Toma Susi

• D.Sc. (Tech)
• Associate Professor at University of Vienna

Single-particle methods based on Kohn-Sham unoccupied states to describe near-edge X-ray absorption (XAS) spectra are routinely applied for the description of K-edge spectra, as there is no complication due to spin-orbit (SO) coupling. L- and M-edge spectra are often addressed via variants of time-dependent density functional theory (TDDFT) based o...

Transmission electron microscopy ( TEM ) is one of the most powerful tools for characterizing a wide variety of materials. Rapid developments in instrumentation are allowing additional information to be gleaned from advanced imaging techniques and bringing many new people into the field. At the same time, open-source code has become an indispensabl...

Accurate computational ptychographic phase reconstructions are enabled by fast direct‐electron cameras with high dynamic ranges used for four‐dimensional scanning transmission electron microscopy (4D‐STEM). The availability of open software packages is making such analyses widely accessible, and especially when implemented in Python, easy to compar...

Density functional theory with linear combination of atomic orbitals (LCAO) basis sets is useful for studying large atomic systems, especially when it comes to computationally highly demanding time-dependent dynamics. We have implemented the Ehrenfest molecular dynamics (ED) method with the approximate approach of Tomfohr and Sankey within the proj...

Electronic charge transfer at the atomic scale can reveal fundamental information about chemical bonding, but is far more challenging to directly image than the atomic structure. The charge density is dominated by the atomic nuclei, with bonding causing only a small perturbation. Thus detecting any change due to bonding requires a higher level of s...

We substitute individual Pt atoms into monolayer MoS$_2$ and study the resulting atomic structures with single-sideband (SSB) ptychography supported by ab initio simulations. We demonstrate that while high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) imaging provides excellent Z-contrast, distinguishing some def...

Accurate computational ptychographic phase reconstructions are enabled by fast direct-electron cameras with high dynamic ranges used for four-dimensional scanning transmission electron microscopy (4D-STEM). The availability of open software packages is making such analyses widely accessible, and especially when implemented in Python, easy to compar...

We measure the two-dimensional elastic modulus $E^\text{2D}$ of atomically clean defect-engineered graphene with a known defect distribution and density in correlated ultra-high vacuum experiments. The vacancies are introduced via low-energy (< 200 eV) Ar ion irradiation and the atomic structure is obtained via semi-autonomous scanning transmission...

Interferometry of atomic matter waves is an essential tool in fundamental sciences [1-5] and for applied quantum sensors [6-10]. The sensitivity of interferometers scales with the momentum separation of the diffracted matter waves, leading to the development of large-momentum transfer beam splitters [11,12]. However, despite decades of research, cr...

Density functional theory with linear combination of atomic orbitals (LCAO) basis sets is useful for studying large atomic systems, especially when it comes to computationally highly demanding time-dependent dynamics. We have implemented the Ehrenfest molecular dynamics (ED) method with the approximate approach of Tomfohr and Sankey within the proj...

Defect-engineered and even amorphous two-dimensional (2D) materials have recently gained interest due to properties that differ from their pristine counterparts. Since these properties are highly sensitive to the exact atomic structure, it is crucial to be able to characterize them at atomic resolution over large areas. This is only possible when t...

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three repr...

Replacing traditional journals with a more modern solution is not a new idea. Here, we propose ways to overcome the social dilemma underlying the decades of inaction. Any solution needs to not only resolve the current problems but also be capable of preventing takeover by corporations: it needs to replace traditional journals with a decentralized,...

Understanding electron irradiation effects is vital not only for reliable transmission electron microscopy characterization, but increasingly also for the controlled manipulation of 2D materials. The displacement cross sections of monolayer hexagonal boron nitride (hBN) are measured using aberration‐corrected scanning transmission electron microsco...

We present a method that lowers the dose required for an electron ptychographic reconstruction by adaptively scanning the specimen, thereby providing the required spatial information redundancy in the regions of highest importance. The proposed method is built upon a deep learning model that is trained by reinforcement learning, using prior knowled...

Electron irradiation-induced damage is often the limiting factor in imaging materials prone to ionization or electronic excitations due to inelastic electron scattering. Quantifying the related processes at the atomic scale has only become possible with the advent of aberration-corrected (scanning) transmission electron microscopes and two-dimensio...

