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We present the design and implementation of a side entry laser system designed for an ultra-high vacuum scanning transmission electron microscope. This system uses a versatile probe design enclosed in a vacuum envelope such that parts can be easily aligned, modified, or exchanged without disturbing the vacuum. The system uses a mirror mounted on the sample holder such that the sample can be illuminated without being tilted. Notably the mirror can be removed and replaced with an ablation target and a higher power laser used to ablate material directly onto the sample. We argue that new capabilities hold the potential to transform the electron microscope from an analysis tool towards a more flexible synthesis system, where atomic scale fabrication and atom-by-atom experiments can be performed.

Efforts aimed at scaling fabrication processes to the level of single atoms, dubbed atom-by-atom fabrication or atomic fabrication, invariably encounter the obstacle of atomic scale cleanliness. When considering atomic fabrication, cleanliness of the base material and purity of the source reservoir from which atomic structures will be built are invariable constraints imposed by laws of physics and chemistry. As obvious as such statements may be, and regardless of the inevitable consequences for successful atomic fabrication, there is a poignant lack of understanding of the "dirt" (contamination/impurities). Here, we examine hydrocarbon contamination on graphene. Graphene has formed the base substrate for many e-beam-based atomic fabrication studies and many strategies for cleaning graphene have been presented in the literature. One popular method is heating to high temperatures (>500 {\deg}C). It is usually inferred that volatile hydrocarbons evaporate into the microscope vacuum system leaving behind pristine graphene. Here, we show through direct image intensity analysis that what appears to be clean graphene can be coated with a thin layer of dynamically diffusing hydrocarbons. This result holds significant implications for approaches to e-beam based atomic fabrication, updates the conceptual model of e-beam induced hydrocarbon deposition, and may extend to hot surfaces generally.

Microscopy, in particular scanning probe and electron microscopy, has been pivotal in improving our understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most research characterization labs and facilities. However, traditional microscopy operations are still limited largely by a human-centric click-and-go paradigm utilizing vendor-provided software, which necessarily limits the scope, utility, efficiency, effectiveness, and at times reproducibility of microscopy experiments. Here, we develop a coupled hardware-software platform that consists of a field-programmable gate array (FPGA) device, with LabView-built customized acquisition scripts, along with a software package termed AEcroscoPy (short for Automated Experiments in Microscopy driven by Python) that overcome these limitations and provide the necessary abstractions towards full automation of microscopy platforms. The platform works across multiple vendor devices on scanning probe microscopes and scanning transmission electron microscopes. It enables customized scan trajectories, processing functions that can be triggered locally or remotely on processing servers, user-defined excitation waveforms, standardization of data models, and completely seamless operation through simple Python commands to enable a plethora of microscopy experiments to be performed in a reproducible, automated manner. This platform can be readily coupled with existing machine learning libraries as well as simulations, to provide automated decision-making and active theory-experiment optimization loops to turn microscopes from characterization tools to instruments capable of autonomous model refinement and physics discovery., Comment: 19 pages, 9 figures

Color centers in diamond play a central role in the development of quantum photonic technologies, and their importance is only expected to grow in the near future. For many quantum applications, high collection efficiency from individual emitters is required, but the refractive index mismatch between diamond and air limits the optimal collection efficiency with conventional diamond device geometries. While different out-coupling methods with near-unity efficiency exist, many have yet to be realized due to current limitations in nanofabrication methods, especially for mechanically hard materials like diamond. Here, we leverage electron-beam-induced etching to modify Sn-implanted diamond quantum microchiplets containing integrated waveguides with width and thickness of 280 nm and 200 nm, respectively. This approach allows for simultaneous high-resolution imaging and modification of the host matrix with an open geometry and direct writing. When coupled with the cathodoluminescence signal generated from the electron-emitter interactions, we can monitor the enhancement of the quantum emitters in real-time with nanoscale spatial resolution. The operando measurement and manipulation of single photon emitters demonstrated here provides a new foundation for the control of emitter-cavity interactions in integrated quantum photonics., Comment: 7 pages, 4 figures

