Pub Date : 2026-01-20DOI: 10.1016/j.ultramic.2026.114320
Wojciech Marciniak , Joanna Marciniak , José Ángel Castellanos-Reyes , Ján Rusz
Time-resolved pump-probe experiments offer unique possibilities for studying ultrafast processes; however, simulation tools for interpreting phonon dynamics in electron diffraction patterns at the sub-picosecond scale remain limited. We introduce the frozen trajectory excitation (FTE) method of exciting phonons beyond their thermal equilibrium population by modifying a molecular dynamics trajectory in the ()-space, and couple it with a new approach to ensemble sampling that extends frozen phonon multislice simulations into the time domain. In this approach, phonons with a certain natural frequency () and located within an arbitrarily selected range of phonon wave vector () are first selectively excited within a single molecular dynamics trajectory. Subsequently, several parallel relaxation runs are started at random points, and snapshots from these trajectories serve as inputs for multislice simulations at defined time delays.
We apply this framework to fcc Ni with relaxation time resolution of 10 fs. The simulations reveal multi-phonon scattering processes as well as strong mode dependence in phonon relaxation, highlighting the importance of considering phonon-specific behavior in ultrafast dynamics. Our results show that mode-dependent relaxation leaves measurable signatures in diffraction patterns, providing predictive guidance for future time-resolved TEM studies.
{"title":"Mode-dependent phonon relaxation in time-resolved electron diffraction pattern simulations","authors":"Wojciech Marciniak , Joanna Marciniak , José Ángel Castellanos-Reyes , Ján Rusz","doi":"10.1016/j.ultramic.2026.114320","DOIUrl":"10.1016/j.ultramic.2026.114320","url":null,"abstract":"<div><div>Time-resolved pump-probe experiments offer unique possibilities for studying ultrafast processes; however, simulation tools for interpreting phonon dynamics in electron diffraction patterns at the sub-picosecond scale remain limited. We introduce the frozen trajectory excitation (FTE) method of exciting phonons beyond their thermal equilibrium population by modifying a molecular dynamics trajectory in the (<span><math><mrow><mover><mrow><mi>q</mi></mrow><mo>→</mo></mover><mo>,</mo><mi>ω</mi></mrow></math></span>)-space, and couple it with a new approach to ensemble sampling that extends frozen phonon multislice simulations into the time domain. In this approach, phonons with a certain natural frequency (<span><math><mi>ω</mi></math></span>) and located within an arbitrarily selected range of phonon wave vector (<span><math><mover><mrow><mi>q</mi></mrow><mo>→</mo></mover></math></span>) are first selectively excited within a single molecular dynamics trajectory. Subsequently, several parallel relaxation runs are started at random points, and snapshots from these trajectories serve as inputs for multislice simulations at defined time delays.</div><div>We apply this framework to fcc Ni with relaxation time resolution of 10<!--> <!-->fs. The simulations reveal multi-phonon scattering processes as well as strong mode dependence in phonon relaxation, highlighting the importance of considering phonon-specific behavior in ultrafast dynamics. Our results show that mode-dependent relaxation leaves measurable signatures in diffraction patterns, providing predictive guidance for future time-resolved TEM studies.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114320"},"PeriodicalIF":2.0,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146024162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-17DOI: 10.1016/j.ultramic.2026.114322
Alan J. Craven, Bianca Sala , Ian MacLaren
It is demonstrated that the low loss region of the electron energy loss spectrum can successfully map (V,Ti,Nb)C precipitates in the matrix of a steel including determining their thicknesses, volume, number density, volume fraction and size distribution. A comparison is made of the results obtained using both the low loss (mainly plasmon-type losses and low-lying semi-core-loss edges) and high loss signals (principally more classic core-loss edges) from the same dataset. The agreement between the two sets of results is excellent. While the high loss results are more element specific, the data takes much longer to acquire. When acquiring only the low loss data, the acquisition time is much shorter and would therefore allow mapping of much larger areas of a specimen, with obvious potential for making statistically significant measurements of precipitate size distributions and volume fractions. Provided that an initial study which includes high loss data is made, such large area maps can be quantified. The residual diffraction contrast in the low loss signal also provides a link connecting the precipitates and the microstructure of the matrix. While the approach here is applied to steels, it has potential for much wider applicability.
