arXiv subjects

Toma Susi

Publications and source records attributed to Toma Susi.

At least 19 recordsLinked to original sources

arXiv2026

Competition between vacancy creation and filling in defect-engineering of hBN

Hexagonal boron nitride (hBN) has recently become the focus of intense research as a material that can host quantum emitters. It is known that such emission is related to point defects, but in order to conclusively correlate specific defects to their spectra, having control over the defect creation mechanism is required. Here, we prepare freestanding, monolayer hBN samples and irradiate them with ultra-low-energy (150 eV) Ar+ ions. The samples are characterized before and after irradiation via scanning transmission electron microscopy to assess the defect density and distribution. Contrary to what analytical potential molecular dynamics simulations have predicted, we predominantly observe boron single vacancies after ion irradiation, followed by double vacancies at half the count. Moreover, we also observe that vacancy filling with Si and C impurity atoms plays a more significant role in the created defects than previously assumed, potentially posing a problem for selective creation of quantum emitters in hBN.

cond-mat.mtrl-sci↗

arXiv2026

Simulating Continuous-Rotation 3D Electron Diffraction: A Multislice and Bloch Wave Framework

To improve the agreement between measured and calculated intensities of three-dimensional electron diffraction (3D ED) experiments, a simulation pipeline is needed to assess and quantify the influence of various structural and experimental parameters. We present a computational pipeline, built upon the abTEM Python package, to simulate continuous-rotation 3D electron diffraction data based on either the Bloch wave or the multislice formalism. Multislice calculations in arbitrary orientations are achieved through large supercells and windowing. We investigate the convergence of key simulation parameters and test their consistency, establishing suitable parameters for accurate and efficient simulations. The pipeline's applicability and robustness are demonstrated through case studies on cubic silicon as well as stretched and sheared variants, analyzing the influence of electron kinetic energy, sample thickness, orientation, and symmetry on simulated diffraction intensities. Finally, we investigate a representative selection of seven compounds, including cubic $\mathrm{SrTiO_3}$, monoclinic $\alpha$-glycine $\mathrm{C_2H_5NO_2}$, and triclinic kyanite $\mathrm{Al_2SiO_5}$ to validate the method. This framework for the simulation of 3D electron diffraction data establishes an approach to investigate the dependence of diffracted intensities on experimentally relevant parameters which are difficult to systematically investigate in experiments.

cond-mat.mtrl-sci↗

arXiv2026

Atom diffraction in the strong-coupling regime

Analytic methods based on matter-wave diffraction are a cornerstone in condensed-matter research, providing access to static and dynamic materials properties down to the atomic level. In these experiments, the shape of the diffraction pattern is largely determined by the lattice at equilibrium whereas vibrationally-induced distortions are treated perturbatively. Here, we show that the perturbative approach does not hold for helium diffracted at kiloelectronvolt energy through freestanding single-layer graphene. In this case, we enter a new regime of strong coupling where the projectile strongly interacts with the electron density of several lattice atoms simultaneously, leading to phase shifts of several radians. In consequence, lattice distortions introduce a significant phase spread that cannot be described by the typically employed Debye-Waller factor. We show that the weak-coupling regime is retained for atomic hydrogen diffraction. The experimental results are supported by simulations, providing a regime-independent approach to describe the influence of phonons on atom diffraction phenomena.

quant-ph↗

arXiv2026

Electron-beam induced methane decomposition for in-situ carbon doping of hexagonal boron nitride

