and self-sputtering with noble gas ions. Moreover, results from in situ tip characterization by field emission and STM experiments were compared to ex situ scanning electron microscopy. Using the so-prepared tips, high resolution STM images and tunneling spectra were obtained in a temperature range from ambient down to 350 mK, partially with applied magnetic field, on a variety of materials.},
   author = {S Ernst and S Wirth and M Rams and V Dolocan and F Steglich},
   doi = {10.1016/j.stam.2007.05.008},
   issn = {1878-5514},
   journal = {Science and Technology of Advanced Materials},
   keywords = {Au(1 1 1),NbSe 2,STM tip preparation,Scanning tunneling microscopy (STM),Superconductor},
   pages = {347-351},
   title = {Science and Technology of Advanced Materials Tip preparation for usage in an ultra-low temperature UHV scanning tunneling microscope Tip preparation for usage in an ultra-low temperature UHV scanning tunneling microscope},
   volume = {8},
   url = {https://www.tandfonline.com/action/journalInformation?journalCode=tsta20},
   year = {2007}
}
@article{Leinen2015,
   abstract = {Controlled manipulation of single molecules is an important step towards the fabrication of single molecule devices and nanoscale molecular machines. Currently, scanning probe microscopy (SPM) is the only technique that facilitates direct imaging and manipulations of nanometer-sized molecular compounds on surfaces. The technique of hand-controlled manipulation (HCM) introduced recently in Beilstein J. Nanotechnol. 2014, 5, 1926-1932 simplifies the identification of successful manipulation protocols in situations when the interaction pattern of the manipulated molecule with its environment is not fully known. Here we present a further technical development that substantially improves the effectiveness of HCM. By adding Oculus Rift virtual reality goggles to our HCM setup we provide the experimentalist with 3D visual feedback that displays the currently executed trajectory and the position of the SPM tip during manipulation in real time, while simultaneously plotting the experimentally measured frequency shift (Δf) of the non-contact atomic force microscope (NC-AFM) tuning fork sensor as well as the magnitude of the electric current (I) flowing between the tip and the surface. The advantages of the setup are demonstrated by applying it to the model problem of the extraction of an individual PTCDA molecule from its hydrogen-bonded monolayer grown on Ag(111) surface. 2148},
   author = {Philipp Leinen and Matthew F B Green and Taner Esat and Christian Wagner and F Stefan Tautz and Ruslan Temirov},
   doi = {10.3762/bjnano.6.220},
   journal = {Beilstein J. Nanotechnol},
   keywords = {Oculus Rift,non-contact atomic force microscopy (NC-AFM),perylene-3,4,9,10-tetracarboxylic dianhydride (PTC,scanning probe microscopy (SPM),scanning tunnelling microscopy (STM),single-molecule manipulation,virtual reality interface},
   pages = {2148-2153},
   title = {Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules},
   volume = {6},
   year = {2015}
}
@article{Cogswell2015,
   abstract = {One major challenge in training Deep Neural Networks is preventing overfitting. Many techniques such as data augmentation and novel regularizers such as Dropout have been proposed to prevent overfitting without requiring a massive amount of training data. In this work, we propose a new regularizer called DeCov which leads to significantly reduced overfitting (as indicated by the difference between train and val performance), and better generalization. Our regularizer encourages diverse or non-redundant representations in Deep Neural Networks by minimizing the cross-covariance of hidden activations. This simple intuition has been explored in a number of past works but surprisingly has never been applied as a regularizer in supervised learning. Experiments across a range of datasets and network architectures show that this loss always reduces overfitting while almost always maintaining or increasing generalization performance and often improving performance over Dropout.},
   author = {Michael Cogswell and Faruk Ahmed and Ross Girshick and Larry Zitnick and Dhruv Batra},
   journal = {4th International Conference on Learning Representations},
   publisher = {International Conference on Learning Representations, ICLR},
   title = {Reducing Overfitting in Deep Networks by Decorrelating Representations},
   url = {http://arxiv.org/abs/1511.06068},
   year = {2016}
}
@book{Goodfellow2016,
   author = {Ian Goodfellow and Yoshua Bengio and Aaron Courville},
   note = {\url\{http://www.deeplearningbook.org\}},
   publisher = {MIT Press},
   title = {Deep Learning},
   year = {2016}
}
@article{Silver2017,
   abstract = {A long-standing goal of artificial intelligence is an algorithm that learns, tabula rasa, superhuman proficiency in challenging domains. Recently, AlphaGo became the first program to defeat a world champion in the game of Go. The tree search in AlphaGo evaluated positions and selected moves using deep neural networks. These neural networks were trained by supervised learning from human expert moves, and by reinforcement learning from self-play. Here we introduce an algorithm based solely on reinforcement learning, without human data, guidance or domain knowledge beyond game rules. AlphaGo becomes its own teacher: a neural network is trained to predict AlphaGo's own move selections and also the winner of AlphaGo's games. This neural network improves the strength of the tree search, resulting in higher quality move selection and stronger self-play in the next iteration. Starting tabula rasa, our new program AlphaGo Zero achieved superhuman performance, winning 100-0 against the previously published, champion-defeating AlphaGo.},
   author = {David Silver and Julian Schrittwieser and Karen Simonyan and Ioannis Antonoglou and Aja Huang and Arthur Guez and Thomas Hubert and Lucas Baker and Matthew Lai and Adrian Bolton and Yutian Chen and Timothy Lillicrap and Fan Hui and Laurent Sifre and George Van Den Driessche and Thore Graepel and Demis Hassabis},
   doi = {10.1038/nature24270},
   issn = {14764687},
   issue = {7676},
   journal = {Nature},
   keywords = {Computational science,Computer science,Reward},
   pages = {354-359},
   pmid = {29052630},
   publisher = {Nature Publishing Group},
   title = {Mastering the game of Go without human knowledge},
   volume = {550},
   url = {https://www.nature.com/articles/nature24270},
   year = {2017}
}
@inbook{Paul2015,
   abstract = {Scanning probe microscopy (SPM) is a widely used tool for investigating the nanoscale structure of materials, as well as their electronic and mechanical properties with its related spectroscopic modes of operation. In SPM experiments, the sharp tip which probes the material under investigation is usually uncharacterized; however, its geometry and chemical composition play a large role in the SPM’s lateral imaging resolution and the features recorded in electronic and force spectroscopies. To carry out comparisons with modeling, one must consider a set of plausible tip structures and choose the one which best reproduces the experimental data recorded with the uncharacterized tip. With an atomically defined tip prepared by FIM, the electronic and mechanical properties of the SPM probe are predetermined before the experiment, permitting direct comparison with theory, as well as the quantitative determination of parameters which depend on tip radius, such as stresses during indentation. Here we describe the implementation of FIM for the characterization of scanning probe apices. This includes topics of tip integrity, characterization, advanced preparation methodologies, and key research findings from experiments which combine FIM and SPM techniques.},
   author = {William Paul and Peter Grütter},
   doi = {10.1007/978-3-662-44551-8_5},
   isbn = {9783662445518},
   booktitle = {Surface Science Tools for Nanomaterials Characterization},
   keywords = {Atomic Force Microscopy (Afm),Field Emission,Field Ion Microscopy (Fim),Nanoelectronics,Nanomechanics,Scanning Probe Microscopy (Spm),Scanning Tunneling Microscopy (Stm),Single-Atom Tips,Tip Characterization},
   pages = {159-198},
   publisher = {Springer Berlin Heidelberg},
   title = {Field ion microscopy for the characterization of scanning probes},
   url = {https://link.springer.com/chapter/10.1007/978-3-662-44551-8_5},
   year = {2015}
}
@article{Aversa2015,
   abstract = {Buckminsterfullerene (C60) is a molecule fully formed of carbon that can be used, owing to its electronic and mechanical properties, as “clean” precursor for the growth of carbon-based materials, ranging from π-conjugated systems (graphenes) to synthesized species, e.g., carbides such as silicon carbide (SiC). To this goal, C60 cage rupture is the main physical process that triggers material growth. Cage breaking can be obtained either thermally by heating up the substrate to high temperatures (630°C), after C60 physisorption, or kinetically by using supersonic molecular beam epitaxy techniques. In this work, aiming at demonstrating the growth of SiC thin films by C60 supersonic beams, we present the experimental investigation of C60 impacts on Si(111) 7 × 7 kept at 500°C for translational kinetic energies (KEs) ranging from 18 to 30 eV. The attained kinetically activated synthesis of SiC submonolayer films is probed by in situ surface electron spectroscopies (X-ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy). Furthermore, in these experimental conditions, the C60-Si(111) 7 × 7 collision has been studied by computer simulations based on a tight-binding approximation to density-functional theory. Our theoretical and experimental findings point toward a kinetically driven growth of SiC on Si, where C60 precursor KE plays a crucial role, while temperature is relevant only after cage rupture to enhance Si and carbon reactivity. In particular, we observe a counterintuitive effect in which for low KE (below 22 eV), C60 bounces back without breaking more effectively at high temperature due to energy transfer from excited phonons. At higher KE (22 < K < 30 eV), for which cage rupture occurs, temperature enhances reactivity without playing a major role in the cage break. These results are in good agreement with ab initio molecular dynamics simulations. Supersonic molecular beam epitaxy is thus a technique able to drive material growth at low-temperature regime.},
   author = {Lucrezia Aversa and Simone Taioli and Marco Vittorio Nardi and Roberta Tatti and Roberto Verucchi and Salvatore Iannotta},
   doi = {10.3389/fmats.2015.00046},
   issn = {22968016},
   journal = {Frontiers in Materials},
   keywords = {First-principle simulations,Fullerene,Silicon carbide,Surface dynamics,Thin film},
   pages = {46},
   publisher = {Frontiers Media S.A.},
   title = {The interaction of C60 on Si(111) 7 × 7 studied by supersonic molecular beams: Interplay between precursor kinetic energy and substrate temperature in surface activated processes},
   volume = {2},
   url = {www.frontiersin.org},
   year = {2015}
}
@article{Sweeney2013,
   abstract = {Google ads, black names and white names, racial discrimination, and click advertising.},
   author = {Latanya Sweeney},
   doi = {10.1145/2460276.2460278},
   issn = {15427730},
   issue = {3},
   journal = {Queue},
   pages = {10-29},
   publisher = {ACM PUB27 New York, NY, USA},
   title = {Discrimination in Online Ad Delivery: Google Ads, black names and white names, racial discrimination, and click advertising},
   volume = {11},
   url = {https://dl.acm.org/doi/abs/10.1145/2460276.2460278},
   year = {2013}
}
@article{LeLay1981,
   author = {G. Le Lay},
   doi = {10.1016/0167-2584(81)90010-4},
   issn = {01672584},
   issue = {1},
   journal = {Surface Science Letters},
   pages = {L429-L433},
   publisher = {Elsevier BV},
   title = {New model for the reconstructed Si(111)7×7 and Si(111)$\sqrt\{19\}$×$\sqrt\{19\}$ - R(±23°5) surfaces},
   volume = {108},
   year = {1981}
}
@article{Pollmann1982,
   abstract = {An entirely new, very general, atomically smooth, and optically symmetry-adapted reconstruction model for the Si(111)-7×7 surface is proposed. It consists of parallel rows of nontouching, π-bonded, hexagonal rings with center atoms and seems to be a realization of a static commensurate phase of a nonlinear lattice. An overwhelming number of experimental findings on the Si(111) surface finds an intuitive, simple, and natural explanation by the model. © 1982 The American Physical Society.},
   author = {Johannes Pollmann},
   doi = {10.1103/PhysRevLett.49.1649},
   issn = {00319007},
   issue = {22},
   journal = {Physical Review Letters},
   pages = {1649-1653},
   publisher = {American Physical Society},
   title = {New hexagonal ring model for the reconstruction of the Si(111)-7 × 7 surface},
   volume = {49},
   url = {https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.49.1649},
   year = {1982}
}
@article{Himpsel1983,
   abstract = {A new structure is proposed for the Si(111)-(7×7) surface which is consistent with recent tunneling microscopy and ion-scattering data. It consists of 12 trimers which are located near the points (1,1), (3,1), (1,3), (5,1), (1,5), (3,3), (4,4), (6,2), (2,6), (6,4), (4,6), (6,6) of a (7×7) unit cell. The bonding of the trimers is similar to the -bonded chain model for Si(111)-(2×1) but only half as many bond flips are required to reconstruct the surface. Broken bonds are eliminated by removing atoms along the boundaries between eclipsed and staggered structures. © 1983 The American Physical Society.},
   author = {F. J. Himpsel},
   doi = {10.1103/PhysRevB.27.7782},
   issn = {01631829},
   issue = {12},
   journal = {Physical Review B},
   pages = {7782-7785},
   publisher = {American Physical Society},
   title = {Structural model for Si(111)-(7×7)},
   volume = {27},
   url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.27.7782},
   year = {1983}
}
@article{Roccapriore2021,
   abstract = {The adatom arrays on surfaces offer an ideal playground to explore the mechanisms of chemical bonding via changes in the local electronic tunneling spectra. While this information is readily availa...},
   author = {Kevin M. Roccapriore and Qiang Zou and Lizhi Zhang and Rui Xue and Jiaqiang Yan and Maxim Ziatdinov and Mingming Fu and David G. Mandrus and Mina Yoon and Bobby G. Sumpter and Zheng Gai and Sergei V. Kalinin},
   doi = {10.1021/ACSNANO.1C02902},
   journal = {ACS Nano},
   keywords = {adatoms,machine learning,scanning probe microscopy,scanning tunneling spectroscopy,topological insulator},
   pages = {acsnano.1c02902},
   publisher = {American Chemical Society},
   title = {Revealing the Chemical Bonding in Adatom Arrays via Machine Learning of Hyperspectral Scanning Tunneling Spectroscopy Data},
   url = {https://pubs.acs.org/doi/pdf/10.1021/acsnano.1c02902},
   year = {2021}
}
@phdthesis{Etheridge2020,
   author = {Henry Etheridge},
   school = {University of Bath},
   title = {Nonlocal manipulation on Si(111)-7x7 using the scanning tunnelling microscope, from charge injection to decay},
   url = {https://purehost.bath.ac.uk/ws/portalfiles/portal/219864220/HGE_Thesis_with_corrections.pdf},
   year = {2020}
}
@article{Stroscio2004,
   abstract = {We studied the dynamics of a single cobalt (Co) atom during lateral manipulation on a copper (111) surface in a low-temperature scanning tunneling microscope. The Co binding site locations were revealed in a detailed image that resulted from lateral Co atom motion within the trapping potential of the scanning tip. Random telegraph noise, corresponding to the Co atom switching between hexagonal close-packed (hcp) and face-centered cubic (fcc) sites, was seen when the tip was used to try to position the Co atom over the higher energy hcp site. Varying the probe tip height modified the normal copper (111) potential landscape and allowed the residence time of the Co atom in these sites to be varied. At low tunneling voltages (less than ∼5 millielectron volts), the transfer rate between sites was independent of tunneling voltage, current, and temperature. At higher voltages, the transfer rate exhibited a strong dependence on tunneling voltage, indicative of vibrational heating by inelastic electron scattering.},
   author = {Joseph A. Stroscio and Robert J. Celotta},
   doi = {10.1126/SCIENCE.1102370},
   issn = {0036-8075},
   issue = {5694},
   journal = {Science},
   pages = {242-247},
   pmid = {15358867},
   publisher = {American Association for the Advancement of Science},
   title = {Controlling the Dynamics of a Single Atom in Lateral Atom Manipulation},
   volume = {306},
   url = {https://science.sciencemag.org/content/306/5694/242 https://science.sciencemag.org/content/306/5694/242.abstract},
   year = {2004}
}
@techReport{Siam2017,
   abstract = {Semantic segmentation was seen as a challenging computer vision problem few years ago. Due to recent advancements in deep learning, relatively accurate solutions are now possible for its use in automated driving. In this paper, the semantic segmentation problem is explored from the perspective of automated driving. Most of the current semantic segmentation algorithms are designed for generic images and do not incorporate prior structure and end goal for automated driving. First, the paper begins with a generic taxonomic survey of semantic segmentation algorithms and then discusses how it fits in the context of automated driving. Second, the particular challenges of deploying it into a safety system which needs high level of accuracy and robustness are listed. Third, different alternatives instead of using an independent semantic segmentation module are explored. Finally, an empirical evaluation of various semantic segmentation architectures was performed on CamVid dataset in terms of accuracy and speed. This paper is a preliminary shorter version of a more detailed survey which is work in progress.},
   author = {Mennatullah Siam and Sara Elkerdawy and Martin Jagersand and Senthil Yogamani},
   title = {Deep Semantic Segmentation for Automated Driving: Taxonomy, Roadmap and Challenges},
   year = {2017}
}
@article{Moriarty1998,
   abstract = {We have investigated the interactions of C60 molecules adsorbed on Si(100)-(2 × 1) through their response to manipulation induced by a scanning tunneling microscope operating at room temperature. Intramolecular features are resolved which vary as a molecule is displaced showing that C60 undergoes rotation during tip-induced displacement. For translation to and from certain bonding sites, the apparent size of a molecule may change following lateral manipulation. Furthermore, reversible changes in dimer buckling are observed as a molecule is moved across the surface. Our experimental observations show that the C60/Si(100)-(2 × 1) interaction is dominant over the C60-C60 interaction and attempts to move a molecular pair result in the transfer of one molecule across a dimer row due to barrier lowering by the intermolecular interaction. We also show that transfer of a molecule from sample to tip (or vice versa) changes both the imaging and manipulation properties of the tip. © 1998 Elsevier Science B.V. All rights reserved.},
   author = {P. Moriarty and Y. R. Ma and M. D. Upward and P. H. Beton},
   doi = {10.1016/S0039-6028(98)00082-X},
   issn = {0039-6028},
   issue = {1-3},
   journal = {Surface Science},
   keywords = {Chemisorption,Fullerenes,Scanning tunnelling microscopy,Silicon},
   pages = {27-35},
   publisher = {North-Holland},
   title = {Translation, rotation and removal of C60 on Si(100)-2 × 1 using anisotropic molecular manipulation},
   volume = {407},
   year = {1998}
}
@article{Vieira1986,
   abstract = {The high resolution and displacement measurement in the scanning tunneling microscope are dependent upon the behavior of the piezoelectric ceramics used for moving the tip. In this paper certain characteristics and features of piezoelectric ceramics relevant to the desired precision are discussed. These characteristics are the relaxation aftereffects that follow the change of the applied electric field, and the temperature dependence of the piezoelectric response. The above effects have been analyzed in four commercial piezoelectric ceramics by the three-terminal capacitance measurement technique.},
   author = {S. Vieira},
   doi = {10.1147/RD.305.0553},
   issue = {5},
   journal = {IBM Journal of Research and Development},
   pages = {553-556},
   title = {BEHAVIOR AND CALIBRATION OF SOME PIEZOELECTRIC CERAMICS USED IN THE STM.},
   volume = {30},
   year = {1986}
}
@article{Morgan2018,
   abstract = {For the collidine analogues of Barluenga's Reagent (IPy2BF4) reported, a flat cation is necessary for the generation of a modulated phase, in keeping with the “Ratchet Model” theory [Kim et al., Crystal Growth \& Design, 2014, 14, 6294]. Attempts to study “diffuse modulation” in Br(Coll)2ClO4 have shown that these non-Bragg features disappear very rapidly on exposure to synchrotron radiation, an effect thought to be caused by the radiation damage disrupting the lattice vibrations that cause the modulation.},
   author = {Lewis C. F. Morgan and Yejin Kim and Jack N. Blandy and Claire A. Murray and Kirsten E. Christensen and Amber L. Thompson},
   doi = {10.1039/C8CC05430D},
   issn = {1364-548X},
   issue = {70},
   journal = {Chemical Communications},
   pages = {9849-9852},
   publisher = {The Royal Society of Chemistry},
   title = {Unexpected behaviour in derivatives of Barluenga's reagent, Hal(Coll)2X (Coll = 2,4,6-trimethyl pyridine, collidine; Hal = I, Br; X = PF6, ClO4 \& BF4)},
   volume = {54},
   url = {https://pubs.rsc.org/en/content/articlehtml/2018/cc/c8cc05430d https://pubs.rsc.org/en/content/articlelanding/2018/cc/c8cc05430d},
   year = {2018}
}
@article{Welbery2002,
   author = {T. R. Welberry and B. D. Butler},
   doi = {10.1021/CR00039A005},
   issue = {7},
   journal = {Chemical Reviews},
   pages = {2369-2403},
   publisher = {American Chemical Society},
   title = {Diffuse X-ray Scattering from Disordered Crystals},
   volume = {95},
   url = {https://pubs.acs.org/doi/abs/10.1021/cr00039a005},
   year = {2002}
}
@article{Welberry2015,
   abstract = {Over the 100 years since the discovery of the diffraction of X-rays by crystals, structure determination based on the analysis of Bragg peaks has grown into a very precise, widely applicable, and d...},
   author = {T.R. Welberry and T. Weber},
   doi = {10.1080/0889311X.2015.1046853},
   issue = {1},
   journal = {http://dx.doi.org/10.1080/0889311X.2015.1046853},
   keywords = {Monte Carlo,X-rays,diffuse scattering,disorder,moleculardynamics,neutrons,single crystal},
   pages = {2-78},
   publisher = {Taylor & Francis},
   title = {One hundred years of diffuse scattering},
   volume = {22},
   url = {https://www.tandfonline.com/doi/abs/10.1080/0889311X.2015.1046853},
   year = {2015}
}
@article{Chen2021,
   abstract = {Neutron and X-ray scattering represent two state-of-the-art materials characterization techniques that measure materials' structural and dynamical properties with high precision. These techniques play critical roles in understanding a wide variety of materials systems, from catalysis to polymers, nanomaterials to macromolecules, and energy materials to quantum materials. In recent years, neutron and X-ray scattering have received a significant boost due to the development and increased application of machine learning to materials problems. This article reviews the recent progress in applying machine learning techniques to augment various neutron and X-ray scattering techniques. We highlight the integration of machine learning methods into the typical workflow of scattering experiments. We focus on scattering problems that faced challenge with traditional methods but addressable using machine learning, such as leveraging the knowledge of simple materials to model more Page 2 of 56 complicated systems, learning with limited data or incomplete labels, identifying meaningful spectra and materials' representations for learning tasks, mitigating spectral noise, and many others. We present an outlook on a few emerging roles machine learning may play in broad types of scattering and spectroscopic problems in the foreseeable future.},
   author = {Zhantao Chen and Nina Andrejevic and Nathan Drucker and Thanh Nguyen and R Patrick Xian and Tess Smidt and Yao Wang and Ralph Ernstorfer and Alan Tennant and Maria Chan and Mingda Li},
   doi = {10.1063/5.0049111},
   issue = {3},
   journal = {Chemical Physics Reviews},
   keywords = {Neutron scattering,X-ray scattering,machine learning},
   pages = {031301},
   title = {Machine Learning on Neutron and X-Ray Scattering},
   volume = {2},
   year = {2021}
}
@article{Wang2017,
   abstract = {Visual inspection of x-ray scattering images is a powerful technique for probing the physical structure of materials at the molecular scale. In this paper, we explore the use of deep learning to develop methods for automatically analyzing x-ray scattering images. In particular, we apply Convolutional Neural Networks and Convolutional Autoencoders for x-ray scattering image classification. To acquire enough training data for deep learning, we use simulation software to generate synthetic x-ray scattering images. Experiments show that deep learning methods outperform previously published methods by 10\% on synthetic and real datasets.},
   author = {Boyu Wang and Kevin Yager and Dantong Yu and Minh Hoai},
   doi = {10.1109/WACV.2017.83},
   journal = {Proceedings - 2017 IEEE Winter Conference on Applications of Computer Vision, WACV 2017},
   pages = {697-704},
   publisher = {Institute of Electrical and Electronics Engineers Inc.},
   title = {X-Ray scattering image classification using deep learning},
   year = {2017}
}
@article{Demuth2021,
   abstract = {The diffraction features of Si(111) 7 × 7 are analyzed and related to various structural models of the Si(111) 7 × 7 surface as one part of a multivariate analysis of this system. The limitations in early sample preparation and measurements produce some uncertainty in previously proposed structures. More recent data is considered here. In addition, models used early on to evaluate the structure of 7 × 7 have been over simplified, idealized models. More complex models are considered within the projection rod method as used for surface crystallography. The origin of numerous diffraction features can be determined via their Fourier components for a wide range of 2-D layers, which provides new insight into the structure as well as the limitations of prior projection analyses. Structures which produce the key elements of the 7 × 7 diffraction are presented and various distortions are considered consistent with other experimental results. In general it is found that the presence of a strong set of 3/7th order beams and near extinction of neighbouring fractional order beams are features which are found experimentally and distinguish an important class of structures. This class has a particular type of 3-fold mirror symmetry, which is not apparent in the widely accepted dimer-adatom-stacking fault, DAS, model. Higher order diffraction features, of which many are weak, are also considered and provide important new structural information. Several new polymorphs of the 7 × 7 are identified which may also satisfy the diffraction derived features and possess some degree of pi-bonding so as to enable magnetic surface states not possible in a pure covalently bonded system such as DAS. The Patterson map of the 7 × 7 surface provide insight into the lost phase information encoded in diffraction and reveal why the DAS structure was experimentally favored. An unusual non-primitive 7 × 7 unit cell is also derived from the Patterson map that possesses unusual symmetry properties, a non-standard surface Brillouin zone with potentially unusual electronic properties.},
   author = {J. E. Demuth},
   doi = {10.1039/D0CP05431C},
   issn = {1463-9084},
   issue = {13},
   journal = {Physical Chemistry Chemical Physics},
   pages = {8043-8074},
   publisher = {The Royal Society of Chemistry},
   title = {A re-evaluation of diffraction from Si(111) 7 × 7: decoding the encoded phase information in the 7 × 7 diffraction pattern},
   volume = {23},
   url = {https://pubs.rsc.org/en/content/articlehtml/2021/cp/d0cp05431c https://pubs.rsc.org/en/content/articlelanding/2021/cp/d0cp05431c},
   year = {2021}
}
@article{Tersoff1985,
   abstract = {We present a theory for tunneling between a real surface and a model probe tip, applicable to the recently developed "scanning tunneling microscope. " The tu,nneling current is found to be proportional to the local density of states of the surface, at the position of the tip. The effective lateral resolution is related to the tip radius 8 and the vacuum gap distance d approximately as [(2 A)(R+d)]'~2. The theory is applied to the 2\&\&1 and 3\&(1 reconstructions of Au(110); results for the respective corrugation ainplitudes and for the gap distance are all in excellent agreement with 0 experimental results of Binnig et al. if a 9-A tip radius is assumed. In addition, a convenient approximate calculational method based on atom superposition is tested; it gives reasonable agreement with the self-consistent calculation and with experiment for Au(110). This method is used to test the structure sensitivity of the microscope. We conclude that for the Au(110) measurements the experimental "image" is relatively insensitive to the positions of atoms beyond the first atomic layer. Finally , tunneling to semiconductor surfaces is considered. Calculations for GaAs(110) illustrate interesting qualitative differences from tunneling to metal surfaces.},
   author = {J. Tersoff and D. R. Hamann},
   doi = {10.1103/PhysRevB.31.805},
   issue = {2},
   journal = {Physical Review B},
   pages = {805-813},
   title = {Theory of the scanning tunneling microscope},
   volume = {31},
   url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.31.805},
   year = {1985}
}
@article{Kawai2020,
   abstract = {Recent advances in state-of-the-art probe microscopy allow us to conduct single molecular chemistry via tip-induced reactions and direct imaging of the inner structure of the products. Here, we synthesize three-dimensional graphene nanoribbons by on-surface chemical reaction and take advantage of tip-induced assembly to demonstrate their capability as a playground for local probe chemistry. We show that the radical caused by tip-induced debromination can be reversibly terminated by either a bromine atom or a fullerene molecule. The experimental results combined with theoretical calculations pave the way for sequential reactions, particularly addition reactions, by a local probe at the single-molecule level decoupled from the surface.},
   author = {Shigeki Kawai and Ondřej Krejčí and Tomohiko Nishiuchi and Keisuke Sahara and Takuya Kodama and Rémy Pawlak and Ernst Meyer and Takashi Kubo and Adam S. Foster},
   doi = {10.1126/SCIADV.AAY8913},
   issue = {9},
   journal = {Science Advances},
   publisher = {American Association for the Advancement of Science},
   title = {Three-dimensional graphene nanoribbons as a framework for molecular assembly and local probe chemistry},
   volume = {6},
   url = {https://www.science.org},
   year = {2020}
}
@article{Nieuwenhuizen2013,
   abstract = {A method for computing the intrinsic resolution of a super-resolution image that accounts for localization uncertainty, labeling density and image anisotropy is described. This work extends and builds on the Fourier ring correlation method used in cryoelectron microscopy. Resolution in optical nanoscopy (or super-resolution microscopy) depends on the localization uncertainty and density of single fluorescent labels and on the sample's spatial structure. Currently there is no integral, practical resolution measure that accounts for all factors. We introduce a measure based on Fourier ring correlation (FRC) that can be computed directly from an image. We demonstrate its validity and benefits on two-dimensional (2D) and 3D localization microscopy images of tubulin and actin filaments. Our FRC resolution method makes it possible to compare achieved resolutions in images taken with different nanoscopy methods, to optimize and rank different emitter localization and labeling strategies, to define a stopping criterion for data acquisition, to describe image anisotropy and heterogeneity, and even to estimate the average number of localizations per emitter. Our findings challenge the current focus on obtaining the best localization precision, showing instead how the best image resolution can be achieved as fast as possible.},
   author = {Robert P J Nieuwenhuizen and Keith A Lidke and Mark Bates and Daniela Leyton Puig and David Grünwald and Sjoerd Stallinga and Bernd Rieger},
   doi = {10.1038/nmeth.2448},
   issn = {1548-7105},
   issue = {6},
   journal = {Nature Methods 2013 10:6},
   keywords = {Cellular imaging,Fluorescence imaging,Nanoscale biophysics,Super,resolution microscopy},
   pages = {557-562},
   publisher = {Nature Publishing Group},
   title = {Measuring image resolution in optical nanoscopy},
   volume = {10},
   url = {https://www.nature.com/articles/nmeth.2448},
   year = {2013}
}
@article{Jones2018,
   abstract = {The usual way to present images from a scanning tunneling microscope (STM) is to take multiple images of the same area, to then manually select the one that appears to be of the highest quality, and then to discard the other almost identical images. This is in contrast to most other disciplines where the signal to noise ratio (SNR) of a data set is improved by taking repeated measurements and averaging them. Data averaging can be routinely performed for 1D spectra, where their alignment is straightforward. However, for serial-acquired 2D STM images the nature and variety of image distortions can severely complicate accurate registration. Here, we demonstrate how a significant improvement in the resolving power of the STM can be achieved through automated distortion correction and multi-frame averaging (MFA) and we demonstrate the broad utility of this approach with three examples. First, we show a sixfold enhancement of the SNR of the Si(111)-(7 × 7) reconstruction. Next, we demonstrate that images with sub-picometre height precision can be routinely obtained and show this for a monolayer of Ti 2 O 3 on Au(111). Last, we demonstrate the automated classification of the two chiral variants of the surface unit cells of the (4 × 4) reconstructed SrTiO 3 (111) surface. Our new approach to STM imaging will allow a wealth of structural and electronic information from surfaces to be extracted that was previously buried in noise. (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.},
   author = {Lewys Jones and Shuqiu Wang and Xiao Hu and Shams ur Rahman and Martin R Castell},
   doi = {10.1186/s40679-018-0056-7},
   issue = {111},
   journal = {Adv Struct Chem Imag},
   keywords = {Multi-frame averaging,SPM,STM,Si(111)-(7 × 7) reconstruction,Signal to noise ratio improvement,SrTiO3(111)-(4 × 4) reconstruction,Sub-picometre height resolution,Ti2O3 monolayer on Au(111)},
   pages = {7},
   title = {Maximising the resolving power of the scanning tunneling microscope},
   volume = {4},
   url = {https://doi.org/10.1186/s40679-018-0056-7},
   year = {2018}
}
@article{Blundell2021,
   abstract = {Understanding the structure of a protein complex is crucial in determining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional. Recent advances in Artificial Intelligence have been applied to this problem, primarily using voxel based approaches to analyse sets of electron microscopy images. Here we present a deep learning solution for reconstructing the protein complexes from a number of 2D single molecule localization microscopy images, with the solution being completely unconstrained. Our convolutional neural network coupled with a differentiable renderer predicts pose and derives a single structure. After training, the network is discarded, with the output of this method being a structural model which fits the data-set. We demonstrate the performance of our system on two protein complexes: CEP152 (which comprises part of the proximal toroid of the centriole) and centrioles.},
   author = {Benjamin J. Blundell and Christian Sieben and Suliana Manley and Ed Rosten and QueeLim Ch'ng and Susan Cox},
   doi = {10.3389/FBINF.2021.740342/BIBTEX},
   journal = {Frontiers in Bioinformatics},
   keywords = {AI,Deep-learning,SMLM,Structure,storm},
   pages = {62},
   publisher = {Frontiers},
   title = {3D Structure from 2D Microscopy images using Deep Learning},
   volume = {0},
   url = {http://arxiv.org/abs/2110.07608 http://dx.doi.org/10.3389/fbinf.2021.740342},
   year = {2021}
}
@article{Jager2018,