{"title":"Towards large-area EELS mapping of precipitates in a steel matrix: Comparing low loss and high loss quantification","authors":"Alan J. Craven, Bianca Sala , Ian MacLaren","doi":"10.1016/j.ultramic.2026.114322","DOIUrl":"10.1016/j.ultramic.2026.114322","url":null,"abstract":"<div><div>It is demonstrated that the low loss region of the electron energy loss spectrum can successfully map (V,Ti,Nb)C precipitates in the matrix of a steel including determining their thicknesses, volume, number density, volume fraction and size distribution. A comparison is made of the results obtained using both the low loss (mainly plasmon-type losses and low-lying semi-core-loss edges) and high loss signals (principally more classic core-loss edges) from the same dataset. The agreement between the two sets of results is excellent. While the high loss results are more element specific, the data takes much longer to acquire. When acquiring only the low loss data, the acquisition time is much shorter and would therefore allow mapping of much larger areas of a specimen, with obvious potential for making statistically significant measurements of precipitate size distributions and volume fractions. Provided that an initial study which includes high loss data is made, such large area maps can be quantified. The residual diffraction contrast in the low loss signal also provides a link connecting the precipitates and the microstructure of the matrix. While the approach here is applied to steels, it has potential for much wider applicability.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114322"},"PeriodicalIF":2.0,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146024161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-16DOI: 10.1016/j.ultramic.2026.114318
David Lamprecht , Shrirang Chokappa , Alissa M. Freilinger , Barbara Maria Mayer , Maximilian Melchior , Jana Dzíbelová , Darwin Lorber , Luiz H.G. Tizei , Mathieu Kociak , Clemens Mangler , Lado Filipovic , Jani Kotakoski
There is a growing interest in identifying the origin of single-photon emission in hexagonal boron nitride (hBN), with proposed candidates including boron and nitrogen vacancies as well as carbon substitutional dopants. Because photon emission intensity often increases with sample thickness, hBN flakes used in these studies commonly exceed 30 atomic layers. To identify potential emitters at the atomic scale, annular dark-field scanning transmission electron microscopy (ADF-STEM) is frequently employed. However, due to the intrinsic AA’ stacking of hBN with vertically alternating boron and nitrogen atoms, this approach is complicated even in few-layer systems. Here, we demonstrate using STEM image simulations and experiments that, even under idealized conditions, the intensity differences between boron- and nitrogen-dominated columns and carbon substitutions become indistinguishable at thicknesses beyond 17 atomic layers (ca. 6 nm). While vacancy-type defects can remain detectable at somewhat larger thicknesses, also their detection becomes unreliable at thicknesses typically used in photonic studies. We further show that common residual aberrations, particularly threefold astigmatism, can lead to artificial contrast differences between columns, which may result in misidentification of atomic defects. We systematically study the effects of non-radially symmetric aberrations on multilayer hBN and demonstrate that even small residual threefold astigmatism can significantly distort the STEM contrast, leading to misleading interpretations.
