Electron-Beam Manipulation of Silicon Dopants in Graphene

Single atoms and metal nanoclusters anchored to graphene vacancies

Fabricating dispersed single atoms and size-controlled metal nanoclusters remains a difficult challenge due to sintering. Here, we demonstrate that atoms and clusters can be immobilized using atomically clean defect-engineered graphene as the matrix. The graphene is first cleaned of surface contamination with laser heating, after which low-energy Ar irradiation is used to create spatially well-separated vacancies into it. Metal atoms are then evaporated either via thermal or ebeam evaporation onto graphene, where they diffuse until being trapped into a vacancy. The density of embedded structures can be controlled through irradiation dose, and the size of the structures through evaporation time. The resulting structures are confirmed through atomic-resolution scanning transmission electron microscopy and electron energy loss spectroscopy. We demonstrate here incorporation of Al, Ti, Fe, Ag and Au single atoms or nanoclusters, but the method should work equally well for other elements.

Probing the interaction range of electron beam-induced etching in STEM by a non-contact electron beam

Beside its main purpose as a high-end tool in material analysis reaching the atomic scale for structure, chemical and electronic properties, aberration-corrected scanning transmission electron microscopy (STEM) is increasingly used as a tool to manipulate materials down to that very same scale. In order to obtain exact and reproducible results, it is essential to consider the interaction processes and interaction ranges between the electron beam and the involved materials. Here, we show in situ that electron beam-induced etching in a low-pressure oxygen atmosphere can extend up to a distance of several nm away from the Ångström-size electron beam, usually used for probing the sample. This relatively long-range interaction is related to beam tails and inelastic scattering involved in the etching process. To suppress the influence of surface diffusion, we measure the etching effect indirectly on isolated nm-sized holes in a 2 nm thin amorphous carbon foil that is commonly used as sample support in STEM. During our experiments, the electron beam is placed inside the nanoholes so that most electrons cannot directly participate in the etching process. We characterize the etching process from measuring etching rates at multiple nanoholes with different distances between the hole edge and the electron beam.

Direct Fabrication of Atomically Defined Pores in MXenes Using Feedback-Driven STEM

Controlled fabrication of nanopores in 2D materials offer the means to create robust membranes needed for ion transport and nanofiltration. Techniques for creating nanopores have relied upon either plasma etching or direct irradiation; however, aberration-corrected scanning transmission electron microscopy (STEM) offers the advantage of combining a sub-Å sized electron beam for atomic manipulation along with atomic resolution imaging. Here, a method for automated nanopore fabrication is utilized with real-time atomic visualization to enhance the mechanistic understanding of beam-induced transformations. Additionally, an electron beam simulation technique, Electron-Beam Simulator (E-BeamSim) is developed to observe the atomic movements and interactions resulting from electron beam irradiation. Using the MXene Ti3C2Tx, the influence of temperature on nanopore fabrication is explored by tracking atomic transformations and find that at room temperature the electron beam irradiation induces random displacement and results in titanium pileups at the nanopore edge, which is confirmed by E-BeamSim. At elevated temperatures, after removal of the surface functional groups and with the increased mobility of atoms results in atomic transformations that lead to the selective removal of atoms layer by layer. This work can lead to the development of defect engineering techniques within functionalized MXene layers and other 2D materials.

The Case for a Defect Genome Initiative

The Materials Genome Initiative (MGI) has streamlined the materials discovery effort by leveraging generic traits of materials, with focus largely on perfect solids. Defects such as impurities and perturbations, however, drive many attractive functional properties of materials. The rich tapestry of charge, spin, and bonding states hosted by defects are not accessible to elements and perfect crystals, and defects can thus be viewed as another class of "elements" that lie beyond the periodic table. Accordingly, a Defect Genome Initiative (DGI) to accelerate functional defect discovery for energy, quantum information, and other applications is proposed. First, major advances made under the MGI are highlighted, followed by a delineation of pathways for accelerating the discovery and design of functional defects under the DGI. Near-term goals for the DGI are suggested. The construction of open defect platforms and design of data-driven functional defects, along with approaches for fabrication and characterization of defects, are discussed. The associated challenges and opportunities are considered and recent advances towards controlled introduction of functional defects at the atomic scale are reviewed. It is hoped this perspective will spur a community-wide interest in undertaking a DGI effort in recognition of the importance of defects in enabling unique functionalities in materials.

Disproportionation chemistry in K2PtCl4 visualized at atomic resolution using scanning transmission electron microscopy

The direct observation of a solid-state chemical reaction can reveal otherwise hidden mechanisms that control the reaction kinetics. However, probing the chemical bond breaking and formation at the molecular level remains challenging because of the insufficient spatial-temporal resolution and composition analysis of available characterization methods. Using atomic-resolution differential phase-contrast imaging in scanning transmission electron microscopy, we have visualized the decomposition chemistry of K2PtCl4 to identify its transient intermediate phases and their interfaces that characterize the chemical reduction process. The crystalline structure of K2PtCl4 is found to undergo a disproportionation reaction to form K2PtCl6, followed by gradual reduction to crystalline Pt metal and KCl. By directly imaging different Pt─Cl bond configurations and comparing them to models predicted via density functional theory calculations, a causal connection between the initial and final states of a chemical reaction is established, showcasing new opportunities to resolve reaction pathways through atomistic experimental visualization.