   abstract = {Catalytic activity of the hydrogen evolution reaction on nanoclusters depends on diverse adsorption site structures. Machine learning reduces the cost for modelling those sites with the aid of descriptors. We analysed the performance of state-of-the-art structural descriptors Smooth Overlap of Atomic Positions, Many-Body Tensor Representation and Atom-Centered Symmetry Functions while predicting the hydrogen adsorption (free) energy on the surface of nanoclusters. The 2D-material molybdenum disulphide and the alloy copper–gold functioned as test systems. Potential energy scans of hydrogen on the cluster surfaces were conducted to compare the accuracy of the descriptors in kernel ridge regression. By having recourse to data sets of 91 molybdenum disulphide clusters and 24 copper–gold clusters, we found that the mean absolute error could be reduced by machine learning on different clusters simultaneously rather than separately. The adsorption energy was explained by the local descriptor Smooth Overlap of Atomic Positions, combining it with the global descriptor Many-Body Tensor Representation did not improve the overall accuracy. We concluded that fitting of potential energy surfaces could be reduced significantly by merging data from different nanoclusters. The accuracy and efficiency of descriptors for machine learning are tested for hydrogen evolution reaction in nanocatalytic systems. A team led by Adam Foster at Aalto University analysed the performance of SOAP, MBTR and ACSF structural descriptors used to gain insight to the free energy of hydrogen adsorption on the surface of nanoclusters relevant to catalysis applications. Using atomically thin MoS2 and AuxCuy metallic alloys as test systems, the accuracy of the predictors was evaluated when used as features in kernel ridge regression. Analysis on a dataset of 91 MoS2 clusters and 24 AuxCuy clusters (x + y = 13) indicated that while none of the descriptors which had been designed for molecules and crystals was optimized for nanoclusters, SOAP performed significantly better, making it a more suitable candidate for adsorption energy prediction.},
   author = {Marc O.J. Jäger and Eiaki V. Morooka and Filippo Federici Canova and Lauri Himanen and Adam S. Foster},
   doi = {10.1038/s41524-018-0096-5},
   issn = {2057-3960},
   issue = {1},
   journal = {npj Computational Materials 2018 4:1},
   keywords = {Characterization and analytical techniques,Electrocatalysis,Nanoparticles},
   pages = {1-8},
   publisher = {Nature Publishing Group},
   title = {Machine learning hydrogen adsorption on nanoclusters through structural descriptors},
   volume = {4},
   url = {https://www.nature.com/articles/s41524-018-0096-5},
   year = {2018}
}
@article{Oinonen2021,
   abstract = {While offering high resolution atomic and electronic structure, scanning probe microscopy techniques have found greater challenges in providing reliable electrostatic characterization on the same s...},
   author = {Niko Oinonen and Chen Xu and Benjamin Alldritt and ⊥ Filippo and Federici Canova and Fedor Urtev and Shuning Cai and Ondř Ej Krejč and Juho Kannala and Peter Liljeroth and Adam S Foster},
   doi = {10.1021/ACSNANO.1C06840},
   issn = {1936-0851},
   journal = {ACS Nano},
   keywords = {atomic force microscopy,chemical identification,electrostatics,machine learning,tip functionalization},
   pages = {acsnano.1c06840},
   publisher = {American Chemical Society},
   title = {Electrostatic Discovery Atomic Force Microscopy},
   url = {https://pubs.acs.org/doi/abs/10.1021/acsnano.1c06840},
   year = {2021}
}
@article{Jones2015,
   abstract = {Many microscopic investigations of materials may benefit from the recording of multiple successive images. This can include techniques common to several types of microscopy such as frame averaging to improve signal-to-noise ratios (SNR) or time series to study dynamic processes or more specific applications. In the scanning transmission electron microscope, this might include focal series for optical sectioning or aberration measurement, beam damage studies or camera-length series to study the effects of strain; whilst in the scanning tunnelling microscope, this might include bias-voltage series to probe local electronic structure. Whatever the application, such investigations must begin with the careful alignment of these data stacks, an operation that is not always trivial. In addition, the presence of low-frequency scanning distortions can introduce intra-image shifts to the data. Here, we describe an improved automated method of performing non-rigid registration customised for the challenges unique to scanned microscope data specifically addressing the issues of low-SNR data, images containing a large proportion of crystalline material and/or local features of interest such as dislocations or edges. Careful attention has been paid to artefact testing of the non-rigid registration method used, and the importance of this registration for the quantitative interpretation of feature intensities and positions is evaluated.},
   author = {Lewys Jones and Hao Yang and Timothy J. Pennycook and Matthew S.J. Marshall and Sandra Van Aert and Nigel D. Browning and Martin R. Castell and Peter D. Nellist},
   doi = {10.1186/S40679-015-0008-4/FIGURES/11},
   issn = {21980926},
   issue = {1},
   journal = {Advanced Structural and Chemical Imaging},
   keywords = {Image registration,Non-rigid registration,Principle component analysis,Quantitative ADF,Scanning tunnelling microscopy (STM),Strain mapping},
   pages = {1-16},
   publisher = {Springer},
   title = {Smart Align—a new tool for robust non-rigid registration of scanning microscope data},
   volume = {1},
   url = {https://ascimaging.springeropen.com/articles/10.1186/s40679-015-0008-4},
   year = {2015}
}
@article{Keeling2002,
   abstract = {We have investigated the manipulation of C60 molecules on Si(1 0 0)-2 × 1 using the tip of a scanning tunnelling microscope. An attractive mode of manipulation has been identified in which molecules hop across the Si(1 0 0)-2 × 1 surface in steps of two lattice constants. An abrupt transition to repulsive manipulation occurs as the tip is lowered towards the surface. The attractive interaction is attributed to chemical forces between the tip and molecule. © 2002 Elsevier Science B.V. All rights reserved.},
   author = {D. L. Keeling and M. J. Humphry and P. Moriarty and P. H. Beton},
   doi = {10.1016/S0009-2614(02)01588-9},
   issn = {0009-2614},
   issue = {3-4},
   journal = {Chemical Physics Letters},
   pages = {300-304},
   publisher = {North-Holland},
   title = {Attractive mode manipulation of covalently bound molecules},
   volume = {366},
   year = {2002}
}
@article{Banterle2013,
   abstract = {Optical nanoscopy techniques using localization based image reconstruction, also termed super-resolution microscopy (SRM), have become a standard tool to bypass the diffraction limit in fluorescence light microscopy. The localization precision measured for the detected fluorophores is commonly used to describe the maximal attainable resolution. However, this measure takes not all experimental factors, which impact onto the finally achieved resolution, into account. Several other methods to measure the resolution of super-resolved images were previously suggested, typically relying on intrinsic standards, such as molecular rulers, or on a priori knowledge about the specimen, e.g. its spatial frequency content. Here we show that Fourier ring correlation provides an easy-to-use, laboratory consistent standard for measuring the resolution of SRM images. We provide a freely available software tool that combines resolution measurement with image reconstruction. © 2013 Elsevier Inc.},
   author = {Niccolò Banterle and Khanh Huy Bui and Edward A. Lemke and Martin Beck},
   doi = {10.1016/J.JSB.2013.05.004},
   issn = {1047-8477},
   issue = {3},
   journal = {Journal of Structural Biology},
   keywords = {Fourier ring correlation,Resolution,Super-resolution microscopy},
   pages = {363-367},
   pmid = {23684965},
   publisher = {Academic Press},
   title = {Fourier ring correlation as a resolution criterion for super-resolution microscopy},
   volume = {183},
   year = {2013}
}
@article{Koho2019,
   abstract = {Fourier ring correlation (FRC) has recently gained popularity among fluorescence microscopists as a straightforward and objective method to measure the effective image resolution. While the knowledge of the numeric resolution value is helpful in e.g., interpreting imaging results, much more practical use can be made of FRC analysis—in this article we propose blind image restoration methods enabled by it. We apply FRC to perform image de-noising by frequency domain filtering. We propose novel blind linear and non-linear image deconvolution methods that use FRC to estimate the effective point-spread-function, directly from the images. We show how FRC can be used as a powerful metric to observe the progress of iterative deconvolution. We also address two important limitations in FRC that may be of more general interest: how to make FRC work with single images (within certain practical limits) and with three-dimensional images with highly anisotropic resolution. Fourier ring correlation (FRC) analysis is commonly used in fluorescence microscopy to measure effective image resolution. Here, the authors demonstrate that FRC can also be leveraged in blind image restoration methods, such as image deconvolution.},
   author = {Sami Koho and Giorgio Tortarolo and Marco Castello and Takahiro Deguchi and Alberto Diaspro and Giuseppe Vicidomini},
   doi = {10.1038/s41467-019-11024-z},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications 2019 10:1},
   keywords = {Cellular imaging,Image processing,Super,resolution microscopy},
   pages = {1-9},
   pmid = {31308370},
   publisher = {Nature Publishing Group},
   title = {Fourier ring correlation simplifies image restoration in fluorescence microscopy},
   volume = {10},
   url = {https://www.nature.com/articles/s41467-019-11024-z},
   year = {2019}
}
@article{Cowie2022,
   abstract = {Transition metal dichalcogenides (TMDCs) have attracted significant attention for optoelectronic, photovoltaic and photoelectrochemical applications. The properties of TMDCs are highly dependent on the number of stacked atomic layers, which is usually counted post-fabrication, using a combination of optical methods and atomic force microscopy height measurements. Here, we use photoluminescence spectroscopy, Raman spectroscopy, and three different AFM methods to demonstrate significant discrepancies in height measurements of exfoliated MoSe 2 flakes on SiO 2 depending on the method used. We also highlight the often overlooked effect that electrostatic forces can be misleading when measuring the height of a MoSe 2 flake using AFM.},
   author = {Megan Cowie and Rikke Plougmann and Yacine Benkirane and Léonard Schué and Zeno Schumacher and Peter Grütter},
   doi = {10.1088/1361-6528/ac40bd},
   issn = {0957-4484},
   issue = {12},
   journal = {Nanotechnology},
   pages = {125706},
   title = {How high is a MoSe 2 monolayer?},
   volume = {33},
   url = {https://doi.org/10.1088/1361-6528/ac40bd https://iopscience.iop.org/article/10.1088/1361-6528/ac40bd},
   year = {2022}
}
@phdthesis{Alldritt2021,
   abstract = {Atomic force microscopy (AFM) with functionalized tips has emerged as the primary experimental technique for understanding the atomic structure of organic molecules on surfaces. Additionally, when combined with atom ma- nipulation, AFM provides the opportunity to explore the atomic structures of single molecules with high precision. As the molecule size increases, the need for accurate computational simulations becomes more burdensome. This thesis explores the capabilities of combining deep learning via neural networks with experimental non-contact atomic force microscopy (nc-AFM), addressing issues with tip functionalization, adsorption configuration, and molecular characteristics, such as electrostatics. To understand integration ofmachine learning methods with experimen- tal nc-AFM, CO molecules were manipulated onto the end of a metallic tip after identification utilizing computer vision (CV) and convolution neu- ral networks (CNN). This provided an automated way of preparing the AFM tips for later experiments and addressed a common issue in many experiments utilizing nc-AFM, particularly regarding the time involved to prepare a tip. Most molecules studied with nc-AFM are planar, but knowledge on the properties non-planar molecules was limited due to the challenges inter- preting the resulting data. To address this, a deep learning infrastructure with a CNN was developed which matches a set of AFM images with a molecular configuration descriptor. This infrastructure was then applied to 1S-camphor on Cu(111), which demonstrated a rapid and reliable method for interpreting AFM images as well as reducing the potential adsorption configurations for future detailed studies. Approaching from a similar perspective, the conventional structure search process, even for small pla- nar molecules, is computationally intensive. By employing Bayesian opti- mization, first-principles simulations with unbiased structure inference for multiple adsorption configurations became possible. To provide a reliable electrostatic characterization ofindividual molecules, experiments ofPTCDA and benzene derivatives on Cu(111) were combined with a machine learning method to provide quantitative maps of the elec- trostatic potential directly from AFM data. Machine learning methods combined with atomic-scale AFM images provide a straightforward path- way to quantitatively understanding molecular properties with reduced bias.},
   author = {Benjamin William Alldritt},
   school = {Aalto University},
   pages = {68 + app. 56},
   title = {Characterization and reconstruction of sin- gle molecules utilizing atomic force mi- croscopy and machine learning},
   url = {https://aaltodoc.aalto.fi/handle/123456789/111926},
   year = {2021}
}
@article{Chen2022_old,
   abstract = {Atomic-scale manipulation in scanning tunneling microscopy 1 has enabled the creation of quantum states of matter based on artificial structures 2-4 and extreme minia-turization of computational circuitry based on individual atoms. 5-7 The ability to autonomously arrange atomic structures with precision will enable the scaling up of nanoscale fabrication 8 and expand the range of artificial structures hosting exotic quantum states. However, the a priori unknown manipulation parameters, the possibility of spontaneous tip apex changes, and the difficulty of modeling tip-atom interactions make it challenging to select manipulation parameters that can achieve atomic precision throughout extended operations. Here we use deep reinforcement learning (DRL) 9 to control the real-world atom manipulation process. Several state-of-the-art reinforcement learning techniques are used jointly to boost data efficiency. The reinforcement learning agent learns to manipulate Ag adatoms on Ag(111) surfaces with optimal precision and is integrated with path planning algorithms 10,11 to complete an autonomous},
   author = {I-Ju Chen and Markus Aapro and Abraham Kipnis and Alexander Ilin and Peter Liljeroth and Adam S Foster},
   title = {Precise atom manipulation through deep reinforcement learning},
   year = {2022}
}
@article{Kawai2014,
   abstract = {Atomic manipulation enables us to fabricate a unique structure at the atomic scale. So far, many atomic manipulations have been reported on conductive surfaces, mainly at low temperature with scanning tunnelling microscopy, but atomic manipulation on an insulator at room temperature is still a long-standing challenge. Here we present a systematic atomic manipulation on an insulating surface by advanced atomic force microscopy, enabling construction of complex patterns such as a ‘Swiss cross’ of substitutional bromine ions in the sodium chloride surface. Atomic manipulation can be used to fabricate unique structures at the atomic level but has previously been limited to conductive surfaces, mainly at low temperatures. Here, the authors present a systematic manipulation on an insulating surface using atomic force microscopy to construct complex patterns.},
   author = {Shigeki Kawai and Adam S. Foster and Filippo Federici Canova and Hiroshi Onodera and Shin Ichi Kitamura and Ernst Meyer},
   doi = {10.1038/ncomms5403},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications 2014 5:1},
   keywords = {Design,Surface chemistry,Surfaces,interfaces and thin films,synthesis and processing},
   pages = {1-7},
   publisher = {Nature Publishing Group},
   title = {Atom manipulation on an insulating surface at room temperature},
   volume = {5},
   url = {https://www.nature.com/articles/ncomms5403},
   year = {2014}
}
@article{Fishlock2000,
   abstract = {Since the realization that the tips of scanning probe microscopes can interact with atoms at surfaces, there has been much interest in the possibility of building or modifying nanostructures or molecules directly from single atoms. Individual large molecules can be positioned on surfaces, and atoms can be transferred controllably between the sample and probe tip. The most complex structures are produced at cryogenic temperatures by sliding atoms across a surface to chosen sites. But there are problems in manipulating atoms laterally at higher temperatures - atoms that are sufficiently well bound to a surface to be stable at higher temperatures require a stronger tip interaction to be moved. This situation differs significantly from the idealized weakly interacting tips of scanning tunnelling or atomic force microscopes. Here we demonstrate that precise positioning of atoms on a copper surface is possible at room temperature. The triggering mechanism for the atomic motion unexpectedly depends on the tunnelling current density, rather than the electric field or proximity of tip and surface.},
   author = {T. W. Fishlock and A. Oral and R. G. Egdell and J. B. Pethica},
   doi = {10.1038/35008030},
   issn = {00280836},
   issue = {6779},
   journal = {Nature},
   pages = {743-745},
   title = {Manipulation of atoms across a surface at room temperature},
   volume = {404},
   year = {2000}
}
@article{Whitman1991,
   abstract = {A general method of manipulating adsorbed atoms and molecules on room-temperature surfaces with the use of a scanning tunneling microscope is described. By applying an appropriate voltage pulse bet...},
   author = {L. J. Whitman and Joseph A. Stroscio and R. A. Dragoset and R. J. Celotta},
   doi = {10.1126/SCIENCE.251.4998.1206},
   issn = {00368075},
   issue = {4998},
   journal = {Science},
   pages = {1206-1210},
   pmid = {17799280},
   publisher = {American Association for the Advancement of Science},
   title = {Manipulation of Adsorbed Atoms and Creation of New Structures on Room-Temperature Surfaces with a Scanning Tunneling Microscope},
   volume = {251},
   url = {https://www.science.org/doi/10.1126/science.251.4998.1206},
   year = {1991}
}
@article{Sloan2005,
   abstract = {Using the tip of a scanning tunnelling microscope (STM) to mechanically manipulate individual atoms and molecules on a surface is now a well established procedure1,2. Similarly, selective vibrational excitation of adsorbed molecules with an STM tip to induce motion or dissociation has been widely demonstrated3,4. Such experiments are usually performed on weakly bound atoms that need to be stabilized by operating at cryogenic temperatures. Analogous experiments at room temperature5 are more difficult, because they require relatively strongly bound species that are not perturbed by random thermal fluctuations. But manipulation can still be achieved through electronic excitation of the atom or molecule by the electron current6,7,8,9,10,11 tunnelling between STM tip and surface at relatively high bias voltages10,11, typically 1–5 V. Here we use this approach to selectively dissociate chlorine atoms from individual oriented chlorobenzene molecules adsorbed on a Si(111)-7 × 7 surface. We map out the final destination of the chlorine daughter atoms, finding that their radial and angular distributions depend on the tunnelling current and hence excitation rate. In our system, one tunnelling electron has nominally sufficient energy to induce dissociation, yet the process requires two electrons. We explain these observations by a two-electron mechanism that couples vibrational excitation and dissociative electron attachment steps.},
   author = {P. A. Sloan and R. E. Palmer},
   doi = {10.1038/nature03385},
   issn = {1476-4687},
   issue = {7031},
   journal = {Nature 2005 434:7031},
   keywords = {Humanities and Social Sciences,Science,multidisciplinary},
   pages = {367-371},
   publisher = {Nature Publishing Group},
   title = {Two-electron dissociation of single molecules by atomic manipulation at room temperature},
   volume = {434},
   url = {https://www.nature.com/articles/nature03385},
   year = {2005}
}
@article{Houselt2008,
   abstract = {The scanning tunnelling microscope (STM) can be used as a tool for assembling nanostructures at the atomic level. In this article we briefly review several pathways for controlled manipulation of atoms and molecules on semiconductor surfaces at room temperature. As an illustrative example we discuss the controlled manipulation of atomic platinum chains. We were able to carry the constituting dimers of the atomic Pt chains from point to point with atomic precision at room temperature. Besides the ultimate control of the surface structure we also show that the manipulated Pt dimer can be attached to the apex of the STM tip in various stable configurations.},
   author = {Arie Van Houselt and Henricus J W Zandvliet},
   issn = {2049-4424},
   issue = {2},
   journal = {Microscopy and analysis (E MEA edition)},
   keywords = {IR-73054,METIS-249956},
   pages = {S5--S8},
   publisher = {Wiley},
   title = {Atomic manipulation on semiconductor surfaces at room temperature by Scanning Tunneling Microscopy},
   volume = {22},
   year = {2008}
}
@article{Uchida1993,
   abstract = {Using a scanning tunneling microscope, single adatoms can be extracted from a Si(111)7X7surface by field evaporation, when the sample voltage is pulsed at 4 V or more in either polarity. Statistically, adatoms at the center of the 7X 7 unit cell are more frequently removed than those near the corner holes, by a ratio of 1.6:1. This difference can be explained by assuming that the binding energy of center ada-toms is approximately 0. 1 eV less than for corner adatoms. The relationship of this result to previous observations of greater chemical reactivity at center adatom sites is discussed.},
   author = {Hironaga Uchida and Dehuan Huang and Franqois Grey and Masakazu Aono},
   doi = {10.1103/PhysRevLett.70.2040},
   issn = {00319007},
   issue = {13},
   journal = {Physical Review Letters},
   keywords = {-Japan,5-9-9 Tohkohdai,Aono Atomcraft Project,ERATO,JRDC,Tsukuba sh-iJb,araki 300 26},
   pages = {2040},
   title = {Site-Specific Measurement of Adatom Binding Energy Differences by Atom Extraction with the STM},
   volume = {70},
   url = {https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.70.2040},
   year = {1993}
}
@article{Yannoni1991,
   abstract = {The controlled manipulation of silicon at the nanometer scale will facilitate the fabrication of new types of electronic devices. The scanning tunneling microscope (STM) can be used to manipulate s...},
   author = {C S Yannoni and R D Johnson and G Meijer and D S Bethune and J R Salem and J Phys Chem and In-whan Lyo and Phaedon AvouRis},
   doi = {10.1126/SCIENCE.253.5016.173},
   issn = {00368075},
   issue = {5016},
   journal = {Science},
   pages = {173-176},
   pmid = {17779133},
   publisher = {American Association for the Advancement of Science},
   title = {Field-Induced Nanometer- to Atomic-Scale Manipulation of Silicon Surfaces with the STM},
   volume = {253},
   url = {https://www.science.org/doi/10.1126/science.253.5016.173},
   year = {1991}
}
@article{Kolmer2013,
   abstract = {We describe a complete protocol for atomically precise dangling bond (DB) logic gate construction on a hydrogenated Ge(0 0 1):H surface. Starting from the preparation of the reconstructed Ge(0 0 1) surface followed by its passivation with hydrogen atoms we end up with the platform for scanning tunneling microscopy (STM) atomic-scale lithography. Finally with the use of dimer-by-dimer STM tip-induced hydrogen desorption from the Ge(0 0 1) - (2 × 1):H surface the DB nanostructures of pre-designed form are fabricated. Furthermore, the STM tip manipulation provides the control over the buckling phase of a single DB dimer incorporated into the DB logic gate structure, which is of crucial importance for the final electronic properties of the system. Our results prove feasibility of DB atomic scale logic gate implementation on the passivated semiconductor surfaces. © 2013 Elsevier Ltd. All rights reserved.},
   author = {Marek Kolmer and Szymon Godlewski and Jakub Lis and Bartosz Such and Lev Kantorovich and Marek Szymonski},
   doi = {10.1016/J.MEE.2013.03.061},
   issn = {0167-9317},
   journal = {Microelectronic Engineering},
   keywords = {Atomic-scale logic gates,Dangling bond nanostructures,Hydrogen passivated germanium,STM},
   pages = {262-265},
   publisher = {Elsevier},
   title = {Construction of atomic-scale logic gates on a surface of hydrogen passivated germanium},
   volume = {109},
   year = {2013}
}
@article{Berger2015,
   abstract = {A single atomic manipulation on the delta-doped B:Si(111)-(√3 × √3)R30 surface using a low temperature dynamic atomic force microscopy based on the Kolibri sensor is investigated. Through a controlled vertical displacement of the probe, a single Si adatom in order to open a vacancy is removed. It is shown that this process is completely reversible, by accurately placing a Si atom back into the vacancy site. In addition, density functional theory simulations are carried out to understand the underlying mechanism of the atomic manipulation in detail. This process also rearranges the atoms at the tip apex, which can be effectively sharpened in this way. Such sharper tips allow for a deeper look into the Si adatom vacancy site. Namely, high-resolution images of the vacancy showing subsurface Si dangling bond triplets, which surround the substitutional B dopant atom in the first bilayer, are achieved. A double tip approaches a silicon surface, passivated by subsurface boron atoms. Vertical manipulation with a surface atom causes sharpening of the tip and opening of a vacancy on the surface. By the newly formed atomically sharp tip, the detailed inner structure of the surface vacancy is observed.},
   author = {Jan Berger and Evan J Spadafora and Pingo Mutombo and Pavel Jelínek and Martin S ˘ Vec and J Berger and E J Spadafora and P Mutombo and P Jelínek},
   doi = {10.1002/SMLL.201500092},
   issn = {1613-6829},
   issue = {30},
   journal = {Small},
   keywords = {AFM,STM,functionalization,manipulation,semiconducting surfaces},
   pages = {3686-3693},
   publisher = {John Wiley & Sons, Ltd},
   title = {Force-Driven Single-Atom Manipulation on a Low-Reactive Si Surface for Tip Sharpening},
   volume = {11},
   url = {https://onlinelibrary.wiley.com/doi/full/10.1002/smll.201500092 https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201500092 https://onlinelibrary.wiley.com/doi/10.1002/smll.201500092},
   year = {2015}
}
@article{Lewis1994,
   abstract = {Although it is well known that cross correlation can be efficiently implemented in the transform domain, the normalized form of cross correlation preferred for template matching applications does not have a simple frequency domain expression. Normalized cross correlation is usually computed in the spatial domain for this reason. This short paper shows that unnormalized cross correlation can be efficiently normalized using precomputed tables containing the integral of the image and image2 over the search window},
   author = {J.P. Lewis},
   journal = {Vis. Interface},
   pages = {120-123},
   title = {Fast Template Matching},
   volume = {95},
   url = {https://www.researchgate.net/publication/242325076_Fast_Template_Matching},
   year = {1994}
}
@article{Kapoor2022,
   abstract = {The use of machine learning (ML) methods for prediction and forecasting has become widespread across the quantitative sciences. However, there are many known methodological pitfalls, including data leakage, in ML-based science. In this paper, we systematically investigate reproducibility issues in ML-based science. We show that data leakage is indeed a widespread problem and has led to severe reproducibility failures. Specifically, through a survey of literature in research communities that adopted ML methods, we find 17 fields where errors have been found, collectively affecting 329 papers and in some cases leading to wildly overoptimistic conclusions. Based on our survey, we present a fine-grained taxonomy of 8 types of leakage that range from textbook errors to open research problems. We argue for fundamental methodological changes to ML-based science so that cases of leakage can be caught before publication. To that end, we propose model info sheets for reporting scientific claims based on ML models that would address all types of leakage identified in our survey. To investigate the impact of reproducibility errors and the efficacy of model info sheets, we undertake a reproducibility study in a field where complex ML models are believed to vastly outperform older statistical models such as Logistic Regression (LR): civil war prediction. We find that all papers claiming the superior performance of complex ML models compared to LR models fail to reproduce due to data leakage, and complex ML models don't perform substantively better than decades-old LR models. While none of these errors could have been caught by reading the papers, model info sheets would enable the detection of leakage in each case.},
   author = {Sayash Kapoor and Arvind Narayanan},
   doi = {https://doi.org/10.48550/arXiv.2207.07048},
   title = {Leakage and the Reproducibility Crisis in ML-based Science},
   url = {http://arxiv.org/abs/2207.07048},
   year = {2022}
}
@article{Shi2005,
   abstract = {A method for reproducible site-specific force spectroscopic measurements at room temperature by combining frequency modulation atomic force microscopy and the atom tracking technique is proposed. The atom tracking enables us to compensate the change in the tip-sample relative position induced by the thermal drift as well as to precisely position the tip over the same spot of the surface within sub-Ångström stability. Here, we describe our atom-tracking implementation and the protocol we have followed for the reproducible room-temperature acquisition of series of frequency shift versus tip-sample distance (f-Z) curves using this technique. With this acquisition protocol, a large number of equivalent f-Z curves can be averaged, resulting in a considerable noise reduction, and therefore avoiding its propagation to the corresponding calculated force curve.},
   author = {Chen Shi and Marco Velli and Ryota Suenaga and Masashi Suzuki and Shoji Kakio and Masayuki Abe and Yoshiaki Sugimoto and Oscar Custance and Seizo Morita},
   doi = {10.1088/0957-4484/16/12/050},
   journal = {Nanotechnology},
   pages = {3029-3034},
   title = {Atom tracking for reproducible force spectroscopy at room temperature with non-contact atomic force microscopy},
   volume = {16},
   year = {2005}
}
@article{Heath2021,
   abstract = {Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM)1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules2. Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset. A localization algorithm is applied to datasets obtained with conventional and high-speed atomic force microscopy to increase image resolution beyond the limits set by the radius of the tip used.},
   author = {George R. Heath and Ekaterina Kots and Janice L. Robertson and Shifra Lansky and George Khelashvili and Harel Weinstein and Simon Scheuring},
   doi = {10.1038/s41586-021-03551-x},
   issn = {1476-4687},
   issue = {7863},
   journal = {Nature 2021 594:7863},
   keywords = {Atomic force microscopy,Imaging techniques,Nanoscale biophysics,Single,molecule biophysics},
   pages = {385-390},
   pmid = {34135520},
   publisher = {Nature Publishing Group},
   title = {Localization atomic force microscopy},
   volume = {594},
   url = {https://www.nature.com/articles/s41586-021-03551-x},
   year = {2021}
}
@article{Wang2016,
   abstract = {The atomic force microscopy (AFM) allows the measurement of interactions at interfaces with nanoscale resolution. Imperfections in the shape of the tip often lead to the presence of imaging artifacts, such as the blurring and repetition of objects within images. In general, these artifacts can only be avoided by discarding data and replacing the probe. Under certain circumstances (e.g., rare, high-value samples, or extensive chemical/physical tip modification), such an approach is not feasible. Here, we apply a novel deblurring technique, using a Bayesian framework, to yield a reliable estimation of the real surface topography without any prior knowledge of the tip geometry (blind reconstruction). A key contribution is to leverage the significant recently successful body of work in natural image deblurring to solve this problem. We focus specifically on the double-tip effect, where two asperities1 are present on the tip, each contributing to the image formation mechanism. Finally, we demonstrate that the proposed technique successfully removes the double-tip effect from high-resolution AFM images, which demonstrate this artifact while preserving feature resolution.1An asperity is a localized sharp peak in the surface of an object.},
   author = {Yun Feng Wang and Jason I. Kilpatrick and Suzanne P. Suzi Jarvis and Francis M. Frank Boland and Anil Kokaram and David Corrigan},
   doi = {10.1109/TIP.2016.2532239},
   issn = {10577149},
   issue = {6},
   journal = {IEEE Transactions on Image Processing},
   keywords = {Amyloid,Atomic Force Microscopy,Bayesian,Blind Deconvolution,Deblurring,Deconvolution,Image Restoration},
   pages = {2774-2788},
   publisher = {Institute of Electrical and Electronics Engineers Inc.},
   title = {Double-Tip Artifact Removal from Atomic Force Microscopy Images},
   volume = {25},
   year = {2016}
}
@article{Straton2014,
   abstract = {Scanning probe microscopy (SPM) images can be obscured by signals from blunt and multiple probe tips. We show why crystallographic image processing (CIP) techniques may be utilized to restore obscured images that are periodic in two dimensions. The image-forming current for double tips in scanning tunneling microscopy (STM) is derived in a more straightforward manner than prior approaches. The Fourier spectrum of the tunneling current for p4mm Bloch surface wave functions and a pair of delta function tips reveals the tip-separation dependence. Our analysis clarifies why crystallographic averaging works well in removing such effects from the recorded 2D periodic images and also outlines the limitations of this image processing technique for certain spatial separations of STM double-tips. Classical simulations of double tip effects in STM images (that ignore electron interference effects) may be understood as modeling double tip effects in images that were recorded with other types of SPMs. Appendix A demonstrates how double tip effects on scanning probe microscope images are detected unambiguously.},
   author = {Jack C. Straton and Taylor T. Bilyeu and Bill Moon and Peter Moeck},
   doi = {10.1002/CRAT.201300240},
   issn = {1521-4079},
   issue = {9},
   journal = {Crystal Research and Technology},
   keywords = {atomic force microscopy,crystallographic image processing,scanning tunneling microscopy},
   pages = {663-680},
   publisher = {John Wiley & Sons, Ltd},
   title = {Double-tip effects on scanning tunneling microscopy imaging of 2D periodic objects: unambiguous detection and limits of their removal by crystallographic averaging in the spatial frequency domain},
   volume = {49},
   url = {https://onlinelibrary.wiley.com/doi/full/10.1002/crat.201300240 https://onlinelibrary.wiley.com/doi/abs/10.1002/crat.201300240 https://onlinelibrary.wiley.com/doi/10.1002/crat.201300240},
   year = {2014}
}
@article{Ternes2008,
   abstract = {Manipulation of individual atoms and molecules by scanning probe microscopy offers the ability of controlled assembly at the single-atom scale. However, the driving forces behind atomic manipulation have not yet been measured. We used an atomic force microscope to measure the vertical and lateral forces exerted on individual adsorbed atoms or molecules by the probe tip. We found that the force that it takes to move an atom depends strongly on the adsorbate and the surface. Our results indicate that for moving metal atoms on metal surfaces, the lateral force component plays the dominant role. Furthermore, measuring spatial maps of the forces during manipulation yielded the full potential energy landscape of the tip-sample interaction.},
   author = {Markus Ternes and Christopher P. Lutz and Cyrus F. Hirjibehedin and Franz J. Giessibl and Andreas J. Heinrich},
   doi = {10.1126/SCIENCE.1150288/SUPPL_FILE/TERNES.SOM.PDF},
   issn = {00368075},
   issue = {5866},
   journal = {Science},
   pages = {1066-1069},
   publisher = {American Association for the Advancement of Science},
   title = {The force needed to move an atom on a surface},
   volume = {319},
   url = {https://www.science.org/doi/10.1126/science.1150288},
   year = {2008}
}
@article{Sugimoto2007,