{"title":"Single photon emitters in hBN: Limitations of atomic resolution imaging and potential sources of error","authors":"David Lamprecht , Shrirang Chokappa , Alissa M. Freilinger , Barbara Maria Mayer , Maximilian Melchior , Jana Dzíbelová , Darwin Lorber , Luiz H.G. Tizei , Mathieu Kociak , Clemens Mangler , Lado Filipovic , Jani Kotakoski","doi":"10.1016/j.ultramic.2026.114318","DOIUrl":"10.1016/j.ultramic.2026.114318","url":null,"abstract":"<div><div>There is a growing interest in identifying the origin of single-photon emission in hexagonal boron nitride (hBN), with proposed candidates including boron and nitrogen vacancies as well as carbon substitutional dopants. Because photon emission intensity often increases with sample thickness, hBN flakes used in these studies commonly exceed 30 atomic layers. To identify potential emitters at the atomic scale, annular dark-field scanning transmission electron microscopy (ADF-STEM) is frequently employed. However, due to the intrinsic AA’ stacking of hBN with vertically alternating boron and nitrogen atoms, this approach is complicated even in few-layer systems. Here, we demonstrate using STEM image simulations and experiments that, even under idealized conditions, the intensity differences between boron- and nitrogen-dominated columns and carbon substitutions become indistinguishable at thicknesses beyond 17 atomic layers (ca. 6 nm). While vacancy-type defects can remain detectable at somewhat larger thicknesses, also their detection becomes unreliable at thicknesses typically used in photonic studies. We further show that common residual aberrations, particularly threefold astigmatism, can lead to artificial contrast differences between columns, which may result in misidentification of atomic defects. We systematically study the effects of non-radially symmetric aberrations on multilayer hBN and demonstrate that even small residual threefold astigmatism can significantly distort the STEM contrast, leading to misleading interpretations.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114318"},"PeriodicalIF":2.0,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146019890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-13DOI: 10.1016/j.ultramic.2026.114319
Chen Liu , Jingkai Xu , Qingxiao Wang , Tianchao Guo , Maolin Chen , Dongxing Zheng , Husam N. Alshareef , Xixiang Zhang
The preparation of high-quality plan-view transmission electron microscopy (TEM) lamellae is essential for investigating the in-plane properties of thin films. However, current focused ion beam (FIB) techniques are limited by ion-beam damage, surface contamination, and time-consuming workflows. Here, we introduce NaCl microcrystals as a sacrificial protective layer, which effectively shields the surface from ion irradiation and can be completely removed by simple dissolution in water, leaving a pristine surface. Building on this, we established a universal and streamlined FIB workflow for plan-view lamellae fabrication from thin films that eliminates the need for conventional Pt/C deposition and avoids custom hardware, relying solely on standard commercial components. Using a classic metal multilayer and an ultrathin epitaxial oxide film as representative model systems, we demonstrate that the prepared plan-view lamellae exhibit large uniform areas, preserved film structures, and contamination-free surfaces, enabling reliable surface-sensitive TEM analyses. This time-efficient and user-friendly approach offers a powerful solution for the contamination- and damage-free preparation of plan-view TEM lamellae across diverse thin-film systems, paving the way for in-depth investigations of their in-plane properties.
{"title":"A universal FIB approach for contamination- and damage-free plan-view TEM lamellae using NaCl sacrificial layers","authors":"Chen Liu , Jingkai Xu , Qingxiao Wang , Tianchao Guo , Maolin Chen , Dongxing Zheng , Husam N. Alshareef , Xixiang Zhang","doi":"10.1016/j.ultramic.2026.114319","DOIUrl":"10.1016/j.ultramic.2026.114319","url":null,"abstract":"<div><div>The preparation of high-quality plan-view transmission electron microscopy (TEM) lamellae is essential for investigating the in-plane properties of thin films. However, current focused ion beam (FIB) techniques are limited by ion-beam damage, surface contamination, and time-consuming workflows. Here, we introduce NaCl microcrystals as a sacrificial protective layer, which effectively shields the surface from ion irradiation and can be completely removed by simple dissolution in water, leaving a pristine surface. Building on this, we established a universal and streamlined FIB workflow for plan-view lamellae fabrication from thin films that eliminates the need for conventional Pt/C deposition and avoids custom hardware, relying solely on standard commercial components. Using a classic metal multilayer and an ultrathin epitaxial oxide film as representative model systems, we demonstrate that the prepared plan-view lamellae exhibit large uniform areas, preserved film structures, and contamination-free surfaces, enabling reliable surface-sensitive TEM analyses. This time-efficient and user-friendly approach offers a powerful solution for the contamination- and damage-free preparation of plan-view TEM lamellae across diverse thin-film systems, paving the way for in-depth investigations of their in-plane properties.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114319"},"PeriodicalIF":2.0,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145979276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-03DOI: 10.1016/j.ultramic.2026.114309