Directed atomic fabrication using an aberration-corrected scanning transmission electron microscope (STEM) opens new pathways for atomic engineering of functional materials. In this approach, the electron beam is used to actively alter the atomic structure through electron beam induced irradiation processes. One of the impediments that has limited widespread use thus far has been the ability to understand the fundamental mechanisms of atomic transformation pathways at high spatiotemporal resolution. Here, we develop a workflow for obtaining and analyzing high-speed spiral scan STEM data, up to 100 fps, to track the atomic fabrication process during nanopore milling in monolayer MoS2. An automated feedback-controlled electron beam positioning system combined with deep convolution neural network (DCNN) was used to decipher fast but low signal-to-noise datasets and classify time-resolved atom positions and nature of their evolving atomic defect configurations. Through this automated decoding, the initial atomic disordering and reordering processes leading to nanopore formation was able to be studied across various timescales. Using these experimental workflows a greater degree of speed and information can be extracted from small datasets without compromising spatial resolution. This approach can be adapted to other 2D materials systems to gain further insights into the defect formation necessary to inform future automated fabrication techniques utilizing the STEM electron beam.

Focused electron beam induced deposition (FEBID) is a direct write technique for depositing materials on a support substrate akin to 3D printing with an electron beam (e-beam). Opportunities exist for merging this existing technique with aberration-corrected scanning transmission electron microscopy to achieve molecular- or atomic-level spatial precision. Several demonstrations have been performed using graphene as the support substrate. A common challenge that arises during this process is e-beam-induced hydrocarbon deposition, suggesting greater control over the sample environment is needed. Various strategies exist for cleaning graphene in situ. One of the most effective methods is to rapidly heat to high temperatures, e.g., 600 C or higher. While this can produce large areas of what appears to be atomically clean graphene, mobile hydrocarbons can still be present on the surfaces. Here, we show that these hydrocarbons are primarily limited to surface migration and demonstrate an effective method for interrupting the flow using e-beam deposition to form corralled hydrocarbon regions. This strategy is effective for maintaining atomically clean graphene at high temperatures where hydrocarbon mobility can lead to substantial accumulation of unwanted e-beam deposition.

Atomic-scale fabrication is an outstanding challenge and overarching goal for the nanoscience community. The practical implementation of moving and fixing atoms to a structure is non-trivial considering that one must spatially address the positioning of single atoms, provide a stabilizing scaffold to hold structures in place, and understand the details of their chemical bonding. Free-standing graphene offers a simplified platform for the development of atomic-scale fabrication and the focused electron beam in a scanning transmission electron microscope can be used to locally induce defects and sculpt the graphene. In this scenario, the graphene forms the stabilizing scaffold and the experimental question is whether a range of dopant atoms can be attached and incorporated into the lattice using a single technique and, from a theoretical perspective, we would like to know which dopants will create technologically interesting properties. Here, we demonstrate that the electron beam can be used to selectively and precisely insert a variety of transition metal atoms into graphene with highly localized control over the doping locations. We use first-principles density functional theory calculations with direct observation of the created structures to reveal the energetics of incorporating metal atoms into graphene and their magnetic, electronic, and quantum topological properties.

Chromium atoms in graphene have been proposed to exhibit magnetic moments and spin-selective conducting states depending on the local bonding geometry within the graphene structure, which could lead to interesting applications in spintronics. Despite this interest, there are few direct experimental reports of Cr dopants in graphene even though it is theorized to be stable. Here, we demonstrate the introduction of single Cr dopant atoms into the graphene lattice and onto graphene edges through the controlled use of a focused electron beam in a scanning transmission electron microscope. We show local control of doping locations and when coupled with targeted in situ milling during scanning of the e-beam, these strategies demonstrate an important component of the fabrication of tailored nanostructured devices in the electron microscope. The approach is validated with first principles calculations to understand synthesis pathways during fabrication and reveal the energetics and local properties of Cr atoms embedded in graphene; e.g., Cr doping can convert graphene into a magnetic and semiconducting material, which suggests Cr-doped graphene can be used as a building block for potential electronic devices and a means to construct them.