   abstract = {Dynamic force microscopy, which works by detecting the interaction force between the oscillating tip of an atomic force microscope (AFM) and a surface, has been refined to the extent that it can achieve true atomic resolution of insulator, semiconductor and metal surfaces. In a landmark publication in this issue this technique has been used to perform the chemical identification of individual atoms in a multi-element system. The method involves precise quantification of short-range chemical forces between the probed atoms and the AFM tip, and provides a robust and general recognition tool suitable for both cryogenic and room temperature environments. The cover shows a topographic image of a surface alloy made up of silicon (red), tin (blue), and lead atoms (green) in equal proportions on a silicon (111) substrate. This atomic identification method is relevant to a wide range of research areas such as catalysis, materials science and semiconductor technology. Scanning probe microscopy is a versatile and powerful method that uses sharp tips to image, measure and manipulate matter at surfaces with atomic resolution1,2. At cryogenic temperatures, scanning probe microscopy can even provide electron tunnelling spectra that serve as fingerprints of the vibrational properties of adsorbed molecules3,4,5 and of the electronic properties of magnetic impurity atoms6,7, thereby allowing chemical identification. But in many instances, and particularly for insulating systems, determining the exact chemical composition of surfaces or nanostructures remains a considerable challenge. In principle, dynamic force microscopy should make it possible to overcome this problem: it can image insulator, semiconductor and metal surfaces with true atomic resolution8,9,10, by detecting and precisely measuring11,12,13 the short-range forces that arise with the onset of chemical bonding between the tip and surface atoms14,15 and that depend sensitively on the chemical identity of the atoms involved. Here we report precise measurements of such short-range chemical forces, and show that their dependence on the force microscope tip used can be overcome through a normalization procedure. This allows us to use the chemical force measurements as the basis for atomic recognition, even at room temperature. We illustrate the performance of this approach by imaging the surface of a particularly challenging alloy system and successfully identifying the three constituent atomic species silicon, tin and lead, even though these exhibit very similar chemical properties and identical surface position preferences that render any discrimination attempt based on topographic measurements impossible.},
   author = {Yoshiaki Sugimoto and Pablo Pou and Masayuki Abe and Pavel Jelinek and Rubén Pérez and Seizo Morita and Óscar Custance},
   doi = {10.1038/nature05530},
   issn = {1476-4687},
   issue = {7131},
   journal = {Nature 2006 446:7131},
   keywords = {Humanities and Social Sciences,Science,multidisciplinary},
   pages = {64-67},
   publisher = {Nature Publishing Group},
   title = {Chemical identification of individual surface atoms by atomic force microscopy},
   volume = {446},
   url = {https://www.nature.com/articles/nature05530},
   year = {2007}
}
@article{Gross2009,
   abstract = {Resolving individual atoms has always been the ultimate goal of surface microscopy. The scanning tunneling microscope images atomic-scale features on surfaces, but resolving single atoms within an adsorbed molecule remains a great challenge because the tunneling current is primarily sensitive to the local electron density of states close to the Fermi level. We demonstrate imaging of molecules with unprecedented atomic resolution by probing the short-range chemical forces with use of noncontact atomic force microscopy. The key step is functionalizing the microscope's tip apex with suitable, atomically well-defined terminations, such as CO molecules. Our experimental findings are corroborated by ab initio density functional theory calculations. Comparison with theory shows that Pauli repulsion is the source of the atomic resolution, whereas van der Waals and electrostatic forces only add a diffuse attractive background.},
   author = {Leo Gross and Fabian Mohn and Nikolaj Moll and Peter Liljeroth and Gerhard Meyer},
   doi = {10.1126/SCIENCE.1176210/SUPPL_FILE/GROSS.SOM.PDF},
   issn = {00368075},
   issue = {5944},
   journal = {Science},
   pages = {1110-1114},
   pmid = {19713523},
   publisher = {American Association for the Advancement of Science},
   title = {The chemical structure of a molecule resolved by atomic force microscopy},
   volume = {325},
   url = {https://www.science.org/doi/10.1126/science.1176210},
   year = {2009}
}
@article{Binnig1982,
   abstract = {We report on the first successful tunneling experiment with an externally and reproducibly adjustable vacuum gap. The observation of vacuum tunneling is established by the exponential dependence of the tunneling resistance on the width of the gap. The experimental setup allows for simultaneous investigation and treatment of the tunnel electrode surfaces.},
   author = {G. Binnig and H. Rohrer and Ch Gerber and E. Weibel},
   doi = {10.1063/1.92999},
   issn = {0003-6951},
   issue = {2},
   journal = {Applied Physics Letters},
   pages = {178-180},
   publisher = {AIP Publishing},
   title = {Tunneling through a controllable vacuum gap},
   volume = {40},
   url = {/aip/apl/article/40/2/178/1023077/Tunneling-through-a-controllable-vacuum-gap},
   year = {1982}
}
@article{Floridi2020,
   abstract = {In this commentary, we discuss the nature of reversible and irreversible questions, that is, questions that may enable one to identify the nature of the source of their answers. We then introduce GPT-3, a third-generation, autoregressive language model that uses deep learning to produce human-like texts, and use the previous distinction to analyse it. We expand the analysis to present three tests based on mathematical, semantic (that is, the Turing Test), and ethical questions and show that GPT-3 is not designed to pass any of them. This is a reminder that GPT-3 does not do what it is not supposed to do, and that any interpretation of GPT-3 as the beginning of the emergence of a general form of artificial intelligence is merely uninformed science fiction. We conclude by outlining some of the significant consequences of the industrialisation of automatic and cheap production of good, semantic artefacts.},
   author = {Luciano Floridi and Massimo Chiriatti},
   doi = {10.1007/S11023-020-09548-1/FIGURES/5},
   issn = {15728641},
   issue = {4},
   journal = {Minds and Machines},
   keywords = {Artificial Intelligence,Automation,GPT-3,Irreversibility,Semantics,Turing Test},
   pages = {681-694},
   publisher = {Springer Science and Business Media B.V.},
   title = {GPT-3: Its Nature, Scope, Limits, and Consequences},
   volume = {30},
   url = {https://link.springer.com/article/10.1007/s11023-020-09548-1},
   year = {2020}
}
@article{Brown2022,
   abstract = {Acquisition of dense, three-dimensional, force fields with intramolecular resolution via noncontact atomic force microscopy (NC-AFM) has yielded enormous progress in our ability to characterize molecular and two-dimensional materials at the atomic scale. To date, intramolecular force mapping has been performed exclusively at cryogenic temperatures, due to the stability afforded by low temperature operation, and as the carbon monoxide functionalization of the metallic scanning probe tip, normally required for submolecular resolution, is only stable at low temperature. In this paper we show that high-resolution, three-dimensional force mapping of a single organic molecule is possible even at room temperature. The physical limitations of room temperature operation are overcome using semiconducting materials to inhibit molecular diffusion and create robust tip apexes, while challenges due to thermal drift are overcome with atom tracking based feedforward correction. Three-dimensional force maps comparable in spatial and force resolution to those acquired at low temperature are demonstrated, permitting a quantitative analysis of the adsorption induced changes in the geometry of the molecule at the picometer level.},
   author = {Timothy Brown and Philip James Blowey and Jack Henry and Adam Sweetman},
   doi = {10.1021/ACSNANO.2C09463/SUPPL_FILE/NN2C09463_SI_002.ZIP},
   issn = {1936086X},
   journal = {ACS Nano},
   keywords = {NC-AFM,SPM,force mapping,force spectroscopy,single molecule,submolecular},
   pages = {1298-1304},
   publisher = {American Chemical Society},
   title = {Intramolecular Force Mapping at Room Temperature},
   volume = {17},
   url = {https://pubs.acs.org/doi/full/10.1021/acsnano.2c09463},
   year = {2022}
}
@article{Liebig2020,
   abstract = {Traditionally, atomic force microscopy (AFM) experiments are conducted at tip-sample distances where the tip strongly interacts with the surface. This increases the signal-to-noise ratio, but poses the problem of relaxations in both tip and sample that hamper the theoretical description of experimental data. Here, we employ AFM at relatively large tip-sample distances where forces are only on the piconewton and subpiconewton scale to prevent tip and sample distortions. Acquiring data relatively far from the surface requires low noise measurements. We probed the CaF2(111) surface with an atomically-characterized metal tip and show that the experimental data can be reproduced with an electrostatic model. By experimentally characterizing the second layer of tip atoms, we were able to reproduce the data with 99.5\% accuracy. Our work links the capabilities of non-invasive imaging at large tip-sample distances and controlling the tip apex at the atomic scale.},
   author = {A. Liebig and A. Peronio and D. Meuer and A. J. Weymouth and F. J. Giessibl},
   doi = {10.1088/1367-2630/AB8EFD},
   issn = {1367-2630},
   issue = {6},
   journal = {New Journal of Physics},
   pages = {063040},
   publisher = {IOP Publishing},
   title = {High-precision atomic force microscopy with atomically-characterized tips},
   volume = {22},
   url = {https://iopscience.iop.org/article/10.1088/1367-2630/ab8efd https://iopscience.iop.org/article/10.1088/1367-2630/ab8efd/meta},
   year = {2020}
}
@article{Ziatdinov2017b,
   abstract = {Recent advances in scanning transmission electron and scanning probe microscopies have opened exciting opportunities in probing the materials structural parameters and various functional properties in real space with angstrom-level precision. This progress has been accompanied by an exponential increase in the size and quality of data sets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large data sets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent. Here we demonstrate an application of deep neural networks to extract information from atomically resolved images including location of the atomic species and type of defects. We develop a "weakly supervised" approach that uses information on the coordinates of all atomic species in the image, extracted via a deep neural network, to identify a rich variety of defects that are not part of an initial training set. We further apply our approach to interpret complex atomic and defect transformation, including switching between different coordination of silicon dopants in graphene as a function of time, formation of peculiar silicon dimer with mixed 3-fold and 4-fold coordination, and the motion of molecular "rotor". This deep learning-based approach resembles logic of a human operator, but can be scaled leading to significant shift in the way of extracting and analyzing information from raw experimental data.},
   author = {Maxim Ziatdinov and Ondrej Dyck and Artem Maksov and Xufan Li and Xiahan Sang and Kai Xiao and Raymond R Unocic and Rama Vasudevan and Stephen Jesse and Sergei V Kalinin},
   doi = {10.1021/acsnano.7b07504},
   issue = {12},
   journal = {ACS Nano},
   keywords = {graphene,neural networks,scanning transmission electron microscopy (STEM),transition-metal dichalcogenide (TMDC),weakly supervised learning},
   pages = {12742-12752},
   title = {Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations},
   volume = {11},
   url = {www.acsnano.org},
   year = {2017}
}
@article{Yoshida2015,
   abstract = {Scaling down materials to an atomic-layer level produces rich physical and chemical properties as exemplified in various two-dimensional (2D) crystals including graphene, transition metal dichalcogenides, and black phosphorus. This is caused by the dramatic modification of electronic band structures. In such reduced dimensions, the electron correlation effects are also expected to be significantly changed from bulk systems. However, there are few attempts to realize novel phenomena in correlated 2D crystals. We report memristive phase switching in nano-thick crystals of 1T-type tantalum disulfide (1T-TaS2), a first-order phase transition system. The ordering kinetics of the phase transition were found to become extremely slow as the thickness is reduced, resulting in an emergence of metastable states. Furthermore, we realized unprecedented memristive switching to multistep nonvolatile states by applying an in-plane electric field. The reduction of thickness is essential to achieve such nonvolatile electrical switching behavior. The thinning-induced slow kinetics possibly make the various metastable states robust and consequently realize the nonvolatile memory operation. The present result indicates that a 2D crystal with correlated electrons is a novel nano-system to explore and functionalize multiple metastable states that are inaccessible in its bulk form.},
   author = {Masaro Yoshida and Ryuji Suzuki and Yijin Zhang and Masaki Nakano and Yoshihiro Iwasa},
   doi = {10.1126/SCIADV.1500606/ASSET/8F780BF8-006A-458D-B4F8-0E584572CA84/ASSETS/GRAPHIC/1500606-F4.JPEG},
   issn = {23752548},
   issue = {9},
   journal = {Science Advances},
   keywords = {Tantalum disulfide (TaS2),electrical phase switching,first-order phase transition,memristor,metastable states,nonvolatile memory,two-dimensional materials},
   publisher = {American Association for the Advancement of Science},
   title = {Memristive phase switching in two-dimensional 1T-TaS2 crystals},
   volume = {1},
   url = {https://www.science.org/doi/10.1126/sciadv.1500606},
   year = {2015}
}
@article{Liu2016,
   abstract = {Transition-metal dichalcogenides (TMDs) MX 2 (M = Ti, Nb, Ta; X = S, Se, Te) exhibit a rich set of charge density wave (CDW) orders, which usually coexist and/or compete with superconductivity. The mechanisms of CDWs and superconductivity in TMDs are still under debate. Here we perform an investigation on a typical TMD system, 1T-TaSe 2−x Te x (0 x 2). Doping-induced disordered distribution of Se/Te suppresses CDWs in 1T-TaSe 2. A domelike superconducting phase with the maximum T onset c of 2.5 K was observed near CDWs. The superconducting volume is very small inside the CDW phase and becomes very large instantly when the CDW phase is fully suppressed. The observations can be understood based on the strong q-dependent electron-phonon coupling-induced periodic-lattice-distortion (PLD) mechanism of CDWs. The volume variation of superconductivity implies the emergence of domain walls in the suppressing process of CDWs. Our concluded scenario makes a fundamental understanding about CDWs and related superconductivity in TMDs.},
   author = {Y Liu and D F Shao and L J Li and W J Lu and X D Zhu and P Tong and R C Xiao and L S Ling and C Y Xi and L Pi and H F Tian and H X Yang and J Q Li and W H Song and X B Zhu and Y P Sun},
   doi = {10.1103/PhysRevB.94.045131},
   issue = {4},
   journal = {Physical Review B},
   pages = {045131},
   title = {Nature of charge density waves and superconductivity in 1T-TaSe2-xTex},
   volume = {94},
   year = {2016}
}
@article{Sethi2017,
   abstract = {A brief review of some of the most recent experiments on the charge density wave (CDW) transition in 1T-TiSe 2 is presented. With increasing pressure or intercalation, the CDW can be suppressed and a superconduct-ing (SC) phase emerges. In the pristine 1T-TiSe 2 , a commensurate CDW develops around 202 K. These experiments show that by tuning these external parameters like pressure, or doping, the commensurate CDW melts into an incommensurate CDW phase through the formation of domain walls. The incipient incommensurate CDW phase coincides with the onset of supercon-ductivity, thus providing insight into the importance of incommensurability in formation of SC phase.},
   author = {Astha Sethi},
   title = {Role of Incommensuration in the charge density wave and superconducting states of 1T-TiSe 2},
   year = {2017}
}
@article{Trieste,
   author = {Elletra Sincrotrone Trieste and Firstly Stm},
   pages = {1-37},
   title = {Chapter 1 STM}
}
@misc{PyTorch,
   title = {https://pytorch.org/},
   url = {https://pytorch.org/}
}
@misc{TensorFlow,
   title = {https://www.tensorflow.org/},
   url = {https://www.tensorflow.org/}
}
@misc{Ismail2023,
   author = {Maneesha Ismail},
   title = {Personal Communication},
   year = {2023}
}
@article{Saxton1982,
   abstract = {An adaptation of the ‘correlation averaging’ method is described which allows reliable and almost fully automatic image averaging in the case of near‐periodic structures notwithstanding the presence of substantial crystal imperfections; methods for assessing resolution and symmetry without reliance on crystallinity are also discussed. Electron micrographs of negatively stained and rotary shadowed preparations of the HPI‐layer protein from the cell envelope of Micrococcus radiodurans have been averaged using the method, and the projected structure is described to a resolution of about 1·9 nm. 1982 Blackwell Science Ltd},
   author = {W. O. Saxton and W. Baumeister},
   doi = {10.1111/J.1365-2818.1982.TB00405.X},
   issn = {1365-2818},
   issue = {2},
   journal = {Journal of Microscopy},
   keywords = {Correlation averaging,cell envelopes,crystal distortions,regular proteins,resolution assessment,symmetry assessment},
   pages = {127-138},
   pmid = {7120365},
   publisher = {John Wiley & Sons, Ltd},
   title = {The correlation averaging of a regularly arranged bacterial cell envelope protein},
   volume = {127},
   url = {https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2818.1982.tb00405.x https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2818.1982.tb00405.x https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.1982.tb00405.x},
   year = {1982}
}
@article{Alldritt2022,
   abstract = {Auto-CO-AFM is an open-source software package for scanning probe microscopes that enables the automatic functionalization of scanning probe tips with carbon monoxide molecules. This enables machine operators to specify the quality of the tip needed utilizing a pre-trained library with off-the-shelf software. From a single image, the software package can determine which molecules on a surface are carbon monoxide, perform the necessary tip functionalization procedures, interface with microscope software to control the tip position, and determines the centeredness of the tip after a successful functionalization. This is of particular interest for atomic force microscopy imaging of molecules on surfaces, where the tip functionalization is a necessary and time consuming step needed for sub-molecular resolution imaging. This package is freely available under the MIT License. Program summary: Program Title: Auto-CO-AFM CPC Library link to program files: https://doi.org/10.17632/khfvjhx4vb.1 Developer's repository link: https://github.com/SINGROUP/Auto-CO-AFM Licensing provisions: MIT Programming language: Python Supplementary material: Supplementary Information as PDF Nature of problem: Scanning probe microscopy experiments are limited by the lack of automated tools in tip preparation, particularly when functionalizing an adatom or molecule on the end of a tip. These tip functionalizations are commonly manually-driven processes that are time-consuming for the operator. Solution method: We have developed an automated solution for tip functionalization for carbon monoxide molecules, which combines machine learning descriptors with automated software control of the tip preparation process. The Python program interfaces with a major vendor's software to scan, functionalize, and verify the tip quality for the operator. The source code, documentation, and basic program are posted online. Additional comments including restrictions and unusual features: Current version of software in publication requires STMAFM software from CreaTec GmbH in physical connection with a CreaTec DSP.},
   author = {Benjamin Alldritt and Fedor Urtev and Niko Oinonen and Markus Aapro and Juho Kannala and Peter Liljeroth and Adam S. Foster},
   doi = {10.1016/J.CPC.2021.108258},
   issn = {0010-4655},
   journal = {Computer Physics Communications},
   keywords = {Atomic force microscopy,Automation,Carbon monoxide,Machine learning,Tip preparation},
   pages = {108258},
   publisher = {North-Holland},
   title = {Automated tip functionalization via machine learning in scanning probe microscopy},
   volume = {273},
   year = {2022}
}
@article{Herz2003,
   abstract = {The structure of single atoms in real space is investigated by scanning tunneling microscopy. Very high resolution can be obtained by a dramatic reduction of the tip-sample distance. The instabilities which are normally encountered while using small tip-sample distances are avoided by oscillating the tip of the scanning tunneling microscope vertically with respect to the sample. The surface atoms of Si(111)-(7×7) with their well-known electronic configuration are used to image individual samarium, cobalt, iron, and silicon atoms. The resulting images resemble the charge density corresponding to 4f, 3d, and 3p atomic orbitals. © 2003 The American Physical Society.},
   author = {M. Herz and J. Giessibl and J. Mannhart},
   doi = {10.1103/PhysRevB.68.045301},
   issn = {1550235X},
   issue = {4},
   journal = {Physical Review B},
   pages = {045301},
   publisher = {American Physical Society},
   title = {Probing the shape of atoms in real space},
   volume = {68},
   url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.68.045301},
   year = {2003}
}
@article{Welker2013a,
   abstract = {The force between two atoms depends not only on their chemical species and distance, but also on the configuration of their chemical bonds to other atoms. This strongly affects atomic force spectroscopy, in which the force between the tip of an atomic force microscope and a sample is measured as a function of distance. We show that the short-range forces between tip and sample atoms depend strongly on the configuration of the tip, to the point of preventing atom identification with a poorly defined tip. Our solution is to control the tip apex before using it for spectroscopy. We demonstrate a method by which a CO molecule on Cu can be used to characterize the tip. In combination with gentle pokes, this can be used to engineer a specific tip apex. This CO Front atom Identification (COFI) method allows us to use a well-defined tip to conduct force spectroscopy. © 2013 American Chemical Society.},
   author = {Joachim Welker and Alfred John Weymouth and Franz J. Giessibl},
   doi = {10.1021/NN403106V/SUPPL_FILE/NN403106V_SI_001.PDF},
   issn = {19360851},
   issue = {8},
   journal = {ACS Nano},
   keywords = {atomic force microscopy,atomic forces,chemical identification},
   pages = {7377-7382},
   publisher = {American Chemical Society},
   title = {The influence of chemical bonding configuration on atomic identification by force spectroscopy},
   volume = {7},
   url = {https://pubs.acs.org/doi/full/10.1021/nn403106v},
   year = {2013}
}
@article{Sawada2009,
   abstract = {We have performed simultaneous scanning tunneling microscopy and atomic force microscopy measurements in the dynamic mode using metal-coated Si cantilevers at room temperature. Frequency shift (Δf) and time-average tunneling current (〈 It 〉) images are obtained by tip scanning on the Si (111) - (7×7) surface at constant height mode. By measuring site-specific Δf (〈 It 〉) versus tip-surface distance curves, we derive the force (tunneling current) at the closest separation between the sample surface and the oscillating tip. We observe the drop in the tunneling current due to the chemical interaction between the tip apex atom and the surface adatom, which was found recently, and estimate the value of the chemical bonding force. Scanning tunneling spectroscopy using the same tip shows that the tip is metallic enough to measure local density of states of electrons on the surface. © 2009 American Institute of Physics.},
   author = {Daisuke Sawada and Yoshiaki Sugimoto and Ken Ichi Morita and Masayuki Abe and Seizo Morita},
   doi = {10.1063/1.3127503/321345},
   issn = {00036951},
   issue = {17},
   journal = {Applied Physics Letters},
   month = {4},
   publisher = {AIP Publishing},
   title = {Simultaneous measurement of force and tunneling current at room temperature},
   volume = {94},
   url = {/aip/apl/article/94/17/173117/321345/Simultaneous-measurement-of-force-and-tunneling},
   year = {2009}
}
@article{Leinen2020,
   abstract = {The ability to handle single molecules as effectively as macroscopic building blocks would enable the construction of complex supramolecular structures inaccessible to self-assembly. The fundamental challenges obstructing this goal are the uncontrolled variability and poor observability of atomic-scale conformations. Here, we present a strategy to work around both obstacles and demonstrate autonomous robotic nanofabrication by manipulating single molecules. Our approach uses reinforcement learning (RL), which finds solution strategies even in the face of large uncertainty and sparse feedback. We demonstrate the potential of our RL approach by removing molecules autonomously with a scanning probe microscope from a supramolecular structure. Our RL agent reaches an excellent performance, enabling us to automate a task that previously had to be performed by a human. We anticipate that our work opens the way toward autonomous agents for the robotic construction of functional supramolecular structures with speed, precision, and perseverance beyond our current capabilities. c 2020 The Authors, some rights reserved.},
   author = {Philipp Leinen and Malte Esders and Kristof T. Schütt and Christian Wagner and Klaus Robert Müller and F. Stefan Tautz},
   doi = {10.1126/SCIADV.ABB6987},
   issn = {23752548},
   issue = {36},
   journal = {Science Advances},
   pmid = {32917594},
   publisher = {American Association for the Advancement of Science},
   title = {Autonomous robotic nanofabrication with reinforcement learning},
   volume = {6},
   url = {https://www.science.org/doi/10.1126/sciadv.abb6987},
   year = {2020}
}
@misc{LabVIEW,
   title = {What is LabVIEW? Graphical Programming for Test and Measurement - NI},
   url = {https://www.ni.com/en/shop/labview.html?cid=PSEA-7013q000001rC7oAAE-CONS-GOGSE_102713975033&utm_keyword=labview&s_kwcid=AL%216304%213%21449107487712%21e%21%21g%21%21labview&gad=1&gclid=Cj0KCQjwpc-oBhCGARIsAH6ote-wq8ciHsI21NslRSSoiqH-_piRP8Zx14jkgX4F4HtkgZ}
}
@article{Nathans1959,
   abstract = {triangles. Reasonable agreement is thus obtained between the experimental form factor values and those computed assuming the unpaired electrons to be in a state of pure e symmetry. It is important to observe that the scale factor, k, here determined experimentally, is such as to make the unpaired Sd charge distribution for Ni++ much more compact in the solid than it is for the free atom. This is in contrast to the case of Mn++ where experiments" show that the charge distribution is expanded in the solid. These experimental results may be compared with the recent calculations of Watson and Free-man' for the Ni++ ion. These Hartree-Fock self-consistent field calculations allow the wave functions of electrons with opposite spins to have different radial dependencies (spin polarization) and lead to a contraction of the charge distribution (both for the free-atom ca.se and the case where the Ni~ ion is placed in an octahedral array of point charges). '4 Unfortunately, the magnitude of the contraction is much too small to explain the observations reported here. Nevertheless , the important fact that the relation of the observed f& to the free-atom f~ is just opposite for the cases of Ni++ and Mn~ would lead one to look for the origin of this effect in the outstanding difference between the two ions: namely their differing spin configurations. These experimental results also serve to suggest that whereas effects such as spin polarization and crystalline environment have a large influence on f~, their effect on f~ is small. Solids 3, 20 (1957). '%e are assuming here that the radial part of the wave functions is the same for all eight electrons so that the three electrons of t2 symmetry with their g4 PP spina in one direction canoe the three electrons of like symmetry with oppositely directed spine.to be published). Their result, which is for a powder measurement, is in approximate agreement with the curve presented here. J. N. Hastings, N. Elliott, and L. M. Corliss, Phys. Rev. 115, 13 (1959). ~4It should be noted that Nn++ which has all its spins in the same direction has no spin polarization effect. Giaever' and more recently Nicol, Shapiro, and Smith' have observed the tunnelling current flowing between two metals separated by a thin oxide layer. The most interesting results are obtained when one or both of the metals are superconduc-ting, in which case they find direct evidence for a gap in the quasi-particle spectrum of the super-conductor. They were able to account for the data quantitatively on the assumption that the only relevant factor is the density of states in energy. This is to be expected if the transition probability for transfer of an electron from one side to the other is given by the familiar expression (2m/&) IM I'pf, where I is the matrix element and pf the energy density of final states, and if it is further assumed that M can be treated as a constant. It is implied that M is not only independent of energy for the small energy differences involved, but is also unchanged when the metal goes from normal to superconducting.},
   author = {R Nathans and A Paoletti},
   issue = {2},
   journal = {3S. J. Pickart and R. Nathans, Suppl. J. Appl. Phys},
   pages = {350},
   title = {PHYSICAL REVIEW LETTERS (unpublished). TUNNELLING FROM A MANY-PARTICLE POINT OF VIEW},
   volume = {6},
   year = {1959}
}
@article{Bardeen1961,
   author = {J. Bardeen},
   doi = {10.1103/PhysRevLett.6.57},
   issn = {00319007},
   issue = {2},
   journal = {Physical Review Letters},
   pages = {57},
   publisher = {American Physical Society},
   title = {Tunnelling from a Many-Particle Point of View},
   volume = {6},
   url = {https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.6.57},
   year = {1961}
}
@article{Sweetman2012,
   abstract = {Background: Noncontact atomic force microscopy (NC-AFM) now regularly produces atomic-resolution images on a wide range of surfaces, and has demonstrated the capability for atomic manipulation solely using chemical forces. Nonetheless, the role of the tip apex in both imaging and manipulation remains poorly understood and is an active area of research both experimentally and theoretically. Recent work employing specially functionalised tips has provided additional impetus to elucidating the role of the tip apex in the observed contrast.},
   author = {Adam Sweetman and Sam Jarvis and Rosanna Danza and Philip Moriarty},
   doi = {10.3762/bjnano.3.3},
   journal = {Beilstein J. Nanotechnol},
   keywords = {Si(001),Si(100),force spectroscopy,image contrast,noncontact AFM,qPlus,tip (apex) structure},
   pages = {25-32},
   title = {Effect of the tip state during qPlus noncontact atomic force microscopy of Si(100) at 5 K: Probing the probe},
   volume = {3},
   year = {2012}
}
@book{Bai,
   abstract = {Second revised edition. 1. Introduction -- Advantages of STM Compared with Other Techniques -- From Optical Microscopy to Scanning Tunneling Microscopy -- 2. The Tunneling Effect -- Historical Remarks -- Tunneling-Current Theory -- Tip-Surface Interaction Model -- 3. Spectroscopy, and Spectroscopic Imaging -- Concepts of Tunneling Spectroscopies -- Experimental Modes -- Energy Resolution -- Examples -- 4. STM Instrumentation -- The Vibration Isolation System -- Mechanical Designs -- Tip Preparation -- Electronics -- Computer Automation -- 5. Other Related Scanning Probe Microscopes -- Atomic Force Microscope -- Other Scanning-Force Microscopies -- Ballistic-Electron-Emission Microscopy -- Scanning Ion-Conductance Microscope -- Scanning Thermal Microscope -- Scanning Tunneling Potentiometry and Scanning Noise Microscopy -- Photon Scanning Tunneling Microscopy and Scanning Plasmon Near-Field Microscopy -- Near-Field Scanning Optical Microscopy and Spectroscopy -- 6. STM Studies of Clean Surfaces -- Metal Surfaces -- Elemental Semiconductor Surfaces -- Compound Semiconductors and Layered Compounds -- 7. Surface Adsorbates and Surface Chemistry -- Adsorption on Metal Surfaces -- Adsorption on Semiconductor Surfaces -- Molecules, and Molecular Adsorbates -- Observation of Clusters -- Nucleation and Growth -- Chemical Reactions on Metals -- Chemical Reaction on Semiconductors -- 8. Biological Applications -- Advantages and Problems -- Preparation -- Nucleic Acids -- Proteins -- Biological Membranes -- Imaging Cells and Other Applications -- Force Spectrum Analysis of Biological Materials -- 9. Surface Modification -- Overview -- Direct Indentation with the Tunneling Tip -- Nanolithography on Resist Films -- Nanofabrication in Solution and in Gaseous Environments -- Atomic-Scale Manipulation -- Quantization of Conductance in Nano-Contacts Produced by STM -- Fabrication with Other Scanning-Probe Microscopes -- The Future.},
   author = {Chunli Bai},
   edition = {2nd},
   isbn = {9783540657156},
   pages = {368},
   publisher = {Springer},
   title = {Scanning Tunneling Microscopy and its Application},
   url = {https://link.springer.com/book/9783540657156},
   year = {2000}
}
@article{Peng2013,
   abstract = {Piezoelectric actuators (PEAs) have been widely used in micro- and nanopositioning applications due to their fine resolution, fast responses, and large actuating forces. However, the existence of nonlinearities such as hysteresis makes modeling and control of PEAs challenging. This paper reviews the recent achievements in modeling and control of piezoelectric actuators. Specifically, various methods for modeling linear and nonlinear behaviors of PEAs, including vibration dynamics, hysteresis, and creep, are examined; and the issues involved are identified. In the control of PEAs as applied to positioning, a review of various control schemes of both model-based and non-model-based is presented along with their limitations. The challenges associated with the control problem are also discussed. This paper is concluded with the emerging issues identified in modeling and control of PEAs for future research.},
   author = {Jingyang Peng and Xiongbiao Chen},
   doi = {10.4236/MME.2013.31001},
   issn = {2164-0165},
   issue = {01},
   journal = {Modern Mechanical Engineering},
   pages = {1-20},
   publisher = {Scientific Research Publishing, Inc,},
   title = {A Survey of Modeling and Control of Piezoelectric Actuators},
   volume = {03},
   year = {2013}
}
@article{Rahe2011,
   abstract = {The acquisition of dense 3D data sets is of great importance, but also a challenge for scanning probe microscopy (SPM). Thermal drift often induces severe distortions in the data, which usually constrains the acquisition of dense data sets to experiments under ultra-high vacuum and low-temperature conditions. Atom tracking is an elegant approach to compensate for thermal drift and to position the microscope tip with highest precision. Here, we present a flexible drift compensation system which can easily be connected to existing SPM hardware. Furthermore, we describe a 3D data acquisition and position correction protocol, which is capable of handling large and non-linear drift as typically present in room temperature measurements. This protocol is based on atom-tracking for precise positioning of the tip and we are able to acquire dense 3D data sets over several hours at room temperature.},
   author = {Philipp Rahe and Jens Schütte and Werner Schniederberend and Michael Reichling and Masayuki Abe and Yoshiaki Sugimoto and Angelika Kühnle},
   doi = {10.1063/1.3600453},
   journal = {REVIEW OF SCIENTIFIC INSTRUMENTS},
   pages = {63704},
   title = {Flexible drift-compensation system for precise 3D force mapping in severe drift environments},
   volume = {82},
   url = {http://rsi.aip.org/about/rights_and_permissions},
   year = {2011}
}
@article{Byabazaire2019,
   author = {John Byabazaire and Cristian Olariu and Mohit Taneja and Alan Davy},
   doi = {10.1109/CCNC.2019.8651681},
   isbn = {9781538655535},
   journal = {2019 16th IEEE Annual Consumer Communications and Networking Conference, CCNC 2019},
   keywords = {Data Analytics,Fog Computing,Internet of Things (IoT),Lameness,Machine Learning,Micro services,Smart Agriculture},
   publisher = {Institute of Electrical and Electronics Engineers Inc.},
   title = {Lameness Detection as a Service: Application of Machine Learning to an Internet of Cattle},
   year = {2019}
}
@article{Fiscutean2021,
   author = {Andrada Fiscutean},
   doi = {10.1038/D41586-021-00818-1},
   issn = {14764687},
   issue = {7852},
   journal = {Nature},
   keywords = {Machine learning,Physiology},
   pages = {S10-S11},
   pmid = {33790457},
   publisher = {NLM (Medline)},
   title = {Data scientists are predicting sports injuries with an algorithm},
   volume = {592},
   year = {2021}
}
@article{Kim2020,
   abstract = {Users of social media often share their feelings or emotional states through their posts. In this study, we developed&nbsp;a deep learning model to identify a user’s mental state based on his/her posting information. To this end, we collected posts from mental health communities in Reddit. By analyzing and learning posting information written by users, our proposed model could accurately identify whether a user’s post belongs to a specific mental disorder, including depression, anxiety, bipolar, borderline personality disorder, schizophrenia, and autism. We believe our model can help identify potential sufferers with mental illness based on their posts. This study further discusses the implication of our proposed model, which can serve as a supplementary tool for monitoring mental health states of individuals who frequently use social media.},