Understanding electron irradiation effects is vital not only for reliable characterization of materials using transmission electron microscopy, but increasingly also for the controlled manipulation of two-dimensional materials. Knock-on displacements due to elastic electron backscattering are theoretically straightforward to model, and appear to co...

Electron irradiation-induced damage is often the limiting factor in imaging materials prone to ionization or electronic excitations due to inelastic electron scattering. Quantifying the related processes at the atomic scale has only become possible with the advent of aberration-corrected (scanning) transmission electron microscopes and 2D materials...

The presence of metal atoms at the edges of graphene nanoribbons (GNRs) opens new possibilities toward tailoring their physical properties. We present here formation and high-resolution characterization of indium (In) chains on the edges of graphene-supported GNRs. The GNRs are formed when adsorbed hydrocarbon contamination crystallizes via laser h...

Electronic charge transfer at the atomic scale can reveal fundamental information about chemical bonding, but is far more challenging to directly image than the atomic structure. Bonding generally involves a relatively small perturbation of the total charge density dominated by the atomic nuclei, and thus detecting any change due to bonding require...

Machine learning and artificial intelligence (ML/AI) are rapidly becoming an indispensable part of physics research, with 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 an...

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 ab...

We introduce a novel method to improve the computational efficiency for (S)TEM image simulation by employing matrix diagonalization of the mixed envelope function (MEF). The MEF is derived by taking the finite size and the energy spread of the effective electron source into account, and is a component of the transmission cross-coefficient that acco...

We compare the ion-induced electron emission from freestanding monolayers of graphene and MoS2 to find a sixfold higher number of emitted electrons for graphene even though both materials have similar work functions. An effective single-band Hubbard model explains this finding by a charge-up in MoS2 that prevents low energy electrons from escaping...

We present a quantitatively accurate machine-learning (ML) model for the computational prediction of core-electron binding energies, from which X-ray photoelectron spectroscopy (XPS) spectra can be readily obtained. Our model combines density functional theory (DFT) with GW and uses kernel ridge regression for the ML predictions. We apply the new a...

Transmission electron microscopy characterization may damage materials, but an electron beam can also induce interesting dynamics. Elastic knock-on is the main electron irradiation damage mechanism in metals including graphene, and although atomic vibrations influence its cross section, only the out-of-plane direction has been considered so far. He...

Although surface diffusion is critical for many physical and chemical processes, including the epitaxial growth of crystals and heterogeneous catalysis, it is particularly challenging to directly study. Here, we estimate the carbon adatom migration barrier on freestanding monolayer graphene by quantifying its temperature-dependent electron knock-on...

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 s...

As a one-atom thick, mechanically strong, and chemically stable material with unique electronic properties, graphene can serve as the basis for a large number of applications. One way to tailor its properties is the controlled introduction of covalently bound heteroatoms into the lattice. In this study, we demonstrate efficient implantation of indivi...

Although surface diffusion is critical for many physical and chemical processes, including the epitaxial growth of crystals and heterogeneous catalysis, it is particularly challenging to directly study. Here, we estimate the carbon adatom migration barrier on freestanding monolayer graphene by quantifying its temperature-dependent electron knock-on...

Heterostructures composed of two-dimensional (2D) materials are already opening many new possibilities in such fields of technology as electronics and magnonics, but far more could be achieved if the number and diversity of 2D materials is increased. So far, only a few dozen 2D crystals have been extracted from materials that exhibit a layered phas...

Doping of the graphene lattice with transition metal atoms resulting in high magnetic anisotropy energy (MAE) is an important goal of materials research owing to its potential application in spintronics. In this article, by using spin-polarized density functional theory including spin-orbit coupling, we examined magnetic properties of graphene with...

For more than twenty years, the international research community has affirmed its support for open and collaborative practices that improve the quality, transparency, reproducibility and inclusiveness of science. In France, this orientation has been reflected in the adoption of two National Plans for Open Science, in 2018 and 2021. In this context...

We present a quantitatively accurate machine-learning (ML) model for the computational prediction of core-electron binding energies, from which x-ray photoelectron spectroscopy (XPS) spectra can be readily obtained. Our model combines density functional theory (DFT) with $GW$ and uses kernel ridge regression for the ML predictions. We apply the new...