Sylvain Laforet , Corentin Le Guillou , Adrien Teurtrie , Maya Marinova , Francisco de la Peña , Anne-Marie Blanchenet , Sylvain Bernard , Hugues Leroux
Characterizing organic compounds using STEM-EELS at high spatial resolution is crucial in materials science and geosciences, especially for organics intricately mixed with minerals at the nanoscale, as is the case in carbonaceous meteorites. However, the high spatial resolution provided by TEM comes with the challenge of electron beam sensitivity, which has long hindered the study of these fragile compounds. Here, we take advantage of direct electron detectors to revisit analytical strategies, searching for the best compromise to prevent beam damage and reach the highest spatial resolution. Our STEM-EELS parametric survey focuses on two reference polymers (PEEK and PES) which differ in their molecular structures and susceptibility to radiation-induced damage. We sequentially acquire low loss and carbon K-edge spectra at low dwell time using a multi-frame protocol, possible thanks to noiseless direct electron detectors. Results show that PES is much more sensitive than PEEK and that the main damage mechanism is radiolysis coupled to recombination. Damage rates are lower when working at an accelerating voltage of 200 keV rather than at 80 keV. Cooling the sample (- 100 °C) helps reducing mass loss and amorphization, but can also lead to the formation of undesired functional groups through recombination. The pixel size affects beam damage independently of the electron dose. Using the fastest dwell-time permitted by the detectors (80 µs) and pixel sizes of 1.5, 7.5, 15 and 30 nm, we show that PEEK resists at 15 nm pixel but is rapidly amorphized at 1 nm while PES is already unstable at 30 nm pixel size. We understand this as damage delocalization effect on successive pixels. The insoluble organic matter extracted from the Orgueil meteorite also appears to better resist damages at 200 keV, but its aliphatic groups are nevertheless affected at pixel size of 15 nm. A reasonable spectral agreement is found between STEM-EELS and synchrotron-based XANES-STXM, paving the road for investigating extra-terrestrial samples such as those returned by space mission from carbonaceous asteroids Ryugu and Bennu.
{"title":"STEM-EELS study of beam damage in polymers and extra-terrestrial organic matter using direct electron detectors","authors":"Sylvain Laforet , Corentin Le Guillou , Adrien Teurtrie , Maya Marinova , Francisco de la Peña , Anne-Marie Blanchenet , Sylvain Bernard , Hugues Leroux","doi":"10.1016/j.ultramic.2026.114309","DOIUrl":"10.1016/j.ultramic.2026.114309","url":null,"abstract":"<div><div>Characterizing organic compounds using STEM-EELS at high spatial resolution is crucial in materials science and geosciences, especially for organics intricately mixed with minerals at the nanoscale, as is the case in carbonaceous meteorites. However, the high spatial resolution provided by TEM comes with the challenge of electron beam sensitivity, which has long hindered the study of these fragile compounds. Here, we take advantage of direct electron detectors to revisit analytical strategies, searching for the best compromise to prevent beam damage and reach the highest spatial resolution. Our STEM-EELS parametric survey focuses on two reference polymers (PEEK and PES) which differ in their molecular structures and susceptibility to radiation-induced damage. We sequentially acquire low loss and carbon K-edge spectra at low dwell time using a multi-frame protocol, possible thanks to noiseless direct electron detectors. Results show that PES is much more sensitive than PEEK and that the main damage mechanism is radiolysis coupled to recombination. Damage rates are lower when working at an accelerating voltage of 200 keV rather than at 80 keV. Cooling the sample (- 100 °C) helps reducing mass loss and amorphization, but can also lead to the formation of undesired functional groups through recombination. The pixel size affects beam damage independently of the electron dose. Using the fastest dwell-time permitted by the detectors (80 µs) and pixel sizes of 1.5, 7.5, 15 and 30 nm, we show that PEEK resists at 15 nm pixel but is rapidly amorphized at 1 nm while PES is already unstable at 30 nm pixel size. We understand this as damage delocalization effect on successive pixels. The insoluble organic matter extracted from the Orgueil meteorite also appears to better resist damages at 200 keV, but its aliphatic groups are nevertheless affected at pixel size of 15 nm. A reasonable spectral agreement is found between STEM-EELS and synchrotron-based XANES-STXM, paving the road for investigating extra-terrestrial samples such as those returned by space mission from carbonaceous asteroids Ryugu and Bennu.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114309"},"PeriodicalIF":2.0,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-03DOI: 10.1016/j.ultramic.2026.114308
Marco Santucci, Ute Kolb
Nanocrystalline materials are the basis of many novel engineered systems, including batteries, nanocomposites, and glass ceramics. Three-dimensional electron diffraction (3D ED) has become a key technique for structural analysis of such materials, offering clear advantages over conventional X-ray diffraction. Commercial routine 3D ED acquisition allowing for measurements of crystals down to ∼750 nm is now standard, but pushing the measurable size towards a few tens of nanometers introduces new challenges, requiring robust crystal-tracking methods. At this scale, TEM automation, reliable object detection, and high mechanical precision of the goniometer are essential.