   author = {Jina Kim and Jieon Lee and Eunil Park and Jinyoung Han},
   doi = {10.1038/s41598-020-68764-y},
   isbn = {0123456789},
   issn = {2045-2322},
   issue = {1},
   journal = {Scientific Reports 2020 10:1},
   keywords = {Engineering,Health care},
   pages = {1-6},
   pmid = {32678250},
   publisher = {Nature Publishing Group},
   title = {A deep learning model for detecting mental illness from user content on social media},
   volume = {10},
   url = {https://www.nature.com/articles/s41598-020-68764-y},
   year = {2020}
}
@article{Mousavi2020,
   abstract = {Earthquake signal detection and seismic phase picking are challenging tasks in the processing of noisy data and the monitoring of microearthquakes. Here we present a global deep-learning model for simultaneous earthquake detection and phase picking. Performing these two related tasks in tandem improves model performance in each individual task by combining information in phases and in the full waveform of earthquake signals by using a hierarchical attention mechanism. We show that our model outperforms previous deep-learning and traditional phase-picking and detection algorithms. Applying our model to 5 weeks of continuous data recorded during 2000 Tottori earthquakes in Japan, we were able to detect and locate two times more earthquakes using only a portion (less than 1/3) of seismic stations. Our model picks P and S phases with precision close to manual picks by human analysts; however, its high efficiency and higher sensitivity can result in detecting and characterizing more and smaller events.},
   author = {S. Mostafa Mousavi and William L. Ellsworth and Weiqiang Zhu and Lindsay Y. Chuang and Gregory C. Beroza},
   doi = {10.1038/S41467-020-17591-W},
   issn = {20411723},
   issue = {1},
   journal = {Nature Communications},
   pmid = {32770023},
   publisher = {Nature Research},
   title = {Earthquake transformer—an attentive deep-learning model for simultaneous earthquake detection and phase picking},
   volume = {11},
   url = {https://news.stanford.edu/2020/10/21/ai-detects-hidden-earthquakes/},
   year = {2020}
}
@article{Widner2023,
   abstract = {The application of an artificial intelligence (AI)-based screening tool for retinal disease in India and Thailand highlighted the myths and reality of introducing medical AI, which may form a framework for subsequent tools},
   author = {Kasumi Widner and Sunny Virmani and Jonathan Krause and Jay Nayar and Richa Tiwari and Elin Rønby Pedersen and Divleen Jeji and Naama Hammel and Yossi Matias and Greg S. Corrado and Yun Liu and Lily Peng and Dale R. Webster},
   doi = {10.1038/s41591-023-02293-9},
   issn = {1546-170X},
   issue = {6},
   journal = {Nature Medicine 2023 29:6},
   keywords = {Biomedical engineering,Translational research},
   pages = {1304-1306},
   pmid = {37248297},
   publisher = {Nature Publishing Group},
   title = {Lessons learned from translating AI from development to deployment in healthcare},
   volume = {29},
   url = {https://www.nature.com/articles/s41591-023-02293-9},
   year = {2023}
}
@article{Grote2020,
   abstract = {In recent years, a plethora of high-profile scientific publications has been reporting about machine learning algorithms outperforming clinicians in medical diagnosis or treatment recommendations. This has spiked interest in deploying relevant algorithms with the aim of enhancing decision-making in healthcare. In this paper, we argue that instead of straightforwardly enhancing the decision-making capabilities of clinicians and healthcare institutions, deploying machines learning algorithms entails trade-offs at the epistemic and the normative level. Whereas involving machine learning might improve the accuracy of medical diagnosis, it comes at the expense of opacity when trying to assess the reliability of given diagnosis. Drawing on literature in social epistemology and moral responsibility, we argue that the uncertainty in question potentially undermines the epistemic authority of clinicians. Furthermore, we elucidate potential pitfalls of involving machine learning in healthcare with respect to paternalism, moral responsibility and fairness. At last, we discuss how the deployment of machine learning algorithms might shift the evidentiary norms of medical diagnosis. In this regard, we hope to lay the grounds for further ethical reflection of the opportunities and pitfalls of machine learning for enhancing decision-making in healthcare.},
   author = {Thomas Grote and Philipp Berens},
   doi = {10.1136/MEDETHICS-2019-105586},
   isbn = {2019105586},
   issn = {0306-6800},
   issue = {3},
   journal = {Journal of Medical Ethics},
   keywords = {autonomy,decision-making,machine learning,paternalism,uncertainty},
   pages = {205-211},
   pmid = {31748206},
   publisher = {Institute of Medical Ethics},
   title = {On the ethics of algorithmic decision-making in healthcare},
   volume = {46},
   url = {https://jme.bmj.com/content/46/3/205 https://jme.bmj.com/content/46/3/205.abstract},
   year = {2020}
}
@article{McKinney2020,
   author = {Scott Mayer McKinney and Marcin Sieniek and Varun Godbole and Jonathan Godwin and Natasha Antropova and Hutan Ashrafian and Trevor Back and Mary Chesus and Greg C. Corrado and Ara Darzi and Mozziyar Etemadi and Florencia Garcia-Vicente and Fiona J. Gilbert and Mark Halling-Brown and Demis Hassabis and Sunny Jansen and Alan Karthikesalingam and Christopher J. Kelly and Dominic King and Joseph R. Ledsam and David Melnick and Hormuz Mostofi and Lily Peng and Joshua Jay Reicher and Bernardino Romera-Paredes and Richard Sidebottom and Mustafa Suleyman and Daniel Tse and Kenneth C. Young and Jeffrey De Fauw and Shravya Shetty},
   doi = {10.1038/S41586-019-1799-6},
   issn = {1476-4687},
   issue = {7788},
   journal = {Nature},
   keywords = {Artificial Intelligence / standards*,Breast Neoplasms / diagnostic imaging*,Early Detection of Cancer / methods*,Early Detection of Cancer / standards*,Evaluation Study,Extramural,Female,Humans,MEDLINE,Mammography / standards,Marcin Sieniek,N.I.H.,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,PubMed Abstract,Reproducibility of Results,Research Support,Scott Mayer McKinney,Shravya Shetty,United Kingdom,United States,doi:10.1038/s41586-019-1799-6,pmid:31894144},
   pages = {89-94},
   pmid = {31894144},
   publisher = {Nature},
   title = {International evaluation of an AI system for breast cancer screening},
   volume = {577},
   url = {https://pubmed.ncbi.nlm.nih.gov/31894144/},
   year = {2020}
}
@misc{AndroidP,
   author = {Sameer Samat},
   note = {Web, 2018},
   title = {Android P: Packed with smarts and simpler than ever},
   url = {https://blog.google/products/android/android-p/},
   year = {2018}
}
@article{McCulloch1943,
   abstract = {Because of the "all-or-none" character of nervous activity, neural events and the relations among them can be treated by means of propositional logic. It is found that the behavior of every net can be described in these terms, with the addition of more complicated logical means for nets containing circles; and that for any logical expression satisfying certain conditions, one can find a net behaving in the fashion it describes. It is shown that many particular choices among possible neurophysiological assumptions are equivalent, in the sense that for every net behaving under one assumption, there exists another net which behaves under the other and gives the same results, although perhaps not in the same time. Various applications of the calculus are discussed. © 1943 The University of Chicago Press.},
   author = {Warren S. McCulloch and Walter Pitts},
   doi = {10.1007/BF02478259/METRICS},
   issn = {00074985},
   issue = {4},
   journal = {The Bulletin of Mathematical Biophysics},
   keywords = {Cell Biology,Life Sciences,Mathematical and Computational Biology,general},
   month = {12},
   pages = {115-133},
   publisher = {Kluwer Academic Publishers},
   title = {A logical calculus of the ideas immanent in nervous activity},
   volume = {5},
   url = {https://link.springer.com/article/10.1007/BF02478259},
   year = {1943}
}
@article{MNIST,
   author = {L. Deng},
   issue = {6},
   journal = {IEEE Signal Processing Magazine},
   pages = {141-142},
   title = {The mnist database of handwritten digit images for machine learning research},
   volume = {29},
   url = {http://yann.lecun.com/exdb/mnist/},
   year = {2012}
}
@article{Goodfellow2010,
   author = {Ian J. Goodfellow and Nate Koenig and Marius Muja and Caroline Pantofaru and Alexander Sorokin and Leila Takayama},
   doi = {10.1145/1734454.1734536},
   isbn = {9781424448937},
   journal = {5th ACM/IEEE International Conference on Human-Robot Interaction, HRI 2010},
   keywords = {HRI,Information theory,Mobile user interface},
   pages = {187-188},
   title = {Help me help you: Interfaces for personal robots},
   url = {https://www.researchgate.net/publication/221473379_Help_me_help_you_Interfaces_for_personal_robots},
   year = {2010}
}
@book{Geron,
   abstract = {Through a series of recent breakthroughs, deep learning has boosted the entire field of machine learning. Now, even programmers who know close to nothing about this technology can use simple, efficient tools to implement programs capable of learning from data. This practical book shows you how. Using concrete examples, minimal theory, and two production-ready Python frameworks—scikit-learn and TensorFlow—author Aurélien Géron helps you gain an intuitive understanding of the concepts and tools for building intelligent systems. You’ll learn a range of techniques, starting with simple linear regression and progressing to deep neural networks.},
   author = {Aurélien Géron},
   isbn = {9781491962299},
   publisher = {O'Reilly},
   title = {Hands-On Machine Learning with Scikit-Learn and TensorFlow},
   year = {2019}
}
@article{Zhuo2023,
   abstract = {We present an automation system for conditioning a scanning probe microscopy (SPM) probe into different states on a Si(111)–(7 × 7) surface at room temperature. Topography images representing multiple surface states and probe condition states divided into 11 categories and trained by a convolution neural network with an accuracy of 87\% were used to estimate the effectiveness of the probe with an accuracy of 98\%. We demonstrate the responsiveness of the method by experimentally reforming a probe into different conditions defined by preset categories. This system will promote advancements in autonomous SPM experiments at atomic scale and room temperature.},
   author = {Diao Zhuo and Linfeng Hou and Abe Masayuki},
   doi = {10.35848/1882-0786/acecd6},
   issue = {085002},
   journal = {Applied Physics Express},
   pages = {1-5},
   title = {Probe conditioning via convolution neural network for scanning probe microscopy automation Hybrid strategies in nanolithography},
   volume = {16},
   url = {https://doi.org/10.35848/1882-0786/acecd6},
   year = {2023}
}
@article{Sugimoto2008,
   abstract = {We perform vacancy-mediated lateral manipulations of Si adatoms on the Si (111) - (7×7) surface by atomic force microscopy at room temperature. A variety of line profiles associated with different atom hopping processes is observed in successive topographic line scans for the atom manipulations. Atom manipulation statistics show stochastic behavior in atom movements. The probability of atom movement increases with a decrease in the tip-surface distance. Moreover, it depends on the scan direction, even with crystallographic equivalence, because of tip apex asymmetry. In addition, the hopping rate reflects the difference in stability of the adsorption sites of the manipulated atoms. © 2008 The American Physical Society.},
   author = {Yoshiaki Sugimoto and Koutaro Miki and Masayuki Abe and Seizo Morita},
   doi = {10.1103/PHYSREVB.78.205305/FIGURES/2/MEDIUM},
   issn = {10980121},
   issue = {20},
   journal = {Physical Review B - Condensed Matter and Materials Physics},
   pages = {205305},
   publisher = {American Physical Society},
   title = {Statistics of lateral atom manipulation by atomic force microscopy at room temperature},
   volume = {78},
   url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.78.205305},
   year = {2008}
}
@article{Sugimoto2013,
   abstract = {The effect of tip chemical reactivity on the lateral manipulation of intrinsic Si adatoms toward a vacancy site on a Si(111)-(7×7) surface has been investigated by noncontact atomic force microscopy at room temperature. Here we measure the atom-hopping probabilities associated with different manipulation processes as a function of the tip-surface distance by means of constant height scans with chemically different types of tips. The interactions between different tips and Si atoms are evaluated by force spectroscopic measurements. Our results demonstrate that the ability to manipulate Si adatoms depends extremely on the chemical nature of the tip apex and is correlated with the maximal attractive force measured over Si adatoms. We rationalize the observed dependence of the atom manipulation process on tip-apex chemical reactivity by means of density functional theory calculations. The results of these calculations suggest that the ability to reduce the energy barrier associated with the Si adatom movement depends profoundly on tip chemical reactivity and that the level of energy barrier reduction is higher with tips that exhibit high chemical reactivity with Si adatoms. The results of this study provide a better way to control the efficiency of the atomic manipulation process for chemisorption systems. © 2013 American Chemical Society.},
   author = {Yoshiaki Sugimoto and Ayhan Yurtsever and Masayuki Abe and Seizo Morita and Martin Ondráček and Pablo Pou and Ruben Pérez and Pavel Jelínek},
   doi = {10.1021/NN403097P/SUPPL_FILE/NN403097P_SI_001.PDF},
   issn = {19360851},
   issue = {8},
   journal = {ACS Nano},
   keywords = {atomic manipulation,chemical interaction force,density functional theory,dynamic force microscopy,force spectroscopy,noncontact atomic force microscopy,nudged elastic band},
   pages = {7370-7376},
   publisher = {American Chemical Society},
   title = {Role of tip chemical reactivity on atom manipulation process in dynamic force microscopy},
   volume = {7},
   url = {https://pubs.acs.org/doi/full/10.1021/nn403097p},
   year = {2013}
}
@article{Simonyan2014,
   abstract = {In this work we investigate the effect of the convolutional network depth on its accuracy in the large-scale image recognition setting. Our main contribution is a thorough evaluation of networks of increasing depth using an architecture with very small (3x3) convolution filters, which shows that a significant improvement on the prior-art configurations can be achieved by pushing the depth to 16-19 weight layers. These findings were the basis of our ImageNet Challenge 2014 submission, where our team secured the first and the second places in the localisation and classification tracks respectively. We also show that our representations generalise well to other datasets, where they achieve state-of-the-art results. We have made our two best-performing ConvNet models publicly available to facilitate further research on the use of deep visual representations in computer vision.},
   author = {Karen Simonyan and Andrew Zisserman},
   journal = {3rd International Conference on Learning Representations, ICLR 2015 - Conference Track Proceedings},
   keywords = {()},
   publisher = {International Conference on Learning Representations, ICLR},
   title = {Very Deep Convolutional Networks for Large-Scale Image Recognition},
   url = {https://arxiv.org/abs/1409.1556v6},
   year = {2014}
}
@article{Kingma2014,
   abstract = {We introduce Adam, an algorithm for first-order gradient-based optimization of stochastic objective functions, based on adaptive estimates of lower-order moments. The method is straightforward to implement, is computationally efficient, has little memory requirements, is invariant to diagonal rescaling of the gradients, and is well suited for problems that are large in terms of data and/or parameters. The method is also appropriate for non-stationary objectives and problems with very noisy and/or sparse gradients. The hyper-parameters have intuitive interpretations and typically require little tuning. Some connections to related algorithms, on which Adam was inspired, are discussed. We also analyze the theoretical convergence properties of the algorithm and provide a regret bound on the convergence rate that is comparable to the best known results under the online convex optimization framework. Empirical results demonstrate that Adam works well in practice and compares favorably to other stochastic optimization methods. Finally, we discuss AdaMax, a variant of Adam based on the infinity norm.},
   author = {Diederik P. Kingma and Jimmy Lei Ba},
   journal = {3rd International Conference on Learning Representations, ICLR 2015 - Conference Track Proceedings},
   publisher = {International Conference on Learning Representations, ICLR},
   title = {Adam: A Method for Stochastic Optimization},
   url = {https://arxiv.org/abs/1412.6980v9},
   year = {2014}
}
@article{Barnard2019,
   abstract = {The combination of computational chemistry and computational materials science with machine learning and artificial intelligence provides a powerful way of relating structural features of nanomaterials with functional properties. However, combining these fundamentally different scientific approaches is not as straightforward as it seems. Machine learning methods were developed for large data sets with small numbers of consistent features. Typically nanomaterials data sets are small, with high dimensionality and high variance in the feature space, and suffer from numerous destructive biases. None of the established data science or machine learning methods in widespread use today were devised with (nano)materials data sets in mind, but there are ways to overcome these challenges and use them reliably. In this review we will discuss domain-specific constraints on data-driven nanomaterials design, and explore the differences between nanomaterials simulation and nanoinformatics that can be leveraged for greater impact.},
   author = {A. S. Barnard and B. Motevalli and A. J. Parker and J. M. Fischer and C. A. Feigl and G. Opletal},
   doi = {10.1039/C9NR05912A},
   issn = {2040-3372},
   issue = {41},
   journal = {Nanoscale},
   pages = {19190-19201},
   pmid = {31397835},
   publisher = {The Royal Society of Chemistry},
   title = {Nanoinformatics, and the big challenges for the science of small things},
   volume = {11},
   url = {https://pubs.rsc.org/en/content/articlehtml/2019/nr/c9nr05912a https://pubs.rsc.org/en/content/articlelanding/2019/nr/c9nr05912a},
   year = {2019}
}
@article{Belianinov2018,
   abstract = {Multimodal chemical imaging simultaneously offers high-resolution chemical and physical information with nanoscale and, in select cases, atomic resolution. By coupling modalities that collect physical and chemical information, we can address scientific problems in biological systems, battery and fuel cell research, catalysis, pharmaceuticals, photovoltaics, medicine, and many others. The combined systems enable the local correlation of material properties with chemical makeup, making fundamental questions of how chemistry and structure drive functionality approachable. In this Review, we present recent progress and offer a perspective for chemical imaging used to characterize a variety of samples by a number of platforms. Specifically, we present cases of infrared and Raman spectroscopies combined with scanning probe microscopy; optical microscopy and mass spectrometry; nonlinear optical microscopy; and, finally, ion, electron, and probe microscopies with mass spectrometry. We also discuss the challenges associated with the use of data originated by the combinatorial hardware, analysis, and machine learning as well as processing tools necessary for the interpretation of multidimensional data acquired from multimodal studies.},
   author = {Alex Belianinov and Anton V. Ievlev and Matthias Lorenz and Nikolay Borodinov and Benjamin Doughty and Sergei V. Kalinin and Facundo M. Fernández and Olga S. Ovchinnikova},
   doi = {10.1021/ACSNANO.8B07292/ASSET/IMAGES/LARGE/NN-2018-07292T_0015.JPEG},
   issn = {1936086X},
   issue = {12},
   journal = {ACS Nano},
   keywords = {Raman spectroscopy,chemical imaging,data analytics,electron microscopy,infrared spectroscopy,ion microscopy,mass spectrometry,nonlinear optical microscopy,optical microscopy,scanning probe microscopy},
   pages = {11798-11818},
   pmid = {30422627},
   publisher = {American Chemical Society},
   title = {Correlated Materials Characterization via Multimodal Chemical and Functional Imaging},
   volume = {12},
   url = {https://pubs.acs.org/doi/full/10.1021/acsnano.8b07292},
   year = {2018}
}
@article{Stirling2013,
   abstract = {We describe SPIW (scanning probe image wizard), a new image processing toolbox for SPM (scanning probe microscope) images. SPIW can be used to automate many aspects of SPM data analysis, even for images with surface contamination and step edges present. Specialised routines are available for images with atomic or molecular resolution to improve image visualisation and generate statistical data on surface structure. © 2013 © 2013 Author(s).},
   author = {Julian Stirling and Richard A.J. Woolley and Philip Moriarty},
   doi = {10.1063/1.4827076/358730},
   issn = {00346748},
   issue = {11},
   journal = {Review of Scientific Instruments},
   pages = {113701},
   publisher = {AIP Publishing},
   title = {Scanning probe image wizard: A toolbox for automated scanning probe microscopy data analysis},
   volume = {84},
   url = {/aip/rsi/article/84/11/113701/358730/Scanning-probe-image-wizard-A-toolbox-for},
   year = {2013}
}
@article{Chen2022,
   abstract = {Atomic-scale manipulation in scanning tunneling microscopy has enabled the creation of quantum states of matter based on artificial structures and extreme miniaturization of computational circuitry based on individual atoms. The ability to autonomously arrange atomic structures with precision will enable the scaling up of nanoscale fabrication and expand the range of artificial structures hosting exotic quantum states. However, the a priori unknown manipulation parameters, the possibility of spontaneous tip apex changes, and the difficulty of modeling tip-atom interactions make it challenging to select manipulation parameters that can achieve atomic precision throughout extended operations. Here we use deep reinforcement learning (DRL) to control the real-world atom manipulation process. Several state-of-the-art reinforcement learning (RL) techniques are used jointly to boost data efficiency. The DRL agent learns to manipulate Ag adatoms on Ag(111) surfaces with optimal precision and is integrated with path planning algorithms to complete an autonomous atomic assembly system. The results demonstrate that state-of-the-art DRL can offer effective solutions to real-world challenges in nanofabrication and powerful approaches to increasingly complex scientific experiments at the atomic scale. Engineering quantum states requires precise manipulations at the atomic level. Here, the authors use deep reinforcement learning to manipulate Ag adatoms on Ag surfaces, which combined with path planning algorithms enables autonomous atomic assembly.},
   author = {I. Ju Chen and Markus Aapro and Abraham Kipnis and Alexander Ilin and Peter Liljeroth and Adam S. Foster},
   doi = {10.1038/s41467-022-35149-w},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications 2022 13:1},
   keywords = {Computational science,Surface patterning,Synthesis and processing},
   pages = {1-8},
   pmid = {36470857},
   publisher = {Nature Publishing Group},
   title = {Precise atom manipulation through deep reinforcement learning},
   volume = {13},
   url = {https://www.nature.com/articles/s41467-022-35149-w},
   year = {2022}
}
@article{Weber2012,
   abstract = {As silicon electronics approaches the atomic scale, interconnects and circuitry become comparable in size to the active device components. Maintaining low electrical resistivity at this scale is challenging because of the presence of confining surfaces and interfaces. We report on the fabrication of wires in silicon-only one atom tall and four atoms wide - with exceptionally low resistivity (∼0.3 milliohm-centimeters) and the current-carrying capabilities of copper. By embedding phosphorus atoms within a silicon crystal with an average spacing of less than 1 nanometer, we achieved a diameter-independent resistivity, which demonstrates ohmic scaling to the atomic limit. Atomistic tight-binding calculations confirm the metallicity of these atomic-scale wires, which pave the way for single-atom device architectures for both classical and quantum information processing.},
   author = {B. Weber and S. Mahapatra and H. Ryu and S. Lee and A. Fuhrer and T. C.G. Reusch and D. L. Thompson and W. C.T. Lee and G. Klimeck and L. C.L. Hollenberg and M. Y. Simmons},
   doi = {10.1126/SCIENCE.1214319/SUPPL_FILE/64.MP3},
   issn = {10959203},
   issue = {6064},
   journal = {Science},
   pages = {64-67},
   publisher = {American Association for the Advancement of Science},
   title = {Ohm's law survives to the atomic scale},
   volume = {335},
   url = {https://www.science.org/doi/10.1126/science.1214319},
   year = {2012}
}
@article{ElSallab2017,
   abstract = {Reinforcement learning is considered to be a strong AI paradigm which can be used to teach machines through interaction with the environment and learning from their mistakes. Despite its perceived utility, it has not yet been successfully applied in automotive applications. Motivated by the successful demonstrations of learning of Atari games and Go by Google DeepMind, we propose a framework for autonomous driving using deep reinforcement learning. This is of particular relevance as it is difficult to pose autonomous driving as a supervised learning problem due to strong interactions with the environment including other vehicles, pedestrians and roadworks. As it is a relatively new area of research for autonomous driving, we provide a short overview of deep reinforcement learning and then describe our proposed framework. It incorporates Recurrent Neural Networks for information integration, enabling the car to handle partially observable scenarios. It also integrates the recent work on attention models to focus on relevant information, thereby reducing the computational complexity for deployment on embedded hardware. The framework was tested in an open source 3D car racing simulator called TORCS. Our simulation results demonstrate learning of autonomous maneuvering in a scenario of complex road curvatures and simple interaction of other vehicles.},
   author = {Ahmad El Sallab and Mohammed Abdou and Etienne Perot and Senthil Yogamani},
   doi = {10.2352/issn.2470-1173.2017.19.avm-023},
   issn = {24701173},
   journal = {IS and T International Symposium on Electronic Imaging Science and Technology},
   pages = {70-76},
   publisher = {Society for Imaging Science and Technology},
   title = {Deep Reinforcement Learning framework for Autonomous Driving},
   url = {https://arxiv.org/abs/1704.02532v1},
   year = {2017}
}
@article{Binnig1986,
   abstract = {We report a new type of three-dimensional mechanical scanner fabricated from a single piezoelectric tube. It has a typical response of 5 nm/V in each orthogonal direction and mechanical resonances at 8 kHz (bending perpendicular to the tube axis) and 40 kHz (motion parallel to the tube axis). When used in a scanning tunneling microscope it is the higher frequency mode which is most critical since it corresponds to motion perpendicular to the sample surface. We show an image of the atomic surface of graphite taken in air using a tube scanner incorporated into a scanning tunneling microscope. The tube scanner allows the development of smaller, simpler, and faster scanning tunneling microscopes.},
   author = {G. Binnig and D. P.E. Smith},
   doi = {10.1063/1.1139196},
   issn = {0034-6748},
   issue = {8},
   journal = {Review of Scientific Instruments},
   pages = {1688-1689},
   publisher = {AIP Publishing},
   title = {Single‐tube three‐dimensional scanner for scanning tunneling microscopy},
   volume = {57},
   url = {/aip/rsi/article/57/8/1688/110698/Single-tube-three-dimensional-scanner-for-scanning},
   year = {1986}
}
@article{Binnig1983a,
   abstract = {Scanning tunneling microscopy, a novel technique based on vacuum tunneling, yields surface topographies in real space and work function profiles on an atomic sale. Surfaces are shown for Au(110), Si(111) and GaAs(111). © 1983.},
   author = {G. Binnig and H. Rohrer},
   doi = {10.1016/0039-6028(83)90716-1},
   issn = {0039-6028},
   issue = {1-3},
   journal = {Surface Science},
   pages = {236-244},
   publisher = {North-Holland},
   title = {Scanning tunneling microscopy},
   volume = {126},
   year = {1983}
}
@article{Wiesendanger1990,
   author = {R Wiesendanger and D Anselmetti and H.-J Guntherodt},
   issue = {4},
   journal = {Europhysics News},
   pages = {72-73},
   title = {Advances in STM Design and Instrumentation},
   volume = {21},
   year = {1990}
}
@article{Frohn1989,
   abstract = {We report on a new coarse tip distance adjustment and positioner for a scanning tunneling microscope, which was designed with ease of sample manipulation and UHV compatibility in mind. It has no mechanical connections in UHV and has been successfully used for measurements of microfaceted platinum surfaces in air and cleaved Si(111) surfaces under liquids.},
   author = {J. Frohn and J. F. Wolf and K. Besocke and M. Teske},
   doi = {10.1063/1.1140287},
   isbn = {202316:02:27},
   issn = {0034-6748},
   issue = {6},
   journal = {Review of Scientific Instruments},
   pages = {1200-1201},
   publisher = {AIP Publishing},
   title = {Coarse tip distance adjustment and positioner for a scanning tunneling microscope},
   volume = {60},
   url = {/aip/rsi/article/60/6/1200/324888/Coarse-tip-distance-adjustment-and-positioner-for},
   year = {1989}
}
@article{Iandola2016,
   abstract = {Recent research on deep neural networks has focused primarily on improving accuracy. For a given accuracy level, it is typically possible to identify multiple DNN architectures that achieve that accuracy level. With equivalent accuracy, smaller DNN architectures offer at least three advantages: (1) Smaller DNNs require less communication across servers during distributed training. (2) Smaller DNNs require less bandwidth to export a new model from the cloud to an autonomous car. (3) Smaller DNNs are more feasible to deploy on FPGAs and other hardware with limited memory. To provide all of these advantages, we propose a small DNN architecture called SqueezeNet. SqueezeNet achieves AlexNet-level accuracy on ImageNet with 50x fewer parameters. Additionally, with model compression techniques we are able to compress SqueezeNet to less than 0.5MB (510x smaller than AlexNet). The SqueezeNet architecture is available for download here: https://github.com/DeepScale/SqueezeNet},
   author = {Forrest N. Iandola and Song Han and Matthew W. Moskewicz and Khalid Ashraf and William J. Dally and Kurt Keutzer},
   title = {SqueezeNet: AlexNet-level accuracy with 50x fewer parameters and <0.5MB model size},
   url = {https://arxiv.org/abs/1602.07360v4},
   year = {2016}
}
@article{Khajetoorians2019,
   abstract = {With the advances in high resolution and spin-resolved scanning tunneling microscopy as well as atomic-scale manipulation, it has become possible to create and characterize quantum states of matter bottom-up, atom-by-atom. This is largely based on controlling the particle- or wave-like nature of electrons, as well as the interactions between spins, electrons, and orbitals and their interplay with structure and dimensionality. We review the recent advances in creating artificial electronic and spin lattices that lead to various exotic quantum phases of matter, ranging from topological Dirac dispersion to complex magnetic order. We also project future perspectives in non-equilibrium dynamics, prototype technologies, engineered quantum phase transitions and topology, as well as the evolution of complexity from simplicity in this newly developing field.},
   author = {Alexander A. Khajetoorians and Daniel Wegner and Alexander F. Otte and Ingmar Swart},
   doi = {10.1038/s42254-019-0108-5},
   issue = {12},
   journal = {Nature Reviews Physics},
   pages = {703-715},
   publisher = {Springer Nature},
   title = {Designer quantum states of matter created atom-by-atom},
   volume = {1},
   url = {http://arxiv.org/abs/1904.11680 http://dx.doi.org/10.1038/s42254-019-0108-5},
   year = {2019}
}
@article{Kim2018,
   abstract = {Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantumcomputing. As a promising platform, one-dimensionalmagnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends.We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing.},
   author = {Howon Kim and Alexandra Palacio-Morales and Thore Posske and Levente Rózsa and Krisztián Palotás and László Szunyogh and Michael Thorwart and Roland Wiesendanger},
   doi = {10.1126/SCIADV.AAR5251/SUPPL_FILE/AAR5251_SM.PDF},
   issn = {23752548},
   issue = {5},
   journal = {Science Advances},
   pmid = {29756034},
   publisher = {American Association for the Advancement of Science},
   title = {Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors},
   volume = {4},
   url = {https://www.science.org/doi/10.1126/sciadv.aar5251},
   year = {2018}
}
@article{Liebhaber2021,
   abstract = {Magnetic adatom chains on surfaces constitute fascinating quantum spin systems. Superconducting substrates suppress interactions with bulk electronic excitations but couple the adatom spins to a chain of subgap Yu-Shiba-Rusinov (YSR) quasiparticles. Using a scanning tunneling microscope, we investigate such correlated spin-fermion systems by constructing Fe chains adatom by adatom on superconducting NbSe$_2$. The adatoms couple entirely via the substrate, retaining their quantum spin nature. In dimers, we observe that the deepest YSR state undergoes a quantum phase transition due to Ruderman-Kittel-Kasuya-Yosida interactions, a distinct signature of quantum spins. Chains exhibit coherent hybridization and band formation of the YSR excitations, indicating ferromagnetic coupling. Longer chains develop separate domains due to coexisting charge-density-wave order of NbSe$_2$. Despite the spin-orbit-coupled substrate, we find no signatures of Majoranas, possibly because quantum spins reduce the parameter range for topological superconductivity. We suggest that adatom chains are versatile systems for investigating correlated-electron physics and its interplay with topological superconductivity.},
   author = {Eva Liebhaber and Lisa M. Rütten and Gaël Reecht and Jacob F. Steiner and Sebastian Rohlf and Kai Rossnagel and Felix von Oppen and Katharina J. Franke},
   doi = {10.1038/s41467-022-29879-0},
   issue = {1},
   journal = {Nature Communications},
   publisher = {Nature Research},
   title = {Quantum spins and hybridization in artificially-constructed chains of magnetic adatoms on a superconductor},
   volume = {13},
   url = {http://arxiv.org/abs/2107.06361 http://dx.doi.org/10.1038/s41467-022-29879-0},
   year = {2021}
}
@article{Gonzalez-Herrero2020,
   abstract = {Isolated hydrogen atoms absorbed on graphene are predicted to induce magnetic moments. Here we demonstrate that the adsorption of a single hydrogen atom on graphene induces a magnetic moment characterized by a ~20 meV spin-split state at the Fermi energy. Our scanning tunneling microscopy (STM) experiments, complemented by first-principles calculations, show that such a spin-polarized state is essentially localized on the carbon sublattice complementary to the one where the H atom is chemisorbed. This atomically modulated spin-texture, which extends several nanometers away from the H atom, drives the direct coupling between the magnetic moments at unusually long distances. Using the STM tip to manipulate H atoms with atomic precision, we demonstrate the possibility to tailor the magnetism of selected graphene regions.},
   author = {H. González-Herrero and J. M. Gómez-Rodríguez and P. Mallet and M. Moaied and J. J. Palacios and C. Salgado and M. M. Ugeda and J. Y. Veuillen and F. Yndurain and I. Brihuega},
   doi = {10.1126/science.aad8038},
   issue = {6284},
   journal = {Science},
   pages = {437-441},
   publisher = {American Association for the Advancement of Science},
   title = {Atomic-scale control of graphene magnetism using hydrogen atoms},
   volume = {352},
   url = {http://arxiv.org/abs/2009.13150 http://dx.doi.org/10.1126/science.aad8038},
   year = {2020}
}
@article{Wyrick2016,
