Pub Date : 2026-04-01Epub 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":"2026-04-01","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 : 2026-04-01Epub 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":"2026-04-01","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}
We report the development of a chromatic and spherical aberration corrector based on combinations of hexapole and quadrupole fields. Thick hexapole fields are used to generate negative third order spherical aberration and to correct residual axial and off-axial aberrations. As an alternative to the use of round transfer lenses placed between the hexapoles, a quadrupole multiplet producing superimposed electric and magnetic quadrupole fields is used to produce negative chromatic aberration. This quadrupole multiplet also functions as a transfer doublet within the corrector. The simultaneous correction of chromatic and spherical aberrations using this corrector design is described, and a resolution improvement is demonstrated for cases where the energy spread is limiting.
{"title":"Chromatic and spherical aberration correction with hexapole and quadrupole fields","authors":"Shigeyuki Morishita , Hidetaka Sawada , Norihiro Okoshi , Shunsaku Waki , Hironori Tanaka , Katsunori Ichikawa , Angus Kirkland","doi":"10.1016/j.ultramic.2026.114331","DOIUrl":"10.1016/j.ultramic.2026.114331","url":null,"abstract":"<div><div>We report the development of a chromatic and spherical aberration corrector based on combinations of hexapole and quadrupole fields. Thick hexapole fields are used to generate negative third order spherical aberration and to correct residual axial and off-axial aberrations. As an alternative to the use of round transfer lenses placed between the hexapoles, a quadrupole multiplet producing superimposed electric and magnetic quadrupole fields is used to produce negative chromatic aberration. This quadrupole multiplet also functions as a transfer doublet within the corrector. The simultaneous correction of chromatic and spherical aberrations using this corrector design is described, and a resolution improvement is demonstrated for cases where the energy spread is limiting.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114331"},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146173532","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 : 2026-04-01Epub Date: 2026-02-06DOI: 10.1016/j.ultramic.2026.114329
Ali Mostaed , Chen Huang , Amirafshar Moshtaghpour , Emanuela Liberti , Mohammed Yusuf , Judy S. Kim , Angus I. Kirkland
Phase contrast imaging in (scanning) transmission electron microscopy ((S)TEM) is among the most effective approach for investigating local structures, at near atomic resolution in beam-sensitive weakly scattering materials including biological samples. However, they often show poor contrast and low signal-to-noise ratio (SNR) at low electron fluence. Multi-pass data acquisition can be used to improve the SNR, however sample drift between data acquisition often complicates the multi-pass approach, particularly at high magnifications. Although numerous drift correction methods have been developed for conventional phase contrast imaging in the TEM, effective drift correction for multi-pass 4D-STEM data acquisition for low fluence electron ptychography has not been extensively explored. In this paper, we report on two approaches for calculating drift vectors at each probe position between passes; one based on the reconstructed ptychographic phase in real space and the other using diffraction patterns. We demonstrate that both methods are effective in calculating and correcting drift when a defocused probe is used for 4D-STEM data acquisition and improve the contrast of low SNR ptychographic phase reconstructions.