Electronic and magnetic properties of transition-metal-doped monolayer B2S2 within GGA + U framework

Considering the significant role of magnetism induction in two-dimensional (2D) semiconductor materials, we systematically investigate the effects of various dopants from the 3d and 4d transition metal (TM) series, including Ti, V, Mn, Fe, Co, Ni, Cu, Zn, Zr, Nb, Mo, Ru, Rh, Pd, Ag and Cd, on the electronic and magnetic properties of monolayer B2S2 through first-principles calculations. The calculated formation energies indicate that substitutional doping at the B site with various TM atoms could be achieved under S-rich growth conditions. What matters is that with the exception of systems doped with Cu, Tc, and Ag elements, which exhibit non-magnetic semiconductor properties, all other doped systems demonstrate magnetism. Specifically, the Cr-, Ni- and Pd-doped monolayers are magnetic half-metals, while the rest are magnetic semiconductors. We have also performed calculations of magnetic couplings between two TM atoms with an impurity concentration of 3.12%, revealing the prevalence of weak magnetic coupling in the majority of the magnetic systems examined. Moreover, the monolayers doped with Cr, Zr and Pd atoms exhibit ferromagnetic ground states. These findings strongly support the high potential for inducing magnetism in the B2S2 monolayer through B-site doping.

A Platform for Atomic Fabrication and In Situ Synthesis in a Scanning Transmission Electron Microscope

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. Atomic-scale modification will be a key enabling factor for engineering quantum materials where desired phenomena are critically determined by 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, progress on this front is presented with a view toward performing synthesis (deposition and growth) processes in a scanning transmission electron microscope in combination with top-down control over the reaction region. An in situ thermal deposition platform is presented, tested, and deposition and growth processes are demonstrated. In particular, it is shown that isolated Sn atoms can be evaporated from a filament and caught on the nearby sample, demonstrating atomized material delivery. This platform is envisioned to facilitate real-time atomic resolution imaging of growth processes and open new pathways toward atomic fabrication.

Top-Down Fabrication of Atomic Patterns in Twisted Bilayer Graphene

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, the application of global and local parameters is combined 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.

Atomically Precise Detection and Manipulation of Nitrogen-Vacancy Centers in Nanodiamonds

Nitrogen-vacancy (NV) centers in nanodiamonds are a promising quantum communication system offering robust and discrete single photon emission, but a more thorough understanding of properties of the NV centers is critical for real world implementation in functional devices. The first step to understanding how factors such as surface, depth, and charge state affect NV center properties is to directly characterize these defects on the atomic scale. Here we use Angstrom-resolution scanning transmission electron microscopy (STEM) to identify a single NV center in a ∼4 nm natural nanodiamond through simultaneous acquisition of electron energy loss and energy dispersive X-ray spectra, which provide a characteristic NV center peak and a nitrogen peak, respectively. In addition, we identify NV centers in larger, ∼15 nm synthetic nanodiamonds, although without the single-defect resolution afforded by the lower background of the smaller natural nanodiamonds. We have further demonstrated the potential to directly position these technologically relevant defects at the atomic scale using the scanning electron beam to "herd" NV centers and nitrogen atoms across their host nanodiamonds.

The Atomic Drill Bit: Precision Controlled Atomic Fabrication of 2D Materials

The ability to deterministically fabricate nanoscale architectures with atomic precision is the central goal of nanotechnology, whereby highly localized changes in the atomic structure can be exploited to control device properties at their fundamental physical limit. Here, an automated, feedback-controlled atomic fabrication method is reported and the formation of 1D-2D heterostructures in MoS₂ is demonstrated through selective transformations along specific crystallographic orientations. The atomic-scale probe of an aberration-corrected scanning transmission electron microscope (STEM) is used, and the shape and symmetry of the scan pathway relative to the sample orientation are controlled. The focused and shaped electron beam is used to reliably create Mo₆ S₆ nanowire (MoS-NW) terminated metallic-semiconductor 1D-2D edge structures within a pristine MoS₂ monolayer with atomic precision. From these results, it is found that a triangular beam path aligned along the zig-zag sulfur terminated (ZZS) direction forms stable MoS-NW edge structures with the highest degree of fidelity without resulting in disordering of the surrounding MoS₂ monolayer. Density functional theory (DFT) calculations and ab initio molecular dynamic simulations (AIMD) are used to calculate the energetic barriers for the most stable atomic edge structures and atomic transformation pathways. These discoveries provide an automated method to improve understanding of atomic-scale transformations while opening a pathway toward more precise atomic-scale engineering of materials.

Atom-by-Atom Direct Writing

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.

A Core-Shell MWCNT-Pt Nanowire Electron Source with Anomalously Long-Term Stable Field Emission

A hybrid core-shell structured nanowire is proposed for a long-term stable electron source based on an isolated platinum/multi-walled carbon nanotube (Pt/MWCNT). This hybrid nanowire is prepared by growing a Pt shell on a metallic MWCNT through a field-emission-induced deposition (FEID) method. An in situ field emission (FE) platform was constructed inside a scanning electron microscope (SEM) equipped with two nanorobotic manipulators (NRMs) for the preparation and testing of the hybrid nanowire. An in situ fatigue test was conducted with high current intensity (500 nA) to show the influence of the Pt shell. Compared with the pristine bare MWCNT, our hybrid-nanowire-based electron source has a lifetime of hundreds of times longer and can work continuously for up to 48 h under relatively high pressure (3.6×10-3 Pa) without having an apparent change in its structure or emission currents, demonstrating good stability and tolerance to poor working conditions. The anomalous long-term stability is attributed mainly to the shielding of oxygen by Pt from the carbon shells and less heating due to the work function lowering by Pt.