   abstract = {Our ability to access and explore the quantum world has been greatly advanced by the power of atomic manipulation and local spectroscopy with scanning tunneling and atomic force microscopes, where the key technique is the use of atomically sharp probe tips to interact with an underlying substrate. Here we employ atomic manipulation to modify and quantify the interaction between the probe and the system under study that can strongly affect any measurement in low charge density systems, such as graphene. We transfer Co atoms from a graphene surface onto a probe tip to change and control the probe’s physical structure, enabling us to modify the induced potential at a graphene surface. We utilize single Co atoms on a graphene field-effect device as atomic scale sensors to quantitatively map the modified potential exerted by the scanning probe over the whole relevant spatial and energy range.},
   author = {Jonathan Wyrick and Fabian D. Natterer and Yue Zhao and Kenji Watanabe and Takashi Taniguchi and William G. Cullen and Nikolai B. Zhitenev and Joseph A. Stroscio},
   doi = {10.1021/ACSNANO.6B05823},
   issn = {1936-086X},
   issue = {12},
   journal = {ACS nano},
   keywords = {Fabian D Natterer,Jonathan Wyrick,Joseph A Stroscio,MEDLINE,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-P.H.S.,Non-U.S. Gov't,PMC5469406,PubMed Abstract,Research Support,U.S. Gov't,doi:10.1021/acsnano.6b05823,pmid:28024319},
   pages = {10698-10705},
   pmid = {28024319},
   publisher = {ACS Nano},
   title = {Tomography of a Probe Potential Using Atomic Sensors on Graphene},
   volume = {10},
   url = {https://pubmed.ncbi.nlm.nih.gov/28024319/},
   year = {2016}
}
@article{Cortes-delRio2020,
   abstract = {Quantum confinement of graphene Dirac-like electrons in artificially crafted nanometer structures is a long sought goal that would provide a strategy to selectively tune the electronic properties of graphene, including bandgap opening or quantization of energy levels. However, creating confining structures with nanometer precision in shape, size, and location remains an experimental challenge, both for top-down and bottom-up approaches. Moreover, Klein tunneling, offering an escape route to graphene electrons, limits the efficiency of electrostatic confinement. Here, a scanning tunneling microscope (STM) is used to create graphene nanopatterns, with sub-nanometer precision, by the collective manipulation of a large number of H atoms. Individual graphene nanostructures are built at selected locations, with predetermined orientations and shapes, and with dimensions going all the way from 2 nm up to 1 µm. The method permits the patterns to be erased and rebuilt at will, and it can be implemented on different graphene substrates. STM experiments demonstrate that such graphene nanostructures confine very efficiently graphene Dirac quasiparticles, both in 0D and 1D structures. In graphene quantum dots, perfectly defined energy bandgaps up to 0.8 eV are found that scale as the inverse of the dot’s linear dimension, as expected for massless Dirac fermions.},
   author = {Eva Cortés-del Río and Pierre Mallet and Héctor González-Herrero and José Luis Lado and Joaquín Fernández-Rossier and José María Gómez-Rodríguez and Jean Yves Veuillen and Iván Brihuega},
   doi = {10.1002/ADMA.202001119},
   issn = {1521-4095},
   issue = {30},
   journal = {Advanced Materials},
   keywords = {atomic manipulation,graphene,graphene quantum dots,nanopatterning,scanning tunneling microscopy},
   pages = {2001119},
   pmid = {32567110},
   publisher = {John Wiley & Sons, Ltd},
   title = {Quantum Confinement of Dirac Quasiparticles in Graphene Patterned with Sub-Nanometer Precision},
   volume = {32},
   url = {https://onlinelibrary.wiley.com/doi/full/10.1002/adma.202001119 https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.202001119 https://onlinelibrary.wiley.com/doi/10.1002/adma.202001119},
   year = {2020}
}
@article{Schofield2013,
   abstract = {Individual atoms and ions are now routinely manipulated using scanning tunnelling microscopes or electromagnetic traps for the creation and control of artificial quantum states. For applications such as quantum information processing, the ability to introduce multiple atomic-scale defects deterministically in a semiconductor is highly desirable. Here we use a scanning tunnelling microscope to fabricate interacting chains of dangling bond defects on the hydrogen-passivated silicon (001) surface. We image both the ground-state and the excited-state probability distributions of the resulting artificial molecular orbitals, using the scanning tunnelling microscope tip bias and tip-sample separation as gates to control which states contribute to the image. Our results demonstrate that atomically precise quantum states can be fabricated on silicon, and suggest a general model of quantum-state fabrication using other chemically passivated semiconductor surfaces where single-atom depassivation can be achieved using scanning tunnelling microscopy. The ability to add and move individual atoms on a surface with a scanning tunnelling microscope enables precise control over the electronic quantum states of the surface. Schofield et al. show that removing hydrogen atoms from a passivated silicon surface can be used to generate and control such states.},
   author = {S. R. Schofield and P. Studer and C. F. Hirjibehedin and N. J. Curson and G. Aeppli and D. R. Bowler},
   doi = {10.1038/ncomms2679},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications 2013 4:1},
   keywords = {Quantum physics,Semiconductors,Techniques and instrumentation},
   pages = {1-7},
   publisher = {Nature Publishing Group},
   title = {Quantum engineering at the silicon surface using dangling bonds},
   volume = {4},
   url = {https://www.nature.com/articles/ncomms2679},
   year = {2013}
}
@article{Folsch2009,
   abstract = {The vertical manipulation of native adatoms on a III-V semiconductor surface was achieved in a scanning tunneling microscope at 5K. Reversible repositioning of individual In atoms on InAs(111)A allows us to construct one-atom-wide In chains. Tunneling spectroscopy reveals that these chains host quantum states deriving from an adatom-induced electronic state and substantial substrate-mediated coupling. Our results show that the combined approach of atom manipulation and local spectroscopy is capable to explore atomic-scale quantum structures on semiconductor platform. © 2009 The American Physical Society.},
   author = {Stefan Fölsch and Jianshu Yang and Christophe Nacci and Kiyoshi Kanisawa},
   doi = {10.1103/PHYSREVLETT.103.096104/FIGURES/3/MEDIUM},
   issn = {00319007},
   issue = {9},
   journal = {Physical Review Letters},
   pages = {096104},
   publisher = {American Physical Society},
   title = {Atom-by-atom quantum state control in adatom chains on a semiconductor},
   volume = {103},
   url = {https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.103.096104},
   year = {2009}
}
@article{Loptien2014,
   abstract = {The electrostatic behavior of a prototypical three-dimensional topological insulator, Bi2Se3(111), is investigated by a scanning tunneling microscopy (STM) study of the distribution of Rb atoms adsorbed on the surface. The positively charged ions are screened by both free electrons residing in the topological surface state as well as band bending induced quantum well states of the conduction band, leading to a surprisingly short screening length. Combining a theoretical description of the potential energy with STM-based atomic manipulation, we demonstrate the ability to create tailored electronic potential landscapes on topological surfaces with atomic-scale control. © 2014 American Physical Society.},
   author = {P. Löptien and L. Zhou and J. Wiebe and A. A. Khajetoorians and J. L. Mi and B. B. Iversen and Ph Hofmann and R. Wiesendanger},
   doi = {10.1103/PHYSREVB.89.085401/FIGURES/6/MEDIUM},
   issn = {10980121},
   issue = {8},
   journal = {Physical Review B - Condensed Matter and Materials Physics},
   pages = {085401},
   publisher = {American Physical Society},
   title = {Screening and atomic-scale engineering of the potential at a topological insulator surface},
   volume = {89},
   url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.89.085401},
   year = {2014}
}
@article{Huff2017,
   abstract = {It has long been anticipated that the ultimate in miniature circuitry will be crafted of single atoms. Despite many advances made in scanned probe microscopy studies of molecules and atoms on surfaces, challenges with patterning and limited thermal stability have remained. Here we make progress toward those challenges and demonstrate rudimentary circuit elements through the patterning of dangling bonds on a hydrogen terminated silicon surface. Dangling bonds sequester electrons both spatially and energetically in the bulk band gap, circumventing short circuiting by the substrate. We deploy paired dangling bonds occupied by one movable electron to form a binary electronic building block. Inspired by earlier quantum dot-based approaches, binary information is encoded in the electron position allowing demonstration of a binary wire and an OR gate.},
   author = {Taleana Huff and Hatem Labidi and Mohammad Rashidi and Roshan Achal and Lucian Livadaru and Thomas Dienel and Jason Pitters and Robert A. Wolkow},
   doi = {10.1038/s41928-018-0180-3},
   issue = {12},
   journal = {Nature Electronics},
   pages = {636-643},
   publisher = {Nature Publishing Group},
   title = {Binary Atomic Silicon Logic},
   volume = {1},
   url = {http://arxiv.org/abs/1706.07427 http://dx.doi.org/10.1038/s41928-018-0180-3},
   year = {2017}
}
@article{Broome2011,
   abstract = {An ultimate goal of spintronic research is the realization of concepts for atomic-scale all-spin-based devices. We combined bottom-up atomic fabrication with spin-resolved scanning tunneling microscopy to construct and read out atomic-scale model systems performing logic operations. Our concept uses substrate-mediated indirect exchange coupling to achieve logical interconnection between individual atomic spins. Combined with spin frustration, this concept enables various logical operations between inputs, such as NOT and OR.},
   author = {Alexander Ako Khajetoorians and Jens Wiebe and Bruno Chilian and Roland Wiesendanger},
   doi = {10.1126/SCIENCE.1201725},
   issn = {1095-9203},
   issue = {6033},
   journal = {Science (New York, N.Y.)},
   keywords = {Alexander Ako Khajetoorians,Jens Wiebe,MEDLINE,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-U.S. Gov't,PubMed Abstract,Research Support,Roland Wiesendanger,doi:10.1126/science.1201725,pmid:21551029},
   pages = {1062-1064},
   pmid = {21551029},
   publisher = {Science},
   title = {Realizing all-spin-based logic operations atom by atom},
   volume = {332},
   url = {https://pubmed.ncbi.nlm.nih.gov/21551029/},
   year = {2011}
}
@article{Broome2018,
   abstract = {Substitutional donor atoms in silicon are promising qubits for quantum computation with extremely long relaxation and dephasing times demonstrated. One of the critical challenges of scaling these systems is determining inter-donor distances to achieve controllable wavefunction overlap while at the same time performing high fidelity spin readout on each qubit. Here we achieve such a device by means of scanning tunnelling microscopy lithography. We measure anti-correlated spin states between two donor-based spin qubits in silicon separated by 16 ± 1 nm. By utilising an asymmetric system with two phosphorus donors at one qubit site and one on the other (2P−1P), we demonstrate that the exchange interaction can be turned on and off via electrical control of two in-plane phosphorus doped detuning gates. We determine the tunnel coupling between the 2P−1P system to be 200 MHz and provide a roadmap for the observation of two-electron coherent exchange oscillations. Donor impurities in silicon are promising candidates as qubits but in order to create a large-scale quantum computer inter-qubit coupling must be introduced by precise positioning of the donors. Here the authors demonstrate the fabrication, manipulation and readout of a two qubit phosphorous donor device.},
   author = {M. A. Broome and S. K. Gorman and M. G. House and S. J. Hile and J. G. Keizer and D. Keith and C. D. Hill and T. F. Watson and W. J. Baker and L. C.L. Hollenberg and M. Y. Simmons},
   doi = {10.1038/s41467-018-02982-x},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications 2018 9:1},
   keywords = {Physics,Qubits},
   pages = {1-7},
   pmid = {29515115},
   publisher = {Nature Publishing Group},
   title = {Two-electron spin correlations in precision placed donors in silicon},
   volume = {9},
   url = {https://www.nature.com/articles/s41467-018-02982-x},
   year = {2018}
}
@article{Achal2018,
   abstract = {At the atomic scale, there has always been a trade-off between the ease of fabrication of structures and their thermal stability. Complex structures that are created effortlessly often disorder above cryogenic conditions. Conversely, systems with high thermal stability do not generally permit the same degree of complex manipulations. Here, we report scanning tunneling microscope (STM) techniques to substantially improve automated hydrogen lithography (HL) on silicon, and to transform state-of-the-art hydrogen repassivation into an efficient, accessible error correction/editing tool relative to existing chemical and mechanical methods. These techniques are readily adapted to many STMs, together enabling fabrication of error-free, room-temperature stable structures of unprecedented size. We created two rewriteable atomic memories (1.1 petabits per in2), storing the alphabet letter-by-letter in 8 bits and a piece of music in 192 bits. With HL no longer faced with this trade-off, practical silicon-based atomic-scale devices are poised to make rapid advances towards their full potential. Manipulation at the atomic scale comes with a trade-off between simplicity and thermal stability. Here, Achal et al. demonstrate improved automated hydrogen lithography and repassivation, enabling error-corrected atomic writing of large-scale structures/memories that are stable at room temperature.},
   author = {Roshan Achal and Mohammad Rashidi and Jeremiah Croshaw and David Churchill and Marco Taucer and Taleana Huff and Martin Cloutier and Jason Pitters and Robert A. Wolkow},
   doi = {10.1038/s41467-018-05171-y},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications 2018 9:1},
   keywords = {Electronics,Semiconductors,Surface patterning,photonics and device physics},
   pages = {1-8},
   pmid = {30038236},
   publisher = {Nature Publishing Group},
   title = {Lithography for robust and editable atomic-scale silicon devices and memories},
   volume = {9},
   url = {https://www.nature.com/articles/s41467-018-05171-y},
   year = {2018}
}
@article{Kiraly2021,
   abstract = {The quest to implement machine learning algorithms in hardware has focused on combining various materials, each mimicking a computational primitive, to create device functionality. Ultimately, these piecewise approaches limit functionality and efficiency, while complicating scaling and on-chip learning, necessitating new approaches linking physical phenomena to machine learning models. Here, we create an atomic spin system that emulates a Boltzmann machine directly in the orbital dynamics of one well-defined material system. Utilizing the concept of orbital memory based on individual cobalt atoms on black phosphorus, we fabricate the prerequisite tuneable multi-well energy landscape by gating patterned atomic ensembles using scanning tunnelling microscopy. Exploiting the anisotropic behaviour of black phosphorus, we realize plasticity with multi-valued and interlinking synapses that lead to tuneable probability distributions. Furthermore, we observe an autonomous reorganization of the synaptic weights in response to external electrical stimuli, which evolves at a different time scale compared to neural dynamics. This self-adaptive architecture paves the way for autonomous learning directly in atomic-scale machine learning hardware.},
   author = {Brian Kiraly and Elze J. Knol and Werner M.J. van Weerdenburg and Hilbert J. Kappen and Alexander A. Khajetoorians},
   doi = {10.1038/S41565-020-00838-4},
   issn = {1748-3395},
   issue = {4},
   journal = {Nature nanotechnology},
   keywords = {Alexander A Khajetoorians,Brian Kiraly,Elze J Knol,MEDLINE,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-P.H.S.,Non-U.S. Gov't,PubMed Abstract,Research Support,U.S. Gov't,doi:10.1038/s41565-020-00838-4,pmid:33526837},
   pages = {414-420},
   pmid = {33526837},
   publisher = {Nat Nanotechnol},
   title = {An atomic Boltzmann machine capable of self-adaption},
   volume = {16},
   url = {https://pubmed.ncbi.nlm.nih.gov/33526837/},
   year = {2021}
}
@phdthesis{Brown2022a,
   abstract = {Acquisition of dense, three-dimensional, force fields with intramolecular resolution via noncontact atomic force microscopy (NC-AFM) has yielded enormous progress in our ability to characterize molecular and two-dimensional materials at the atomic scale. To date, intramolecular force mapping has been performed exclusively at cryogenic temperatures, due to the stability afforded by low temperature operation, and as the carbon monoxide functionalization of the metallic scanning probe tip, normally required for submolecular resolution, is only stable at low temperature. In this paper we show that high-resolution, three-dimensional force mapping of a single organic molecule is possible even at room temperature. The physical limitations of room temperature operation are overcome using semiconducting materials to inhibit molecular diffusion and create robust tip apexes, while challenges due to thermal drift are overcome with atom tracking based feedforward correction. Three-dimensional force maps comparable in spatial and force resolution to those acquired at low temperature are demonstrated, permitting a quantitative analysis of the adsorption induced changes in the geometry of the molecule at the picometer level.},
   author = {Timothy Brown},
   doi = {10.1021/acsnano.2c09463},
   issn = {1936086X},
   keywords = {NC-AFM,SPM,force mapping,force spectroscopy,single molecule,submolecular},
   title = {Intramolecular Force Mapping at Room Temperature},
   year = {2022}
}
@article{Gordon2022,
   abstract = {Although scanning probe microscopy (SPM) techniques have allowed researchers to interact with the nanoscale for decades now, little improvement has been made to the incredibly manual, time consuming process of setting up, running, and analysing the results of these experiments, often arising due to the constantly varying shape of the probe apex. Unlike traditional computing methods, machine learning methods (with neural networks in particular) are considerably more capable of automating subjective tasks such as these, and we are only just beginning to explore the potential applications of this technology in SPM. In this thesis we explore a number of areas where machine learning could potentially massively change the way we go about SPM experimentation. We begin by discussing the history, theory, and experimental concepts of scanning tunnelling microscopy (STM), atomic force microscopy (AFM), and normal-incidence-x-ray standing wave (NIXSW). We then explore the makeup of a neural network and demonstrate how they can be applied to a variety of use-cases in SPM, including classification and policy prediction. Moving to the experimental chapters, we first discuss how we can successfully distinguish between STM tip states of the H:Si(100), Au(111) and Cu(111) surfaces. We also show that by adapting this network to work in real time, we improve performance while requiring on the order of 100x less data. We next discuss our attempts to combine these networks with expert examples to intelligently maintain tip apex sharpness during experimentation, envisioning an end-to-end automatic experiment. Because one of the main difficulties in applying machine learning is the frequent need to manually label data, we then show how we can use Monte Carlo simulations of self-organised AFM nanostructures to automatically label training data for a network, and then combine it with classical statistics and preprocessing to find specific structures in a mixed, messy dataset of real, experimental AFM images. As part of this, we also build a network to denoise experimental images. Finally, we present NIXSW results from an investigation into the temperature dependence of H20@C60, discussing the potential to use unsupervised clustering techniques to distinguish between noisy human-indistinguishable spectra to overcome limitations in data collection.},
   author = {Oliver Miles Gordon},
   title = {Machine learning at the nanoscale},
   year = {2022}
}
@article{Bonnet1994,
   abstract = {In the nanometer resolution range, image formation in STM and AFM cannot be described by a convolution process but is essentially governed by the geometrical interaction between the specimen surface and the tip surface. This non-linear process can be simply described by a dilation of the surface profile by a three-dimensional structuring element which has the shape of the tip. Accordingly, the restoration procedure using these concepts consists in performing the erosion of the image by the same structuring element. A preliminary investigation of a possible blind restoration procedure (i.e. restoration without a very precise knowledge of the tip shape and without the need of using a known test object) is performed.},
   author = {Noël Bonnet and Samuel Dongmo and Philippe Vautrot and Michel Troyon},
   doi = {10.1051/MMM:0199400504-6047700},
   issn = {1154-2799},
   issue = {4-6},
   journal = {Microscopy Microanalysis Microstructures},
   keywords = {Atomic force microscopy,EDP Sciences,Image forming,Image processing,Image restoration,Images,Mathematical morphology,Metrology,Microscopy Microanalysis Microstructures,Optics,Physics,STM,Scanning probe microscopy,journal},
   pages = {477-487},
   publisher = {Société Française de Microscopie Electronique},
   title = {A mathematical morphology approach to image formation and image restoration in scanning tunnelling and atomic force microscopies},
   volume = {5},
   url = {http://dx.doi.org/10.1051/mmm:0199400504-6047700},
   year = {1994}
}
@article{Gordon2020T,
   author = {Gordon Oliver M.},
   issn = {21976619},
   title = {Machine Learning at the Nanoscale},
   year = {2020}
}
@article{Moriarty1998b,
   abstract = {We have investigated the interactions of C60 molecules adsorbed on Si(100)-(2 × 1) through their response to manipulation induced by a scanning tunneling microscope operating at room temperature. Intramolecular features are resolved which vary as a molecule is displaced showing that C60 undergoes rotation during tip-induced displacement. For translation to and from certain bonding sites, the apparent size of a molecule may change following lateral manipulation. Furthermore, reversible changes in dimer buckling are observed as a molecule is moved across the surface. Our experimental observations show that the C60/Si(100)-(2 × 1) interaction is dominant over the C60-C60 interaction and attempts to move a molecular pair result in the transfer of one molecule across a dimer row due to barrier lowering by the intermolecular interaction. We also show that transfer of a molecule from sample to tip (or vice versa) changes both the imaging and manipulation properties of the tip. © 1998 Elsevier Science B.V. All rights reserved.},
   author = {P. Moriarty and Y. R. Ma and M. D. Upward and P. H. Beton},
   doi = {10.1016/S0039-6028(98)00082-X},
   issn = {0039-6028},
   issue = {1-3},
   journal = {Surface Science},
   keywords = {Chemisorption,Fullerenes,Scanning tunnelling microscopy,Silicon},
   pages = {27-35},
   publisher = {North-Holland},
   title = {Translation, rotation and removal of C60 on Si(100)-2 × 1 using anisotropic molecular manipulation},
   volume = {407},
   year = {1998}
}
@article{Keeling2002a,
   abstract = {We have investigated the manipulation of C60 molecules on Si(1 0 0)-2 × 1 using the tip of a scanning tunnelling microscope. An attractive mode of manipulation has been identified in which molecules hop across the Si(1 0 0)-2 × 1 surface in steps of two lattice constants. An abrupt transition to repulsive manipulation occurs as the tip is lowered towards the surface. The attractive interaction is attributed to chemical forces between the tip and molecule. © 2002 Elsevier Science B.V. All rights reserved.},
   author = {D. L. Keeling and M. J. Humphry and P. Moriarty and P. H. Beton},
   doi = {10.1016/S0009-2614(02)01588-9},
   issn = {0009-2614},
   issue = {3-4},
   journal = {Chemical Physics Letters},
   pages = {300-304},
   publisher = {North-Holland},
   title = {Attractive mode manipulation of covalently bound molecules},
   volume = {366},
   year = {2002}
}
@article{Humphry2000,
   abstract = {A versatile digital controller for scanning probe microscopy capable of data acquisition during molecular manipulation has been constructed. A commercially available digital signal processor (DSP) board connected to a Pentium PC and custom-built high voltage amplifiers were used to control a commercial ultrahigh vacuum scanning tunneling microscope and to perform molecular manipulations. Use of the DSP system to produce all analog outputs resulted in an extremely flexible system with complete control of the probe tip. © 2000 American Institute of Physics.},
   author = {M. J. Humphry and R. Chettle and P. J. Moriarty and M. D. Upward and P. H. Beton},
   doi = {10.1063/1.1150522},
   issn = {0034-6748},
   issue = {4},
   journal = {Review of Scientific Instruments},
   pages = {1698-1701},
   publisher = {AIP Publishing},
   title = {Digital scanning probe microscope controller for molecular manipulation applications},
   volume = {71},
   url = {/aip/rsi/article/71/4/1698/442508/Digital-scanning-probe-microscope-controller-for},
   year = {2000}
}
@article{Meyer2001,
   abstract = {We briefly survey our recent studies on the soft lateral manipulation of atoms and small molecules with the scanning tunneling microscope (STM), whereby mainly the tip-surface forces are employed. Repulsive (pushing) as well as discontinuous (pulling) and continuous (sliding) attractive manipulation modes could be distinguished on Cu(2 1 1) for CO molecules and metal atoms, respectively. In the case of pulling of Cu atoms on Cu(1 1 1) even finer details could be discerned: the adparticle may show various movement patterns visiting different surface sites upon applying different tip forces. Lateral manipulation also allows modifications of the Cu(2 1 1) substrate itself in an atom-by-atom manner by releasing atoms from six-fold coordinated kink sites and even seven-fold coordinated regular step sites. Furthermore, investigations concerning controlled vertical manipulation with emphasis on picking up single CO molecules are reported. The mechanism behind vertical transfer of CO molecules relates to ultrafast chemical processes. Vertical manipulation implies besides extending the possibilities for the build-up of nanostructures the important possibility of creating structurally and compositionally well defined tips, which may eventually lead to chemical sensitivity with the STM. © 2001 Elsevier Science B.V. All rights reserved.},
   author = {Gerhard Meyer and Ludwig Bartels and Karl Heinz Rieder},
   doi = {10.1016/S0927-0256(00)00205-6},
   issn = {0927-0256},
   issue = {3-4},
   journal = {Computational Materials Science},
   keywords = {Atomic/molecular manipulation,Carbon monooxide,Scanning tunneling microscopy},
   pages = {443-450},
   publisher = {Elsevier},
   title = {Atom manipulation with the STM: nanostructuring, tip functionalization, and femtochemistry},
   volume = {20},
   year = {2001}
}
@article{Hofer2012,
   abstract = {We show by a statistical analysis of high-resolution scanning tunneling microscopy (STM) experiments, that the interpretation of the density of electron charge as a statistical quantity leads to a conflict with the Heisenberg uncertainty principle. Given the precision in these experiments we find that the uncertainty principle would be violated by close to two orders of magnitude, if this interpretation were correct. We are thus forced to conclude that the density of electron charge is a physically real, i. e., in principle precisely measurable quantity. © 2012 Higher Education Press and Springer-Verlag Berlin Heidelberg.},
   author = {Werner A. Hofer},
   doi = {10.1007/S11467-012-0246-Z/METRICS},
   issn = {20950462},
   issue = {2},
   journal = {Frontiers of Physics},
   keywords = {density functional theory,electron charge,scanning tunneling microscope,uncertainty relations},
   pages = {218-222},
   publisher = {Springer},
   title = {Heisenberg, uncertainty, and the scanning tunneling microscope},
   volume = {7},
   url = {https://link.springer.com/article/10.1007/s11467-012-0246-z},
   year = {2012}
}
@article{Spadafora2014,
   abstract = {We have studied the near surface defects of the delta-doped B:Si(111)-(√3 × √3)R30° system using a combination of scanning tunneling microscopy, non-contact atomic force microscopy, Kelvin probe force spectroscopy, total energy DFT, and STM theoretical simulations. We positively identify and characterize two near surface defects: the adatom vacancy and a B substitutional defect located in the second Si bilayer. We also confirm the assignment of the dangling-bond defect. Additionally, the influence that the subsurface B dopants have on the surface electronic structure, the modulation of the surface potential and the chemical activity of the surface is investigated. © 2014 American Chemical Society.},
   author = {E. J. Spadafora and J. Berger and P. Mutombo and M. Telychko and M. Švec and Z. Majzik and A. B. McLean and P. Jelínek},
   doi = {10.1021/JP503410J/ASSET/IMAGES/LARGE/JP-2014-03410J_0009.JPEG},
   issn = {19327455},
   issue = {29},
   journal = {Journal of Physical Chemistry C},
   pages = {15744-15753},
   publisher = {American Chemical Society},
   title = {Identification of surface defects and subsurface dopants in a delta-doped system using simultaneous nc-AFM/STM and DFT},
   volume = {118},
   url = {https://pubs.acs.org/doi/full/10.1021/jp503410j},
   year = {2014}
}
@article{Baris2012,
   abstract = {Two-dimensional supramolecular multicomponent networks on surfaces are of major interest for the building of highly ordered functional materials with nanometer-sized features especially designed for applications in nanoelectronics, energy storage, sensors, etc. If such molecular edifices have been previously built on noble metals or HOPG surfaces, we have successfully realized a 2D open supramolecular framework on a silicon adatom-based surface under ultrahigh vacuum with thermal stability up to 400 K by combining molecule-molecule and molecule-silicon substrate interactions. One of these robust open networks was further used to control both the growth and the periodicity of the first bicomponent arrays without forming any covalent bond with a silicon surface. Our strategy allows the formation of a well-controlled long-range periodic array of single fullerenes by site-specificity inclusion into a bicomponent supramolecular network. © 2012 American Chemical Society.},
   author = {Bulent Baris and Judicaël Jeannoutot and Vincent Luzet and Frank Palmino and Alain Rochefort and Frédéric Chérioux},
   doi = {10.1021/NN301827E/SUPPL_FILE/NN301827E_SI_001.PDF},
   issn = {19360851},
   issue = {8},
   journal = {ACS Nano},
   keywords = {bicomponent network,scanning probe microscopy,semiconductors,supramolecular self-assembly,surface chemistry},
   pages = {6905-6911},
   pmid = {22746840},
   publisher = {American Chemical Society},
   title = {Noncovalent bicomponent self-assemblies on a silicon surface},
   volume = {6},
   url = {https://pubs.acs.org/doi/full/10.1021/nn301827e},
   year = {2012}
}
@article{Russakovsky2015,
   abstract = {The ImageNet Large Scale Visual Recognition Challenge is a benchmark in object category classification and detection on hundreds of object categories and millions of images. The challenge has been run annually from 2010 to present, attracting participation from more than fifty institutions. This paper describes the creation of this benchmark dataset and the advances in object recognition that have been possible as a result. We discuss the challenges of collecting large-scale ground truth annotation, highlight key breakthroughs in categorical object recognition, provide a detailed analysis of the current state of the field of large-scale image classification and object detection, and compare the state-of-the-art computer vision accuracy with human accuracy. We conclude with lessons learned in the 5 years of the challenge, and propose future directions and improvements.},
   author = {Olga Russakovsky and Jia Deng and Hao Su and Jonathan Krause and Sanjeev Satheesh and Sean Ma and Zhiheng Huang and Andrej Karpathy and Aditya Khosla and Michael Bernstein and Alexander C. Berg and Li Fei-Fei},
   doi = {10.1007/S11263-015-0816-Y/FIGURES/16},
   issn = {15731405},
   issue = {3},
   journal = {International Journal of Computer Vision},
   keywords = {Benchmark,Dataset,Large-scale,Object detection,Object recognition},
   month = {12},
   pages = {211-252},
   publisher = {Springer New York LLC},
   title = {ImageNet Large Scale Visual Recognition Challenge},
   volume = {115},
   url = {https://link.springer.com/article/10.1007/s11263-015-0816-y},
   year = {2015}
}
@phdthesis{Treier2009,
   author = {Matthias Treier},
   title = {Novel Approaches to the Bottom-up Fabrication of Ordered Organic Nanostructures on Metal Surfaces},
   year = {2009}
}
@article{Zhu2022,
   abstract = {Computer vision as a subcategory of deep learning tackles complex vision tasks by dealing with data of images. Molecular images with exceptionally high resolution have been achieved thanks to the development of techniques like scanning probe microscopy (SPM). However, extracting useful information from SPM image data requires careful analysis which heavily relies on human supervision. In this work, we develop a deep learning framework using an advanced computer vision algorithm, Mask R-CNN, to address the challenge of molecule detection, classification and instance segmentation in binary molecular nanostructures. We employ the framework to determine two triangular-shaped molecules of similar STM appearance. Our framework could accurately differentiate two molecules and label their positions. We foresee that the application of computer vision in SPM images will become an indispensable part in the field, accelerating data mining and the discovery of new materials.},
   author = {Zhiwen Zhu and Jiayi Lu and Fengru Zheng and Cheng Chen and Yang Lv and Hao Jiang and Yuyi Yan and Akimitsu Narita and Klaus Müllen and Xiao Ye Wang and Qiang Sun},
   doi = {10.1002/ANIE.202213503},
   issn = {1521-3773},
   issue = {49},
   journal = {Angewandte Chemie International Edition},
   keywords = {CNN,Computer Vision,Machine Learning,Mask R,Molecular Recognitions,Scanning Tunneling Microscopy},
   month = {12},
   pages = {e202213503},
   pmid = {36178779},
   publisher = {John Wiley & Sons, Ltd},
   title = {A Deep-Learning Framework for the Automated Recognition of Molecules in Scanning-Probe-Microscopy Images},
   volume = {61},
   url = {https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202213503 https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202213503 https://onlinelibrary.wiley.com/doi/10.1002/anie.202213503},
   year = {2022}
}
@article{Olsson2004,
   abstract = {The Cu adatom-induced localization of the two-dimensional Shockley surface state at the Cu(111) surface was identified from experimental and simulated scanning tunneling microscopy spectra. The localization gives rise to a resonance located just below the surface state band edge. The adatom-induced surface state localization is discussed in terms of the existence theorem for bound states in any attractive two-dimensional potential. We also identify adatom-induced resonance states deriving from atomic orbitals in both experimental and simulated spectra. Shockley surface states at noble metal surfaces provide an ideal model system for electrons propagating in two dimensions (2D). Direct real space information on these states at the atomic scale is provided by scanning tunnel-ing microscopy (STM), revealing the properties of the surface states from standing wave patterns around defects at the surface. The ability of the STM to assemble nano-structures, such as quantum corrals [1,2], from single ad-sorbates provides means to tailor the propagation of surface states in confined geometries with potential use in nanotechnology. The scattering of surface states from adsorbates introduces also a long-range adsorbate-adsor-bate interaction that affects, for example, growth [3,4]. Thus there is a need to characterize the scattering properties of surface states from elementary defects at surfaces , such as single adatoms. STM and scanning tun-neling spectroscopy (STS) have provided detailed information about adatoms interacting with surface states, for example, standing wave patterns around adatoms [5] and Kondo resonances induced by magnetic adatoms [2,6,7]. A most important fundamental physical effect associated with a 2D surface state interacting with an adatom that has not yet been demonstrated is the possibility of an adatom-induced localization of the surface state [8]. The localization is a direct consequence of the 2D character of the surface state. A theorem by Simon [9] states that any attractive 2D potential has a bound state. In an earlier investigation based on model potentials for Cs on Cu(111), we suggested that adatom-induced localization of the surface state may be observed in STS as a peak appearing just below the surface state band edge [10]. Since the 2D surface state is embedded in the 3D bulk states, this peak corresponds to a resonance state decaying into the bulk state continuum rather than to a 2D bound state. The existence of surface state localization by an adatom has not yet been demonstrated for a real system. In the present work, we present STS experiments combined with detailed theoretical simulations of electronic states for single Cu adatoms on Cu(111) that demonstrate the localization of the Cu(111) Shockley surface state by a Cu adatom. The simulations were carried out in a parameter-free scheme, where the adatom-induced effects on the electronic states were obtained from wave packet and density functional calculations [11]. These calculations show that the observed peaks in the STS data can be assigned to either surface state localization or resonances deriving from atomic orbitals. In search of experimental evidence for adatom-induced resonances, we carried out low-temperature STM investigations at 7 K. Standard procedures were applied for sample preparation in ultrahigh vacuum as described in Ref. [12]. In the spectroscopic measurement, the differential tunneling conductance dI=dV was recorded at constant STM tip height by conventional lock-in technique. This experimental quantity provides a measure of the local density of states (LDOS) of the sample at the tip apex [13]. dI=dV spectra were measured on top of the adatom and at positions close to the adatom at an estimated tip height of 6 A. The STM image in Fig. 1(a) shows a single Cu adatom characterized by an apparent height of 0:7 A and a full width at half maximum (FWHM) of 5:2 A at the indicated tunneling parameters; the faint wave pattern around the adatom arises from standing waves of the surface state. As shown in Fig. 1, the topmost dI=dV spectra recorded over the adatom exhibits a clear peak at a sample bias of ÿ0:49 V with a FWHM of 150 mV.},