Graphene is of great scientific interest due to a variety of unique properties such as ballistic transport, spin selectivity, the quantum hall effect, and other quantum properties. Nanopatterning and atomic scale modifications of graphene are expected to enable further control over its intrinsic properties, providing ways to tune the electronic properties through geometric and strain effects, introduce edge states and other local or extended topological defects, and sculpt circuit paths. The focused beam of a scanning transmission electron microscope (STEM) can be used to remove atoms, enabling milling, doping, and deposition. Utilization of a STEM as an atomic scale fabrication platform is increasing; however, a detailed understanding of beam-induced processes and the subsequent cascade of aftereffects is lacking. Here, we examine the electron beam effects on atomically clean graphene at a variety of temperatures ranging from 400 to 1000 C. We find that temperature plays a significant role in the milling rate and moderates competing processes of carbon adatom coalescence, graphene healing, and the diffusion (and recombination) of defects. The results of this work can be applied to a wider range of 2D materials and introduce better understanding of defect evolution in graphite and other bulk layered materials.

Optimization of experimental materials synthesis and characterization through active learning methods has been growing over the last decade, with examples ranging from measurements of diffraction on combinatorial alloys at synchrotrons, to searches through chemical space with automated synthesis robots for perovskites. In virtually all cases, the target property of interest for optimization is defined apriori with limited human feedback during operation. In contrast, here we present the development of a new type of human in the loop experimental workflow, via a Bayesian optimized active recommender system (BOARS), to shape targets on the fly, employing human feedback. We showcase examples of this framework applied to pre-acquired piezoresponse force spectroscopy of a ferroelectric thin film, and then implement this in real time on an atomic force microscope, where the optimization proceeds to find symmetric piezoresponse amplitude hysteresis loops. It is found that such features appear more affected by subsurface defects than the local domain structure. This work shows the utility of human-augmented machine learning approaches for curiosity-driven exploration of systems across experimental domains. The analysis reported here is summarized in Colab Notebook for the purpose of tutorial and application to other data: https://github.com/arpanbiswas52/varTBO, Comment: 7 figures in main text, 3 figures in Supp Material

The engineering of quantum materials requires the development of tools able to address various synthesis and characterization challenges. These include the establishment and refinement of growth methods, material manipulation, and defect engineering. Material modification at the atomic level will be a key enabling factor for the engineering of quantum materials where desired phenomena are critically determined by local atomic structures. Successful use of scanning transmission electron microscopes (STEMs) for atomic scale material manipulation has opened the door for a transformed view of what can be accomplished using electron-beam-based strategies. However, serious obstacles exist on the pathway from possibility to practical reality. One such obstacle is the in situ delivery of atomized material in the STEM to the region of interest for further fabrication processes. Here, we present progress on this front with a view toward performing synthesis (deposition and growth) processes in a scanning transmission electron microscope. An in situ thermal deposition platform is presented, tested, and deposition and growth processes are demonstrated. In particular, we show that isolated Sn atoms can be evaporated from a filament and caught on the nearby sample, demonstrating atomized material delivery. This platform, and future variations, are envisioned to facilitate real-time atomic resolution imaging of growth processes and open new pathways toward atomic fabrication.

The scanning transmission electron microscope, a workhorse instrument in materials characterization, is being transformed into an atomic-scale material manipulation platform. With an eye on the trajectory of recent developments and the obstacles toward progress in this field, we provide a vision for a path toward an expanded set of capabilities and applications. We reconceptualize the microscope as an instrument for fabrication and synthesis with the capability to image and characterize atomic-scale structural formation as it occurs. Further development and refinement of this approach may have substantial impact on research in microelectronics, quantum information science, and catalysis where precise control over atomic scale structure and chemistry of a few "active sites" can have a dramatic impact on larger scale functionality and where developing a better understanding of atomic scale processes can help point the way to larger scale synthesis approaches.

Direct-write processes enable the alteration or deposition of materials in a continuous, directable, sequential fashion. In this work we demonstrate an electron beam direct-write process in an aberration-corrected scanning transmission electron microscope. This process has several fundamental differences from conventional electron beam induced deposition techniques, where the electron beam dissociates precursor gases into chemically reactive products that bond to a substrate. Here, we use elemental tin (Sn) as a precursor and employ a different mechanism to facilitate deposition. The atomic-sized electron beam is used to generate chemically reactive point defects at desired locations in a graphene substrate. Temperature control of the sample is used to enable the precursor atoms to migrate across the surface and bond to the defect sites thereby enabling atom-by-atom direct-writing.

