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	Author	Pedrazo-Tardajos, A.; Arslan Irmak, E.; Kumar, V.; Sánchez-Iglesias, A.; Chen, Q.; Wirix, M.; Freitag, B.; Albrecht, W.; Van Aert, S.; Liz-Marzán, L.M.; Bals, S.
	Title	Thermal Activation of Gold Atom Diffusion in Au@Pt Nanorods			Type	A1 Journal article
	Year	2022	Publication	ACS nano	Abbreviated Journal	Acs Nano
	Volume		Issue		Pages
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	Understanding the thermal stability of bimetallic nanoparticles is of vital importance to preserve their functionalities during their use in a variety of applications. In contrast to well-studied bimetallic systems such as Au@Ag, heat-induced morphological and compositional changes in Au@Pt nanoparticles are insufficiently understood, even though Au@Pt is an important material for catalysis. To investigate the thermal instability of Au@Pt nanorods at temperatures below their bulk melting point, we combined in situ heating with two- and three-dimensional electron microscopy techniques, including three-dimensional energy-dispersive X-ray spectroscopy. The experimental results were used as input for molecular dynamics simulations, to unravel the mechanisms behind the morphological transformation of Au@Pt core–shell nanorods. We conclude that thermal stability is influenced not only by the degree of coverage of Pt on Au but also by structural details of the Pt shell.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000819246800001	Publication Date	2022-06-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1936-0851	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	17.1	Times cited	8	Open Access	OpenAccess
	Notes	S.B., S.V.A., L.M.L.-M. and A.P.-T. acknowledge financial support from the European Commission under the Horizon 2020 Programme by grant nos. 731019 (EUSMI) and 823717 (ESTEEM3) and ERC Consolidator grant nos. 815128 (REALNANO) and 770887 (PICOMETRICS). L.M.L.-M. acknowledges funding from MCIN/AEI/10.13039/501100011033 through grants no. PID2020-117779RB-I00 and Maria de Maeztu Unit of Excellence no. MDM-2017-0720. The authors acknowledge the resources and services used for the simulations in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government.; esteem3reported; esteem3JRA			Approved	Most recent IF: 17.1
	Call Number	EMAT @ emat @c:irua:188540			Serial	7072
Permanent link to this record



	Author	Fatermans, J.; Romolini, G.; Altantzis, T.; Hofkens, J.; Roeffaers, M.B.J.; Bals, S.; Van Aert, S.
	Title	Atomic-scale detection of individual lead clusters confined in Linde Type A zeolites			Type	A1 Journal article
	Year	2022	Publication	Nanoscale	Abbreviated Journal	Nanoscale
	Volume		Issue		Pages
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT)
	Abstract	Structural analysis of metal clusters confined in nanoporous materials is typically performed by X-ray-driven techniques. Although X-ray analysis has proved its strength in the characterization of metal clusters, it provides averaged structural information. Therefore, we here present an alternative workflow for bringing the characterization of confined metal clusters towards the local scale. This workflow is based on the combination of aberration-corrected transmission electron microscopy (TEM), TEM image simulations, and powder X-ray diffraction (XRD) with advanced statistical techniques. In this manner, we were able to characterize the clustering of Pb atoms in Linde Type A (LTA) zeolites with Pb loadings as low as 5 wt%. Moreover, individual Pb clusters could be directly detected. The proposed methodology thus enables a local-scale characterization of confined metal clusters in zeolites. This is important for further elucidation of the connection between the structure and the physicochemical properties of such systems.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000809619900001	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.7	Times cited	2	Open Access	OpenAccess
	Notes	The authors acknowledge the Research Foundation Flanders through project fundings (FWO, G026718N, G050218N, ZW15_09-G0H6316N, and W002221N) and through a PhD scholarship to G.R. (grant 11C6920N), as well as iBOF-21-085 PERSIST. T.A. and S.V.A. acknowledge funding from the University of Antwerp Research fund (BOF). J.H. acknowledges the Flemish government through long-term structural funding Methusalem (CASAS2, Meth/15/04) and the MPI as MPI fellow. M.R. acknowledges funding by the KU Leuven Research Fund (C14/19/079). S.B. and S.V.A. acknowledge funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (ERC Consolidator Grants No. 815128−REALNANO and No. 770887−PICOMETRICS). The authors thank Dr. D. Chernyshov for the collection of XRD measurements.			Approved	Most recent IF: 6.7
	Call Number	EMAT @ emat @c:irua:189061			Serial	7076
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	Author	Hao, Y.; Velpula, G.; Kaltenegger, M.; Bodlos, W.R.; Vibert, F.; Mali, K.S.; De Feyter, S.; Resel, R.; Geerts, Y.H.; Van Aert, S.; Beljonne, D.; Lazzaroni, R.