   author = {F E Olsson and M Persson and A G Borisov and J.-P Gauyacq and J Lagoute and S Fölsch},
   doi = {10.1103/PhysRevLett.93.206803},
   issue = {20},
   journal = {Physical Review Letters},
   title = {Localization of the Cu(111) Surface State by Single Cu Adatoms},
   volume = {93},
   year = {2004}
}
@article{Li1997,
   abstract = {Electron scattering from steps on the Ag111 surface has been studied by scanning tunneling microscopy STM and spectroscopic STM images of the differential conductance (dI/dV). The amplitudes and positions of maxima of dI/dV deviate significantly from those of the local density of states LDOS. These deviations are due to variations of the vertical tip position which exponentially affect the tunneling barrier transmission and, hence, dI/dV. We show that the LDOS can be recovered from simultaneous topographic and spectro-scopic measurements. S0163-18299703236-0 A knowledge of the local density of states LDOS at solid surfaces is fundamental for an understanding of their local physical and chemical properties. In particular, surface states play a crucial role for the chemical reactivity of some catalytically relevant metals. 1 A measurement of the energy dispersion as a function of the electron wave vector E(K) of such confined electron states is usually performed by techniques such as angle-resolved photoemission spectroscopy PES for occupied states or inverse photoemission spectros-copy for empty states, which are selective in both energy and k space. 2 Recently, scanning tunneling microscopy STM has been used to determine E(K) from standing waves near steps. 3,4 The STM images can often be interpreted as maps of the sample LDOS s near the Fermi energy E F. 5 Spectro-scopic information on s can be extracted from the variation of the tunneling current I with the sample bias voltage V. Since I and hence the constant-current image involve an integral over a range of electron energies its derivative dI/dV is commonly used to unravel the spectroscopic information, e.g., in spatial maps of dI/dV. The perhaps most spectacular applications of this spectroscopic measurement have been the direct imaging of superconductor vortices 6 and of electron scattering and confined electronic states on noble metal surfaces. 3,4 dI/dV mapping is widely used on semiconductor surfaces and interfaces. 7,8 A caveat commonly mentioned in this context is that dI/dV is affected, e.g., by local variations of the tip-sample distance z and therefore does not exactly represent s. 3,4,8-10 Stroscio et al. suggested that this effect can approximately be corrected for by normalization of dI/dV images with I/V, a procedure that had proved to be useful for local dI/dV spectra. 8 Recently, in a theoretical study, Hö rmandinger demonstrated that neither maps of dI/dV nor of the normalized quantity (dI/dV)/(I/V) are good approximations of the LDOS. 10 Later on Ukraintsev pointed out the decisive role of the barrier transmission probability for recovering the LDOS from dI/dV spectra. 11 As a consequence, the surface state dispersion evaluated directly from either dI/dV or (dI/dV)/(I/V) maps deviates from PES results. Hö rmand-inger suggested that the preferable way for measuring the dispersion was to observe dI/dV at constant tip height and far away from a step. Unfortunately, at large distances from the step edge, the oscillatory signal becomes smaller. More importantly, while a constant height can be approximated experimentally by constant current operation at a suitable voltage such a voltage is not known a priori. 8 Here we use simultaneous measurements of z and dI/dV to recover the oscillating LDOS s on a close-packed metal surface. Moreover , experimental dI/dV data are compared to WKB model calculations which take the barrier transmission into account. The agreement of the dispersion thus determined and PES data is very encouraging. The experiments were performed with a custom-built ul-trahigh vacuum UHV STM at T50 K. 12 The Ag111 surface and W tips were prepared in UHV by standard procedures. 12 Spectroscopic dI/dV using lock-in detection and constant current images were acquired simultaneously. With modulation amplitudes of 3.5 mV rms, frequencies of 23 kHz and lock-in time constants of 20 ms, the image data were taken at 80 ms per pixel in order to avoid time-constant effects. Figure 1 shows cross sections of both a constant current and a dI/dV image of a monatomic step on Ag111 at V 20 mV. While a clear oscillatory behavior of dI/dV with a wavelength of 32 Å is observed the constant current data display a small undulation only with 0.1 Å corrugation inset of Fig. 1a. The physical origin of both oscillations has been discussed by Crommie, Lutz, and Eigler 3 and by Hasegawa and Avouris. 4 Scattering of surface state electrons from the step edge leads to interference of the incident and the scattered waves 13 which results in a standing wave pattern in s. At low V, constant current images may be interpreted as maps of s Ref. 5 and thus exhibit oscillations. At larger V the tunneling current represents a weighted integral over a range of energies. 9 Since these energies correspond to varying wavelengths the oscillatory pattern is washed out in the constant current data. In a one-dimensional model dI/dV is given by 9},
   author = {Jiutao Li and Wolf-Dieter Schneider and Richard Berndt},
   issue = {12},
   journal = {Phys Rev B},
   pages = {7656},
   title = {Local density of states from spectroscopic scanning-tunneling-microscope images: Ag(111)},
   volume = {56},
   year = {1997}
}
@article{Tautz2007,
   abstract = {Recent efforts to understand the interaction of large aromatic molecules with metal surfaces are discussed. We focus exclusively on work involving the model molecule 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) and the noble metal surfaces of Cu, Ag, and Au. Using this material system as an example, salient features of the (chemical) bond between an extended π-conjugated electron system and a metallic substrate are illustrated. Interface structures are a valuable indicator of the metal-molecule interaction strength. Consistent with the trend observed for small molecule adsorption, they indicate that the interaction strength of PTCDA with the metal substrate decreases in the order Cu-Ag-Au. The interfaces of PTCDA with the Au(1 1 1) and Ag(1 1 1) surfaces have been studied in particular detail. The interaction of Au(1 1 1) with PTCDA is weak, leading to point-on-line coincidence between the lattices of the substrate and the molecular overlayer. Experimental results on this surface are generally consistent with a predominantly physisorptive bonding of PTCDA. The situation is different on Ag surfaces, and in particular on Ag(1 1 1), where clear signs of PTCDA chemisorption are observed in many ensemble averaging and single molecule spectroscopies. Issues of electronic and geometric structure as well as electron-vibron interaction, and their relation to the chemical molecule-substrate interaction, are discussed in detail. © 2007 Elsevier Ltd. All rights reserved.},
   author = {F. S. Tautz},
   doi = {10.1016/J.PROGSURF.2007.09.001},
   issn = {0079-6816},
   issue = {9-12},
   journal = {Progress in Surface Science},
   month = {9},
   pages = {479-520},
   publisher = {Pergamon},
   title = {Structure and bonding of large aromatic molecules on noble metal surfaces: The example of PTCDA},
   volume = {82},
   year = {2007}
}
@article{Nicoara2006,
   abstract = {We have studied the electronic properties at the interface of a PTCDA molecular film on Au(1 1 1) by means of scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS) and angle resolved ultraviolet photoelectron spectroscopy (ARUPS). Measurements were performed for the clean Au(1 1 1) surface as well as for 1 ML and multilayer coverage of PTCDA. STS curves recorded for 1 ML PTCDA film show a feature at the density of states inside the PTCDA gap and a metallic behavior, in contrast to higher coverage, where a semiconductor behavior is observed. By relating this information to the band dispersion of the electronic states close to the Fermi edge, we can assign this electronic feature to the Au(1 1 1) Shockley surface state. By comparison of intramolecularly resolved STM images with first-principles calculations of the free molecule we show that the electronic molecular states at the interface are not altered by the gold surface. All these facts indicate a weak interaction of the PTCDA molecules with the Au surface and we conclude that the observed metallicity of the interface is provided by the gold substrate rather than by the organic layer. © 2006 Elsevier B.V. All rights reserved.},
   author = {Nicoleta Nicoara and Elisa Román and José M. Gómez-Rodríguez and José A. Martín-Gago and Javier Méndez},
   doi = {10.1016/J.ORGEL.2006.03.010},
   issn = {1566-1199},
   issue = {5},
   journal = {Organic Electronics},
   keywords = {Organic molecules,PTCDA,Photoemission spectroscopy,Scanning tunneling microscopy,Scanning tunneling spectroscopy,Surface states},
   month = {10},
   pages = {287-294},
   publisher = {North-Holland},
   title = {Scanning tunneling and photoemission spectroscopies at the PTCDA/Au(1 1 1) interface},
   volume = {7},
   year = {2006}
}
@article{Mendez2016,
   author = {J Méndez and J M Gómez-Rodríguez},
   doi = {10.1088/0957-4484/27/47/475707},
   journal = {Nanotechnology},
   pages = {475707},
   title = {Visualizing the interface state of PTCDA on Au(111) by scanning tunneling microscopy},
   volume = {27},
   year = {2016}
}
@article{Sabitova2018,
   abstract = {A modified scheme of scanning tunneling spectroscopy data analysis has been used to reconstruct the band structure of a strongly dispersive two-dimensional unoccupied electronic state located at the commensurate interface between a monolayer of 3,4,9,10-perylene-tetracarboxylic dianhydride (PTCDA) and Ag(111) surface up to the fourth band in the reduced Brillouin zone of the molecular monolayer. The two-dimensional scattering potential, evaluated with the help of the measured band structure data, is highly corrugated. This shows that the accepted picture, describing the interface state of PTCDA/Ag(111) as an upshifted Shockley state of Ag(111), is incomplete. Our findings indicate that the hybridization of unoccupied molecular orbitals of PTCDA on one of the two sublattices with the metal states of Ag(111) substantially influences the interface state properties.},
   author = {A Sabitova and R Temirov and F S Tautz},
   doi = {10.1103/PhysRevB.98.205429},
   journal = {PHYSICAL REVIEW B},
   keywords = {doi:10.1103/PhysRevB.98.205429 url:https://doi.org},
   pages = {205429},
   title = {Lateral scattering potential of the PTCDA/Ag(111) interface state},
   volume = {98},
   year = {2018}
}
@article{Hormandinger,
   abstract = {Scanning-tunneling-microscopy (STM) data for the Cu(111) surface have been calculated theoretically , based on Bardeen's approximation and a layer-Korringa-Kohn-Rostoker-like approach to describe the sample. The onset of the surface state gives rise to a steplike increase in the conductivity in very good agreement with recent experimental data, which demonstrates the ability of Bardeen s approximation to describe surface states in spite of its failure regarding surface states in one dimension. The STM conductivity can be approximated in terms of the local density of states (LDOS) of the sample at the voltage V, plus a background term which involves states at all energies, and which is frequently neglected in the interpretation of STM images. In the presence of a step edge, the LDOS of the Cu(111) surface state displays standing wave oscillations. In this case, the background term shows oscillations of the Friedel type which drop as Jq(2kz)/kx for a two-dimensional electron gas. This has important implications for determining the surface state dispersion relation and for the interpretation of standing wave patterns in terms of the LDOS.},
   author = {G Hormandinger},
   journal = {PHYSICAL REVIEW B},
   pages = {15-1994},
   title = {Imaging of the Cu(111) surface state in scanning tunneling microscopy},
   volume = {49},
   year = {1994}
}
@article{DiazAlvarez2016,
   abstract = {Low temperature scanning tunnelling spectroscopy and Raman spectroscopy were used to study the electronic and vibrational properties of silicene formed on the Ag(111) surface for coverage up to one monolayer in the temperature range 230-250 °C. The tunnelling spectra reveal the strong contribution of silver states in the measured density of states around the Fermi level. The Raman spectra are found to evolve as a function of the submonolayer coverages, giving rise at one monolayer coverage to peaks that are characteristic of chemical bonds with distorted sp3 hybrid orbitals. Such properties account for the electronic transparency of the silicene/Ag(111) interface.},
   author = {A. Díaz Álvarez and T. Zhu and J. P. Nys and M. Berthe and M. Empis and J. Schreiber and B. Grandidier and T. Xu},
   doi = {10.1016/J.SUSC.2016.06.005},
   issn = {0039-6028},
   journal = {Surface Science},
   keywords = {Raman spectroscopy,Scanning tunnelling spectroscopy,Silicene},
   month = {11},
   pages = {92-96},
   publisher = {North-Holland},
   title = {Scanning tunnelling spectroscopy and Raman spectroscopy of monolayer silicene on Ag(111)},
   volume = {653},
   year = {2016}
}
@article{Li2010,
   abstract = {To develop new functional materials and nanoscale electronics, researchers would like to accurately describe and precisely control the quantum state of a single molecule on a surface. Scanning tunneling microscopy (STM), combined with first-principles simulations, provides a powerful technique for acquiring this level of understanding. Traditionally, metal phthalocyanine (MPc) molecules, composed of a metal atom surrounded by a ligand ring, have been used as dyes and pigments. Recently, MPc molecules have shown great promise as components of light-emitting diodes, field-effect transistors, photovoltaic cells, and single-molecule devices. In this Account, we describe recent research on the characterization and control of adsorption and electronic states of a single MPc molecule on noble metal surfaces. In general, the electronic and magnetic properties of a MPc molecule largely depend on the type of metal ion within the phthalocyanine ligand and the type of surface on which the molecule is adsorbed. However, with the STM technique, we can use on-site molecular "surgery" to manipulate the structure and the properties of the molecule. For example, STM can induce a dehydrogenation reaction of the MPc, which allows us to control the Kondo effect, which describes the spin polarization of the molecule and its interaction with the complex environment. A specially designed STM tip can allow researchers to detect certain molecule?surface hybrid states that are not accessible by other techniques. By matching the local orbital symmetry of the STM tip and the molecule, we can generate the negative differential resistance effect in the formed molecular junction. This orbital symmetry based mechanism is extremely robust and does not critically depend on the geometry of the STM tip. In summary, this simple model system, a MPc molecule absorbed on a noble metal surface, demonstrates the power of STM for quantum characterization and manipulation of single molecules, highlighting the potential of this technique in a variety of applications. © 2010 American Chemical Society.},
   author = {Zhenyu Li and Bin Li and Jinlong Yang and Jian Guo Hou},
   doi = {10.1021/AR9001558/ASSET/IMAGES/MEDIUM/AR-2009-001558_0010.GIF},
   issn = {00014842},
   issue = {7},
   journal = {Accounts of Chemical Research},
   month = {7},
   pages = {954-962},
   publisher = {American Chemical Society},
   title = {Single-molecule chemistry of metal phthalocyanine on noble metal surfaces},
   volume = {43},
   url = {https://pubs.acs.org/doi/epdf/10.1021/ar9001558},
   year = {2010}
}
@article{Toader2012,
   abstract = {The organic/metal interface formed upon adsorption of cobalt(II) phthalocyanine (CoPc) molecules on a flat Ag(111) single crystal was investigated using a combination of scanning tunneling microscopy (STM) and photoemission spectroscopy (PES). A flat-lying molecular adsorption with the π conjugated phthalocyanine ligand parallel to the substrate was found to lead to an effective molecule-substrate coupling which governs a template-guided molecular growth. A voltage polarity dependence at the cobalt ion site was emphasized and correlated with the Co 2p core level spectra evolution which sustains an interface-confined reduction effect of the cobalt oxidation state. The formation of interface dipoles was observed via monitoring the changes in the work function (WF) upon deposition. The observations are discussed on the basis of a site-dependent donation/backdonation charge transfer at the molecule-substrate interface. © 2012 American Chemical Society.},
   author = {Marius Toader and Pavel Shukrynau and Martin Knupfer and Dietrich R.T. Zahn and Michael Hietschold},
   doi = {10.1021/LA302792Z},
   issn = {07437463},
   issue = {37},
   journal = {Langmuir},
   month = {9},
   pages = {13325-13330},
   publisher = {American Chemical Society},
   title = {Site-dependent donation/backdonation charge transfer at the CoPc/Ag(111) interface},
   volume = {28},
   url = {https://pubs.acs.org/doi/abs/10.1021/la302792z},
   year = {2012}
}
@article{Green2014,
   abstract = {One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM), which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s) is largely unknown. 1926},
   author = {Matthew F B Green and Taner Esat and Christian Wagner and Philipp Leinen and Alexander Grötsch and F Stefan Tautz and Ruslan Temirov},
   doi = {10.3762/bjnano.5.203},
   journal = {Beilstein J. Nanotechnol},
   keywords = {3,4,9,10-perylene tetracarboxylic acid dianhydride,atomic force microscopy (AFM),scanning tunneling microscopy (STM),single-molecule manipulation},
   pages = {1926-1932},
   title = {Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope},
   volume = {5},
   year = {2014}
}
@article{Yongfeng2009,
   abstract = {Molecule-based functional devices on surfaces may take advantage of bistable molecular switches. The conformational dynamics and efficiency of switches are radically different on surfaces compared to the liquid phase. We present a design of molecular layers which enables bistable switching on a surface and, for the first time, demonstrate control of a single switch in a dense and ordered array at the spatial limit. Up and down motion of a central Sn ion through the frame of a phthalocyanine molecule is achieved via resonant electron or hole injection into molecular orbitals. © 2009 American Chemical Society.},
   author = {Wang Yongfeng and Jörg Kröger and Richard Berndt and Werner A. Hofer},
   doi = {10.1021/JA807876C},
   issn = {00027863},
   issue = {10},
   journal = {Journal of the American Chemical Society},
   month = {3},
   pages = {3639-3643},
   publisher = { American Chemical Society},
   title = {Pushing and pulling a Sn Ion through an adsorbed phthalocyanine molecule},
   volume = {131},
   url = {https://pubs.acs.org/doi/full/10.1021/ja807876c},
   year = {2009}
}
@article{VanStraaten2018,
   abstract = {Molecular monolayer films containing two different types of molecules (so-called heteromolecular films) are promising candidates for the controlled functionalization of metal-organic hybrid interfaces. This is particularly true for blends formed by charge donor and acceptor molecules. Here we study heteromolecular monolayer systems containing 3,4,9,10-perylene-tetra-carboxylic-dianhydride (PTCDA) as charge acceptor, and either copper(II) or tin(II) phthalocyanine (CuPc or SnPc) as charge donor, adsorbed on Ag(111). We find that both systems exhibit structural phases with identical lateral ordering (isostructural phases), which is an important prerequisite for studying the role of the central metal atom without competing effects caused by different lateral structures. Using normal incidence X-ray standing waves and photoemission tomography we find distinct differences in the (vertical) geometric and electronic structure for the heteromolecular systems under study: While the vertical structure of CuPc is essentially unaffected by mixing with PTCDA, the SnPc clearly reacts to the formation of a blend by reducing its adsorption height by approximately 0.2 Å. Also, the vertical structure of the PTCDA anhydride groups changes strongly: While the anhydride oxygen atoms are located below the perylene core for most mixed phases, for one of the PTCDA + CuPc phases it is lying above the perylene core. Regarding the electronic structure we find that while mixing with PTCDA causes a complete depletion of the CuPc former lowest unoccupied molecular orbital (FLUMO), the SnPc FLUMO is pinned to the Fermi level instead, and thus it remains partially filled. We demonstrate that all these differences are driven by the rearrangement of the substrate electron density in the vicinity of the PTCDA molecules, which are caused by the interaction with the metal phthalocyanine molecules.},
   author = {Gerben Van Straaten and Markus Franke and Serguei Soubatch and Benjamin Stadtmüller and David A. Duncan and Tien Lin Lee and F. Stefan Tautz and Christian Kumpf},
   doi = {10.1021/ACS.JPCC.8B02689/ASSET/IMAGES/LARGE/JP-2018-026894_0010.JPEG},
   issn = {19327455},
   issue = {15},
   journal = {Journal of Physical Chemistry C},
   month = {4},
   pages = {8491-8504},
   publisher = {American Chemical Society},
   title = {Role of the Central Metal Atom in Substrate-Mediated Molecular Interactions in Phthalocyanine-Based Heteromolecular Monolayers},
   volume = {122},
   url = {https://pubs.acs.org/doi/full/10.1021/acs.jpcc.8b02689},
   year = {2018}
}
@article{Wang2012,
   abstract = {This review mainly focuses on progress recently achieved in the growth of phthalocyanine molecules on single-crystal surfaces of sub-monolayer up to few-monolayer thin films studied by scanning tunneling microscopy in our groups. On metallic surfaces such as Au(111), Ag(111) and Cu(111), molecular superstructures are determined by combining directional intermolecular interactions caused by symmetry reduction, molecule-substrate interactions and indirect long-range interactions due to quantum interference of surface state electrons. On semiconducting TiO2 surface, molecular assembling structures are dictated by the strong molecule-substrate interaction. However, on insulating NaCl film, molecule-molecule interaction dominates over the molecule-NaCl coupling, leading to molecular growth behavior. Knowledge obtained from these studies would help people better understand the physicochemical properties of the phthalocyanine molecules at surfaces so that their new applications could be further explored and uncovered in the future. © 2012 Copyright 2012 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported license. © Author 2012.},
   author = {Yongfeng Wang and Kai Wu and Jörg Kröger and Richard Berndt},
   doi = {10.1063/1.4773458/21748},
   issn = {21583226},
   issue = {4},
   journal = {AIP Advances},
   month = {12},
   pages = {41402},
   publisher = {American Institute of Physics Inc.},
   title = {Review article: Structures of phthalocyanine molecules on surfaces studied by STM},
   volume = {2},
   url = {/aip/adv/article/2/4/041402/21748/Review-Article-Structures-of-phthalocyanine},
   year = {2012}
}
@article{Lackinger2002,
   abstract = {Adsorption of the non-planar molecule tin-phthalocyanine (SnPc) on a Ag(1 1 1) single crystalline surface was studied by means of VT-STM under UHV conditions. For coverage less than one monolayer and deposition on a substrate held at room temperature, a disordered and an ordered phase were found. The disordered phase showed short range ordering in terms of molecular chains and agglomerates. For the ordered phase a rectangular unit cell with a two-molecular base was found. Submolecularly resolved images allow to distinguish between two different adsorption states of the shuttlecock shaped molecule. In these states the central Sn-atom was pointing either towards or off the surface. In case of the densely packed phase an azimuthal rotation of the "up" and "down" adsorbed molecules enables a high packing density. © 2002 Elsevier Science B.V. All rights reserved.},
   author = {Markus Lackinger and Michael Hietschold},
   doi = {10.1016/S0039-6028(02)02269-0},
   issn = {0039-6028},
   issue = {1-2},
   journal = {Surface Science},
   keywords = {Adsorption kinetics,Scanning tunneling microscopy,Silver,Tin},
   month = {11},
   pages = {L619-L624},
   publisher = {North-Holland},
   title = {Determining adsorption geometry of individual tin–phthalocyanine molecules on Ag(111)––a STM study at submonolayer coverage},
   volume = {520},
   year = {2002}
}
@article{Tsubokura2024,
   abstract = {The functionalities of materials are governed by the atom type and arrangement, and perturbations caused by defects and adsorbate interactions often significantly alter the behavior of materials. Scanning probe microscopy (SPM) can capture complex interactions caused by the structures on surfaces. It is, however, difficult to analyze such interactions appearing there. In this paper, an image-processing technique that employs template matching to recognize local structures in SPM images and calculate positional correlations is reported. This approach opens new avenues for investigating intricate perturbations in the sciences and provides detailed insights into materials science. T he functionalities of solid materials are determined by the type and arrangement of their constituent atoms. However, perturbations induced by factors such as defects and interactions between adsorbates can often cause significant alterations of their functionality. Such perturbations have been well documented in various fields such as catalysis, superconductivity, and carrier transport, 1-6) demonstrating their considerable impact on the behavior of solids. Understanding these subtle perturbations is crucial because they often hold the key to unlocking new possibilities in materials science. 7-16) However, detecting them is challenging because of their inherent weaknesses. In the quest to understand the mechanism of perturbations, the analysis of local structures using microscopic images of materials has emerged as a potent tool. 17-25) Among the microscopic techniques available, scanning probe microscopy (SPM) stands out as a premier choice due to its exceptional resolution, including the ability to achieve atomic resolution. 26,27) Moreover, SPM can reveal minute physical properties, encompassing phenomena such as molecule-molecule interactions, electronic interactions, lattice-electron interactions, and spin-orbit interactions. 26,27) Despite the fact that SPM images provide us with the treasure trove of information, the detection and interpretation of these intricate, small-scale interactions often pose significant challenges. To comprehend SPM images better, researchers have traditionally used techniques such as Fourier transform and autocorrelation analysis. 26,27) These methods have proven to be effective in revealing the features of periodic and simple structures. 28-30) However, their applicability diminishes when used in non-periodic and complex structural systems, rendering them inadequate for capturing the full scope of local structural intricacies. In particular, the analysis of positional correlations between local structures is challenging. These positional correlations inherently encapsulate the interactions between distinct species, and thus, we aspire to gain insight into their intricate behavior. Nonetheless, in cases where periodicity is absent within the image or where local structures are entwined with complex counterparts, the application of the analysis proves to be demanding. In response to these challenges, we have developed an image-processing technique that enable us to recognize local structures and analyze the positional correlations among them. In this study, we introduce a method for the automated recognition of structures within SPM images coupled with calculations of positional correlation trends among the identified structures. To verify the validity of our approach, we conducted experiments using SPM images obtained under actual conditions. The results verify the ability of the method to autonomously identify structures and accurately compute their positional correlations. This cutting-edge advancement in image processing not only promises to clarify local structure-function relationships in materials science but also opens new doors for the investigation of intricate perturbations in the sciences. The purpose of this study is to recognize the local structure of SPM images and analyze their positional correlation from complex and non-periodic systems. The proposed method is divided into two steps: (1) recognition of the structure, and (2) calculation of positional correlations in recognized structure groups. In this paper, we describe a method for automatically recognizing the structures in an image. The characteristics of the SPM images with complex structures are as follows: − The structure to be recognized depends on the sample and imaging parameters, each of which exhibits unique characteristics. − Considering the actual experimental situation, we assume that the number of images is less than 1000. 31) Typical methods for automatic recognition include methods that use deep-learning techniques such as convolu-tional neural networks. 32-34) Methods based on the},
   author = {Sota Tsubokura and Shoya Kawano and Yumiko Imai and Tadashi Ueda and Kei-Ichi Nakamoto and Haruo Noma and Hirohisa Hioki and Taketoshi Minato},
   doi = {10.35848/1882-0786/ad2784},
   journal = {Appl. Phys. Express},
   pages = {35003},
   title = {Development of a method for analyzing the positional correlation of local structures in scanning probe microscopy images using template-matching image-procesing method},
   volume = {17},
   url = {https://doi.org/10.35848/1882-0786/ad2784},
   year = {2024}
}
@article{Toader2011,
   abstract = {The tip influence on the energy level alignment at the SnPc/Ag(111) interface has been addressed via scanning tunneling spectroscopy (STS). A collective effect characteristic for both molecular conformations up and down is reported to shift the corresponding first filled and empty levels toward the Fermi energy via a tip-sample distance decrease. The importance of the tin ion coupling to the metal electrodes is emphasized for the newly reported "cross-bending" effect as well as for a controllable tip-induced single-molecule switching and "nano-writing" within densely packed molecular arrays. © 2011 American Chemical Society.},
   author = {Marius Toader and Michael Hietschold},
   doi = {10.1021/JP111478V},
   issn = {19327447},
   issue = {7},
   journal = {Journal of Physical Chemistry C},
   month = {2},
   pages = {3099-3105},
   publisher = {American Chemical Society},
   title = {Tuning the energy level alignment at the SnPc/Ag(111) interface using an STM tip},
   volume = {115},
   url = {https://pubs.acs.org/doi/full/10.1021/jp111478v},
   year = {2011}
}
@article{Zhu2012,
   author = {Yimei Zhu and Hiromi Inada and Achim Hartschuh and Li Shi and Ada Della Pia and Giovanni Costantini and Amadeo L. Vázquez de Parga and Rodolfo Miranda and Antoine Barbier and Cristian Mocuta and Rachid Belkhou and Bharat Bhushan and J. H. Hoo and K. S. Park and R. Baskaran and K. F. Böhringer and Wei Lu and Michael Nosonovsky and Moon-Ho Ham and Ardemis A. Boghossian and Jong Hyun Choi and Michael S. Strano and Amy Lang and Maria Laura Habegger and Philip Motta and Bharat Bhushan and Thomas Bachmann and Hermann Wagner and Donald W. Brenner and Jian Chen and Nika Shakiba and Qingyuan Tan and Yu Sun and Julia R. Greer and M. Laver and S. M. Khaled and Alessandro Parodi and Ennio Tasciotti and Bakul C. Dave and Sarah B. Lockwood and Claudia Musicanti and Paolo Gasco and Fritz Vollrath and Alexander Booth and Andy C. McIntosh and Novid Beheshti and Richard Walker and Lars Uno Larsson and Andrew Copestake and Hyundoo Hwang and Yoon-Kyoung Cho and Jian Chen and Michael Chu and Claudia R. Gordijo and Xiao Yu Wu and Yu Sun and Mathias Kolle and Ullrich Steiner and Szu-Wen Wang and Frederik Ceyssens and Robert Puers and Xiaodong Han and Shengcheng Mao and Ze Zhang and Lei Jiang and Ling Lin and Regina Ragan and Vanni Lughi and Carlos Drummond and Marina Ruths and Weiqiang Mu and John B. Ketterson and Pierre Berini and Ya-Pu Zhao and Feng-Chao Wang and Shaurya Prakash and Simon J. Henley and José V. Anguita and S. Ravi P. Silva and Munish Chanana and Cintia Mateo and Verónica Salgueirino and Miguel A. Correa-Duarte and Swastik Kar and Saikat Talapatra and Javier Calvo Fuentes and José Rivas and M. Arturo López-Quintela and Soichiro Tsuda},
   doi = {10.1007/978-90-481-9751-4_111},
   isbn = {978-90-481-9751-4},
   journal = {Encyclopedia of Nanotechnology},
   pages = {2313-2321},
   publisher = {Springer, Dordrecht},
   title = {Scanning Tunneling Spectroscopy},
   url = {https://link.springer.com/referenceworkentry/10.1007/978-90-481-9751-4_111},
   year = {2012}
}
@article{Wang2017a,
   abstract = {We present an improved way for imaging the density of states of a sample with a scanning tunneling microscope, which consists in mapping the surface topography while keeping the differential conductance (dI/dV) constant. When archetypical C 60 molecules on Cu(111) are imaged with this method, these so-called iso-dI/dV maps are in excellent agreement with theoretical simulations of the isodensity contours of the molecular orbitals. A direct visualization and unambiguous identification of superatomic C 60 orbitals and their hybridization is then possible.},
   author = {Xin Wang and Xuelei Chen and Zhao-Yu Li and Juntai Shen - and Gaël Reecht and Benjamin W Heinrich and Hervé Bulou and Fabrice Scheurer and Laurent Limot and Guillaume Schull},
   doi = {10.1088/1367-2630/aa969a},
   journal = {New J. Phys},
   keywords = {C 60,fulleren,scanning tunneling microscopy,scanning tunneling spectroscopy,super-atomic orbitals},
   pages = {113033},
   title = {Imaging isodensity contours of molecular states with STM},
   volume = {19},
   url = {https://doi.org/10.1088/1367-2630/aa969a},
   year = {2017}
}
@article{Rizzo2018,
   abstract = {Topological insulators are an emerging class of materials that host highly robust in-gap surface or interface states while maintaining an insulating bulk1,2. Most advances in this field have focused on topological insulators and related topological crystalline insulators3 in two dimensions4–6 and three dimensions7–10, but more recent theoretical work has predicted the existence of one-dimensional symmetry-protected topological phases in graphene nanoribbons (GNRs)11. The topological phase of these laterally confined, semiconducting strips of graphene is determined by their width, edge shape and terminating crystallographic unit cell and is characterized by a $$\{\{\mathbb\{Z\}\}\}_\{2\}$$ invariant12 (that is, an index of either 0 or 1, indicating two topological classes—similar to quasi-one-dimensional solitonic systems13–16). Interfaces between topologically distinct GNRs characterized by different\&nbsp;values of $$\{\{\mathbb\{Z\}\}\}_\{2\}$$ are predicted to support half-filled, in-gap localized electronic states that could, in principle, be used as a tool for material engineering11. Here we present the rational design and experimental realization of a topologically engineered GNR superlattice that hosts a one-dimensional array of such states, thus generating otherwise inaccessible electronic structures. This strategy also enables new end states to be engineered directly into the termini of the one-dimensional GNR superlattice. Atomically precise topological GNR superlattices were synthesized from molecular precursors on a gold surface, Au(111), under ultrahigh-vacuum conditions and characterized by low-temperature scanning tunnelling microscopy and spectroscopy. Our experimental results and first-principles calculations reveal that the frontier band structure&nbsp;(the bands bracketing filled and empty states) of these GNR superlattices is defined purely by the coupling between adjacent topological interface states. This manifestation of non-trivial one-dimensional topological phases presents a route to band engineering in one-dimensional materials based on precise control of their electronic topology, and is a promising platform for studies of one-dimensional quantum spin physics. A topologically engineered graphene nanoribbon superlattice is presented that hosts a one-dimensional array of half-filled, in-gap localized electronic states, enabling band engineering.},