Topological Defects Created by Gamma Rays in a Carbon Nanotube Bilayer

Graphene sheets are a highly radiation-resistant material for prospective nuclear applications and nanoscale defect engineering. However, the precise mechanism of graphene radiation hardness has remained elusive. In this paper, we study the origin and nature of defects induced by gamma radiation in a graphene rolled-up plane. In order to reduce the environmental influence on graphene and reveal the small effects of gamma rays, we have synthesized a novel graphene-based nanocomposite material containing a bilayer of highly aligned carbon nanotube assemblies that have been decorated by organometallic compounds and suspended on nanoporous Al2O3 membranes. The bilayer samples were irradiated by gamma rays from a 137Cs source with a fluence rate of the order of 105 m-2s-1. The interaction between the samples and gamma quanta results in the appearance of three characteristic photon escape peaks in the radiation spectra. We explain the mechanism of interaction between the graphene sheets and gamma radiation using a pseudo-Majorana fermion graphene model, which is a quasi-relativistic N=3-flavor graphene model with a Majorana-like mass term. This model admits the existence of giant charge carrier currents that are sufficient to neutralize the impact of ionizing radiation. Experimental evidence is provided for the prediction that the 661.7-keV gamma quanta transfer enough energy to the electron subsystem of graphene to bring about the deconfinement of the bound pseudo-Majorana modes and involve C atoms in a vortical motion of the electron density flows in the graphene plane. We explain the radiation hardness of graphene by the topological non-triviality of the pseudo-Majorana fermion configurations comprising the graphene charge carriers.

Numerical package for QFT calculations of defect-induced phenomena in graphene

We introduce a computationally efficient method based on the path integral formalism to describe defect-modified graphene. By taking into account the entire Brillouin zone, our approach respects the lattice symmetry and can be used to investigate both short-range and long-range effects. The proposed method's key advantage is that the computational complexity does not increase with the system size, scaling, instead, with the number of defects. Our aim is to make the quantum-field calculations in graphene accessible to the experimental community. We demonstrate our method's capabilities by exploring the well-known graphene-mediated Ruderman-Kittel-Kasuya-Yoshida interaction and by performing a detailed study of the atomic collapse in the presence of defects.

Gate-Tunable Resonance State and Screening Effects for Proton-Like Atomic Charge in Graphene

The ability to create a robust and well-defined artificial atomic charge in graphene and understand its carrier-dependent electronic properties represents an important goal toward the development of graphene-based quantum devices. Herein, we devise a new pathway toward the atomically precise embodiment of point charges into a graphene lattice by posterior (N) ion implantation into a back-gated graphene device. The N dopant behaves as an in-plane proton-like charge manifested by formation of the characteristic resonance state in the conduction band. Scanning tunneling spectroscopy measurements at varied charge carrier densities reveal a giant energetic renormalization of the resonance state up to 220 meV with respect to the Dirac point, accompanied by the observation of gate-tunable long-range screening effects close to individual N dopants. Joint density functional theory and tight-binding calculations with modified perturbation potential corroborate experimental findings and highlight the short-range character of N-induced perturbation.

Identifying and manipulating single atoms with scanning transmission electron microscopy

The manipulation of individual atoms has developed from visionary speculation into an established experimental science. Using focused electron irradiation in a scanning transmission electron microscope instead of a physical tip in a scanning probe microscope confers several benefits, including thermal stability of the manipulated structures, the ability to reach into bulk crystals, and the chemical identification of single atoms. However, energetic electron irradiation also presents unique challenges, with an inevitable possibility of irradiation damage. Understanding the underlying mechanisms will undoubtedly continue to play an important role to guide experiments. Great progress has been made in several materials including graphene, carbon nanotubes, and crystalline silicon in the eight years since the discovery of electron-beam manipulation, but the important challenges that remain will determine how far we can expect to progress in the near future.

Electron-Beam Induced Emergence of Mesoscopic Ordering in Layered MnPS3

Ordered mesoscale structures in 2D materials induced by small misorientations have allowed for a wide variety of electronic, ferroelectric, and quantum phenomena to be explored. Until now, the only mechanism to induce this periodic ordering was via mechanical rotations between the layers, with the periodicity of the resulting moiré pattern being directly related to twist angle. Here we report a fundamentally distinct mechanism for emergence of mesoscopic periodic patterns in multilayer sulfur-containing metal phosphorus trichalcogenide, MnPS₃, induced by the electron beam. The formation under the beam of periodic hexagonal patterns with several characteristic length scales, nucleation and transitions between the phases, and local dynamics are demonstrated. The associated mechanisms are attributed to the relative contraction of the layers caused by beam-induced sulfur vacancy formation with subsequent ordering and lattice parameter change. As a result, the plasmonic response of the system is locally altered, suggesting an element of control over plasmon resonances by electron beam patterning. We pose that harnessing this phenomenon provides both insight into fundamental physics of quantum materials and enables device applications by enabling controlled periodic potentials on the atomic scale.