PyFast-ADT is introduced as a modular automation framework for 3D ED data collection, extending the measurable size range through improved crystal tracking routines. Its Python architecture enhances shareability and promotes facility automation within the 3D ED and Cryo-EM communities. The PatchworkCC algorithm combines Cross-Correlation with Kalman Filtering to achieve fully automatic crystal tracking with improved accuracy and minimal user supervision. Characterization of goniometer reproducibility revealed a rapid decrease behaviour degrading precision, addressed by the HiPerGonio procedure, which stabilizes performance and supports optimal TEM/sample holder choices.
Together, these developments enable fully automated 3D ED data collection on 25 nm nanocrystals embedded in a glass-ceramic matrix, increasing throughput up to sixfold and advancing reproducible, high-throughput structure determination at the nanometer scale.
{"title":"Evaluation of the reproducibility and crystal tracking precision of TEM goniometers in tomography experiments","authors":"Marco Santucci, Ute Kolb","doi":"10.1016/j.ultramic.2026.114308","DOIUrl":"10.1016/j.ultramic.2026.114308","url":null,"abstract":"<div><div>Nanocrystalline materials are the basis of many novel engineered systems, including batteries, nanocomposites, and glass ceramics. Three-dimensional electron diffraction (3D ED) has become a key technique for structural analysis of such materials, offering clear advantages over conventional X-ray diffraction. Commercial routine 3D ED acquisition allowing for measurements of crystals down to ∼750 nm is now standard, but pushing the measurable size towards a few tens of nanometers introduces new challenges, requiring robust crystal-tracking methods. At this scale, TEM automation, reliable object detection, and high mechanical precision of the goniometer are essential.</div><div>PyFast-ADT is introduced as a modular automation framework for 3D ED data collection, extending the measurable size range through improved crystal tracking routines. Its Python architecture enhances shareability and promotes facility automation within the 3D ED and Cryo-EM communities. The PatchworkCC algorithm combines Cross-Correlation with Kalman Filtering to achieve fully automatic crystal tracking with improved accuracy and minimal user supervision. Characterization of goniometer reproducibility revealed a rapid decrease behaviour degrading precision, addressed by the HiPerGonio procedure, which stabilizes performance and supports optimal TEM/sample holder choices.</div><div>Together, these developments enable fully automated 3D ED data collection on 25 nm nanocrystals embedded in a glass-ceramic matrix, increasing throughput up to sixfold and advancing reproducible, high-throughput structure determination at the nanometer scale.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114308"},"PeriodicalIF":2.0,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-26DOI: 10.1016/j.ultramic.2025.114305
Dana O. Byrne , Stephanie M. Ribet , Demie Kepaptsoglou , Quentin M. Ramasse , Colin Ophus , Frances I. Allen
Tetravacancies in monolayer hexagonal boron nitride (hBN) with consistent edge termination (boron or nitrogen) form triangular nanopores with electrostatic potentials that can be leveraged for applications such as selective ion transport and neuromorphic computing. In order to quantitatively predict the properties of these structures, an atomic-level understanding of their local electronic and chemical environments is required. Moreover, robust methods for their precision manufacture are needed. Here we use electron irradiation in a scanning transmission electron microscope (STEM) at a high dose rate to drive the formation of boron-terminated tetravacancies in monolayer hBN. Characterization of the defects is achieved using aberration-corrected STEM, monochromated electron energy-loss spectroscopy (EELS), and electron ptychography. Z-contrast in STEM and chemical fingerprinting by core-loss EELS enable identification of the edge terminations, while electron ptychography gives insight into structural relaxation of the tetravacancies and provides evidence of enhanced electron density around the defect perimeters indicative of bonding effects.