   author = {Daniel J. Rizzo and Gregory Veber and Ting Cao and Christopher Bronner and Ting Chen and Fangzhou Zhao and Henry Rodriguez and Steven G. Louie and Michael F. Crommie and Felix R. Fischer},
   doi = {10.1038/s41586-018-0376-8},
   issn = {1476-4687},
   issue = {7717},
   journal = {Nature 2018 560:7717},
   keywords = {Electronic properties and materials,Molecular electronics,Molecular self,Synthesis of graphene,Topological matter,assembly},
   month = {8},
   pages = {204-208},
   pmid = {30089918},
   publisher = {Nature Publishing Group},
   title = {Topological band engineering of graphene nanoribbons},
   volume = {560},
   url = {https://www.nature.com/articles/s41586-018-0376-8},
   year = {2018}
}
@article{Gross2011,
   abstract = {Individual pentacene and naphthalocyanine molecules adsorbed on a bilayer of NaCl grown on Cu(111) were investigated by means of scanning tunneling microscopy using CO-functionalized tips. The images of the frontier molecular orbitals show an increased lateral resolution compared with those of the bare tip and reflect the modulus squared of the lateral gradient of the wave functions. The contrast is explained by tunneling through the p-wave orbitals of the CO molecule. Comparison with calculations using a Tersoff-Hamann approach, including sand p-wave tip states, demonstrates the significant contribution of p-wave tip states. The role of the tip wave function in scanning tunneling microscopy (STM) has been discussed in great detail in several theoretical studies and is of fundamental importance for the interpretation of STM images [1,2]. It was shown early on by Tersoff and Hamann [1] that for s-wave tip states, STM images approximately resemble the local density of states, which is given by the modulus squared of sample wave functions evaluated at the Fermi energy. In contrast, for p-wave tip states, STM images are expected to show spatial derivatives of the sample wave functions, as pointed out by Chen in his derivative rule [2-4]. The character of tip states could in principle be modified by functionalizing the tip by picking up single atoms and molecules. Several groups have shown that a tip termination using either metal atoms, CO, H 2 or organic molecules leads to an enhanced resolution of STM images compared to the bare tip [5-16]. In particular, the lobes of frontier molecular orbitals of planar organic molecules could be resolved with increased resolution using pentacene-terminated tips [9-11]. In the latter case the increased resolution is explained by a decrease of the effective tip-sample distance compared with bare tips [9]. CO-terminated tips could give rise to tunneling through the 2 Ã orbitals of CO and exhibit p-wave character [17]. However, to date no p-wave contributions have been identified in any images recorded using CO tips or any other functionalized tips. By imaging molecular orbitals with a CO-functionalized tip at 5 K, we demonstrate in this Letter that the STM images represent the lateral gradient of the wave function, in agreement with Chen's derivative rule. A comparison with theory corroborates the significant contribution of p-wave tip states. A key finding with wide ramifications for the imaging of individual molecules is the observation that orbitals with closely spaced nodal planes can be imaged with high contrast because of a large lateral gradient of the wave function. As model systems we investigated pentacene and naph-thalocyanine. For each model system, the structure, highest occupied molecular orbital (HOMO), and lowest unoccupied molecular orbital (LUMO) are shown schematically in Fig. 1. To decouple the molecules electronically from the substrate and to suppress direct tunneling into the metal substrate, we used a two-monolayer (ML) thick NaCl film deposited on Cu(111). As shown by Repp et al. [9], two distinct molecular resonances are observable for pentacene on NaClð2 MLÞ=Cuð111Þ in the dI=dV spectra, centered at V ¼ À2:4 V and at V ¼ 1:7 V, corresponding to the positive ion resonance (PIR) and negative ion resonance (NIR), respectively. At these voltages, electrons predominantly tunnel through the HOMO and through the LUMO, respectively , and STM images acquired at these voltages resemble the shape of their orbital densities when using s-wave tips [9]. We created a Cu tip, i.e., an s-wave tip, by bringing a PtIr tip, cut by focused ion beam, into controlled contact with the Cu(111) surface. Finally, to create a CO tip, a single CO molecule was picked up as described previously [5,18]. Compared with images obtained with s-wave tips, the orbital images change drastically when using a CO tip as shown in Figs. 2(a) and 2(b). Calculated constant-height images of the HOMO and LUMO using the Tersoff-Hamann [1] approach with an FIG. 1 (color online). Structure model and molecular frontier orbitals HOMO and LUMO of (a) pentacene and (b) naphthalocyanine. The colors of the atoms correspond to carbon (gray), hydrogen (white) and nitrogen (blue [medium-light gray]). Images were calculated with ArgusLab [31].},
   author = {Leo Gross and Nikolaj Moll and Fabian Mohn and Alessandro Curioni and Gerhard Meyer and Felix Hanke and Mats Persson},
   doi = {10.1103/PhysRevLett.107.086101},
   journal = {PRL},
   keywords = {7115Mb,7320Hb,7361Ng,numbers: 6837Ef},
   pages = {86101},
   title = {High-Resolution Molecular Orbital Imaging Using a p-Wave STM Tip},
   volume = {107},
   year = {2011}
}
@phdthesis{Smalley2024,
   abstract = {The scanning tunneling microscope (STM) is one of the most advanced surface science tools capable of atomic resolution imaging and atomic manipulation. Unfortunately, STM has many time- consuming bottlenecks, like probe conditioning, tip instability, and noise artificing, which causes the technique to have low experimental throughput. This dissertation describes my efforts to address these challenges through automation and machine learning. It consists of two main sections each describing four projects for a total of eight studies. The first section details two studies on nanoscale sample fabrication and two studies on STM tip preparation. The first two studies describe the fabrication of graphene-based Josephson Junction devices and the factorial optimization of patterned carbon nanotube forest synthesis. The second two studies focus on the factorial optimization of electrochemical STM tip etching and automated STM tip functionalization via in-situ silicon nanocolumn growth. The second section details four studies on the use of neural networks for STM image and spectroscopy analysis. The third two studies are on the effectiveness of convolutional neural networks for identifying images of conditioned STM tips on the Au(111) surface and on the detection and metrology of atomic scale defects in single crystal tungsten diselenide, a transition metal dichalcogenide. The fourth two studies are on the use of variational autoencoders to autonomously classify scanning tunneling spectra of various materials, molecules, and surface structures and to identify bismuth and nickel atoms from cross sectional STM images of doped gallium arsenide.},
   author = {Darian Smalley},
   school = {University of Central Florida},
   title = {Enhancing Scanning Tunneling Microscopy with Automation and Machine Learning},
   year = {2024}
}
@article{Chen1998,
   abstract = {We have used scanning tunneling spectroscopy to spatially resolve the electronic structure of clean Au(111) at low temperature. We find that the long-range herringbone reconstruction on Au(111) acts as a superlattice for surface-state electrons, creating a new band structure and modulated electronic density. Low energy electrons respond to the superlattice by localizing in the hexagonal-close-packed (hcp) region of the reconstruction, while higher energy electrons reverse this trend, shifting density back to the adjacent face-centered-cubic (fcc) region. These observations are quantitatively explained by an extended Kronig-Penney model, from which we estimate the well-depth of the reconstruction-induced surface superlattice. © 1998 The American Physical Society.},
   author = {W. Chen and V. Madhavan and T. Jamneala and M. F. Crommie},
   doi = {10.1103/PhysRevLett.80.1469},
   issn = {10797114},
   issue = {7},
   journal = {Physical Review Letters},
   month = {2},
   pages = {1469},
   publisher = {American Physical Society},
   title = {Scanning Tunneling Microscopy Observation of an Electronic Superlattice at the Surface of Clean Gold},
   volume = {80},
   url = {https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.80.1469},
   year = {1998}
}
@article{Ortega2018,
   abstract = {Vicinal surfaces exhibiting arrays of atomic steps are frequently investigated due to their diverse physical-chemical properties and their use as growth templates. However, surfaces featuring steps with a large number of low-coordinated kink-atoms have been widely ignored, despite their higher potential for chemistry and catalysis. Here, the equilibrium structure and the electronic states of vicinal Ag(111) surfaces with densely kinked steps are investigated in a systematic way using a curved crystal. With scanning tunneling microscopy we observe an exceptional structural homogeneity of this class of vicinals, reflected in the smooth probability distribution of terrace sizes at all vicinal angles. This allows us to observe, first, a subtle evolution of the terrace-size distribution as a function of the terrace-width that challenges statistical models of step lattices, and second, lattice fluctuations around resonant modes of surface states. As shown in angle resolved photoemission experiments, surface states undergo stronger scattering by fully-kinked step-edges, which triggers the full depletion of the two-dimensional band at surfaces with relatively small vicinal angles.},
   author = {J. Enrique Ortega and Guillaume Vasseur and Ignacio Piquero-Zulaica and Sonia Matencio and Miguel Angel Valbuena and Julien E. Rault and Frederik Schiller and Martina Corso and Aitor Mugarza and Jorge Lobo-Checa},
   doi = {10.1088/1367-2630/aacbb7},
   issn = {13672630},
   issue = {7},
   journal = {New Journal of Physics},
   keywords = {Ag(111),STM,curved surface,kinked step,photoemission,surface states,vicinal surface},
   publisher = {IOP Publishing},
   title = {Structure and electronic states of vicinal Ag(111) surfaces with densely kinked steps},
   volume = {20},
   year = {2018}
}
@article{Ternes2014,
   author = {Markus Ternes},
   issue = {September},
   title = {Scanning Tunneling Spectroscopy at the Single Atom Scale},
   year = {2014}
}
@article{Farooq2024,
   abstract = {The absence of early diagnosis contributes to oesophageal cancer being the sixth most common cause of global cancer-associated deaths, with a 5-year survival rate of < 20%. Barrett’s oesophagus is the main pre-cancerous condition to adenocarcinoma development, characterised by the morphological transition of oesophageal squamous epithelium to metaplastic columnar epithelium. Early tracking and treatment of oesophageal adenocarcinoma could dramatically improve with diagnosis and monitoring of patients with Barrett’s Oesophagus. Current diagnostic methods involve invasive techniques such as endoscopies and, with only a few identified biomarkers of disease progression, the detection of oesophageal adenocarcinoma is costly and challenging. In this work, single-cell Raman spectroscopy was combined with microfluidic techniques to characterise the development of oesophageal adenocarcinoma through the progression of healthy epithelial, Barrett’s oesophagus and oesophageal adenocarcinoma cell lines. Principal component analysis and linear discriminant analysis were used to classify the different stages of cancer progression. with the ability to differentiate between healthy and cancerous cells with an accuracy of 97%. Whilst the approach could also separate the dysplastic stages from healthy or cancer with high accuracy—the intra-class separation was approximately 68%. Overall, these results highlight the potential for rapid and reliable diagnostic/prognostic screening of Barrett’s Oesophagus patients.},
   author = {Alisha Farooq and Christopher D. Wood and John E. Ladbury and Stephen D. Evans},
   doi = {10.1038/S41598-024-52079-3},
   issn = {20452322},
   issue = {1},
   journal = {Scientific Reports},
   month = {12},
   pages = {1761},
   pmid = {38242991},
   publisher = {Nature Publishing Group},
   title = {On-chip Raman spectroscopy of live single cells for the staging of oesophageal adenocarcinoma progression},
   volume = {14},
   url = {/pmc/articles/PMC10799027/ /pmc/articles/PMC10799027/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10799027/},
   year = {2024}
}
@article{Thomas2022,
   abstract = {Individual atomic defects in 2D materials impact their macroscopic functionality. Correlating the interplay is challenging, however, intelligent hyperspectral scanning tunneling spectroscopy (STS) mapping provides a feasible solution to this technically difficult and time consuming problem. Here, dense spectroscopic volume is collected autonomously via Gaussian process regression, where convolutional neural networks are used in tandem for spectral identification. Acquired data enable defect segmentation, and a workflow is provided for machine-driven decision making during experimentation with capability for user customization. We provide a means towards autonomous experimentation for the benefit of both enhanced reproducibility and user-accessibility. Hyperspectral investigations on WS2 sulfur vacancy sites are explored, which is combined with local density of states confirmation on the Au\{111\} herringbone reconstruction. Chalcogen vacancies, pristine WS2, Au face-centered cubic, and Au hexagonal close-packed regions are examined and detected by machine learning methods to demonstrate the potential of artificial intelligence for hyperspectral STS mapping.},
   author = {John C. Thomas and Antonio Rossi and Darian Smalley and Luca Francaviglia and Zhuohang Yu and Tianyi Zhang and Shalini Kumari and Joshua A. Robinson and Mauricio Terrones and Masahiro Ishigami and Eli Rotenberg and Edward S. Barnard and Archana Raja and Ed Wong and D. Frank Ogletree and Marcus M. Noack and Alexander Weber-Bargioni},
   doi = {10.1038/s41524-022-00777-9},
   issn = {2057-3960},
   issue = {1},
   journal = {npj Computational Materials 2022 8:1},
   keywords = {Imaging techniques,Scanning probe microscopy,Surfaces,interfaces and thin films},
   month = {5},
   pages = {1-7},
   publisher = {Nature Publishing Group},
   title = {Autonomous scanning probe microscopy investigations over WS2 and Au\{111\}},
   volume = {8},
   url = {https://www.nature.com/articles/s41524-022-00777-9},
   year = {2022}
}
@article{Sweetman2020,
   abstract = {In the last decade it has become possible to resolve the geometric structure of organic molecules with intramolecular resolution using high resolution scanning probe microscopy (SPM), and specifically using the subset of SPM known as noncontact atomic force microscopy (ncAFM). In world leading groups it has become routine not only to perform sub-molecular imaging of the chemical, electronic, and electrostatic properties of single molecules, but also to use this technique to track complex on-surface chemical reactions, investigate novel reaction products, and even synthesise new molecular structures one bond at a time. These developments represent the cutting edge of characterisation at the single chemical bond level, and have revolutionised our understanding of surface-based chemical processes.},
   author = {Adam Sweetman and Neil Champness and Alex Saywell and See Adam Sweetman and Neil R Champness and Chem Soc Rev and Chi Zhang and Kanyi Pu},
   doi = {10.1039/D0CS00166J},
   issn = {1460-4744},
   issue = {13},
   journal = {Chemical Society Reviews},
   month = {7},
   pages = {4189-4202},
   pmid = {32510083},
   publisher = {The Royal Society of Chemistry},
   title = {On-surface chemical reactions characterised by ultra-high resolution scanning probe microscopy},
   volume = {49},
   url = {https://pubs.rsc.org/en/content/articlehtml/2020/cs/d0cs00166j https://pubs.rsc.org/en/content/articlelanding/2020/cs/d0cs00166j},
   year = {2020}
}
@article{Repp2005,
   abstract = {Ultrathin insulating NaCl films have been employed to decouple individual pentacene molecules electronically from the metallic substrate. This allows the inherent electronic structure of the free molecule to be preserved and studied by means of low-temperature scanning-tunneling microscopy. Thereby direct images of the unperturbed molecular orbitals of the individual pentacene molecules are obtained. Elastic scattering quantum chemistry calculations substantiate the experimental findings. © 2005 The American Physical Society.},
   author = {Jascha Repp and Gerhard Meyer and Sladjana M. Stojković and André Gourdon and Christian Joachim},
   doi = {10.1103/PHYSREVLETT.94.026803},
   issn = {00319007},
   issue = {2},
   journal = {Physical Review Letters},
   keywords = {6837Ef,7361Ng,numbers: 7320Hb},
   month = {1},
   pages = {026803},
   publisher = {American Physical Society},
   title = {Molecules on insulating films: Scanning-tunneling microscopy imaging of individual molecular orbitals},
   volume = {94},
   url = {https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.94.026803},
   year = {2005}
}
@article{Andreev2004,
   abstract = {The energetic position of the Au(111) Shockley surface state is compared before and after adsorbing different rare gas monolayers (Ar, Kr, and Xe). We used ultraviolet photoelectron spectroscopy (UPS) and scanning tunneling spectroscopy (STS) in combination to get more complete information by using the advantages of both methods. For determining the energetic position and the effective mass of the surface state in UPS an analytic mathematical method is used, which takes the finite angular resolution of the analyzer into account. We performed STS scans for the pure Au(111) surface as well as covered with a monolayer Kr and Xe. For an accurate analysis it is possible to use an extended Kronig-Penney model to take into account the influence of the 23 × √3 reconstruction. We found that the first monolayer of a rare gas induces shifts of around 50-150 meV increasing with the gas atomic number, whereas a second monolayer has only a small influence of about 3-18 meV. Using an image potential model it is possible to characterize these shifts qualitatively. For a semiquantitative analysis the phase accumulation model is applied. Within this model we can describe the experimental data roughly with a Coulomb potential changing in dependence of the electron affinity and the dielectric constant of the rare gas.},
   author = {Thomas Andreev and Ingo Barke and Heinz Hövel},
   doi = {10.1103/PHYSREVB.70.205426},
   issn = {01631829},
   issue = {20},
   pages = {205426},
   journal = {Physical Review B - Condensed Matter and Materials Physics},
   month = {11},
   title = {Adsorbed rare-gas layers on Au(111): Shift of the Shockley surface state studied with ultraviolet photoelectron spectroscopy and scanning tunneling spectroscopy},
   volume = {70},
   url = {https://www.researchgate.net/publication/228783225_Adsorbed_rare-gas_layers_on_Au_111_Shift_of_the_Shockley_surface_state_studied_with_ultraviolet_photoelectron_spectroscopy_and_scanning_tunneling_spectroscopy},
   year = {2004}
}
@article{Barker2024,
   abstract = {The manual identification and in situ correction of the state of the scanning probe tip is one of the most time-consuming and tedious processes in atomic-resolution scanning probe microscopy. This is due to the random nature of the probe tip on the atomic level, and the requirement for a human operator to compare the probe quality via manual inspection of the topographical images after any change in the probe. Previous attempts to automate the classification of the scanning probe state have focused on the use of machine learning techniques, but the training of these models relies on large, labeled data sets for each surface being studied. These data sets are extremely time-consuming to create and are not always available, especially when considering a new substrate or adsorbate system. In this paper, we show that the problem of tip classification from a topographical image can be solved by using only a single image of the surface along with a small amount of prior knowledge of the appearance of the system in question with a method utilizing template matching (TM). We find that by using these TM methods, comparable accuracy and precision can be achieved to values obtained with the use of machine learning. We demonstrate the efficacy of this technique by training a machine learning-based classifier and comparing the classifications with the TM classifier for two prototypical silicon-based surfaces. We also apply the TM classifier to a number of other systems where supervised machine learning-based training was not possible due to the nature of the training data sets. Finally, the applicability of the TM method to surfaces used in the literature, which have been classified using machine learning-based methods, is considered.},
   author = {Dylan Stewart Barker and Philip James Blowey and Timothy Brown and Adam Sweetman},
   doi = {10.1021/ACSNANO.3C10597},
   issn = {1936086X},
   issue = {3},
   journal = {ACS Nano},
   keywords = {atomic resolution,automation,cross-correlation,in situ tip conditioning,machine learning,scanning probe microscopy (SPM),scanning tunneling microscopy (STM)},
   month = {1},
   pages = {2384-2394},
   pmid = {38194226},
   publisher = {American Chemical Society},
   title = {Automated Scanning Probe Tip State Classification without Machine Learning},
   volume = {18},
   url = {https://pubs.acs.org/doi/full/10.1021/acsnano.3c10597},
   year = {2024}
}
@article{Mamin1999,
   abstract = {The atomic force microscope (AFM), with its ability to image and modify surfaces on the nanometer scale, offers the potential for simple, compact, high-density data-storage devices. At the heart of the technique is a microfabricated cantilever with a sharp tip on the end. Using modern micromachining techniques, it is possible to batch fabricate cantilevers with tips that are sharp on the scale of 100 angstrom. We have pursued a particular AFM storage scheme based on mechanical readback of topographic data using high-frequency, piezoresistive silicon cantilevers. Areal densities of 65 Gbit/in2 have been demonstrated, with readback rates greater than 10 Mbit/s. Nanoreplication techniques have been used to produce read-only disks. In addition, a write-once scheme was developed that uses integrated heating elements on the cantilevers in order to perform thermomechanical writing on a polymer substrate. Considerable progress has been made in addressing critical issues such as data rate, reliability, and practical implementation, but significant challenges still remain, both in the technology and in finding the most suitable applications.},
   author = {H. Jonathon Mamin and Robert P. Ried and Bruce D. Terris and Daniel Rugar},
   doi = {10.1109/5.763314},
   issn = {00189219},
   issue = {6},
   journal = {Proceedings of the IEEE},
   pages = {1014-1027},
   publisher = {IEEE},
   title = {High-density data storage based on the atomic force microscope},
   volume = {87},
   year = {1999}
}
@article{Heinz2004,
   abstract = {The power of the combined application of quantitative low-energy electron diffraction (LEED) and scanning tunneling microscopy (STM) is demonstrated for several examples. It is shown that the STM image in most cases provides the key to the applicable structural model type. Such an initial guess is needed by LEED to start a structural search in which the model parameters are varied so that the complete crystallographic structure is obtained. The input from STM is invaluable when a large number of different model types have to be tested or, even more, in cases where the scientist lacks the imagination to think of the correct model type. If a structural misinterpretation of the STM image puts LEED on the wrong track, then the method becomes aware of that by the best fit achieved being unsatisfying. In this sense, the combination of STM and quantitative LEED is almost ideal and provides new power for the access of complex structures.},
   author = {Klaus Heinz and Lutz Hammer},
   doi = {10.1021/JP049289N/ASSET/IMAGES/LARGE/JP049289NF00007.JPEG},
   issn = {15206106},
   issue = {38},
   journal = {Journal of Physical Chemistry B},
   month = {9},
   pages = {14579-14584},
   publisher = { American Chemical Society },
   title = {Combined application of LEED and STM in surface crystallography},
   volume = {108},
   url = {https://pubs.acs.org/doi/full/10.1021/jp049289n},
   year = {2004}
}
@article{Yates1991,
   abstract = {The role of surface dangling bonds in controlling the surface chemistry of Si(100) and Si(ll1) has been investigated using surface science methods. The adsorption and decomposition of arrtylem on Si(1W) has been shown to occur by means of a mobile precursor m&&un. leading to a di-o chemisorbed eth&nic species occupying Si dimer sites on Si(la0). This species decomposes at elevated temperatures to produce adsorbed carban and hydrogen (800K) and then silicon carbide (1000 K). The activity of Si(ll1) for the adsorpbion of species such as ammonia and atomic hydrogen can be sipifieantly reduced by doping of the surface region with boron. It has been shown that subsurface boron ripifi-tly changer the structure of Si(ll1)-(7x7) lo a 6 x ~'3 R30° structure. In addition, the local doping of the surface reduces the chemical activity of the dangling bonds so that neither the dissociation of NH3 nor the adsorption of atomic hydrogen will occur.},
   author = {J T Yates},
   journal = {J. Phys.: Condens. Matter},
   pages = {14-156},
   title = {Surface chemistry of silicon-the behaviour of dangling bonds},
   volume = {3},
   year = {1991}
}
@article{Bedrossian1989,
   abstract = {We have investigated the incorporation of boron into the Si(111)(v3x J3)R30 surface from low bo-ron concentration up to-, monolayer, using tunneling microscopy and spectroscopy and first-principles total-energy calculations. Surprisingly, we find that a (J3x J3)R30' structure composed almost entirely of Si adatoms on a Si double layer can be stabilized by boron doping in near-surface layers. Moreover , when boron atoms are in the surface layers, the adatom site is unfavorable compared with the site underneath the adatom, unlike other group-III elements adsorbed on the Si(111)surface. PACS numbers: 68.35.Dv, 61.16.Di, 73.20.Hb Recent studies have revealed that Al, Ga, and In all show quite similar behavior when adsorbed on Si(111), and it might be thought that adsorption of group-III metals on this surface was well characterized and understood. ' In this Letter, we report two entirely novel features associated with the presence of boron, another group-III element, on the Si(111) surface. Using scanning tunneling microscopy (STM) and spectroscopy, we find that a large subsurface concentration of boron can stabilize a (J3x J3)R30' structure of Si adatoms on a Si double layer. To our knowledge, such stabilization has not previously been reported, and we propose a doping mechanism to explain it. Second, we determine from first-principles total-energy calculations that when boron is observed at the surface, it prefers the site directly underneath the adatom, in dramatic contrast to other group-III adsorbates, all of which occupy the adatom site. ' Our results demonstrate the feasibility of modifying the atomic-scale morphology and electronic structure of semiconductor surfaces by heavily doping the near-surface region.},
   author = {P Bedrossian and Robert D Meade and K Mortensen and D M Chen and J A Golovchenko and David Vanderbilt},
   issue = {12},
   journal = {Phys. Rev. Lett},
   pages = {1257-1260},
   title = {PHYSICAL REVIEW LETTERS Surface Doping and Stabilization of Si(111) with Boron},
   volume = {63},
   year = {1989}
}
@article{Makoudi2017,
   abstract = {Understanding the physical and chemical processes in which local interactions lead to ordered structures is of particular relevance to the realization of supramolecular architectures on surfaces. While spectacular patterns have been demonstrated on metal surfaces, there have been fewer studies of the spontaneous organization of supramolecular networks on semiconductor surfaces, where the formation of covalent bonds between organics and adatoms usually hamper the diffusion of molecules and their subsequent interactions with each other. However, the saturation of the dangling bonds at a semiconductor surface is known to make them inert and offers a unique way for the engineering of molecular patterns on these surfaces. This review describes the physicochemical properties of the passivated B-Si(111)-(√3x√3) R30° surface, that enable the self-assembly of molecules into a rich variety of extended and regular structures on silicon. Particular attention is given to computational methods based on multi-scale simulations that allow to rationalize the relative contribution of the dispersion forces involved in the self-assembled networks observed with scanning tunneling microscopy. A summary of state of the art studies, where a fine tuning of the molecular network topology has been achieved, sheds light on new frontiers for exploiting the construction of supramolecular structures on semiconductor surfaces.},
   author = {Younes Makoudi and Judicaël Jeannoutot and Frank Palmino and Frédéric Chérioux and Guillaume Copie and Christophe Krzeminski and Fabrizio Cleri and Bruno Grandidier},
   doi = {10.1016/J.SURFREP.2017.06.001},
   issn = {0167-5729},
   issue = {4},
   journal = {Surface Science Reports},
   keywords = {Intermolecular forces,Multiscale modelling,Scanning tunneling microscopy,Self-assembly,Semiconductor surfaces,Two-dimensional molecular network},
   month = {9},
   pages = {316-349},
   publisher = {North-Holland},
   title = {Supramolecular self-assembly on the B-Si(111)-(√3x√3) R30° surface: From single molecules to multicomponent networks},
   volume = {72},
   year = {2017}
}
@article{Baumgartel1999,
   abstract = {A quantitative structural analysis of the system Si(111)(33)R30°-B has been performed using photo-electron diffraction in the scanned energy mode. We confirm that the substitutional S 5 adsorption site is occupied and show that the interatomic separations to the three nearest-neighbor Si atoms are 1.98(0.04) Å , 2.14(0.13) Å , and 2.21(0.12) Å. These correspond to the silicon atom immediately below the boron atom, the adatom immediately above, and the three atoms to which it is coordinated symmetrically in the first layer. S0163-18299905819-1},
   author = {P Baumgärtel and J J Paggel and M Hasselblatt and K Horn and V Fernandez and O Schaff and J H Weaver and A M Bradshaw and D P Woodruff and E Rotenberg and J Denlinger},
   issue = {20},
   journal = {Phys. Rev. B},
   pages = {13014-13019},
   title = {Structure determination of the "33…R30° boron phase on the Si"111… surface using photoelectron diffraction},
   volume = {59},
   year = {1999}
}
@article{Youya1996,
   abstract = {The application of scanning tunnelling microscopy (STM) to semiconductor surfaces is reviewed. After a brief description of theoretical models for STM the experimental requirements are summarized. STM results will be shown and discussed for clean semiconductor surfaces (Si(111), Si(100), Si(110), high-index faces of Si, Ge and GaAs). Examples will be given for the more important reconstructions of these surfaces and for temperature dependent phase transitions, e.g., for the high-temperature (7 × 7)/(1 × 1) transition of Si(111) and for the low-temperature c(4 × 2)/(2 × 1) transition of Si(100). The properties of steps will be described for Si(111) and Si(100). The study of adsorption and growth processes is one of the main fields in current STM work on semiconductors and representative examples will be given for homoepitaxy, heteroepitaxy, cross-sectional studies, metal adsorption and adsorption of small molecules which give rise to surface reactions. Finally, more recent applications such as manipulation of semiconductor surfaces, ballistic-electron emission, potentiometry and electrochemistry will briefly be reviewed.},
   author = {Wagatsuma Youya and Kazuya Alam and Al Okada and Wu Li and Shigeo Sato and Hisanao Akima},
   doi = {10.1088/0034-4885/59/6/001},
   issn = {0034-4885},
   issue = {6},
   journal = {Reports on Progress in Physics},
   month = {6},
   pages = {701},
   publisher = {IOP Publishing},
   title = {Scanning tunnelling microscopy of semiconductor surfaces},
   volume = {59},
   url = {https://iopscience.iop.org/article/10.1088/0034-4885/59/6/001 https://iopscience.iop.org/article/10.1088/0034-4885/59/6/001/meta},
   year = {1996}
}
@article{Kalinin2024,
   abstract = {Machine learning (ML) methods are progressively gaining acceptance in the electron microscopy community for de-noising, semantic segmentation, and dimensionality reduction of data post-acquisition. The introduction of the application programming interfaces (APIs) by major instrument manufacturers now allows the deployment of ML workflows in microscopes, not only for data analytics but also for real-time decision-making and feedback for microscope operation. However, the number of use cases for real-time ML remains remarkably small. Here, we discuss some considerations in designing ML-based active experiments and pose that the likely strategy for the next several years will be human-in-the-loop automated experiments (hAE). In this paradigm, the ML learning agent directly controls beam position and image and spectroscopy acquisition functions, and a human operator monitors experiment progression in real and feature space of the system and tunes the policies of the ML agent to steer the experiment toward specific objectives.},
   author = {Sergei V Kalinin and Yongtao Liu and Arpan Biswas and Gerd Duscher and Utkarsh Pratiush and Kevin Roccapriore and Maxim Ziatdinov and Rama Vasudevan},
   doi = {10.1093/MICTOD/QAAD096},
   issn = {1551-9295},
   issue = {1},
   journal = {Microscopy Today},
   keywords = {application programming interfaces,deep kernel learning,electron microscopy,machine learning,scanning tunneling microscopy},
   month = {2},
   pages = {35-41},
   publisher = {Oxford Academic},
   title = {Human-in-the-Loop: The Future of Machine Learning in Automated Electron Microscopy},
   volume = {32},
   url = {https://dx.doi.org/10.1093/mictod/qaad096},
   year = {2024}
}
@article{Temirov2008,
   abstract = {We report a new contrast mechanism in which scanning tunnelling micrographs of a certain class of molecules resemble chemists' structure formulae. The method is based on adding molecular hydrogen below its condensation temperature to the tunnelling junction of a low-temperature scanning tunnelling microscope. In the presence of hydrogen, the scanning tunnelling microscope contrast can be switched between the conventional mapping of the electronic local density of states and the new geometric imaging by selecting the appropriate bias voltage. Scanning tunnelling spectroscopy suggests that the coupling of the electron tunnelling current to an internal degree of freedom in the tunnelling junction is responsible for the geometric contrast. The new scanning tunnelling hydrogen microscopy (STHM) allows the chemical identification of certain molecular species by their structure. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.},
   author = {R. Temirov and S. Soubatch and O. Neucheva and A. C. Lassise and F. S. Tautz},
   doi = {10.1088/1367-2630/10/5/053012},
   issn = {1367-2630},
   issue = {5},
   journal = {New Journal of Physics},
   month = {5},
   pages = {053012},
   publisher = {IOP Publishing},
   title = {A novel method achieving ultra-high geometrical resolution in scanning tunnelling microscopy},
   volume = {10},
   url = {https://iopscience.iop.org/article/10.1088/1367-2630/10/5/053012 https://iopscience.iop.org/article/10.1088/1367-2630/10/5/053012/meta},
   year = {2008}
}
@article{Kichin2011,
   abstract = {Individual Xe atoms as well as single CO and CH4 molecules adsorbed at the tip apex of a scanning tunneling microscope (STM) function as microscopic force sensors that change the tunneling current in response to the forces acting from the surface. An STM equipped with any of these sensors is able to image the short-range Pauli repulsion and thus resolve the inner structure of large organic adsorbate molecules. Differences in the performance of the three studied sensors suggest that the sensor functionality can be tailored by tuning the interaction between the sensor particle and the STM tip. © 2011 American Chemical Society.},