	Title	From 2D to 3D : bridging self-assembled monolayers to a substrate-induced polymorph in a molecular semiconductor			Type	A1 Journal article
	Year	2022	Publication	Chemistry of materials	Abbreviated Journal	Chem Mater
	Volume	34	Issue	5	Pages	2238-2248
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	In this study, a new bottom-up approach is proposed to predict the crystal structure of the substrate-induced polymorph (SIP) of an archetypal molecular semiconductor. In spite of intense efforts, the formation mechanism of SIPs is still not fully understood, and predicting their crystal structure is a very delicate task. Here, we selected lead phthalocyanine (PbPc) as a prototypical molecular material because it is a highly symmetrical yet nonplanar molecule and we demonstrate that the growth and crystal structure of the PbPc SIPs can be templated by the corresponding physisorbed self-assembled molecular networks (SAMNs). Starting from SAMNs of PbPc formed at the solution/graphite interface, the structural and energetic aspects of the assembly were studied by a combination of in situ scanning tunneling microscopy and multiscale computational chemistry approach. Then, the growth of a PbPc SIP on top of the physisorbed monolayer was modeled without prior experimental knowledge, from which the crystal structure of the SIP was predicted. The theoretical prediction of the SIP was verified by determining the crystal structure of PbPc thin films using X-ray diffraction techniques, revealing the formation of a new polymorph of PbPc on the graphite substrate. This study clearly illustrates the correlation between the SAMNs and SIPs, which are traditionally considered as two separate but conceptually connected research areas. This approach is applicable to molecular materials in general to predict the crystal structure of their SIPs.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000812125800001	Publication Date	2022-02-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0897-4756; 1520-5002	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.6	Times cited		Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 8.6
	Call Number	UA @ admin @ c:irua:189086			Serial	7084
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	Author	Friedrich, T.; Yu, C.-P.; Verbeek, J.; Pennycook, T.; Van Aert, S.
	Title	Phase retrieval from 4-dimensional electron diffraction datasets			Type	P1 Proceeding
	Year	2021	Publication	Proceedings T2 – IEEE International Conference on Image Processing (ICIP), SEP 19-22, 2021, Electr. network	Abbreviated Journal
	Volume		Issue		Pages	3453-3457
	Keywords	P1 Proceeding; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	We present a computational imaging mode for large scale electron microscopy data, which retrieves a complex wave from noisy/sparse intensity recordings using a deep learning approach and subsequently reconstructs an image of the specimen from the Convolutional Neural Network (CNN) predicted exit waves. We demonstrate that an appropriate forward model in combination with open data frameworks can be used to generate large synthetic datasets for training. In combination with augmenting the data with Poisson noise corresponding to varying dose-values, we effectively eliminate overfitting issues. The U-NET[1] based architecture of the CNN is adapted to the task at hand and performs well while maintaining a relatively small size and fast performance. The validity of the approach is confirmed by comparing the reconstruction to well-established methods using simulated, as well as real electron microscopy data. The proposed method is shown to be effective particularly in the low dose range, evident by strong suppression of noise, good spatial resolution, and sensitivity to different atom types, enabling the simultaneous visualisation of light and heavy elements and making different atomic species distinguishable. Since the method acts on a very local scale and is comparatively fast it bears the potential to be used for near-real-time reconstruction during data acquisition.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000819455103114	Publication Date	2021-08-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	978-1-6654-4115-5	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:189462			Serial	7089
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	Author	De wael, A.; De Backer, A.; Yu, C.-P.; Sentürk, D.G.; Lobato, I.; Faes, C.; Van Aert, S.
	Title	Three Approaches for Representing the Statistical Uncertainty on Atom-Counting Results in Quantitative ADF STEM			Type	A1 Journal article
	Year	2022	Publication	Microscopy and microanalysis	Abbreviated Journal	Microsc Microanal
	Volume		Issue		Pages	1-9
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000854930500001	Publication Date	2022-09-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1431-9276	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	2.8	Times cited		Open Access	OpenAccess
	Notes	This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N, G.0267.18N, and EOS 30489208. S.V.A. acknowledges TOP BOF funding from the University of Antwerp. The authors are grateful to L.M. Liz-Marzán (CIC biomaGUNE and Ikerbasque) for providing the samples. esteem3reported; esteem3jra			Approved	Most recent IF: 2.8
	Call Number	EMAT @ emat @c:irua:190585			Serial	7119
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	Author	Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S.