Atomic-scale engineering typically involves bottom-up approaches, leveraging parameters such as temperature, partial pressures, and chemical affinity to promote spontaneous arrangement of atoms. These parameters are applied globally, resulting in atomic scale features scattered probabilistically throughout the material. In a top-down approach, different regions of the material are exposed to different parameters resulting in structural changes varying on the scale of the resolution. In this work, we combine the application of global and local parameters in an aberration corrected scanning transmission electron microscope (STEM) to demonstrate atomic scale precision patterning of atoms in twisted bilayer graphene. The focused electron beam is used to define attachment points for foreign atoms through the controlled ejection of carbon atoms from the graphene lattice. The sample environment is staged with nearby source materials, such that the sample temperature can induce migration of the source atoms across the sample surface. Under these conditions, the electron-beam (top-down) enables carbon atoms in the graphene to be replaced spontaneously by diffusing adatoms (bottom-up). Using image-based feedback-control, arbitrary patterns of atoms and atom clusters are attached to the twisted bilayer graphene with limited human interaction. The role of substrate temperature on adatom and vacancy diffusion is explored by first-principles simulations.

Recent studies of secondary electron (SE) emission in scanning transmission electron microscopes suggest that material's properties such as electrical conductivity, connectivity, and work function can be probed with atomic scale resolution using a technique known as secondary electron e-beam-induced current (SEEBIC). Here, we apply the SEEBIC imaging technique to a stacked 2D heterostructure device to reveal the spatially resolved electron orbital ionization cross section of an encapsulated WSe2 layer. We find that the double Se lattice site shows higher emission than the W site, which is at odds with first-principles modelling of ionization of an isolated WSe2 cluster. These results illustrate that atomic level SEEBIC contrast within a single material is possible and that an enhanced understanding of atomic scale SE emission is required to account for the observed contrast. In turn, this suggests that subtle information about interlayer bonding and the effect on electron orbitals can be directly revealed with this technique.

Ferroelectric domain walls have emerged as one of the most fascinating objects in condensed matter physics due to the broad variability of functional behaviors they exhibit. However, the vast majority of domain walls studies have been focused on bias-induced dynamics and transport behaviors. Here, we introduce the scanning probe microscopy approach based on piezoresponse force microscopy (PFM) with a dynamically heated probe, combining local heating and local biasing of the material. This approach is used to explore the thermal polarization dynamics in soft Sn2P2S6 ferroelectrics, and allows for the exploration of phase transitions at individual domain walls. The strong and weak modulation regimes for the thermal PFM are introduced. The future potential applications of heated probe approach for functional SPM measurements including piezoelectric, elastic, microwave, and transport measurements are discussed.

Electron-beam (e-beam) manipulation of single dopant atoms in an aberration-corrected scanning transmission electron microscope is emerging as a method for directed atomic motion and atom-by-atom assembly. Until now, the dopant species have been limited to atoms closely matched to carbon in terms of ionic radius and capable of strong covalent bonding with carbon atoms in the graphene lattice. In situ dopant insertion into a graphene lattice has thus far been demonstrated only for Si, which is ubiquitously present as a contaminant in this material. Here, we achieve in situ manipulation of Pt atoms and their insertion into the graphene host matrix using the e-beam deposited Pt on graphene as a host system. We further demonstrate a mechanism for stabilization of the Pt atom, enabled through the formation of Si-stabilized Pt heteroatomic clusters attached to the graphene surface. This study provides evidence toward the universality of the e-beam assembly approach, opening a pathway for exploring cluster chemistry through direct assembly., Comment: 23 pages, 6 figures

Graphene has been proposed for use in various nanodevice designs, many of which harness emergent quantum properties for device functionality. However, visualization, measurement, and manipulation become non-trivial at nanometer and atomic scales, representing a significant challenge for device fabrication, characterization, and optimization at length scales where quantum effects emerge. Here, we present proof of principle results at the crossroads between 2D nanoelectronic devices, e-beam-induced modulation, and imaging with secondary electron e-beam induced currents (SEEBIC). We introduce a device platform compatible with scanning transmission electron microscopy investigations. We then show how the SEEBIC imaging technique can be used to visualize conductance and connectivity in single layer graphene nanodevices, even while supported on a thicker substrate (conditions under which conventional imaging fails). Finally, we show that the SEEBIC imaging technique can detect subtle differences in charge transport through time in non-ohmic graphene nanoconstrictions indicating the potential to reveal dynamic electronic processes., Comment: 25 pages, 15 figures