Elastic knock-on is the main electron irradiation damage mechanism in metals including graphene. Atomic vibrations influence its cross-section, but only the out-of-plane direction has been considered so far in the literature. Here, we present a full three-dimensional theory of knock-on damage including the effect of temperature and vibrations to de...

A major factor underlying several of scholarship's most pressing problems is its antiquated journal system with its trifecta of reproducibility, affordability and functionality crises. Any solution needs to not only solve the current problems but also be capable of preventing a takeover by corporations. Technically, there is broad agreement on the...

Heterostructures composed of two-dimensional (2D) materials are already opening many new possibilities in such fields of technology as electronics and magnonics, but far more could be achieved if the number and diversity of 2D materials is increased. So far, only a few dozen 2D crystals have been extracted from materials that exhibit a layered phas...

Diamond and graphene are carbon allotropes with starkly different physical characteristics. Their combination into graphene-on-diamond heterostructures could benefit from the complementary properties of both components. Graphitization of single-crystalline diamond surfaces is a promising synthesis route, but a clear understanding of the growth of g...

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 suspende...

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 samp...

The electronic properties of stacked few‐layer 2D materials are highly dependent on their precise structural arrangement. In article number 2100388, featured on the front cover, Michael J. Zachman, Miaofang Chi, and co‐workers describe a four‐dimensional scanning transmission electron microscopy technique that utilizes interference between Bragg di...

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 samp...

Structural engineering is the first step toward changing properties of materials. While this can be at relative ease done for bulk materials, for example, using ion irradiation, similar engineering of 2D materials and other low-dimensional structures remains a challenge. The difficulties range from the preparation of clean and uniform samples to th...

Processes of research evaluation are coming under increasing scrutiny, with detractors arguing that they have adverse effects on research quality, and that they support a research culture of competition to the detriment of collaboration. Based on three personal perspectives, we consider how current systems of research evaluation lock early career r...

Van der Waals materials composed of stacks of individual atomic layers have attracted considerable attention due to their exotic electronic properties that can be altered by, e.g., manipulating the twist angle of bilayer materials or the stacking sequence of trilayer materials. To fully understand and control the unique properties of these few‐laye...

Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret experimental data. Since nuclear cores dominate electron scattering, the scattering potential is typically described using the independent atom model, which completely neglects valence bonding and its effect on the transmitting electro...

Transmission electron microscopy (TEM) and scanning TEM (STEM) are indispensable tools for materials characterization. However, during a typical (S)TEM experiment, the sample is subject to a number of effects that can change its atomic structure. Of these, perhaps the least discussed are chemical modifications due to the non-ideal vacuum around the...

Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret experimental data. Since nuclear cores dominate electron scattering, the scattering potential is typically described using the independent atom model, which completely neglects valence bonding and its effect on the transmitting electro...

The simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret their contrast and extract specimen features. This is especially true for high-resolution phase-contrast imaging of materials, but electron scattering simulations based on atomistic models are widely used in materials science and s...

Vertically stacked low-dimensional heterostructures are outstanding systems both for exploring fundamental physics and creating new devices. Due to nanometerscale building blocks, atomic scale phenomena become for them of fundamental importance, including during device operation. These can be accessed in situ in aberration-corrected scanning transm...

The chemical composition of graphene samples and their dopants, functional groups, and impurities is vital information not only for applications but also for many fundamental studies. Other characterization methods mainly based on core-level techniques including X-ray and electron spectroscopies are the most appropriate tools for determining these...

Transmission electron microscopy (TEM) and scanning TEM (STEM) are indispensable tools for materials characterization. However, during a typical (S)TEM experiment, the sample is subject to a number of effects that can change its atomic structure. Of these, perhaps the least discussed are chemical modifications due to the non-ideal vacuum around the...

Van der Waals materials composed of stacks of individual atomic layers have attracted considerable attention due to their exotic electronic properties that can be altered by, for example, manipulating the twist angle of bilayer materials or the stacking sequence of trilayer materials. To fully understand and control the unique properties of these f...

The simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret their contrast and extract specimen features. This is especially true for high-resolution phase-contrast imaging of materials, but model-based reconstructions in TEM are widely used across the physical and biological sciences. Sinc...