	Title	Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors			Type	A1 Journal article
	Year	2022	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	242	Issue		Pages	113626
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000873778100001	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited		Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra			Approved	Most recent IF: 2.2
	Call Number	EMAT @ emat @c:irua:190925			Serial	7118
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	Author	De Backer, A.; Van Aert, S.; Faes, C.; Arslan Irmak, E.; Nellist, P.D.; Jones, L.
	Title	Experimental reconstructions of 3D atomic structures from electron microscopy images using a Bayesian genetic algorithm			Type	A1 Journal article
	Year	2022	Publication	N P J Computational Materials	Abbreviated Journal	npj Comput Mater
	Volume	8	Issue	1	Pages	216
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	We introduce a Bayesian genetic algorithm for reconstructing atomic models of monotype crystalline nanoparticles from a single projection using Z-contrast imaging. The number of atoms in a projected atomic column obtained from annular dark field scanning transmission electron microscopy images serves as an input for the initial three-dimensional model. The algorithm minimizes the energy of the structure while utilizing a priori information about the finite precision of the atom-counting results and neighbor-mass relations. The results show promising prospects for obtaining reliable reconstructions of beam-sensitive nanoparticles during dynamical processes from images acquired with sufficiently low incident electron doses.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000866500900001	Publication Date	2022-10-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2057-3960	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A. and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N) and a postdoctoral grant to A.D.B. L.J. acknowledges Science Foundation Ireland (SFI – grant number URF/RI/191637), the Royal Society, and the AMBER Centre. The authors acknowledge Aakash Varambhia for his assistance and expertise with the experimental recording and use of characterization facilities within the David Cockayne Centre for Electron Microscopy, Department of Materials, University of Oxford, and in particular the EPSRC (EP/K040375/1 South of England Analytical Electron Microscope).; esteem3reported; esteem3JRA			Approved	Most recent IF: NA
	Call Number	EMAT @ emat @c:irua:191398			Serial	7114
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	Author	De Backer, A.; Zhang, Z.; van den Bos, K.H.W.; Bladt, E.; Sánchez‐Iglesias, A.; Liz‐Marzán, L.M.; Nellist, P.D.; Bals, S.; Van Aert, S.
	Title	Element Specific Atom Counting at the Atomic Scale by Combining High Angle Annular Dark Field Scanning Transmission Electron Microscopy and Energy Dispersive X‐ray Spectroscopy			Type	A1 Journal article
	Year	2022	Publication	Small methods	Abbreviated Journal	Small Methods
	Volume		Issue		Pages	2200875
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	A new methodology is presented to count the number of atoms in multimetallic nanocrystals by combining energy dispersive X-ray spectroscopy (EDX) and high angle annular dark field scanning transmission electron microscopy (HAADF STEM). For this purpose, the existence of a linear relationship between the incoherent HAADF STEM and EDX images is exploited. Next to the number of atoms for each element in the atomic columns, the method also allows quantification of the error in the obtained number of atoms, which is of importance given the noisy nature of the acquired EDX signals. Using experimental images of an Au@Ag core–shell nanorod, it is demonstrated that 3D structural information can be extracted at the atomic scale. Furthermore, simulated data of an Au@Pt core–shell nanorod show the prospect to characterize heterogeneous nanostructures with adjacent atomic numbers.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000862072700001	Publication Date	2022-09-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2366-9608	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	12.4	Times cited	5	Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A., Grant 815128 REALNANO to S.B., and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N) and a postdoctoral grant to A.D.B.; esteem3reported; esteem3JRA			Approved	Most recent IF: 12.4
	Call Number	EMAT @ emat @c:irua:191570			Serial	7109
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	Author	Zhang, Z.; Lobato, I.; De Backer, A.; Van Aert, S.; Nellist, P.
	Title	Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions			Type	A1 Journal article
	Year	2023	Publication	Ultramicroscopy	Abbreviated Journal
	Volume	246	Issue		Pages	113671
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simulations. Based on incoherent imaging, the atomic lensing model previously developed for ADF is now expanded to EDX, which yields ADF-EDX scattering cross-section predictions in good agreement with multislice simulations for mixed columns in a core–shell nanoparticle and a high entropy alloy. The fast and accurate prediction of ADF-EDX scattering cross-sections opens up new opportunities to explore the wide range of ordering possibilities of heterogeneous materials with multiple elements.
	Address
	Corporate Author	Zezhong Zhang			Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000995063900001	Publication Date	2022-12-28
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited		Open Access	OpenAccess
	Notes	European Research Council 770887 PICOMETRICS; Fonds Wetenschappelijk Onderzoek No.G.0502.18N; Horizon 2020, 770887 ; Horizon 2020 Framework Programme; European Research Council, 823717 ESTEEM3 ; esteem3reported; esteem3JRa			Approved	Most recent IF: 2.2; 2023 IF: 2.843
	Call Number	EMAT @ emat @c:irua:195890			Serial	7251
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	Author	De Backer, A.; Bals, S.; Van Aert, S.