Over the last few years, a new mode for imaging in the scanning transmission electron microscope (STEM) has gained attention as it permits the direct visualization of sample conductivity and electrical connectivity. When the electron beam (e-beam) is focused on the sample in the STEM, secondary electrons (SEs) are generated. If the sample is conductive and electrically connected to an amplifier, the SE current can be measured as a function of the e-beam position. This scenario is similar to the better-known scanning electron microscopy (SEM)-based technique, electron beam induced current (EBIC) imaging except the signal in STEM is generated by the emission of SEs, hence the name SEEBIC, and in this case the current flows in the opposite direction. Here, we provide a brief review of recent work in this area, examine the various contrast generation mechanisms associated with SEEBIC, and illustrate its use for the characterization of graphene nanoribbon devices., Comment: 49 pages, 13 figures

Research on two-dimensional materials has expanded over the past two decades to become a central theme in condensed matter research today. Significant advances have been made in the synthesis and subsequent reassembly of these materials using mechanical methods into a vast array of hybrid structures with novel properties and ever-increasing potential applications. The key hurdles in realizing this potential are the challenges in controlling the atomic structure of these layered hybrid materials and the difficulties in harnessing their unique functionality with existing semiconductor nanofabrication techniques. Here we report on high-quality van der Waals epitaxial growth and characterization of a layered topological insulator on freestanding monolayer graphene transferred to different mechanical supports. This templated synthesis approach enables direct interrogation of interfacial atomic structure of these as-grown hybrid structures and opens a route towards creating device structures with more traditional semiconductor nanofabrication techniques., Comment: 13 pages, 4 figures

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.

Polarization dynamics in ferroelectric materials are explored via the automated experiment in Piezoresponse Force Spectroscopy. A Bayesian Optimization framework for imaging is developed and its performance for a variety of acquisition and pathfinding functions is explored using previously acquired data. The optimized algorithm is then deployed on an operational scanning probe microscope (SPM) for finding areas of large electromechanical response in a thin film of PbTiO3, with metrics showing gains of ~3x in the sampling efficiency. This approach opens the pathway to perform more complex spectroscopies in SPM that were previously not possible due to time constraints and sample stability, tip wear, and/or stochastic sample damage that occurs at specific, a priori unknown spatial positions. Potential improvements to the framework to enable the incorporation of more prior information and improve efficiency further are discussed.

We suggest and implement an approach for the bottom-up description of systems undergoing large-scale structural changes and chemical transformations from dynamic atomically resolved imaging data, where only partial or uncertain data on atomic positions are available. This approach is predicated on the synergy of two concepts, the parsimony of physical descriptors and general rotational invariance of non-crystalline solids, and is implemented using a rotationally-invariant extension of the variational autoencoder applied to semantically segmented atom-resolved data seeking the most effective reduced representation for the system that still contains the maximum amount of original information. This approach allowed us to explore the dynamic evolution of electron beam-induced processes in a silicon-doped graphene system, but it can be also applied for a much broader range of atomic-scale and mesoscopic phenomena to introduce the bottom-up order parameters and explore their dynamics with time and in response to external stimuli., Comment: The revised version

Fast scanning probe microscopy enabled via machine learning allows for a broad range of nanoscale, temporally resolved physics to be uncovered. However, such examples for functional imaging are few in number. Here, using piezoresponse force microscopy (PFM) as a model application, we demonstrate a factor of 5.8 improvement in imaging rate using a combination of sparse spiral scanning with compressive sensing and Gaussian processing reconstruction. It is found that even extremely sparse scans offer strong reconstructions with less than 6 % error for Gaussian processing reconstructions. Further, we analyze the error associated with each reconstructive technique per reconstruction iteration finding the error is similar past approximately 15 iterations, while at initial iterations Gaussian processing outperforms compressive sensing. This study highlights the capabilities of reconstruction techniques when applied to sparse data, particularly sparse spiral PFM scans, with broad applications in scanning probe and electron microscopies.