Controlling the spatial incorporation of carbon into hexagonal boron nitride (hBN) is essential for engineering optically active defects, yet existing approaches lack nanoscale precision and control over the carbon supply. Here, we demonstrate a method for carbon doping of hBN using electron-beam irradiation in a low-pressure methane atmosphere, where the beam simultaneously generates vacancies and decomposes methane into individual carbon and hydrogen atoms. Using annular dark-field scanning transmission electron microscopy, we show that increasing the methane partial pressure suppresses pore growth and drives the formation of triangular boron-terminated pores through preferential hydrogen etching of nitrogen. Time-resolved electron energy-loss spectroscopy (EELS) mapping reveals progressive carbon incorporation into the lattice, accompanied by boron and nitrogen depletion. Carbon clustering occurs predominantly within the irradiated area: 84+-7% of carbon-rich regions are confined to the area exposed to the electron beam, while some carbon atoms are also found to diffuse up to an average distance of 4.7+-0.5 nm beyond it. The incorporated carbon atoms arrange in a hexagonal pattern within the lattice, forming patches that do not exceed ~1 nm in size. Analysis of the EELS fine structure indicates modifications to the local electronic environment within these regions, with implications for the optical properties of the resulting carbon-related defects.

cond-mat.mtrl-sci↗

arXiv2025

Origin of circular and triangular pores in electron-irradiated hexagonal boron nitride

For nearly two decades, it has been known that electron irradiation of hexagonal boron nitride (hBN) in a transmission electron microscope leads to the formation of triangular pores. This has been attributed to the lower displacement threshold energy of boron, with or without the assistance of an inelastic scattering event, typically assuming that chemical processes caused by residual gases can be neglected. In this study, in contrast to previous high-vacuum experiments, we show that electron irradiation in ultra-high vacuum leads to circular pores, whereas even small amounts of oxygen in the atmosphere during the experiment drive the pores to grow into triangle shapes with nitrogen-terminated edges. This result is shown to hold for samples of different types and from different manufacturers, and at different electron energies as well as focused scanning and defocused stationary beams. Our results explain the chemical origin of triangular pores in hBN and demonstrate a deterministic way to create atomically defined pores in this important 2D material.

cond-mat.mtrl-sci↗

arXiv2025

Explicit core-hole single-particle methods for L- and M- edge X-ray absorption and electron energy-loss spectra

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 on SO calculations. Here, we present a computationally efficient implementation based on single-particle calculations with core holes within the frozen-core approximation. Combined with a semiempirical energy shift and a fixed spin-orbit splitting for each core level, this allows for a computationally cheap, while overall accurate prediction of experimental spectra on the absolute energy scale. The spectra are compared to about 40 times slower linear-response TDDFT calculations for molecules and show similar or even better match with experiment. An exception are multiplet effects that we analyze in detail and show that they cannot be covered by a single-particle approximation. A similar picture emerges for solids, where good qualitative and sometimes even quantitative agreement to experimental XAS and electron energy-loss spectra is achieved.

cond-mat.mtrl-sci↗

arXiv2025

Uncovering the atomic structure of substitutional platinum dopants in MoS$_2$ with single-sideband ptychography

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 defect types such as single and double sulfur vacancies remains challenging due to their low relative contrast difference. However, SSB with its nearly linear Z-contrast and high phase sensitivity enables reliable identification of these defect configurations as well as various Pt dopant structures at significantly lower electron doses. Our findings uncover the precise atomic placement and highlight the potential of SSB ptychography for detailed structural analysis of dopant-modified 2D materials while minimizing beam-induced damage, offering new pathways for understanding and engineering atomic-scale features in 2D systems.

cond-mat.mtrl-sci↗

arXiv2025

Quantifying Phase Magnitudes of Open-Source Focused-Probe 4D-STEM Ptychography Reconstructions

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 compare in terms of computational efficiency and reconstruction quality. In this contribution, I reconstruct atomic phase shifts from convergent-beam electron diffraction maps of pristine monolayer graphene, which is an ideal dose-robust uniform phase object, acquired on a Dectris ARINA detector installed in a Nion UltraSTEM 100 operated at 60 keV with a focused-probe convergence semi-angle of 34 mrad. For two different recorded maximum scattering angle settings, I compare a range of direct and iterative open-source phase reconstruction algorithms, evaluating their computational efficiency and tolerance to reciprocal-space binning and real-space thinning of the data. The quality of the phase images is assessed by quantifying the variation of atomic phase shifts using a robust parameter-based method revealing an overall agreement with some notable differences in the absolute magnitudes and the variation of the phases. Although such variation is not a major issue when analyzing data with many identical atoms, it does put limits on what level of precision can be relied upon for unique sites such as defects or dopants, which also tend to be more dose-sensitive. Overall, these findings and the accompanying open data and code provide useful guidance for the sampling required for desired levels of phase precision, and suggest particular care is required when relying on electron ptychography for quantitative analyses of atomic-scale electromagnetic properties.