	Title	A decade of atom-counting in STEM: From the first results toward reliable 3D atomic models from a single projection			Type	A1 Journal article
	Year	2023	Publication	Ultramicroscopy	Abbreviated Journal
	Volume		Issue		Pages	113702
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Quantitative structure determination is needed in order to study and understand nanomaterials at the atomic scale. Materials characterisation resulting in precise structural information is a crucial point to understand the structure–property relation of materials. Counting the number of atoms and retrieving the 3D atomic structure of nanoparticles plays an important role here. In this paper, an overview will be given of the atom-counting methodology and its applications over the past decade. The procedure to count the number of atoms will be discussed in detail and it will be shown how the performance of the method can be further improved. Furthermore, advances toward mixed element nanostructures, 3D atomic modelling based on the atom-counting results, and quantifying the nanoparticle dynamics will be highlighted.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000953765800001	Publication Date	2023-02-10
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited	3	Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert, Grant 815128 REALNANO to S. Bals, and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N, and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF) . The authors also thank the colleagues who have contributed to this work over the years, including T. Altantzis, E. Arslan Irmak, K.J. Batenburg, E. Bladt, A. De wael, R. Erni, C. Faes, B. Goris, L. Jones, L.M. Liz-Marzán, I. Lobato, G.T. Martinez, P.D. Nellist, M.D. Rosell, A. Rosenauer, K.H.W. van den Bos, A. Varambhia, and Z. Zhang.; esteem3reported; esteem3JRA			Approved	Most recent IF: 2.2; 2023 IF: 2.843
	Call Number	EMAT @ emat @c:irua:195896			Serial	7236
Permanent link to this record



	Author	Jain, N.; Hao, Y.; Parekh, U.; Kaltenegger, M.; Pedrazo-Tardajos, A.; Lazzaroni, R.; Resel, R.; Geerts, Y.H.; Bals, S.; Van Aert, S.
	Title	Exploring the effects of graphene and temperature in reducing electron beam damage: A TEM and electron diffraction-based quantitative study on Lead Phthalocyanine (PbPc) crystals			Type	A1 Journal article
	Year	2023	Publication	Micron	Abbreviated Journal
	Volume	169	Issue		Pages	103444
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	High-resolution transmission electron microscopy (TEM) of organic crystals, such as Lead Phthalocyanine (PbPc), is very challenging since these materials are prone to electron beam damage leading to the breakdown of the crystal structure during investigation. Quantification of the damage is imperative to enable high-resolution imaging of PbPc crystals with minimum structural changes. In this work, we performed a detailed electron diffraction study to quantitatively measure degradation of PbPc crystals upon electron beam irradiation. Our study is based on the quantification of the fading intensity of the spots in the electron diffraction patterns. At various incident dose rates (e/Å2/s) and acceleration voltages, we experimentally extracted the decay rate (1/s), which directly correlates with the rate of beam damage. In this manner, a value for the critical dose (e/Å2) could be determined, which can be used as a measure to quantify beam damage. Using the same methodology, we explored the influence of cryogenic temperatures, graphene TEM substrates, and graphene encapsulation in prolonging the lifetime of the PbPc crystal structure during TEM investigation. The knowledge obtained by diffraction experiments is then translated to real space high-resolution TEM imaging of PbPc.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000965998800001	Publication Date	2023-03-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0968-4328	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.4	Times cited	1	Open Access	OpenAccess
	Notes	This work is supported by FWO and FNRS within the 2Dto3D network of the EOS (Excellence of Science) program (grant number 30489208) and ERC-CoGREALNANO-815128 (to Prof. Dr. Sara Bals). N.J. would like to thank Dr. Kunal S. Mali and Dr. Da Wang for useful and interesting discussions on sample preparation procedures.			Approved	Most recent IF: 2.4; 2023 IF: 1.98
	Call Number	EMAT @ emat @c:irua:196069			Serial	7379
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	Author	Samal, D.; Gauquelin, N.; Takamura, Y.; Lobato, I.; Arenholz, E.; Van Aert, S.; Huijben, M.; Zhong, Z.; Verbeeck, J.; Van Tendeloo, G.; Koster, G.