{"title":"Fabrication and characterization of boron-terminated tetravacancies in monolayer hBN using STEM, EELS and electron ptychography","authors":"Dana O. Byrne , Stephanie M. Ribet , Demie Kepaptsoglou , Quentin M. Ramasse , Colin Ophus , Frances I. Allen","doi":"10.1016/j.ultramic.2025.114305","DOIUrl":"10.1016/j.ultramic.2025.114305","url":null,"abstract":"<div><div>Tetravacancies in monolayer hexagonal boron nitride (hBN) with consistent edge termination (boron or nitrogen) form triangular nanopores with electrostatic potentials that can be leveraged for applications such as selective ion transport and neuromorphic computing. In order to quantitatively predict the properties of these structures, an atomic-level understanding of their local electronic and chemical environments is required. Moreover, robust methods for their precision manufacture are needed. Here we use electron irradiation in a scanning transmission electron microscope (STEM) at a high dose rate to drive the formation of boron-terminated tetravacancies in monolayer hBN. Characterization of the defects is achieved using aberration-corrected STEM, monochromated electron energy-loss spectroscopy (EELS), and electron ptychography. Z-contrast in STEM and chemical fingerprinting by core-loss EELS enable identification of the edge terminations, while electron ptychography gives insight into structural relaxation of the tetravacancies and provides evidence of enhanced electron density around the defect perimeters indicative of bonding effects.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114305"},"PeriodicalIF":2.0,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145897877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Scanning tunneling microscopy (STM) has significantly influenced the fields of nanoscience and nanotechnology. However, the tip effect and thermal drift cause loss and distortion of data in the STM images. Here, we propose a physics-guided optimization model for extracting STM imaging parameters, including tip shape, thermal drift, depth of field, current, and height. The model uses partial charge densities from density functional theory (DFT) simulation and works based on the mass comparison of experimental and simulated images using a two-dimensional Pearson correlation. Testing the model on Si(111)-7 × 7 reconstruction images provided higher than 96 % correlations for both biases. The fitting showed the highest correlation for only two bands in each image instead of the integration of all bands. Gaussian functions were used in the model to simulate the tip effect, which could recover 1.5-6 % of the lost data due to the blurring effect. Additionally, thermal drift was detected and corrected in the negative bias image, which could linearly distort the data by about 19 %. An important advantage of using this model is increasing the microscopy speed because there is no need to slow down the scanning process in microscopy experiments to evade thermal drift.
{"title":"A correlation-based optimization model to recover lost and distorted data from scanning tunneling microscopy images based on density functional theory","authors":"Ehsan Moradpur-Tari , Andreas Kyritsakis , Mohadeseh Karimkhah , Veronika Zadin","doi":"10.1016/j.ultramic.2025.114306","DOIUrl":"10.1016/j.ultramic.2025.114306","url":null,"abstract":"<div><div>Scanning tunneling microscopy (STM) has significantly influenced the fields of nanoscience and nanotechnology. However, the tip effect and thermal drift cause loss and distortion of data in the STM images. Here, we propose a physics-guided optimization model for extracting STM imaging parameters, including tip shape, thermal drift, depth of field, current, and height. The model uses partial charge densities from density functional theory (DFT) simulation and works based on the mass comparison of experimental and simulated images using a two-dimensional Pearson correlation. Testing the model on Si(111)-7 × 7 reconstruction images provided higher than 96 % correlations for both biases. The fitting showed the highest correlation for only two bands in each image instead of the integration of all bands. Gaussian functions were used in the model to simulate the tip effect, which could recover 1.5-6 % of the lost data due to the blurring effect. Additionally, thermal drift was detected and corrected in the negative bias image, which could linearly distort the data by about 19 %. An important advantage of using this model is increasing the microscopy speed because there is no need to slow down the scanning process in microscopy experiments to evade thermal drift.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114306"},"PeriodicalIF":2.0,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pixelated differential phase contrast (DPC) is a four-dimensional scanning transmission electron microscopy (4D-STEM) technique in which the position of the transmitted beam is tracked to reconstruct the electromagnetic fields of a sample. Although it can provide (semi-) quantitative information for a range of different applications, the measurements are greatly affected by the microscope’s optical and acquisition settings in terms of sensitivity, accuracy, and spatial resolution, particularly when measuring weak electric fields. Herein, we focus on the nano-beam 4D-STEM configuration and systematically study the way in which all the parameters typically selected by users for pixelated-DPC experiments influence the lowest achievable electric field sensitivity. First, we define the metric by which the sensitivity is assessed, discussing the optimal ranges for parameters including convergence semi-angle, electron dose, and camera length in absence of external field, while also evaluating the effect of the scanning system. Next, the sensitivity and its error are assessed under field-bound conditions, realized by a coplanar capacitor that allows the position of the transmitted beam to be shifted controllably using an external bias. Comparison of the experimental results with finite element method calculations yields quantitative information about the accuracy that can be attained for these measurements, while the effects of microscope drift and sample charging are also discussed. Our findings provide a platform for the quantitative assessment of weak electric fields as calculated by pixelated-DPC experiments, while highlighting the challenges associated with these measurements.