With the advent of increasingly elaborate experimental techniques in physics, chemistry and materials sciences, measured data are becoming bigger and more complex. The observables are typically a function of several stimuli resulting in multidimensional data sets spanning a range of experimental parameters. As an example, a common approach to study ferroelectric switching is to observe effects of applied electric field, but switching can also be enacted by pressure and is influenced by strain fields, material composition, temperature, time, etc. Moreover, the parameters are usually interdependent, so that their decoupling toward univariate measurements or analysis may not be straightforward. On the other hand, both explicit and hidden parameters provide an opportunity to gain deeper insight into the measured properties, provided there exists a well-defined path to capture and analyze such data. Here, we introduce a new, two-dimensional approach to represent hysteretic response of a material system to applied electric field. Utilizing ferroelectric polarization as a model hysteretic property, we demonstrate how explicit consideration of electromechanical response to two rather than one control voltages enables significantly more transparent and robust interpretation of observed hysteresis, such as differentiating between charge trapping and ferroelectricity. Furthermore, we demonstrate how the new data representation readily fits into a variety of machinelearning methodologies, from unsupervised classification of the origins of hysteretic response via linear clustering algorithms to neural-network-based inference of the sample temperature based on the specific morphology of hysteresis.

The broad incorporation of microscopic methods is yielding a wealth of information on atomic and mesoscale dynamics of individual atoms, molecules, and particles on surfaces and in open volumes. Analysis of such data necessitates statistical frameworks to convert observed dynamic behaviors to effective properties of materials. Here we develop a method for stochastic reconstruction of effective acting potentials from observed trajectories. Using the Silicon vacancy defect in graphene as a model, we develop a statistical framework to reconstruct the free energy landscape from calculated atomic displacements., Comment: 12 pages, 5 figures. This manuscript is a part of update to previous work (arXiv:1804.03729v1) authors found some of the analysis in the previous work to be not accurate and this manuscript is a partial update to that work

Interface structures in complex oxides remain one of the active areas of condensed matter physics research, largely enabled by recent advances in scanning transmission electron microscopy (STEM). Yet the nature of the STEM contrast in which the structure is projected along the given direction precludes separation of possible structural models. Here, we utilize deep convolutional neural networks (DCNN) trained on simulated 4D scanning transmission electron microscopy (STEM) datasets to predict structural descriptors of interfaces. We focus on the widely studied interface between LaAlO3 and SrTiO3, using dynamical diffraction theory and leveraging high performance computing to simulate thousands of possible 4D STEM datasets to train the DCNN to learn properties of the underlying structures on which the simulations are based. We validate the DCNN on simulated data and show that it is possible (with >95% accuracy) to identify a physically rough from a chemically diffuse interface and achieve 85% accuracy in determination of buried step positions within the interface. The method shown here is general and can be applied for any inverse imaging problem where forward models are present., Comment: 18 pages, 4 figures

The universal tendency in scanning probe microscopy (SPM) over the last two decades is to transition from simple 2D imaging to complex detection and spectroscopic imaging modes. The emergence of complex SPM engines brings forth the challenge of reliable data interpretation, i.e. conversion from detected signal to descriptors specific to tip-surface interactions and subsequently to materials properties. Here, we implemented a Bayesian inference approach for the analysis of the image formation mechanisms in band excitation (BE) SPM. Compared to the point estimates in classical functional fit approaches, Bayesian inference allows for the incorporation of extant knowledge of materials and probe behavior in the form of corresponding prior distribution and return the information on the material functionality in the form of readily interpretable posterior distributions. We note that in application of Bayesian methods, special care should be made for proper setting on the problem as model selection vs. establishing practical parameter equivalence. We further explore the non-linear mechanical behaviors at topological defects in a classical ferroelectric material, PbTiO3. We observe the non-trivial evolution of Duffing resonance frequency and the nonlinearity of the sample surface, suggesting the presence of the hidden elements of domain structure. These observations suggest that the spectrum of anomalous behaviors at the ferroelectric domain walls can be significantly broader than previously believed and can extend to non-conventional mechanical properties in addition to static and microwave conductance., Comment: Supplementary materials is located at the end of the manuscript