	Title	Unusual structural rearrangement and superconductivity in infinite layer cuprate superlattices			Type	A1 Journal Article
	Year	2023	Publication	Physical review materials	Abbreviated Journal
	Volume	7	Issue	5	Pages	054803
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001041792100007	Publication Date	2023-05-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2475-9953	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	3.4	Times cited		Open Access	OpenAccess
	Notes	Air Force Office of Scientific Research; European Office of Aerospace Research and Development, FA8655-10-1-3077 ; Office of Science, DE-AC02-05CH11231 ; National Science Foundation, DMR-1745450 ; Seventh Framework Programme, 278510 ; Bijzonder Onderzoeksfonds UGent;			Approved	Most recent IF: 3.4; 2023 IF: NA
	Call Number	EMAT @ emat @c:irua:196973			Serial	8790
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	Author	Lobato, I.; De Backer, A.; Van Aert, S.
	Title	Real-time simulations of ADF STEM probe position-integrated scattering cross-sections for single element fcc crystals in zone axis orientation using a densely connected neural network			Type	A1 Journal Article
	Year	2023	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	251	Issue		Pages	113769
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag, Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS values for a wide range of input parameters that are commonly used for aberration-corrected transmission electron microscopes.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001011617200001	Publication Date	2023-06-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	2.2	Times cited		Open Access	Open_Access
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N and G0A7723N) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF), Belgium.			Approved	Most recent IF: 2.2; 2023 IF: 2.843
	Call Number	EMAT @ emat @c:irua:197275			Serial	8812
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	Author	Monai, M.; Jenkinson, K.; Melcherts, A.E.M.; Louwen, J.N.; Irmak, E.A.; Van Aert, S.; Altantzis, T.; Vogt, C.; van der Stam, W.; Duchon, T.; Smid, B.; Groeneveld, E.; Berben, P.; Bals, S.; Weckhuysen, B.M.
	Title	Restructuring of titanium oxide overlayers over nickel nanoparticles during catalysis			Type	A1 Journal article
	Year	2023	Publication	Science	Abbreviated Journal
	Volume	380	Issue	6645	Pages	644-651
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT)
	Abstract	Reducible supports can affect the performance of metal catalysts by the formation of suboxide overlayers upon reduction, a process referred to as the strong metal-support interaction (SMSI). A combination of operando electron microscopy and vibrational spectroscopy revealed that thin TiOx overlayers formed on nickel/titanium dioxide catalysts during 400 degrees C reduction were completely removed under carbon dioxide hydrogenation conditions. Conversely, after 600 degrees C reduction, exposure to carbon dioxide hydrogenation reaction conditions led to only partial reexposure of nickel, forming interfacial sites in contact with TiOx and favoring carbon-carbon coupling by providing a carbon species reservoir. Our findings challenge the conventional understanding of SMSIs and call for more-detailed operando investigations of nanocatalysts at the single-particle level to revisit static models of structure-activity relationships.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000999020900010	Publication Date	2023-05-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0036-8075; 1095-9203	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	56.9	Times cited	29	Open Access	Not_Open_Access
	Notes	This work was supported by BASF and NWO CHIPP (research grant to B.M.W.); the MCEC NWO Gravitation Program (B.M.W.); the ARC-CBBC NWO Program (B.M.W.); the European Research Council (grant 770887 PICOMETRICS to S.V.A.); and the European Research Council (grant 815128 REALNANO to S.B.).			Approved	Most recent IF: 56.9; 2023 IF: 37.205
	Call Number	UA @ admin @ c:irua:197432			Serial	8923
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	Author	Arteaga Cardona, F.; Jain, N.; Popescu, R.; Busko, D.; Madirov, E.; Arús, B.A.; Gerthsen, D.; De Backer, A.; Bals, S.; Bruns, O.T.; Chmyrov, A.; Van Aert, S.; Richards, B.S.; Hudry, D.