Single atoms and few-atom nanoclusters are of high interest in catalysis and plasmonics, but pathways for their fabrication and stable 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 s...

Atomistic Understanding of Damage and Beam-Driven Dynamics in 2D Materials - Alexandru Chirita, Alexander Markevich, Jani Kotakoski, Toma Susi

Uncovering the Mechanism for Electron-Beam Manipulation of Dopants in Silicon - Alexander Markevich, Bethany Hudak, Andrew Lupini, Toma Susi

abTEM: ab Initio Transmission Electron Microscopy Image Simulation - Jacob Madsen, Toma Susi

Quantitative Measurement and Utilization of Electron Irradiation Effects in 2D Materials - Gregor Leuthner, Thuy An Bui, Georg Zagler, Bernhard Fickl, Mohammad Monazam, Alexandru Chirita, Toma Susi, Jani Kotakoski

The electronic and magnetic properties of graphene can be modulated by doping it with other elements, especially those with a different number of valence electrons. In this article, we first provide a three-dimensional reconstruction of the atomic structure of a phosphorus substitution in graphene by using aberration-corrected scanning transmission...

The Community of Open Scholarship Grassroots Networks (COSGN), includes 120 grassroots networks, representing virtually every region of the world and every research discipline. These networks communicate and coordinate on topics of common interest. We propose, using an NSF 19-501 Full-Scale implementation grant, to formalize governance and coordina...

Synopsis We have investigated theoretically the possibility to diffract hydrogen atoms through a suspended graphene single layer. Using quantum and semi classical approaches we evaluate the momentum and energy exchange to the electronic and vibrational system and estimate their influence on the coherence and spot size.

Important recent advances in transmission electron microscopy instrumentation and capabilities have made it indispensable for atomic-scale materials characterization. At the same time, the availability of two-dimensional materials has provided ideal samples where each atom or vacancy can be resolved. Recent studies have also revealed new possibilit...

Pertinent existing hydrogen technologies for energy storage require unsustainable amounts of scarce platinum group metals. Here, an electrocatalyst comprising high-aspect-ratio platinum nanowires (PtNWs) on single-walled carbon nanotubes (SWNTs) with ultralow Pt content (340 ngPt cm⁻²) is employed for hydrogen evolution reaction (HER). A comparable...

Along with hydrogen, carbon, nitrogen and oxygen are the arguably most important elements for organic chemistry. Due to their rich variety of possible bonding configurations, they can form a staggering number of compounds. Here, we present a detailed analysis of nitrogen and oxygen bonding configurations in a defective carbon (graphene) lattice. Us...

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 deter...

The established application of graphene in organic/inorganic spin‐valve spintronic assemblies is as a spin‐transport channel for spin‐polarized electrons injected from ferromagnetic substrates. To generate and control spin injection without such substrates, the graphene backbone must be imprinted with spin‐polarized states and itinerant‐like spins....

Automated Real-time Analysis of Atomic-resolution STEM Images - Volume 25 Supplement - Jacob Madsen, Andreas Postl, Toma Susi

Substitutional Si Doping of Graphene and Nanotubes through Ion Irradiation-Induced Vacancies - Volume 25 Supplement - Heena Inani, Kimmo Mustonen, Alexander Markevich, Er-Xiong Ding, Mukesh Tripathi, Aqeel Hussian, Clemens Mangler, Esko I. Kauppinen, Toma Susi, Jani Kotakoski

Electron-Beam Manipulation of Lattice Impurities in Graphene and Single-Walled Carbon Nanotubes - Volume 25 Supplement - Toma Susi, Mukesh Tripathi, Kimmo Mustonen, Alexander Markevich, Clemens Mangler, Cong Su, Ju Li, Juan Carlos Idrobo, Jannik Meyer, Jani Kotakoski

Atomic-scale Chemical Manipulation of Materials in the Scanning Transmission Electron Microscope under Controlled Atmospheres - Volume 25 Supplement - Gregor T Leuthner, Clemens Mangler, Jannik C Meyer, Toma Susi, Jani Kotakoski

Quantifying Elastic and Inelastic Electron Irradiation Damage in Transmission Electron Microscopy of 2D Materials - Volume 25 Supplement - Toma Susi, Tibor Lehnert, Ute Kaiser, Jannik Meyer, Jani Kotakoski