{"title":"Assessing the electric field sensitivity measured by pixelated differential phase contrast imaging in vacuum both in the absence of external fields and under field-bound conditions","authors":"Pierpaolo Ranieri , Reinis Ignatans , Victor Boureau , Vasiliki Tileli","doi":"10.1016/j.ultramic.2025.114307","DOIUrl":"10.1016/j.ultramic.2025.114307","url":null,"abstract":"<div><div>Pixelated differential phase contrast (DPC) is a four-dimensional scanning transmission electron microscopy (4D-STEM) technique in which the position of the transmitted beam is tracked to reconstruct the electromagnetic fields of a sample. Although it can provide (semi-) quantitative information for a range of different applications, the measurements are greatly affected by the microscope’s optical and acquisition settings in terms of sensitivity, accuracy, and spatial resolution, particularly when measuring weak electric fields. Herein, we focus on the nano-beam 4D-STEM configuration and systematically study the way in which all the parameters typically selected by users for pixelated-DPC experiments influence the lowest achievable electric field sensitivity. First, we define the metric by which the sensitivity is assessed, discussing the optimal ranges for parameters including convergence semi-angle, electron dose, and camera length in absence of external field, while also evaluating the effect of the scanning system. Next, the sensitivity and its error are assessed under field-bound conditions, realized by a coplanar capacitor that allows the position of the transmitted beam to be shifted controllably using an external bias. Comparison of the experimental results with finite element method calculations yields quantitative information about the accuracy that can be attained for these measurements, while the effects of microscope drift and sample charging are also discussed. Our findings provide a platform for the quantitative assessment of weak electric fields as calculated by pixelated-DPC experiments, while highlighting the challenges associated with these measurements.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114307"},"PeriodicalIF":2.0,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-21DOI: 10.1016/j.ultramic.2025.114304
T. Ben Britton, Tianbi Zhang
We present a simple ‘shift and add’ based improvement in the angular resolution of single electron backscatter diffraction (EBSD) patterns. Sub-pixel image registration is used to measure the (sub-pixel) difference in projection parameters for patterns collected within a map, and then the pattern is shifted and added together. The resultant EBSD-pattern is shown to contain more angular information than a long-exposure single pattern, via 2D Fast Fourier Transform (FFT)-based analysis. In particular, this method has the potential to enhance the scope of small compact direct electron detectors (DEDs).
{"title":"Angular resolution enhancement of electron backscatter diffraction patterns","authors":"T. Ben Britton, Tianbi Zhang","doi":"10.1016/j.ultramic.2025.114304","DOIUrl":"10.1016/j.ultramic.2025.114304","url":null,"abstract":"<div><div>We present a simple ‘shift and add’ based improvement in the angular resolution of single electron backscatter diffraction (EBSD) patterns. Sub-pixel image registration is used to measure the (sub-pixel) difference in projection parameters for patterns collected within a map, and then the pattern is shifted and added together. The resultant EBSD-pattern is shown to contain more angular information than a long-exposure single pattern, via 2D Fast Fourier Transform (FFT)-based analysis. In particular, this method has the potential to enhance the scope of small compact direct electron detectors (DEDs).</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114304"},"PeriodicalIF":2.0,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145834867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}