	Title	Preventing cation intermixing enables 50% quantum yield in sub-15 nm short-wave infrared-emitting rare-earth based core-shell nanocrystals			Type	A1 Journal Article
	Year	2023	Publication	Nature communications	Abbreviated Journal	Nat Commun
	Volume	14	Issue	1	Pages	4462
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	Short-wave infrared (SWIR) fluorescence could become the new gold standard in optical imaging for biomedical applications due to important advantages such as lack of autofluorescence, weak photon absorption by blood and tissues, and reduced photon scattering coefficient. Therefore, contrary to the visible and NIR regions, tissues become translucent in the SWIR region. Nevertheless, the lack of bright and biocompatible probes is a key challenge that must be overcome to unlock the full potential of SWIR fluorescence. Although rare-earth-based core-shell nanocrystals appeared as promising SWIR probes, they suffer from limited photoluminescence quantum yield (PLQY). The lack of control over the atomic scale organization of such complex materials is one of the main barriers limiting their optical performance. Here, the growth of either homogeneous (α-NaYF<sub>4</sub>) or heterogeneous (CaF<sub>2</sub>) shell domains on optically-active α-NaYF<sub>4</sub>:Yb:Er (with and without Ce<sup>3+</sup>co-doping) core nanocrystals is reported. The atomic scale organization can be controlled by preventing cation intermixing only in heterogeneous core-shell nanocrystals with a dramatic impact on the PLQY. The latter reached 50% at 60 mW/cm<sup>2</sup>; one of the highest reported PLQY values for sub-15 nm nanocrystals. The most efficient nanocrystals were utilized for in vivo imaging above 1450 nm.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001037058500022	Publication Date	2023-07-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2041-1723	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	16.6	Times cited	1	Open Access	OpenAccess
	Notes	D.H. would like to thank Dominique Ectors (Bruker AXS GmbH, Karlsruhe, Germany) for assistance and discussion on the PXRD data and TOPAS evaluations. The authors would like to acknowledge the financial support provided by the Helmholtz Association via: i) the Professorial Recruitment Initiative Funding (B.S.R.); ii) the Research Field Energy – Program Materials and Technologies for the Energy Transition – Topic 1 Photovoltaics (F.A.C., D.B., E.M., B.S.R., D.H.). This project received funding from the European Union’s Horizon 2020 innovation programme under grant agreement 823717. This work was supported by the European Research Council (grant 770887-PICOMETRICS to S.V.A. and Grant 815128-REALNANO to S.B.). The authors acknowledge financial support from the ResearchFoundation Flanders (FWO, Belgium) through project fundings (G.0346.21 N to S.V.A. and S.B.) and a postdoctoral grant (A.D.B.). The authors (B.A.A., O.T.B. and A.C.) acknowledge funding from the Helmholtz Zentrum München, the DFG-Emmy Noether program (BR 5355/2-1) and from the CZI Deep Tissue Imaging (DTI-0000000248). The authors (O.T.B. and D.H.) would like to thank the Helmholtz Imaging (ZT-I-PF-4-038-BENIGN).			Approved	Most recent IF: 16.6; 2023 IF: 12.124
	Call Number	EMAT @ emat @c:irua:198158			Serial	8808
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	Author	Friedrich, T.; Yu, C.-P.; Verbeeck, J.; Van Aert, S.
	Title	Phase object reconstruction for 4D-STEM using deep learning			Type	A1 Journal article
	Year	2023	Publication	Microscopy and microanalysis	Abbreviated Journal
	Volume	29	Issue	1	Pages	395-407
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	In this study, we explore the possibility to use deep learning for the reconstruction of phase images from 4D scanning transmission electron microscopy (4D-STEM) data. The process can be divided into two main steps. First, the complex electron wave function is recovered for a convergent beam electron diffraction pattern (CBED) using a convolutional neural network (CNN). Subsequently, a corresponding patch of the phase object is recovered using the phase object approximation. Repeating this for each scan position in a 4D-STEM dataset and combining the patches by complex summation yields the full-phase object. Each patch is recovered from a kernel of 3x3 adjacent CBEDs only, which eliminates common, large memory requirements and enables live processing during an experiment. The machine learning pipeline, data generation, and the reconstruction algorithm are presented. We demonstrate that the CNN can retrieve phase information beyond the aperture angle, enabling super-resolution imaging. The image contrast formation is evaluated showing a dependence on the thickness and atomic column type. Columns containing light and heavy elements can be imaged simultaneously and are distinguishable. The combination of super-resolution, good noise robustness, and intuitive image contrast characteristics makes the approach unique among live imaging methods in 4D-STEM.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001033590800038	Publication Date	2023-01-12
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1431-9276	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.8	Times cited	1	Open Access	OpenAccess
	Notes	We acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 770887 PICOMETRICS) and funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 823717 ESTEEM3. J.V. and S.V.A acknowledge funding from the University of Antwerp through a TOP BOF project. The direct electron detector (Merlin, Medipix3, Quantum Detectors) was funded by the Hercules fund from the Flemish Government. This work was supported by the FWO and FNRS within the 2Dto3D project of the EOS program (grant number 30489208).			Approved	Most recent IF: 2.8; 2023 IF: 1.891
	Call Number	UA @ admin @ c:irua:198221			Serial	8912
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	Author	Ren, P.; Zhang, T.; Jain, N.; Ching, H.Y.V.; Jaworski, A.; Barcaro, G.; Monti, S.; Silvestre-Albero, J.; Celorrio, V.; Chouhan, L.; Rokicinska, A.; Debroye, E.; Kustrowski, P.; Van Doorslaer, S.; Van Aert, S.; Bals, S.; Das, S.