{"title":"Drift correction methods for multi-pass 4D-STEM","authors":"Ali Mostaed , Chen Huang , Amirafshar Moshtaghpour , Emanuela Liberti , Mohammed Yusuf , Judy S. Kim , Angus I. Kirkland","doi":"10.1016/j.ultramic.2026.114329","DOIUrl":"10.1016/j.ultramic.2026.114329","url":null,"abstract":"<div><div>Phase contrast imaging in (scanning) transmission electron microscopy ((S)TEM) is among the most effective approach for investigating local structures, at near atomic resolution in beam-sensitive weakly scattering materials including biological samples. However, they often show poor contrast and low signal-to-noise ratio (SNR) at low electron fluence. Multi-pass data acquisition can be used to improve the SNR, however sample drift between data acquisition often complicates the multi-pass approach, particularly at high magnifications. Although numerous drift correction methods have been developed for conventional phase contrast imaging in the TEM, effective drift correction for multi-pass 4D-STEM data acquisition for low fluence electron ptychography has not been extensively explored. In this paper, we report on two approaches for calculating drift vectors at each probe position between passes; one based on the reconstructed ptychographic phase in real space and the other using diffraction patterns. We demonstrate that both methods are effective in calculating and correcting drift when a defocused probe is used for 4D-STEM data acquisition and improve the contrast of low SNR ptychographic phase reconstructions.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114329"},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146166846","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 : 2026-04-01Epub Date: 2025-12-18DOI: 10.1016/j.ultramic.2025.114302
Johann Brenner , Jürgen M. Plitzko , Sven Klumpe
Focused ion beams (FIB) are widely used instruments in transmission electron microscopy (TEM) sample preparation across scientific disciplines. Generally, site-specific ablation of material is achieved by scanning a highly focused probe across a selected area, leading to the removal of material. However, the geometries of TEM lamellae milled with the FIB are usually highly non-isometric, with their thickness generally being orders of magnitude smaller than their width and length. Here, we explore a changed probe shape for milling. Instead of using an ion beam with the standard, Gaussian-like probe, we characterize the use of the stigmator as quasi-cylindrical lens to create a highly astigmatic probe that we term ‘ion knife’. Using the ion knife allows for material removal by spreading the current over a larger area and changes the dimension of the probe as observed in spot burn cross-sections. To allow for rapid alignment of parameters in beam shaping, we demonstrate a method to approximate the shapes of our probes by imaging. Finally, exploring shaped probes in cryogenic lamella preparation, we demonstrate the feasibility of cellular lamella milling and sectioning of cryo-lift-out volumes with the ion knife.
{"title":"Exploring shaped focused ion beams for lamella preparation","authors":"Johann Brenner , Jürgen M. Plitzko , Sven Klumpe","doi":"10.1016/j.ultramic.2025.114302","DOIUrl":"10.1016/j.ultramic.2025.114302","url":null,"abstract":"<div><div>Focused ion beams (FIB) are widely used instruments in transmission electron microscopy (TEM) sample preparation across scientific disciplines. Generally, site-specific ablation of material is achieved by scanning a highly focused probe across a selected area, leading to the removal of material. However, the geometries of TEM lamellae milled with the FIB are usually highly non-isometric, with their thickness generally being orders of magnitude smaller than their width and length. Here, we explore a changed probe shape for milling. Instead of using an ion beam with the standard, Gaussian-like probe, we characterize the use of the stigmator as quasi-cylindrical lens to create a highly astigmatic probe that we term ‘ion knife’. Using the ion knife allows for material removal by spreading the current over a larger area and changes the dimension of the probe as observed in spot burn cross-sections. To allow for rapid alignment of parameters in beam shaping, we demonstrate a method to approximate the shapes of our probes by imaging. Finally, exploring shaped probes in cryogenic lamella preparation, we demonstrate the feasibility of cellular lamella milling and sectioning of cryo-lift-out volumes with the ion knife.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114302"},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145967105","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 : 2026-04-01Epub 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":"2026-04-01","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 : 2026-04-01Epub Date: 2025-12-19DOI: 10.1016/j.ultramic.2025.114291
Tom Fraysse, Robin Cours, Hugo Lourenço-Martins, Florent Houdellier
This paper explores the topologies of caustics observed in instruments that employ charged particles, such as electron and ion microscopes. These geometrical figures are studied here using catastrophe theory. The application of this geometrical theory to our optical situation has enabled us to analytically reproduce the behaviours of various caustics. The interest lies mainly in the universal nature of these results since our treatment requires no prior knowledge of the optical configuration, but only a smart definition of the control space. This universal approach has finally made it possible to extract mathematical relationships between the aberration coefficients of any optical system, which were hidden by the complexity of optical trajectories but revealed by the set of catastrophes in the control space. These results provide a glimpse for future applications of caustics in the development of new corrected optical systems, especially for ions-based devices.