Probing Electron Beam Induced Transformations on a Single-Defect Level via Automated Scanning Transmission Electron Microscopy

A robust approach for real-time analysis of the scanning transmission electron microscopy (STEM) data streams, based on ensemble learning and iterative training (ELIT) of deep convolutional neural networks, is implemented on an operational microscope, enabling the exploration of the dynamics of specific atomic configurations under electron beam irradiation via an automated experiment in STEM. Combined with beam control, this approach allows studying beam effects on selected atomic groups and chemical bonds in a fully automated mode. Here, we demonstrate atomically precise engineering of single vacancy lines in transition metal dichalcogenides and the creation and identification of topological defects in graphene. The ELIT-based approach facilitates direct on-the-fly analysis of the STEM data and engenders real-time feedback schemes for probing electron beam chemistry, atomic manipulation, and atom by atom assembly.

Tailoring magnetism in silicon-doped zigzag graphene edges

Recently, the edges of single-layer graphene have been experimentally doped with silicon atoms by means of scanning transmission electron microscopy. In this work, density functional theory is applied to model and characterize a wide range of experimentally inspired silicon doped zigzag-type graphene edges. The thermodynamic stability is assessed and the electronic and magnetic properties of the most relevant edge configurations are unveiled. Importantly, we show that silicon doping of graphene edges can induce a reversion of the spin orientation on the adjacent carbon atoms, leading to novel magnetic properties with possible applications in the field of spintronics.

Beam-driven Dynamics of Aluminium Dopants in Graphene

Substituting heteroatoms into graphene can tune its properties for applications ranging from catalysis to spintronics. The further recent discovery that covalent impurities in graphene can be manipulated at atomic precision using a focused electron beam may open avenues towards sub-nanometer device architectures. However, the preparation of clean samples with a high density of dopants is still very challenging. Here, we report vacancy-mediated substitution of aluminium into laser-cleaned graphene, and without removal from our ultra-high vacuum apparatus, study their dynamics under 60 keV electron irradiation using aberration-corrected scanning transmission electron microscopy and spectroscopy. Three- and four-coordinated Al sites are identified, showing excellent agreement with ab initio predictions including binding energies and electron energy-loss spectrum simulations. We show that the direct exchange of carbon and aluminium atoms predicted earlier occurs under electron irradiation, although unexpectedly it is less probable than the same process for silicon. We also observe a previously unknown nitrogen-aluminium exchange that occurs at Al─N double-dopant sites at graphene divacancies created by our plasma treatment.

Aligned Stacking of Nanopatterned 2D Materials for High-Resolution 3D Device Fabrication

Two-dimensional materials can be combined by placing individual layers on top of each other, so that they are bound only by their van der Waals interaction. The sequence of layers can be chosen arbitrarily, enabling an essentially atomic-level control of the material and thereby a wide choice of properties along one dimension. However, simultaneous control over the structure in the in-plane directions is so far still rather limited. Here, we combine spatially controlled modifications of 2D materials, using focused electron irradiation or electron beam induced etching, with the layer-by-layer assembly of van der Waals heterostructures. The presented assembly process makes it possible to structure each layer with an arbitrary pattern prior to the assembly into the heterostructure. Moreover, it enables a stacking of the layers with accurate lateral alignment, with an accuracy of currently 10 nm, under observation in an electron microscope. Together, this enables the fabrication of almost arbitrary 3D structures with highest spatial resolution.

Towards automating structural discovery in scanning transmission electron microscopy *

Scanning transmission electron microscopy is now the primary tool for exploring functional materials on the atomic level. Often, features of interest are highly localized in specific regions in the material, such as ferroelectric domain walls, extended defects, or second phase inclusions. Selecting regions to image for structural and chemical discovery via atomically resolved imaging has traditionally proceeded via human operators making semi-informed judgements on sampling locations and parameters. Recent efforts at automation for structural and physical discovery have pointed towards the use of ‘active learning’ methods that utilize Bayesian optimization with surrogate models to quickly find relevant regions of interest. Yet despite the potential importance of this direction, there is a general lack of certainty in selecting relevant control algorithms and how to balance a priori knowledge of the material system with knowledge derived during experimentation. Here we address this gap by developing the automated experiment workflows with several combinations to both illustrate the effects of these choices and demonstrate the tradeoffs associated with each in terms of accuracy, robustness, and susceptibility to hyperparameters for structural discovery. We discuss possible methods to build descriptors using the raw image data and deep learning based semantic segmentation, as well as the implementation of variational autoencoder based representation. Furthermore, each workflow is applied to a range of feature sizes including NiO pillars within a La:SrMnO3 matrix, ferroelectric domains in BiFeO3, and topological defects in graphene. The code developed in this manuscript is open sourced and will be released at github.com/nccreang/AE_Workflows.