cond-mat.mtrl-sci↗

arXiv2024

Corrugation-dominated mechanical softening of defect-engineered graphene

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 electron microscopy and image analysis. Based on atomic force microscopy nanoindentation measurements, a decrease of $E^\text{2D}$ from 286 to 158 N/m is observed when measuring the same graphene membrane before and after an ion irradiation-induced vacancy density of $1.0\times 10^{13}$ cm$^{-2}$. This decrease is significantly greater than what is predicted by most theoretical studies and in stark contrast to some measurements presented in the literature. With the assistance of atomistic simulations, we show that this softening is mostly due to corrugations caused by local strain at vacancies with two or more missing atoms, while the influence of single vacancies is negligible. We further demonstrate that the opposite effect can be measured when surface contamination is not removed before defect engineering

cond-mat.mtrl-sci↗

arXiv2024

Diffraction of atomic matter waves through a 2D crystal

Diffraction of atoms from surfaces provides detailed insights into structures, interactions, and dynamical processes. However, currently the method is limited to measurements in reflection - diffraction through materials has only been demonstrated for subatomic particles and is an outstanding challenge for atoms. We diffract helium and hydrogen atoms at kiloelectronvolt energies through single-layer graphene at normal incidence. Despite the atoms' high kinetic energy as well as coupling to the electronic system of graphene, we observe coherent scattering. This preservation of coherence was the result of the limited momentum transfer between the projectile and the lattice, resulting from interaction times on the femtosecond scale.

quant-ph↗

arXiv2024

Ehrenfest dynamics with localized atomic-orbital basis sets within the projector augmented-wave method

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 projector augmented-wave code GPAW. We apply this method to small molecules as well as larger periodic systems, and elucidate its limits, advantages, and disadvantages in comparison to the existing implementation of Ehrenfest dynamics with a real-space grid representation. For modest atomic velocities, LCAO-ED shows satisfactory accuracy at a much reduced computational cost. This method will be particularly useful for modeling ion irradiation processes that require large amounts of vacuum in the simulation cell.

cond-mat.mtrl-sci↗

arXiv2024

GPAW: An open Python package for electronic-structure calculations

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 representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE) providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation (BSE), variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support of GPU acceleration has been achieved with minor modifications of the GPAW code thanks to the CuPy library. We end the review with an outlook describing some future plans for GPAW.

cond-mat.mtrl-sci↗

arXiv2024

Defect-engineering hexagonal boron nitride using low-energy Ar+ irradiation

Monolayer hexagonal boron nitride (hBN) has recently become the focus of intense research as a material to host quantum emitters. Although it is well known that such emission is associated with point defects, so far no conclusive correlation between the spectra and specific defects has been demonstrated. Here, we prepare atomically clean suspended hBN samples and subject them to low-energy ion irradiation. The samples are characterized before and after irradiation via automated scanning transmission electron microscopy imaging to assess the defect concentrations and distributions. We find an intrinsic defect concentration of ca. 0.03/nm2 (with ca. 55% boron and 8% nitrogen single vacancies, 20% double vacancies and 16% more complex vacancy structures). To be able to differentiate between these and irradiation-induced defects, we create a significantly higher (but still moderate) concentration of defects with the ions (0.30/nm2), and now find ca. 55% boron and 12% nitrogen single vacancies, 14% double vacancies, and 18% more complex vacancy structures. The results demonstrate that already the simplest irradiation provides selectivity for the defect types, and open the way for future experiments to explore changing the selectivity by modifying the irradiation parameters.