Imaging mechanisms in contact Kelvin Probe Force Microscopy (cKPFM) are explored via information theory-based methods. Gaussian Processes are used to achieve super-resolution in the cKPFM signal, effectively extrapolating across the spatial and parameter space. Tensor matrix factorization is applied to reduce the multidimensional signal to the tensor convolution of the scalar functions that show clear trending behavior with the imaging parameters. These methods establish a workflow for the analysis of the multidimensional data sets, that can then be related to the relevant physical mechanisms. We also provide an interactive Google Colab notebook (http://bit.ly/39kMtuR) that goes through all the analysis discussed in the paper., Comment: Update with accepted version

Domains walls and topological defects in ferroelectric materials have emerged as a powerful new paradigm for functional electronic devices including memory and logic. Similarly, wall interactions and dynamics underpin a broad range of mesoscale phenomena ranging from giant electromechanical responses to memory effects. Exploring the functionalities of individual domain walls, their interactions, and controlled modifications of the domain structures is crucial for applications and fundamental physical studies. However, the dynamic nature of these features severely limits studies of their local physics since application of local biases or pressures in piezoresponse force microscopy induce wall displacement as a primary response. Here, we introduce a fundamentally new approach for the control and modification of domain structures based on automated experimentation whereby real space image-based feedback is used to control the tip bias during ferroelectric switching, allowing for modification routes conditioned on domain states under the tip. This automated experiment approach is demonstrated for the exploration of domain wall dynamics and creation of metastable phases with large electromechanical response.

We report electron-beam activated motion of a catalytic nanoparticle along a graphene step edge and associated etching of the edge. This approach enables beam-controlled etching of matter through activated electrocatalytic processes. The applications of electron-beam control as a paradigm for molecular-scale robotics are discussed.

Piezoresponse force microscopy (PFM) is a powerful characterization technique to readily image and manipulate ferroelectrics domains. PFM gives insight into the strength of local piezoelectric coupling as well as polarization direction through PFM amplitude and phase, respectively. Converting measured arbitrary units to physical material parameters, however, remains a challenge. While much effort has been spent on quantifying the PFM amplitude signal, little attention has been given to the PFM phase and it is often arbitrarily adjusted to fit expectations or processed as recorded. This is problematic when investigating materials with unknown or potentially negative sign of the probed effective electrostrictive coefficient or strong frequency dispersion of electromechanical responses since assumptions about the phase cannot be reliably made. The PFM phase can, however, provide important information on the polarization orientation and the sign of the electrostrictive coefficient. Most notably, the orientation of the PFM hysteresis loop is determined by the PFM phase. Moreover, when presenting PFM data as a combined signal, the resulting response can be artificially lowered or asymmetric if the phase data has not been correctly processed. Here, we demonstrate a path to identify the phase offset required to extract correct meaning from PFM phase data. We explore different sources of phase offsets including the experimental setup, instrumental contributions, and data analysis. We discuss the physical working principles of PFM and develop a strategy to extract physical meaning from the PFM phase. The proposed procedures are verified on two materials with positive and negative piezoelectric coefficients., Comment: 16 pages, 6 figures

We investigate the ability to reconstruct and derive spatial structure from sparsely sampled 3D piezoresponse force microcopy data, captured using the band-excitation (BE) technique, via Gaussian Process (GP) methods. Even for weakly informative priors, GP methods allow unambiguous determination of the characteristic length scales of the imaging process both in spatial and frequency domains. We further show that BE data set tends to be oversampled, with ~30% of the original data set sufficient for high-quality reconstruction, potentially enabling the faster BE imaging. Finally, we discuss how the GP can be used for automated experimentation in SPM, by combining GP regression with non-rectangular scans. The full code for GP regression applied to hyperspectral data is available at https://git.io/JePGr.

Four-dimensional scanning transmission electron microscopy (4D-STEM) is one of the most rapidly growing modes of electron microscopy imaging. The advent of fast pixelated cameras and the associated data infrastructure have greatly accelerated this process. Yet conversion of the 4D datasets into physically meaningful structure images in real-space remains an open issue. In this work, we demonstrate that, it is possible to systematically create filters that will affect the apparent resolution or even qualitative features of the real-space structure image, reconstructing artificially generated patterns. As initial efforts, we explore statistical model selection algorithms, aiming for robustness and reliability of estimated filters. This statistical model selection analysis demonstrates the need for regularization and cross-validation of inversion methods to robustly recover structure from high-dimensional diffraction datasets.