Exploring electron beam induced atomic assembly via reinforcement learning in a molecular dynamics environment. NANOTECHNOLOGY 2021;33:115301. [PMID: 34768249 DOI: 10.1088/1361-6528/ac394a]

Atom-by-atom assembly of functional materials and devices is perceived as one of the ultimate targets of nanotechnology. Recently it has been shown that the beam of a scanning transmission electron microscope can be used for targeted manipulation of individual atoms. However, the process is highly dynamic in nature rendering control difficult. One possible solution is to instead train artificial agents to perform the atomic manipulation in an automated manner without need for human intervention. As a first step to realizing this goal, we explore how artificial agents can be trained for atomic manipulation in a simplified molecular dynamics environment of graphene with Si dopants, using reinforcement learning. We find that it is possible to engineer the reward function of the agent in such a way as to encourage formation of local clusters of dopants under different constraints. This study shows the potential for reinforcement learning in nanoscale fabrication, and crucially, that the dynamics learned by agents encode specific elements of important physics that can be learned.

Defect-Dependent Corrugation in Graphene

Graphene's intrinsically corrugated and wrinkled topology fundamentally influences its electronic, mechanical, and chemical properties. Experimental techniques allow the manipulation of pristine graphene and the controlled production of defects which allows one to control the atomic out-of-plane fluctuations and thus tune graphene's properties. Here, we perform large scale machine learning-driven molecular dynamics simulations to understand the impact of defects on the structure of graphene. We find that defects cause significantly higher corrugation leading to a strongly wrinkled surface. The magnitude of this structural transformation strongly depends on the defect concentration and specific type of defect. Analyzing the atomic neighborhood of the defects reveals that the extent of these morphological changes depends on the preferred geometrical orientation and the interactions between defects. While our work highlights that defects can strongly affect graphene's morphology, it also emphasizes the differences between distinct types by linking the global structure to the local environment of the defects.

Single Indium Atoms and Few-Atom Indium Clusters Anchored onto Graphene via Silicon Heteroatoms

Single atoms and few-atom nanoclusters are of high interest in catalysis and plasmonics, but pathways for their fabrication and placement remain scarce. We report here the self-assembly of room-temperature-stable single indium (In) atoms and few-atom In clusters (2-6 atoms) that are anchored to substitutional silicon (Si) impurity atoms in suspended monolayer graphene membranes. Using atomically resolved scanning transmission electron microscopy (STEM), we find that the symmetry of the In structures is critically determined by the three- or fourfold coordination of the Si "anchors". All structures are produced without electron-beam induced materials modification. In turn, when activated by electron beam irradiation in the STEM, we observe in situ the formation, restructuring, and translation of the Si-anchored In structures. Our results on In-Si-graphene provide a materials system for controlled self-assembly and heteroatomic anchoring of single atoms and few-atom nanoclusters on graphene.

Mechanism of Electron-Beam Manipulation of Single-Dopant Atoms in Silicon

The precise positioning of dopant atoms within bulk crystal lattices could enable novel applications in areas including solid-state sensing and quantum computation. Established scanning probe techniques are capable tools for the manipulation of surface atoms, but at a disadvantage due to their need to bring a physical tip into contact with the sample. This has prompted interest in electron-beam techniques, followed by the first proof-of-principle experiment of bismuth dopant manipulation in crystalline silicon. Here, we use first-principles modeling to discover a novel indirect exchange mechanism that allows electron impacts to non-destructively move dopants with atomic precision within the silicon lattice. However, this mechanism only works for the two heaviest group V donors with split-vacancy configurations, Bi and Sb. We verify our model by directly imaging these configurations for Bi and by demonstrating that the promising nuclear spin qubit Sb can be manipulated using a focused electron beam.

Antiferromagnetic spin ordering in two-dimensional honeycomb lattice of SiP3

Magnetism in low-dimensional materials has been of sustained interest due to its intriguing quantum mechanical origin and promising device applications. Here, we propose a buckled honeycomb lattice of stoichiometry SiP₃, a two-dimensional binary group-IV and V material that exhibits an antiferromagnetic ground state with itinerant electrons. Here we perform elemental Si substitution in pristine blue phosphorene to downshift the Fermi energy and induce the Fermi instability that results in a spin polarized ground state. Within first-principles calculations, we observe antiferromagnetic spin alignment between adjacent ferromagnetic triangular domains where each Si atom is coupled with three neighboring P atoms with a ferromagnetic interaction. Such unique spin structure and resulting magnetic ground state are unprecedented in defect-free two-dimensional materials made of only p-block elements. This metal-free magnetism can be exploited for advanced spintronic and memory storage applications.

Exploring order parameters and dynamic processes in disordered systems via variational autoencoders

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 noncrystalline 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.

Imaging Secondary Electron Emission from a Single Atomic Layer

Graphene-based devices hold promise for a wide range of technological applications. Yet characterizing the structure and the electrical properties of a material that is only one atomic layer thick still poses technical challenges. Recent investigations indicate that secondary-electron electron-beam-induced current (SE-EBIC) imaging can reveal subtle details regarding electrical conductivity and electron transport with high spatial resolution. Here, it is shown that the SEEBIC imaging mode can be used to detect suspended single layers of graphene and distinguish between different numbers of layers. Pristine and contaminated areas of graphene are also compared to show that pristine graphene exhibits a substantially lower SE yield than contaminated regions. This SEEBIC imaging mode may provide valuable information for the engineering of surface coatings where SE yield is a priority.