{"title":"Morphologies of caustics studied by catastrophe charged-particle optics","authors":"Tom Fraysse, Robin Cours, Hugo Lourenço-Martins, Florent Houdellier","doi":"10.1016/j.ultramic.2025.114291","DOIUrl":"10.1016/j.ultramic.2025.114291","url":null,"abstract":"<div><div>This paper explores the topologies of caustics observed in instruments that employ charged particles, such as electron and ion microscopes. These geometrical figures are studied here using catastrophe theory. The application of this geometrical theory to our optical situation has enabled us to analytically reproduce the behaviours of various caustics. The interest lies mainly in the universal nature of these results since our treatment requires no prior knowledge of the optical configuration, but only a smart definition of the control space. This universal approach has finally made it possible to extract mathematical relationships between the aberration coefficients of any optical system, which were hidden by the complexity of optical trajectories but revealed by the set of catastrophes in the control space. These results provide a glimpse for future applications of caustics in the development of new corrected optical systems, especially for ions-based devices.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114291"},"PeriodicalIF":2.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928659","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 : 2026-04-01Epub 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":"2026-04-01","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 : 2026-04-01Epub 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":"2026-04-01","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 : 2026-03-15DOI: 10.1016/j.ultramic.2026.114352
Vijithkumar Vijayan, Sudhakar Sivasubramaniam
The microscope is an essential tool for biological research. This study introduces a microscope auxiliary device designed to study the morphology of segments in annelid species such as earthworms. The novel, lightweight, portable device enables omni-surface visualization of embedded samples through extensive rotational capabilities. The research details the device design, working principles, and demonstrates its application by capturing fluorescent images of setae patterns in four earthworm species: Eudrilus eugeniae, Lampito mauritii, Pontoscolex corethrurus, and Perionyx ceylanensis. These species represent two distinct setae arrangements: lumbricine (E. eugeniae, P. corethrurus) and perichaetine (L. mauritii, P. ceylanensis). Setae patterns were comprehensively analyzed by measuring the inter-setae arc-distance using the mathematical algorithm, "Euler's approximation" for elliptical arc length. The results demonstrate that the device effectively documents the cylindrical structure of specimens, providing detailed morphological information not readily obtainable with conventional microscopy methods.
显微镜是生物学研究必不可少的工具。本研究介绍了一种用于研究蚯蚓等环节动物节段形态的显微镜辅助装置。这种新颖、轻便、便携的设备可以通过广泛的旋转功能实现嵌入式样品的全表面可视化。本研究详细介绍了该装置的设计、工作原理，并通过捕获四种蚯蚓（Eudrilus eugenae、Lampito mauritii、pontocolex corethrurus和Perionyx ceylanensis）刚毛图案的荧光图像演示了该装置的应用。这些物种代表两种不同的刚毛排列：lumbricine （E. eugenae， P. corethrurus）和perichaetine （L. mauritii， P. ceylanensis）。利用椭圆弧长“欧拉近似”的数学算法，通过测量刚毛间的弧距，对刚毛图案进行了综合分析。结果表明，该装置有效地记录了标本的圆柱形结构，提供了传统显微镜方法难以获得的详细形态学信息。
{"title":"A microscope- auxiliary device to profile the setae patterns of earthworm species; a study on Eudrilus eugeniae, Lampito mauritii, Pontoscolex corethrurus, and Perionyx ceylanensis.","authors":"Vijithkumar Vijayan, Sudhakar Sivasubramaniam","doi":"10.1016/j.ultramic.2026.114352","DOIUrl":"https://doi.org/10.1016/j.ultramic.2026.114352","url":null,"abstract":"<p><p>The microscope is an essential tool for biological research. This study introduces a microscope auxiliary device designed to study the morphology of segments in annelid species such as earthworms. The novel, lightweight, portable device enables omni-surface visualization of embedded samples through extensive rotational capabilities. The research details the device design, working principles, and demonstrates its application by capturing fluorescent images of setae patterns in four earthworm species: Eudrilus eugeniae, Lampito mauritii, Pontoscolex corethrurus, and Perionyx ceylanensis. These species represent two distinct setae arrangements: lumbricine (E. eugeniae, P. corethrurus) and perichaetine (L. mauritii, P. ceylanensis). Setae patterns were comprehensively analyzed by measuring the inter-setae arc-distance using the mathematical algorithm, \"Euler's approximation\" for elliptical arc length. The results demonstrate that the device effectively documents the cylindrical structure of specimens, providing detailed morphological information not readily obtainable with conventional microscopy methods.</p>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"283 ","pages":"114352"},"PeriodicalIF":2.0,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147487307","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号