Materials science is undergoing profound changes due to advances in characterization instrumentation that have resulted in an explosion of data in terms of volume, velocity, variety and complexity. Harnessing these data for scientific research requires an evolution of the associated computing and data infrastructure, bridging scientific instrumentation with super- and cloud- computing. Here, we describe Universal Spectroscopy and Imaging Data (USID), a data model capable of representing data from most common instruments, modalities, dimensionalities, and sizes. We pair this schema with the hierarchical data file format (HDF5) to maximize compatibility, exchangeability, traceability, and reproducibility. We discuss a family of community-driven, open-source, and free python software packages for storing, processing and visualizing data. The first is pyUSID which provides the tools to read and write USID HDF5 files in addition to a scalable framework for parallelizing data analysis. The second is Pycroscopy, which provides algorithms for scientific analysis of nanoscale imaging and spectroscopy modalities and is built on top of pyUSID and USID. The instrument-agnostic nature of USID facilitates the development of analysis code independent of instrumentation and task in Pycroscopy which in turn can bring scientific communities together and break down barriers in the age of open-science. The interested reader is encouraged to be a part of this ongoing community-driven effort to collectively accelerate materials research and discovery through the realms of big data.

Recent advances in scanning transmission electron microscopy (STEM) allow to observe solid-state transformations and reactions in materials induced by thermal stimulus or electron beam on the atomic level. However, despite the rate at which large volumes of data can be generated (sometimes in the gigabyte to terabyte range per single experiment), approaches for the extraction of material-specific knowledge on the kinetics and thermodynamics of these processes are still lacking. One of the critical issues lies in being able to map the evolution of various atomic structures and determine the associated transition probabilities directly from raw experimental data characterized by high levels of noise and missing structural elements. Here, we demonstrate an approach based on the combination of multiple machine learning techniques to study the dynamic behavior of e-beam irradiated Si atoms in the bulk and at the edges of single-layer graphene in STEM experiments. First, a deep learning network is used to convert experimental STEM movies into coordinates of individual Si and carbon atoms. Then, a Gaussian mixture model is further used to establish the elementary atomic configurations of the Si atoms, defining the bonding geometries and chemical species and accounting for the discrete rotational symmetry of the host lattice. Finally, the frequencies and Markov transition probabilities between these states are determined. This analysis enables insight into the thermodynamics of defect populations and chemical reaction networks from the atomically resolved STEM data. Here, we observe a clear tendency for the formation of a 1D Si crystal along zigzag direction of graphene edges and for the Si impurity coupling to topological defects in bulk graphene.

Four-dimensional scanning transmission electron microscopy (4D-STEM) of local atomic diffraction patterns is emerging as a powerful technique for probing intricate details of atomic structure and atomic electric fields. However, efficient processing and interpretation of large volumes of data remain challenging, especially for two-dimensional or light materials because the diffraction signal recorded on the pixelated arrays is weak. Here we employ data-driven manifold leaning approaches for straightforward visualization and exploration analysis of the 4D-STEM datasets, distilling real-space neighboring effects on atomically resolved deflection patterns from single-layer graphene, with single dopant atoms, as recorded on a pixelated detector. These extracted patterns relate to both individual atom sites and sublattice structures, effectively discriminating single dopant anomalies via multi-mode views. We believe manifold learning analysis will accelerate physics discoveries coupled between data-rich imaging mechanisms and materials such as ferroelectric, topological spin and van der Waals heterostructures.

Using electron beam manipulation, we enable deterministic motion of individual Si atoms in graphene along predefined trajectories. Structural evolution during the dopant motion was explored, providing information on changes of the Si atom neighborhood during atomic motion and providing statistical information of possible defect configurations. The combination of a Gaussian mixture model and principal component analysis applied to the deep learning-processed experimental data allowed disentangling of the atomic distortions for two different graphene sublattices. This approach demonstrates the potential of e-beam manipulation to create defect libraries of multiple realizations of the same defect and explore the potential of symmetry breaking physics. The rapid image analytics enabled via a deep learning network further empowers instrumentation for e-beam controlled atom-by-atom fabrication. The analysis described in the paper can be reproduced via an interactive Jupyter notebook at https://git.io/JJ3Bx, Comment: Updated paper with new analysis. Replaced most of the previous analysis. Added a Jupyter notebook that goes through the analysis discussed in the paper