Electron beam triggered single-atom dynamics in two-dimensional materials

Controlling atomic structure and dynamics with single-atom precision is the ultimate goal in nanoscience and nanotechnology. Despite great successes being achieved by scanning tunneling microscopy (STM) over the past a few decades, fundamental limitations, such as ultralow temperature, and low throughput, significantly hinder the fabrication of a large array of atomically defined structures by STM. The advent of aberration correction in scanning transmission electron microscopy (STEM) revolutionized the field of nanomaterials characterization pushing the detection limit down to single-atom sensitivity. The sub-angstrom focused electron beam (e-beam) of STEM is capable of interacting with an individual atom, thereby it is the ideal platform to direct and control matter at the level of a single atom or a small cluster. In this article, we discuss the transfer of energy and momentum from the incident e-beam to atoms and their subsequent potential dynamics under different e-beam conditions in 2D materials, particularly transition metal dichalcogenides (TMDs). Next, we systematically discuss the e-beam triggered structural evolutions of atomic defects, line defects, grain boundaries, and stacking faults in a few representative 2D materials. Their formation mechanisms, kinetic paths, and practical applications are comprehensively discussed. We show that desired structural evolution or atom-by-atom assembly can be precisely manipulated by e-beam irradiation which could introduce intriguing functionalities to 2D materials. In particular, we highlight the recent progress on controlling single Si atom migration in real-time on monolayer graphene along an extended path with high throughput in automated STEM. These results unprecedentedly demonstrate that single-atom dynamics can be realized by an atomically focused e-beam. With the burgeoning of artificial intelligence and big data, we can expect that fully automated microscopes with real-time data analysis and feedback could readily design and fabricate large scale nanostructures with unique functionalities in the near future.

Tracking atomic structure evolution during directed electron beam induced Si-atom motion in graphene via deep machine learning

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.

Electron-Beam-Induced Molecular Plasmon Excitation and Energy Transfer in Silver Molecular Nanowires

We investigate (1) electron-beam-induced plasmon absorption spectra of Ag molecular nanowire dimers and (2) electron-beam-induced energy transfer between two nanowires. We employ linear-response time-dependent density functional theory (TDDFT) and real-time TDDFT methods to simulate the electron-beam-induced plasmonic excitations, dynamics, and corresponding electron energy loss spectrum for small models of a single molecular nanowire with four Ag atoms and for two Ag nanowires. An array of different relative orientations of nanowires and of different initial excitation conditions resulting from applying an electron beam at different positions with respect to the Ag nanowires is investigated. The results demonstrate (1) an electron beam can induce plasmonic excitations from the molecular Ag nanowire ground state to the excited states that are both optically allowed and forbidden, (2) a tunability for selective excitations that can be controlled by the position of a focused electron beam, and (3) kinetic and dynamic behaviors of time-dependent electron-beam-induced energy transfer between two Ag molecular nanowires depend on the position of the beam source and nanowire separation distance, providing insights into the spatial dependences of plasmonic couplings in nanowire arrays.

Nonadiabatic Effects on Defect Diffusion in Silicon-Doped Nanographenes

Single atom impurities in graphene, substitutional silicon defects in particular, have been observed to diffuse under electron beam irradiation. However, the relative importance of elastic and inelastic scattering in facilitating their mobility remains unclear. Here, we employ excited-state electronic structure calculations to explore potential inelastic effects, and find an electronically nonadiabatic excited-state silicon diffusion pathway involving "softened" Si-C bonding that presents an ∼2 eV lower diffusion barrier than the ground-state pathway. Beam-induced transition rates to this state indicate that the excited-state pathway is accessible through irradiation of the defect site. However, even in the limit of fully elastic scattering, upward nonadiabatic transitions are also possible along the diffusion coordinate, increasing the diffusion barrier and further demonstrating the potential for electronic nonadiabaticity to influence beam-induced atomic transformations in materials. We also propose some experimentally testable signatures of such excited-state pathways.

Understanding and controlling the covalent functionalisation of graphene

Chemical functionalisation is one of the most active areas of graphene research, motivated by fundamental science, the opportunities to adjust or supplement intrinsic properties, and the need to assemble materials for a broad array of applications. Historically, the primary consideration has been the degree of functionalisation but there is growing interest in understanding how and where modification occurs. Reactions may proceed preferentially at edges, defects, or on graphitic faces; they may be correlated, uncorrelated, or anti-correlated with previously grafted sites. A detailed collation of existing literature data indicates that steric effects play a strong role in limiting the extent of reaction. However, the pattern of functionalisation may have important effects on the resulting properties. This article addresses the unifying principles of current graphene functionalisation technologies, with emphasis on understanding and controlling the locus of functionalisation.

Direct matter disassembly via electron beam control: electron-beam-mediated catalytic etching of graphene by nanoparticles

We report electron-beam activated motion of a catalytic nanoparticle along a graphene step edge and associated etching of the edge. The catalytic hydrogenation process was observed to be activated by a combination of elevated temperature and electron beam irradiation. Reduction of beam fluence on the particle was sufficient to stop the process, leading to the ability to switch on and off the etching. Such an approach enables the targeting of individual nanoparticles to induce motion and beam-controlled etching of matter through activated electrocatalytic processes. The applications of electron-beam control as a paradigm for molecular-scale robotics are discussed.