cond-mat.mtrl-sci↗

arXiv2023

Creation of single vacancies in hBN with electron irradiation

Understanding electron irradiation effects is vital not only for reliable transmission electron microscopy characterization, but increasingly also for the controlled manipulation of two-dimensional materials. The displacement cross sections of monolayer hBN are measured using aberration-corrected scanning transmission electron microscopy in near ultra-high vacuum at primary beam energies between 50 and 90 keV. Damage rates below 80 keV are up to three orders of magnitude lower than previously measured at edges under poorer residual vacuum conditions where chemical etching appears to have been dominant. Notably, is possible to create single vacancies in hBN using electron irradiation, with boron almost twice as likely as nitrogen to be ejected below 80 keV. Moreover, any damage at such low energies cannot be explained by elastic knock-on, even when accounting for vibrations of the atoms. A theoretical description is developed to account for lowering of the displacement threshold due to valence ionization resulting from inelastic scattering of probe electrons, modelled using charge-constrained density functional theory molecular dynamics. Although significant reductions are found depending on the constrained charge, quantitative predictions for realistic ionization states are currently not possible. Nonetheless, there is potential for defect-engineering of hBN at the level of single vacancies using electron irradiation.

cond-mat.mes-hall↗

arXiv2023

Combined electronic excitation and knock-on damage in monolayer MoS2

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-dimensional materials that allow imaging each lattice atom. While it has been shown for graphene that pure knock-on damage arising from elastic scattering is sufficient to describe the observed damage, the situation is more complicated with two-dimensional semiconducting materials such as MoS2. Here, we measure the displacement cross section for sulfur atoms in MoS2 with primary beam energies between 55 and 90 keV, and correlate the results with existing measurements and theoretical models. Our experimental data suggests that the displacement process can occur from the ground state, or with single or multiple excitations, all caused by the same impinging electron. The results bring light to reports in the recent literature, and add necessary experimental data for a comprehensive description of electron irradiation damage in a two-dimensional semiconducting material. Specifically, the results agree with a combined inelastic and elastic damage mechanism at intermediate energies, in addition to a pure elastic mechanism that dominates above 80 keV. When the inelastic contribution is assumed to arise through impact ionization, the associated excitation lifetime is on the order of picoseconds, on par with expected excitation lifetimes in MoS2, whereas it drops to some tens of femtoseconds when direct valence excitation is considered.

cond-mat.mtrl-sci↗

arXiv2023

Detecting charge transfer at defects in 2D materials with electron ptychography

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 sensitivity than imaging structure and the overall charge density. Here we achieve the sensitivity required to detect charge transfer in both pristine and defected monolayer WS\textsubscript{2} using the high dose efficiency of electron ptychography and its ability to correct for lens aberrations. Excellent agreement is achieved with first-principles image simulations including where thermal diffuse scattering is explicitly modeled via finite-temperature molecular dynamics based on density functional theory. The focused-probe ptychography configuration we use also provides the important ability to concurrently collect the annular dark-field signal, which can be unambiguously interpreted in terms of the atomic structure and chemical identity of the atoms, independently of the charge transfer. Our results demonstrate both the power of ptychographic reconstructions and the importance of quantitatively accurate simulations to aid their interpretation.

cond-mat.mtrl-sci↗

arXiv2022

Accurate computational prediction of core-electron binding energies in carbon-based materials: A machine-learning model combining density-functional theory and $\boldsymbol{GW}$

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 approach to materials and molecules containing carbon, hydrogen and oxygen, and obtain qualitative and quantitative agreement with experiment, resolving spectral features within 0.1 eV of reference experimental spectra. The method only requires the user to provide a structural model for the material under study to obtain an XPS prediction within seconds. Our new tool is freely available online through the XPS Prediction Server.

cond-mat.mtrl-sci↗

arXiv2022

Indirect measurement of the carbon adatom migration barrier on graphene

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 damage. Due to the fast healing of vacancies by diffusing adatoms, the damage rate decreases with increasing temperature. By analyzing the observed damage rates at 300-1073 K using a model describing our finite scanning probe, we find a barrier of (0.33 \pm 0.03) eV.

cond-mat.mtrl-sci↗