	Title	An atomically dispersed Mn-photocatalyst for generating hydrogen peroxide from seawater via the Water Oxidation Reaction (WOR)			Type	A1 Journal article
	Year	2023	Publication	Journal of the American Chemical Society	Abbreviated Journal
	Volume	145	Issue	30	Pages	16584-16596
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Organic synthesis (ORSY); Theory and Spectroscopy of Molecules and Materials (TSM²)
	Abstract	In this work, we have fabricatedan aryl amino-substitutedgraphiticcarbon nitride (g-C3N4) catalyst with atomicallydispersed Mn capable of generating hydrogen peroxide (H2O2) directly from seawater. This new catalyst exhibitedexcellent reactivity, obtaining up to 2230 & mu;M H2O2 in 7 h from alkaline water and up to 1800 & mu;Mfrom seawater under identical conditions. More importantly, the catalystwas quickly recovered for subsequent reuse without appreciable lossin performance. Interestingly, unlike the usual two-electron oxygenreduction reaction pathway, the generation of H2O2 was through a less common two-electron water oxidation reaction(WOR) process in which both the direct and indirect WOR processesoccurred; namely, photoinduced h(+) directly oxidized H2O to H2O2 via a one-step 2e(-) WOR, and photoinduced h(+) first oxidized a hydroxide (OH-) ion to generate a hydroxy radical ((OH)-O-& BULL;), and H2O2 was formed indirectly by thecombination of two (OH)-O-& BULL;. We have characterized thematerial, at the catalytic sites, at the atomic level using electronparamagnetic resonance, X-ray absorption near edge structure, extendedX-ray absorption fine structure, high-resolution transmission electronmicroscopy, X-ray photoelectron spectroscopy, magic-angle spinningsolid-state NMR spectroscopy, and multiscale molecular modeling, combiningclassical reactive molecular dynamics simulations and quantum chemistrycalculations.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001034983300001	Publication Date	2023-07-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0002-7863	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	15	Times cited	21	Open Access	Not_Open_Access
	Notes	S.D. thanks the IOF grant and Francqui start up grant from the University of Antwerp, Belgium, for the financial support. P.R. thanks CSC and T.Z. thanks FWO for their financial assistance to finish this work. E.D. would like to thank the KU Leuven Research Fund for financial support through STG/21/010. J.S.A. acknowledges financial support from MCIN/AEI/10.13039/501100011033 and EU NextGeneration/PRTR (Project PCI2020-111968/3D-Photocat) and Diamond Synchrotron (rapid access proposal SP32609). This work was supported by the European Research Council (grant 770887-PICOMETRICS to S.V.A. and Grant 815128-REALNANO to S.B.). S.B. and S.V.A. acknowledge financial support from the Research Foundation Flanders (FWO, Belgium, project G.0346.21 N). We also thank Mr. Jian Zhu and Mr. Shahid Ullah Khan from the University of Antwerp, Belgium, for helpful discussions.			Approved	Most recent IF: 15; 2023 IF: 13.858
	Call Number	UA @ admin @ c:irua:198426			Serial	8831
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	Author	Şentürk, DG.; Yu, CP.; De Backer, A.; Van Aert, S.
	Title	Atom counting from a combination of two ADF STEM images			Type	A1 Journal Article
	Year	2024	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	255	Issue		Pages	113859
	Keywords	A1 Journal Article; Atomic resolution scanning transmission electron microscopy; Atom counting; Heterogeneous nanostructures; Multivariate Gaussian mixture model; 4D STEM; Electron Microscopy for Materials Science (EMAT) ;
	Abstract	To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001089064200001	Publication Date	2023-09-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	2.2	Times cited		Open Access	Not_Open_Access
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).			Approved	Most recent IF: 2.2; 2024 IF: 2.843
	Call Number	EMAT @ emat @c:irua:201008			Serial	8964
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	Author	Delfino, C.L.; Hao, Y.; Martin, C.; Minoia, A.; Gopi, E.; Mali, K.S.; Van der Auweraer, M.; Geerts, Y.H.; Van Aert, S.; Lazzaroni, R.; De Feyter, S.