Imaging an unsupported metal-metal bond in dirhenium molecules at the atomic scale

Metallic bonds remain one of the most important and least understood of the chemical bonds. In this study, we generated Re₂ molecules in which the Re-Re core is unsupported by ligands. Real-time imaging of the atomic-scale dynamics of Re₂ adsorbed on a graphitic lattice allows direct measurement of Re-Re bond lengths for individual molecules that changes in discrete steps correlating with bond order from one to four. Direct imaging of the Re-Re bond breaking process reveals a new bonding state with the bond order less than one and a high-amplitude vibrational stretch, preceding the bond dissociation. The methodology, based on aberration-corrected transmission electron microscopy imaging, is shown to be a powerful analytical tool for the investigation of dynamics of metallic bonding at the atomic level.

Spatially Controlled Fabrication and Mechanisms of Atomically Thin Nanowell Patterns in Bilayer WS2 Using in Situ High Temperature Electron Microscopy

We show controlled production of atomically thin nanowells in bilayer WS₂ using an in situ heating holder combined with a focused electron beam in a scanning transmission electron microscope (STEM). We systematically study the formation and evolvement mechanism involved in removing a single layer of WS₂ within a bilayer region with 2 nm accuracy in location and without punching through to the other layer to create a hole. Best results are found when using a high temperature of 800 °C, because it enables thermally activated atomic migration and eliminates the interference from surface carbon contamination. We demonstrate precise control over spatial distributions with 5 nm accuracy of patterning and the width of nanowells adjustable by dose-dependent parameters. The mechanism of removing a monolayer of WS₂ within a bilayer region is different than removing equivalent sections in a monolayer film due to the van der Waals interaction of the underlying remaining layer in the bilayer system that stabilizes the excess W atom stoichiometry within the edges of the nanowell structure and facilitates expansion. This study offers insights for the nanoengineering of nanowells in two-dimensional (2D) transitional metal dichalcogenides (TMDs), which could hold potential as selective traps to localize 2D reactions in molecules and ions, underpinning the broader utilization of 2D material membranes.

Toward Electrochemical Studies on the Nanometer and Atomic Scales: Progress, Challenges, and Opportunities

Electrochemical reactions and ionic transport underpin the operation of a broad range of devices and applications, from energy storage and conversion to information technologies, as well as biochemical processes, artificial muscles, and soft actuators. Understanding the mechanisms governing function of these applications requires probing local electrochemical phenomena on the relevant time and length scales. Here, we discuss the challenges and opportunities for extending electrochemical characterization probes to the nanometer and ultimately atomic scales, including challenges in down-scaling classical methods, the emergence of novel probes enabled by nanotechnology and based on emergent physics and chemistry of nanoscale systems, and the integration of local data into macroscopic models. Scanning probe microscopy (SPM) methods based on strain detection, potential detection, and hysteretic current measurements are discussed. We further compare SPM to electron beam probes and discuss the applicability of electron beam methods to probe local electrochemical behavior on the mesoscopic and atomic levels. Similar to a SPM tip, the electron beam can be used both for observing behavior and as an active electrode to induce reactions. We briefly discuss new challenges and opportunities for conducting fundamental scientific studies, matter patterning, and atomic manipulation arising in this context.

Influence of temperature on the displacement threshold energy in graphene

The atomic structure of nanomaterials is often studied using transmission electron microscopy. In addition to image formation, the energetic electrons impinging on the sample may also cause damage. In a good conductor such as graphene, the damage is limited to the knock-on process caused by elastic electron-nucleus scattering. This process is determined by the kinetic energy an atom needs to be sputtered, i.e. its displacement threshold energy E_d. This is typically assumed to have a fixed value for all electron impacts on equivalent atoms within a crystal. Here we show using density functional tight-binding simulations that the displacement threshold energy is affected by thermal perturbations of atoms from their equilibrium positions. This effect can be accounted for in the estimation of the displacement cross section by replacing the constant threshold energy value with a distribution. Our refined model better describes previous precision measurements of graphene knock-on damage, and should be considered also for other low-dimensional materials.

Building and exploring libraries of atomic defects in graphene: Scanning transmission electron and scanning tunneling microscopy study

The presence and configurations of defects are primary components determining materials functionality. Their population and distribution are often nonergodic and dependent on synthesis history, and therefore rarely amenable to direct theoretical prediction. Here, dynamic electron beam-induced transformations in Si deposited on a graphene monolayer are used to create libraries of possible Si and carbon vacancy defects. Deep learning networks are developed for automated image analysis and recognition of the defects, creating a library of (meta) stable defect configurations. Density functional theory is used to estimate atomically resolved scanning tunneling microscopy (STM) signatures of the classified defects from the created library, allowing identification of several defect types across imaging platforms. This approach allows automatic creation of defect libraries in solids, exploring the metastable configurations always present in real materials, and correlative studies with other atomically resolved techniques, providing comprehensive insight into defect functionalities.