   author = {Georgy Kichin and Christian Weiss and Christian Wagner and F. Stefan Tautz and Ruslan Temirov},
   doi = {10.1021/JA204624G/ASSET/IMAGES/LARGE/JA-2011-04624G_0001.JPEG},
   issn = {00027863},
   issue = {42},
   journal = {Journal of the American Chemical Society},
   month = {10},
   pages = {16847-16851},
   publisher = {American Chemical Society},
   title = {Single molecule and single atom sensors for atomic resolution imaging of chemically complex surfaces},
   volume = {133},
   url = {https://pubs.acs.org/doi/full/10.1021/ja204624g},
   year = {2011}
}
@article{Mohn2013,
   abstract = {We explore different tip functionalizations for atomic force microscopy (AFM), scanning tunneling microscopy (STM), and Kelvin probe force microscopy (KPFM) of organic molecules on thin insulating films. We describe in detail how tips terminated with single Br and Xe atoms can be created. The performance of these tips in AFM, STM, and KPFM imaging of single molecules is compared to other tip terminations, and the advantages and disadvantages of the different tips are discussed. The Br tip was found to be particularly useful for AFM and lateral manipulation, whereas the Xe tip excelled in STM and KPFM. © 2013 American Institute of Physics.},
   author = {Fabian Mohn and Bruno Schuler and Leo Gross and Gerhard Meyer},
   doi = {10.1063/1.4793200/24335},
   issn = {00036951},
   issue = {7},
   journal = {Applied Physics Letters},
   month = {2},
   pages = {73109},
   publisher = {AIP Publishing},
   title = {Different tips for high-resolution atomic force microscopy and scanning tunneling microscopy of single molecules},
   volume = {102},
   url = {/aip/apl/article/102/7/073109/24335/Different-tips-for-high-resolution-atomic-force},
   year = {2013}
}
@article{Sweetman2014,
   abstract = {Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism. Hydrogen bonding is an important force in nature, directing and controlling the assembly of numerous natural and synthetic structures. Here the authors show that the interpretation of intermolecular contrast in atomic force microscope images of hydrogen-bonded assemblies necessitates detailed consideration of the coupled tip-molecule system.},
   author = {A. M. Sweetman and S. P. Jarvis and Hongqian Sang and I. Lekkas and P. Rahe and Yu Wang and Jianbo Wang and N. R. Champness and L. Kantorovich and P. Moriarty},
   doi = {10.1038/ncomms4931},
   issn = {2041-1723},
   issue = {1},
   journal = {Nature Communications 2014 5:1},
   keywords = {Physical chemistry},
   month = {5},
   pages = {1-7},
   publisher = {Nature Publishing Group},
   title = {Mapping the force field of a hydrogen-bonded assembly},
   volume = {5},
   url = {https://www.nature.com/articles/ncomms4931},
   year = {2014}
}
@article{Monig2015,
   abstract = {In scanning probe microscopy, the imaging characteristics in the various interaction channels crucially depend on the chemical termination of the probe tip. Here we analyze the contrast signatures of an oxygen-terminated copper tip with a tetrahedral configuration of the covalently bound terminal O atom. Supported by first-principles calculations we show how this tip termination can be identified by contrast analysis in noncontact atomic force and scanning tunneling microscopy (NC-AFM, STM) on a partially oxidized Cu(110) surface. After controlled tip functionalization by soft indentations of only a few angstroms in an oxide nanodomain, we demonstrate that this tip allows imaging an organic molecule adsorbed on Cu(110) by constant-height NC-AFM in the repulsive force regime, revealing its internal bond structure. In established tip functionalization approaches where, for example, CO or Xe is deliberately picked up from a surface, these probe particles are only weakly bound to the metallic tip, leading to lateral deflections during scanning. Therefore, the contrast mechanism is subject to image distortions, artifacts, and related controversies. In contrast, our simulations for the O-terminated Cu tip show that lateral deflections of the terminating O atom are negligible. This allows a detailed discussion of the fundamental imaging mechanisms in high-resolution NC-AFM experiments. With its structural rigidity, its chemically passivated state, and a high electron density at the apex, we identify the main characteristics of the O-terminated Cu tip, making it a highly attractive complementary probe for the characterization of organic nanostructures on surfaces.},
   author = {Harry Mönig and Diego R. Hermoso and Oscar Díaz Arado and Milica Todorović and Alexander Timmer and Simon Schüer and Gernot Langewisch and Rubén Pérez and Harald Fuchs},
   doi = {10.1021/ACSNANO.5B06513/ASSET/IMAGES/NN-2015-06513T_M003.GIF},
   issn = {1936086X},
   issue = {1},
   journal = {ACS Nano},
   keywords = {Contrast mechanism,Copper oxide,High-resolution imaging,Noncontact atomic force microscopy,Organic molecules,Tip functionalization},
   month = {11},
   pages = {1201-1209},
   publisher = {American Chemical Society},
   title = {Submolecular imaging by noncontact atomic force microscopy with an oxygen atom rigidly connected to a metallic probe},
   volume = {10},
   url = {https://pubs.acs.org/doi/full/10.1021/acsnano.5b06513},
   year = {2016}
}
@article{Walen2015,
   abstract = {Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed clean surface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30°from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, derived using a limited cluster expansion based on density functional theory energetics. Models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.},
   author = {Holly Walen and Da Jiang Liu and Junepyo Oh and Hyunseob Lim and J. W. Evans and Yousoo Kim and P. A. Thiel},
   doi = {10.1063/1.4922929},
   issn = {00219606},
   issue = {1},
   journal = {Journal of Chemical Physics},
   month = {7},
   publisher = {American Institute of Physics Inc.},
   title = {Self-organization of S adatoms on Au(111): √3R30°rows at low coverage},
   volume = {143},
   url = {https://www.researchgate.net/publication/279941463_Self-organization_of_S_adatoms_on_Au111_3R30_rows_at_low_coverage},
   year = {2015}
}
@article{Bartels1997a,
   abstract = {A reliable procedure for controlled vertical transfer of single CO molecules between a Cu(111) surface and a scanning tunneling microscope tip and vice versa is demonstrated. It is shown that with a tip having a single CO molecule at its apex, chemical contrast is achieved allowing distinction of adsorbed CO molecules and oxgen atoms, which look very similar to the bare metal tip. © 1997 American Institute of Physics.},
   author = {L. Bartels and G. Meyer and K. H. Rieder},
   doi = {10.1063/1.119503},
   issn = {0003-6951},
   issue = {2},
   journal = {Applied Physics Letters},
   month = {7},
   pages = {213-215},
   publisher = {AIP Publishing},
   title = {Controlled vertical manipulation of single CO molecules with the scanning tunneling microscope: A route to chemical contrast},
   volume = {71},
   url = {/aip/apl/article/71/2/213/67819/Controlled-vertical-manipulation-of-single-CO},
   year = {1997}
}
@article{Lee1999,
   abstract = {A scanning tunneling microscope (STM) was used to manipulate the bonding of a carbon monoxide (CO) molecule and to analyze the structure and vibrational properties of individual products. Individual iron (Fe) atoms were evaporated and coadsorbed with CO molecules on a silver (110) surface at 13 kelvin. A CO molecule was transferred from the surface to the STM tip and bonded with an Fe atom to form Fe(CO). A second CO molecule was similarly transferred and bonded with Fe(CO) to form Fe(CO)2. Controlled bond formation and characterization at the single-bond level probe chemistry at the spatial limit.},
   author = {H. J. Lee and W. Ho},
   doi = {10.1126/SCIENCE.286.5445.1719/ASSET/C348FB04-C84E-416B-9F6C-ED5DC21CE916/ASSETS/GRAPHIC/SE4798049004.JPEG},
   issn = {00368075},
   issue = {5445},
   journal = {Science},
   month = {11},
   pages = {1719-1722},
   publisher = {American Association for the Advancement of Science},
   title = {Single-bond formation and characterization with a scanning tunneling microscope},
   volume = {286},
   url = {https://www.science.org/doi/10.1126/science.286.5445.1719},
   year = {1999}
}
@article{Lagoute2004,
   abstract = {Low-temperature scanning tunneling microscopy at 7 K is used to study the adsorption and manipulation of single pentacene molecules on Cu(111). Controlled lateral translations of the molecule are performed along different high-symmetry directions of the substrate via attractive tip-molecule interactions. By means of a detailed site-mapping technique combining lateral manipulations of the molecule and of native substrate adatoms we determine the adsorptive configuration of the aromatic molecule. We find a planar adsorption geometry with the long molecular axis aligned with the close-packed Cu atom rows and the benzene units centered over hexagonal close-packed hollow sites of the substrate. The interaction of organic molecules with solid surfaces is of central importance for various issues in science and technology. These include, for example, surface chemistry and catalysis, 1 basic steps during organic semiconductor layer growth, 2 and the concept of molecular electronics 3 which aims at utilizing single molecules as functional building blocks with defined switching, sensing, or conduction properties. Especially with respect to the latter issue, low-temperature scanning tunneling microscopy (LT-STM) provides an excellent experimental approach since it allows to address, to characterize, and to manipulate 4,5 single adsorbed atoms and molecules with atomic-scale precision. In this work, we employ LT-STM to explore the detailed adsorptive configuration of single pentacene molecules on the close-packed transition metal surface Cu(111). Pentacene C 22 H 14 is a linear polycyclic hydrocarbon and has recently gained ample attention due to its promising bulk properties as an organic semiconductor. 6 By means of a detailed site-mapping technique which combines lateral manipulations of the molecule and of native substrate adatoms we perform a straightforward determination of the energetically preferred molecular adsorption site. It is demonstrated that LT-STM-based manipulation provides a powerful surface science tool which facilitates a direct real-space determination of the overall ad-sorption geometry of single organic molecules. The experiments were performed with a homebuilt ultrahigh-vacuum (UHV) LT-STM system at a temperature of 7 K. A chemomechanically polished Cu(111) crystal was cleaned in situ by repeated Ne sputtering at 1 keV and an-nealing at 700 K. Molecules were deposited in UHV by thermal sublimation of pentacene after carefully degassing the crystalline source material. Cut Pt-Ir tips were used for the present experiments. Prior to the measurements the final tip condition was optimized by controlled tip-sample contact at 7 K. The metallic character of the tip was checked by spec-troscopic measurements of the differential tunneling conduc-tance dI / dV verifying inherent electronic features of the Cu(111) surface such as the onset of the surface-state band 7 and a smooth variation of the local density of states within the pseudogap of the projected Cu bulk bands. 8 Respective tunneling voltages indicated in the following refer to the sample bias with respect to the tip. Figure 1(a) shows a constant-current STM image of an extended surface area 560 Å 336 Å after depositing 6 10 12 molecules per cm 2 at room temperature and subsequently cooling the specimen to the measuring temperature of 7 K. Single pentacene molecules appear as rodlike protru-sions with lobes of enhanced tunneling conductance located at the ends. The wave pattern between the molecules arises from the Friedel oscillations of the Cu(111) surface-state electrons. As evident, no pronounced tendency of molecular clustering is observed which indicates the absence of appreciable attractive intermolecular interactions. This characteristic is advantageous for the present purpose, since it permits room-temperature sample preparation for experiments fo-cused on single-molecule spectroscopy and manipulation. In contrast to the behavior found on homogeneous terraces, surface defects like steps act as effective sites for molecular aggregation. In detail, we find that quasiperiodic arrays of pentacene molecules with their long axis parallel to the step direction are formed preferably at the upper edge of mon-atomic Cu steps. This specific behavior in heterogeneous nucleation, which was similarly observed for benzene molecules on Cu(111), 9 is likely to arise from the interaction of adsorption-induced molecular dipoles 10,11 with the intrinsic step dipoles present at a metal surface (the latter are due to the well known Smoluchowski effect of electron-charge smoothing 12). At the same time, it indicates a considerable degree of surface diffusion of single pentacene molecules on Cu(111) at room temperature. Turning back to the molecular adsorption on homogeneous terraces, a comparison between the STM image in (b) and the atomic corrugation of bare Cu(111) in (c) shows that the molecules strictly align with the close-packed Cu atom rows along the three equivalent 110 in-plane directions. The characteristic appearance of the molecule when imaged with a bare metallic tip is shown in Fig. 1(d). The diagram on the lower right details the corresponding constant-current profile measured along the long molecular symmetry axis at a tunneling current of 1 nA and a bias of 460 mV. The spacing of the observed double-lobe structure extracted from a large set of STM images is 9.8± 0.2 Å which is close to the separation of the outermost benzene rings of the free mol},
   author = {Jérôme Lagoute and Kiyoshi Kanisawa and Stefan Fölsch},
   doi = {10.1103/PhysRevB.70.245415},
   issue = {24},
   journal = {PHYSICAL REVIEW B},
   keywords = {6837Ef,6847De,8237Gk,number(s): 6843Fg},
   pages = {245415},
   title = {Manipulation and adsorption-site mapping of single pentacene molecules on Cu(111)},
   volume = {70},
   year = {2004}
}
@article{Nishino2005,
   abstract = {A fullerene molecular tip was used to detect electron tunneling from a single porphyrin molecule. Electron tunneling was found to occur locally from an electron-donating moiety of the porphyrin to the fullerene through charge-transfer interaction between them. In addition, electron tunneling within the single fullerene-porphyrin pair exhibited rectifying behavior in which electrons can be driven only at the direction from the porphyrin to the fullerene. It is demonstrated that localized electron tunneling enables us to spatially visualize the frontier orbital of the porphyrin involved in electron tunneling. In addition, rectification demonstrates that the fullerene-porphyrin pair constitutes a molecular rectifier. We believe that molecular tips bring insight into intermolecular electron transmission toward realization of molecular electronics as shown here. © 2005 by The National Academy of Sciences of the USA.},
   author = {Tomoaki Nishino and Takashi Ito and Yoshio Umezawa},
   doi = {10.1073/PNAS.0408474102},
   issn = {00278424},
   issue = {16},
   journal = {Proceedings of the National Academy of Sciences of the United States of America},
   keywords = {Molecular electronics,Nanoscience,Scanning tunneling microscopy},
   month = {4},
   pages = {5659},
   pmid = {15809427},
   publisher = {National Academy of Sciences},
   title = {From the Cover: A fullerene molecular tip can detect localized and rectified electron tunneling within a single fullerene–porphyrin pair},
   volume = {102},
   url = {/pmc/articles/PMC556290/ /pmc/articles/PMC556290/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC556290/},
   year = {2005}
}
@article{Repp2006,
   abstract = {A covalent bond between an individual pentacene molecule and a gold atom was formed by means of single-molecule chemistry inside a scanning tunneling microscope junction. The bond formation is reversible, and different structural isomers can be produced. The single-molecule synthesis was done on ultrathin insulating films that electronically isolated the reactants and products from their environment. Direct imaging of the orbital hybridization upon bond formation provides insight into the energetic shifts and occupation of the molecular resonances.},
   author = {Jascha Repp and Gerhard Meyer and Sami Paavilainen and Fredrik E. Olsson and Mats Persson},
   doi = {10.1126/SCIENCE.1126073},
   issn = {1095-9203},
   issue = {5777},
   journal = {Science (New York, N.Y.)},
   keywords = {Gerhard Meyer,Jascha Repp,MEDLINE,Mats Persson,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,PubMed Abstract,doi:10.1126/science.1126073,pmid:16728636},
   month = {5},
   pages = {1196-1199},
   pmid = {16728636},
   publisher = {Science},
   title = {Imaging bond formation between a gold atom and pentacene on an insulating surface},
   volume = {312},
   url = {https://pubmed.ncbi.nlm.nih.gov/16728636/},
   year = {2006}
}
@article{Liljeroth2007,
   abstract = {The bistability in the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine molecules constitutes a two-level system that was manipulated and probed by low-temperature scanning tunneling microscopy. When adsorbed on an ultrathin insulating film, the molecules can be switched in a controlled fashion between the two states by excitation induced by the inelastic tunneling current. The tautomerization reaction can be probed by resonant tunneling through the molecule and is expressed as considerable changes in the conductivity of the molecule. We also demonstrated a coupling of the switching process so that the charge injection in one molecule induced tautomerization in an adjacent molecule.},
   author = {Peter Liljeroth and Jascha Repp and Gerhard Meyer},
   doi = {10.1126/SCIENCE.1144366},
   issn = {1095-9203},
   issue = {5842},
   journal = {Science (New York, N.Y.)},
   keywords = {Gerhard Meyer,Jascha Repp,MEDLINE,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-U.S. Gov't,Peter Liljeroth,PubMed Abstract,Research Support,doi:10.1126/science.1144366,pmid:17761878},
   month = {8},
   pages = {1203-1206},
   pmid = {17761878},
   publisher = {Science},
   title = {Current-induced hydrogen tautomerization and conductance switching of naphthalocyanine molecules},
   volume = {317},
   url = {https://pubmed.ncbi.nlm.nih.gov/17761878/},
   year = {2007}
}
@article{Schull2009,
   abstract = {The charge flow from a single C60 molecule to another one has been probed. The conformation and electronic states of both molecules on the contacting electrodes have been characterized using a cryogenic scanning tunneling microscope. While the contact conductance of a single molecule between two Cu electrodes can vary up to a factor of 3 depending on electrode geometry, the conductance of the C60-C60 contact is consistently lower by 2 orders of magnitude. First-principles transport calculations reproduce the experimental results, allow a determination of the actual C60-C60 distances, and identify the essential role of the intermolecular link in bi- and trimolecular chains. © 2009 The American Physical Society.},
   author = {Guillaume Schull and Thomas Frederiksen and Mads Brandbyge and Richard Berndt},
   doi = {10.1103/PHYSREVLETT.103.206803},
   issn = {0031-9007},
   issue = {20},
   journal = {Physical Review Letters},
   keywords = {C-60,CONDUCTANCE,MICROSCOPY,TIPS,TRANSPORT,WIRES},
   month = {11},
   pages = {206803},
   pmid = {20365999},
   publisher = {American Physical Society},
   title = {Passing Current  through Touching Molecules},
   volume = {103},
   url = {https://orbit.dtu.dk/en/publications/passing-current-through-touching-molecules},
   year = {2009}
}
@article{Mohn2010,
   abstract = {We report on the formation of a metal-molecule complex that can be used as a molecular switch. Using a cryogenic scanning tunneling microscope, a covalent bond was formed reversibly between a gold atom and a perylene-3,4,9,10-tetracarboxylic dianhydride molecule supported by a thin insulating film. The bonded and the nonbonded state of the complex were found to be associated with different charge states, and the switching between the two states was accompanied by a considerable change in the tunneling current. Atomic force microscopy molecular imaging was employed to determine precisely the atomic structure of the complex, and the experimental results were corroborated by density functional theory calculations. The concept of using single atoms and molecules as memory elements or switches in electronic devices was established long ago [1]. Scanning tunneling microscopy (STM) has been used to investigate and identify promising molecular switches [2-7], due to its capabilities to image and manipulate adsorbates on the atomic scale. Atomic manipulation was also performed with noncontact atomic force microscopy (AFM) a few years ago [8-10], and most recently it was shown that atomic resolution can be achieved on organic molecules by functionalizing an AFM tip with a suitable atomic termination [11]. STM has repeatedly been used for the making and breaking of single chemical bonds between metal atoms and molecules [12-16] and between molecules [17,18]. Those previous examples of bond formation, however, were not suited as molecular switches, because they required complex protocols of STM tip positioning, voltage pulses or current injection, involved various possible configurations of the constituents, or resulted in only a slight change of the tunneling current. Furthermore, in the examples mentioned it was not possible to switch between the bonded and the nonbonded state in a reliable and directed manner (mean-ing that the system can be switched with certainty to the desired state). In this Letter, we present a molecular switch that is based on the reversible bond formation between a Au adatom and an organic admolecule [perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA)] on a thin NaCl film supported by a Cu substrate. The switching between the bonded and the nonbonded configuration was accompanied by a change in the tunneling current of about 2 orders of magnitude. The bond making and breaking were controlled simply by applying voltage pulses of according polarity and did not require an exact tip movement or positioning over a particular part of the molecule. The operation and electronic characterization of the switch were performed with STM, whereas the exact geometry of the complex was deduced from atomically resolved AFM images. The experimental results were combined with density functional theory (DFT) calculations to gain further insight into the details of the bonding geometry and the electronic structure of the complex. Our results strongly suggest that the reliability and directed manner of the switching are based on the fact that a change of the charge state of the complex occurs upon bond formation. The electronic decoupling provided by the insulating NaCl film is crucial to ensure the stability of the different charge states [5,19]. Our experiments were performed with a homebuilt combined STM/AFM system using a qPlus tuning fork sensor [20] operated in UHV and at low temperature (T sample % 5 K). NaCl was evaporated onto a clean Cu(111) single-crystal surface at T sample % 270 K, leading to the formation of (100)-terminated islands of mostly two atomic layers in thickness, denoted as NaClð2MLÞ=Cuð111Þ [21]. Low cov-erages of Au atoms and PTCDA molecules were then evaporated in situ at T sample % 10 K. The tip preparation techniques described in Ref. [11] were employed to obtain well-defined tips for our STM and AFM investigations. In Fig. 1, the reversible switching of a Au-PTCDA complex on NaClð2MLÞ=Cuð111Þ is shown. First of all, we used vibrational excitation by inelastic electron tunnel-ing into a negatively charged Au adatom (identified in the STM image by its characteristic surrounding depression [19]) to successively move it towards a PTCDA molecule. Once the Au À and the PTCDA had been positioned close enough to each other [Fig. 1(a)], it was possible to switch the complex to a different state by ramping the sample bias voltage to V ¼ À1:5 V [Fig. 1(b)]. The switching process was found to be completely reversible [Fig.},
   author = {Fabian Mohn and Jascha Repp and Leo Gross and Gerhard Meyer and Matthew S Dyer and Mats Persson},
   doi = {10.1103/PhysRevLett.105.266102},
   issue = {26},
   journal = {Physical Review Letters},
   keywords = {6837Ps,7115Mb,8237Gk,numbers: 6837Ef},
   pages = {266102},
   title = {Reversible Bond Formation in a Gold-Atom-Organic-Molecule Complex as a Molecular Switch},
   volume = {105},
   year = {2010}
}
@article{Cheng2011,
   abstract = {High-resolution scanning tunneling microscope images of iron phthalocyanine and zinc phthalocyanine molecules on Au(111) have been obtained using a functionalized tip of a scanning tunneling microscope (STM), and show rich intramolecular features that are not observed using clean tips. Ab initio density functional theory calculations and extended Hückel theory calculations revealed that the imaging of detailed electronic states is due specifically to the decoration of the STM tip with O2. The detailed structures are differentiated only when interacting with the highly directional orbitals of the oxygen molecules adsorbed on a truncated, [111]-oriented tungsten tip. Our results indicate a method for increasing the resolution in generic scans and thus, have potential applications in fundamental research based on high-resolution electronic states of molecules on metals, concerning, for example, chemical reactions, and catalysis mechanisms. © 2011 Tsinghua University Press and Springer-Verlag Berlin Heidelberg.},
   author = {Zhihai Cheng and Shixuan Du and Wei Guo and Li Gao and Zhitao Deng and Nan Jiang and Haiming Guo and Hao Tang and H. J. Gao},
   doi = {10.1007/S12274-011-0108-Y/METRICS},
   issn = {19980000},
   issue = {6},
   journal = {Nano Research},
   keywords = {High-resolution scanning tunneling microscope (STM,density functional theory calculation,functionalized STM tip,metal phthalocyanines,molecular orbital},
   month = {2},
   pages = {523-530},
   publisher = {Tsinghua University Press},
   title = {Direct imaging of molecular orbitals of metal phthalocyanines on metal surfaces with an O2-functionalized tip of a scanning tunneling microscope},
   volume = {4},
   url = {https://link.springer.com/article/10.1007/s12274-011-0108-y},
   year = {2011}
}
@misc{AtomBoy,
   title = {IBM Research, A Boy and His Atom},
   url = {https://www.youtube.com/watch?v=oSCX78-8-q0},
   year = {2013}
}
@article{Kobayashi1989,
   abstract = {The tunnel current in the scanning tunneling microscopy (STM) of graphite is numerically simulated using the bonding and the antibonding orbitals of H2 as a model of the tip. The normal image of the triangular lattice is obtained by the bonding orbital. But the image by the antibonding orbital is very much distorted; in an extreme case, it is the shape of linear chain which is often observed in the actual STM. It is caused by the special wave function of graphite near the Fermi level and the interference of the current contributed by the two tip atoms. © 1989, THE PHYSICAL SOCIETY OF JAPAN. All rights reserved.},
   author = {Katsuyoshi Kobayashi and Masaru Tsukada},
   doi = {10.1143/JPSJ.58.2238},
   issn = {13474073},
   issue = {7},
   journal = {Journal of the Physical Society of Japan},
   pages = {2238-2241},
   title = {Effect of microscopic tip electronic state on stm image of graphite},
   volume = {58},
   year = {1989}
}
@article{MasaruTsukada1991,
   abstract = {The current image and the tunnel conductance in the scanning tunneling microscopy/spectroscopy (STM/STS) of graphite are simulated by the first-principles local density functional calculation of the electronic states. As models of the tip, W10[111], W14[110], W13[110] and Pt10[111] clusters are used. For the tips with a single apex atom, normal STM images are obtained. However, abnormal images are generated by the removal of the apex atom. STS spectra are changed in a systematic way by the apex angle of the tip. The negative differential resistance observed in the STS of the Si(111) 3× 3-B/defect surface is reproduced by the theoretical simulation with the cluster models of the tip. © 1991.},
   author = {Masaru Tsukada and Katsuyoshi Kobayashi and Nobuyuki Isshiki},
   doi = {10.1016/0039-6028(91)90234-J},
   issn = {0039-6028},
   issue = {1-3},
   journal = {Surface Science},
   month = {2},
   pages = {12-17},
   publisher = {North-Holland},
   title = {Effect of tip atomic and electronic structure on scanning tunneling microscopy/spectroscopy},
   volume = {242},
   year = {1991}
}
@article{Kobayashi2006,
   abstract = {The structure-dependent edge state of graphite is investigated by ultra-high-vacuum scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) observations. On a hydrogenated zigzag edge, bright spots assigned to edge states are observed together with a (sqrt(3) × sqrt(3)) R30° superlattice. The STS measurement shows that the bright spots originate from a peak near the Fermi level at VS=-30 mV. In contrast, on a hydrogenated armchair edge, such bright spots are not observed. Even in the hydrogenated armchair edge, however, edge states are observed at defect points, where zigzag edges are partially created. The distribution of the edge states is dependent on the detailed structure of the defect. © 2006 Elsevier B.V. All rights reserved.},
   author = {Yousuke Kobayashi and Koichi Kusakabe and Ken ichi Fukui and Toshiaki Enoki},
   doi = {10.1016/J.PHYSE.2006.03.058},
   issn = {1386-9477},
   issue = {1-2},
   journal = {Physica E: Low-dimensional Systems and Nanostructures},
   keywords = {Edge state,Graphene sheet,STM,STS},
   month = {8},
   pages = {678-681},
   publisher = {North-Holland},
   title = {STM/STS observation of peculiar electronic states at graphite edges},
   volume = {34},
   year = {2006}
}
@article{Kwapiski2010,
   abstract = {The influence of STM tip electronic states on the electron transport through an atomic object on a surface is studied both experimentally and theoretically.Wepresent scanning tunnelling spectroscopy (STS) experimental results on Ag islands with two, blunt and sharp, STM tips. The data taken with the sharp tip have an additional peak at positive bias which corresponds to the tip apex atom state. Weshow that sudden tip sharpness variation and corresponding I(V) characteristic change may help to differentiate between electronic states of the tip and the sample. The experimental data are discussed and compared with theoretical calculations performed for two different tips. The current and differential conductance calculations are carried out by means of the Green's function technique and a tight-binding Hamiltonian. © 2010 Elsevier B.V. All rights reserved.},
   author = {T. Kwapiński and M. Jałochowski},
   doi = {10.1016/J.SUSC.2010.06.026},
   issn = {0039-6028},
   issue = {19-20},
   journal = {Surface Science},
   keywords = {Differential conductance,Green's function,STM,Tunneling spectroscopy},
   month = {9},
   pages = {1752-1756},
   publisher = {North-Holland},
   title = {Signature of tip electronic states on tunneling spectra},
   volume = {604},
   year = {2010}
}
@article{Passoni2009,
   abstract = {Scanning tunneling spectroscopy (STS) provides a unique method for the investigation of the local surface-projected electron density of states (DOS), mostly for its capability of reaching atomic resolution. Such information is contained in a nonobvious way in STS data, and a proper understanding of the overall features of the system (sample+tip) is mandatory in order to obtain quantitative information. Several approaches have been proposed in the literature to tackle this problem. A common feature of these methods is that they are mostly based on a one-dimensional (1D) WKB description of the tunneling current. We present a critical analysis and an extension of the methods so far proposed, with the main goal of applying the results to STS experimental data. This study has been conducted by modeling the tip-sample system within the frame of 1D-WKB theory, investigating key open issues, such as the estimation of required but usually experimentally unknown parameters such as the tip-sample distance and the role played by the presence of a nonconstant tip local DOS on STS data. This investigation allows us to ascertain strengths and weaknesses of the existing methods and leads to an optimized and improved strategy which we propose for the analysis of STS data. We tested our conclusions on STS measurements of the Si (111) -7×7 and Au(111) surfaces, acquired with W and Cr tips. © 2009 The American Physical Society.},
   author = {M. Passoni and F. Donati and A. Li Bassi and C. S. Casari and C. E. Bottani},
   doi = {10.1103/PHYSREVB.79.045404},
   issn = {10980121},
   issue = {4},
   journal = {Physical Review B - Condensed Matter and Materials Physics},
   month = {1},
   pages = {045404},
   publisher = {American Physical Society},
   title = {Recovery of local density of states using scanning tunneling spectroscopy},
   volume = {79},
   url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.79.045404},
   year = {2009}
}
@article{Klyachko2000,
   abstract = {The formation of cluster images in a scanning tunneling microscope (STM) has been modeled using isolate C60 molecules deposited on top of crystalline monolayers of C60 on Ge(100) and Si(100) containing vacancies. C60 molecules occupy positions above vacancies and depending on the dimensions of the latter protrude to a different height above the surface. A simple model of the image formation is suggested and the variation of the shape of C60 molecules in STM images as a function of their apparent height is explained by the convolution of their images with that of the tip and by scattering of tunneling electrons on vacancies below C60 molecules.},
   author = {D. Klyachko and D. M. Chen},
   doi = {10.1016/S0039-6028(99)01110-3},
   issn = {0039-6028},
   issue = {1-2},
   journal = {Surface Science},
   month = {2},
   pages = {98-102},
   publisher = {North-Holland},
   title = {Cluster shapes in STM images of isolate clusters and cluster materials},
   volume = {446},
   year = {2000}
}
@article{Hofer1998,
   abstract = {In view of interpreting images obtained by scanning tunnelling microscopes with perturbation methods the electronic properties of the STM tip are of utmost importance. We have calculated with a first-principles method the spin-resolved electronic structure of a tungsten (100) surface with different apex atoms. The results presented show that the electronic states in the vacuum region are in each case considered a mixture of states with s-, p- and d-type symmetries. The relevance of this result for STM imaging and a calculation of the tunnelling current by numerical methods is discussed briefly. © 1998 Taylor & Francis Group, LLC.},
   author = {W. A. Hofer and J. Redinger},
   doi = {10.1080/13642819808206754},
   issn = {13642812},
   issue = {5-6},
   journal = {Philosophical Magazine B: Physics of Condensed Matter; Statistical Mechanics, Electronic, Optical and Magnetic Properties},
   pages = {519-525},
   title = {Electronic structure of a realistic STM tip: The role of different apex atoms},
   volume = {78},
   url = {https://www.tandfonline.com/action/journalInformation?journalCode=tphb20},
   year = {1998}
}
@article{Garcia1993,
   author = {N. Garcia and Vu Thien Binh and S.T. Purcell},
   doi = {10.1016/0167-2584(93)90226-9},
   issn = {0167-2584},
   issue = {3},
   journal = {Surface Science Letters},
   month = {8},
   pages = {L884-L886},
   publisher = {North-Holland},
   title = {Structurally induced FEES from nanotips: implications for scanning tunneling spectroscopy},
   volume = {293},
   year = {1993}
}

@article{Palotas2011,
   abstract = {Based on a simple model for spin-polarized scanning tunneling spectroscopy (SP-STS), we study how tip magnetization and electronic structure affects the differential conductance (dI/dV) tunneling spectrum of an Fe(001) surface. We take into account energy dependence of the vacuum decay of electron states and tip electronic structure either using an ideal model or based on ab initio electronic structure calculation. In the STS approach, topographic and magnetic contributions to dI/dV can clearly be distinguished and analyzed separately. Our results suggest that the sensitivity of STS on a magnetic sample can be tuned and even enhanced by choosing the appropriate magnetic tip and bias set point, and the effect is governed by the effective spin polarization. © 2011 American Physical Society.},
   author = {Krisztián Palotás and Werner A. Hofer and László Szunyogh},
   doi = {10.1103/PHYSREVB.83.214410/FIGURES/4/MEDIUM},
   issn = {10980121},
   issue = {21},
   journal = {Physical Review B - Condensed Matter and Materials Physics},
   month = {6},
   pages = {214410},
   publisher = {American Physical Society},
   title = {Theoretical study of the role of the tip in enhancing the sensitivity of differential conductance tunneling spectroscopy on magnetic surfaces},
   volume = {83},
   url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.83.214410},
   year = {2011}
}