Silicon Substitution in Nanotubes and Graphene via Intermittent Vacancies

The chemical and electrical properties of single-walled carbon nanotubes (SWCNTs) and graphene can be modified by the presence of covalently bound impurities. Although this can be achieved by introducing chemical additives during synthesis, it often hinders growth and leads to limited crystallite size and quality. Here, through the simultaneous formation of vacancies with low-energy argon plasma and the thermal activation of adatom diffusion by laser irradiation, silicon impurities are incorporated into the lattice of both materials. After an exposure of ∼1 ion/nm², we find Si-substitution densities of 0.15 nm^-2 in graphene and 0.05 nm^-2 in nanotubes, as revealed by atomically resolved scanning transmission electron microscopy. In good agreement with predictions of Ar irradiation effects in SWCNTs, we find Si incorporated in both mono- and divacancies, with ∼2/3 being of the first type. Controlled inclusion of impurities in the quasi-1D and -2D carbon lattices may prove useful for applications such as gas sensing, and a similar approach might also be used to substitute other elements with migration barriers lower than that of carbon.

Engineering single-atom dynamics with electron irradiation

Atomic engineering is envisioned to involve selectively inducing the desired dynamics of single atoms and combining these steps for larger-scale assemblies. Here, we focus on the first part by surveying the single-step dynamics of graphene dopants, primarily phosphorus, caused by electron irradiation both in experiment and simulation, and develop a theory for describing the probabilities of competing configurational outcomes depending on the postcollision momentum vector of the primary knock-on atom. The predicted branching ratio of configurational transformations agrees well with our atomically resolved experiments. This suggests a way for biasing the dynamics toward desired outcomes, paving the road for designing and further upscaling atomic engineering using electron irradiation.

Engineering the magnetic properties of PtSe2 monolayer through transition metal doping

Using first-principles calculations, we have studied the energetic feasibility and magnetic properties of transition metal (TM) doped PtSe₂ monolayers. Our study shows that TM doped PtSe₂ layers with 6.25% doping exhibit versatile spintronic behaviour depending on the nature of the dopant TM atoms. Groups IVB and VIII10 TM doped PtSe₂ layers are non magnetic semiconductors, while groups IIIB, VB, VIII8, VIII9, IB TM doped PtSe₂ layers are half-metals and finally, groups VIB, VIIB and IIB TM doped PtSe₂ layers are spin polarized semiconductors. The presence of half-metallic and magnetic semiconducting characteristics suggest that TM doped PtSe₂ layers can be considered as a new kind of dilute magnetic semiconductor and thus have the promise to be used in spintronics. By studying the magnetic interactions between two TM dopants in PtSe₂ monolayers for dopant concentration of 12.5% and dopant distance of 12.85 [Formula: see text], we have found that in particular, Fe and Ru doped PtSe₂ systems are ferromagnetic half-metal having above-room-temperature Curie point of 422 and 379.9 K, respectively. By varying the dopant distance and concentration we have shown that the magnetic interaction is strongly dependent on dopant distance and concentration. Interestingly, the Curie temperature of TM doped PtSe₂ layers is affected by the correlation effects on the TM d states and also spin-orbit coupling. We have also studied the magnetic properties of defect complex composed of one TM dopant and one Pt vacancy (TM_Pt  +  V_Pt) which shows novel magnetism.

Direct Cation Exchange in Monolayer MoS_{2} via Recombination-Enhanced Migration

In addition to their unique optical and electronic properties, two-dimensional materials provide opportunities to directly observe atomic-scale defect dynamics. Here we use scanning transmission electron microscopy to observe substitutional Re impurities in monolayer MoS_{2} undergo direct exchanges with neighboring Mo atoms in the lattice. Density-functional-theory calculations find that the energy barrier for direct exchange, a process that has only been studied as a diffusion mechanism in bulk materials, is too large for either thermal activation or energy directly transferred from the electron beam. The presence of multiple sulfur vacancies next to the exchanged Re-Mo pair, as observed by electron microscopy, does not lower the energy barrier sufficiently to account for the observed atomic exchange. Instead, the calculations find that a Re dopant and surrounding sulfur vacancies introduce an ever-changing set of deep levels in the energy gap. We propose that these levels mediate an "explosive" recombination-enhanced migration via multiple electron-hole recombination events. As a proof of concept, we also show that Re-Mo direct exchange can be triggered via controlled creation of sulfur vacancies. The present experimental and theoretical findings lay a fundamental framework towards manipulating single substitutional dopants in two-dimensional materials.

Defect Engineering in 2D Materials: Precise Manipulation and Improved Functionalities

Two-dimensional (2D) materials have attracted increasing interests in the last decade. The ultrathin feature of 2D materials makes them promising building blocks for next-generation electronic and optoelectronic devices. With reducing dimensionality from 3D to 2D, the inevitable defects will play more important roles in determining the properties of materials. In order to maximize the functionality of 2D materials, deep understanding and precise manipulation of the defects are indispensable. In the recent years, increasing research efforts have been made on the observation, understanding, manipulation, and control of defects in 2D materials. Here, we summarize the recent research progress of defect engineering on 2D materials. The defect engineering triggered by electron beam (e-beam), plasma, chemical treatment, and so forth is comprehensively reviewed. Firstly, e-beam irradiation-induced defect evolution, structural transformation, and novel structure fabrication are introduced. With the assistance of a high-resolution electron microscope, the dynamics of defect engineering can be visualized in situ. Subsequently, defect engineering employed to improve the performance of 2D devices by means of other methods of plasma, chemical, and ozone treatments is reviewed. At last, the challenges and opportunities of defect engineering on promoting the development of 2D materials are discussed. Through this review, we aim to build a correlation between defects and properties of 2D materials to support the design and optimization of high-performance electronic and optoelectronic devices.