	Title	Conformation-Dependent Monolayer and Bilayer Structures of an Alkylated TTF Derivative Revealed using STM and Molecular Modeling			Type	A1 Journal Article
	Year	2023	Publication	The Journal of Physical Chemistry C	Abbreviated Journal	J. Phys. Chem. C
	Volume	127	Issue	47	Pages	23023-23033
	Keywords	A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
	Abstract	In this study, the multi-layer self-assembled molecular network formation of an alkylated tetrathiafulvalene compound is studied at the liquid-solid interface between 1-phenyloctane and graphite. A combined theoretical/experimental approach associating force-field and quantum-chemical calculations with scanning tunnelling microscopy is used to determine the two-dimensional self-assembly beyond the monolayer, but also to further the understanding of the molecular adsorption conformation and its impact on the molecular packing within the assemblies at the monolayer and bilayer level.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001111637100001	Publication Date	2023-11-30
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1932-7447	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	3.7	Times cited		Open Access	Not_Open_Access
	Notes	Financial support from the Research Foundation-Flanders (FWO G081518N, G0A3220N) and KU Leuven–Internal Funds (C14/19/079) is acknowledged. This work was in part supported by FWO and F. R. S.-FNRS under the Excellence of Science EOS program (project 30489208 and 40007495). C.M. acknowledges the financial support: Grants PID2021-128761OA-C22 and CNS2022-136052 funded by MCIN/AEI/10.13039/501100011033 by the “European Union” and SBPLY/21/180501/000127 funded by JCCM and by the EU through “Fondo Europeo de Desarollo Regional” (FEDER). Research in Mons is also supported by the Belgian National Fund for Scientific Research (FRS-FNRS) within the Consortium des Équipements de Calcul Intensif – CÉCI, under Grant 2.5020.11, and by the Walloon Region (ZENOBE Tier-1 supercomputer, under grant 1117545).			Approved	Most recent IF: 3.7; 2023 IF: 4.536
	Call Number	EMAT @ emat @c:irua:201671			Serial	8974
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	Author	Teunissen, J.L.; Braeckevelt, T.; Skvortsova, I.; Guo, J.; Pradhan, B.; Debroye, E.; Roeffaers, M.B.J.; Hofkens, J.; Van Aert, S.; Bals, S.; Rogge, S.M.J.; Van Speybroeck, V.
	Title	Additivity of Atomic Strain Fields as a Tool to Strain-Engineering Phase-Stabilized CsPbI₃Perovskites			Type	A1 Journal Article
	Year	2023	Publication	The Journal of Physical Chemistry C	Abbreviated Journal	J. Phys. Chem. C
	Volume	127	Issue	48	Pages	23400-23411
	Keywords	A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
	Abstract	CsPbI3 is a promising perovskite material for photovoltaic applications in its photoactive perovskite or black phase. However, the material degrades to a photovoltaically inactive or yellow phase at room temperature. Various mitigation strategies are currently being developed to increase the lifetime of the black phase, many of which rely on inducing strains in the material that hinder the black-to-yellow phase transition. Physical insight into how these strategies exactly induce strain as well as knowledge of the spatial extent over which these strains impact the material is crucial to optimize these approaches but is still lacking. Herein, we combine machine learning potential-based molecular dynamics simulations with our in silico strain engineering approach to accurately quantify strained large-scale atomic structures on a nanosecond time scale. To this end, we first model the strain fields introduced by atomic substitutions as they form the most elementary strain sources. We demonstrate that the magnitude of the induced strain fields decays exponentially with the distance from the strain source, following a decay rate that is largely independent of the specific substitution. Second, we show that the total strain field induced by multiple strain sources can be predicted to an excellent approximation by summing the strain fields of each individual source. Finally, through a case study, we illustrate how this additive character allows us to explain how complex strain fields, induced by spatially extended strain sources, can be predicted by adequately combining the strain fields caused by local strain sources. Hence, the strain additivity proposed here can be adopted to further our insight into the complex strain behavior in perovskites and to design strain from the atomic level onward to enhance their sought-after phase stability.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001116862000001	Publication Date	2023-12-07
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1932-7447	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	3.7	Times cited		Open Access
	Notes	This work was supported by iBOF-21-085 PERsist (Special Research Fund of Ghent University, KU Leuven Research Fund, and the Research Fund of the University of Antwerp). S.M.J.R., T.B., and B.P. acknowledge financial support from the Research Foundation-Flanders (FWO) through two postdoctoral fellow- ships [grant nos. 12T3522N (S.M.J.R.) and 1275521N (B.P.)] and an SB-FWO fellowship [grant no. 1SC1319 (T.B.)]. E.D., M.B.J.R., and J.H. acknowledge financial support from the Research Foundation-Flanders (FWO, grant nos. G.0B39.15, G.0B49.15, G098319N, S002019N, S004322N, and ZW15_09- GOH6316). J.H. acknowledges support from the Flemish government through long-term structural funding Methusalem (CASAS2, Meth/15/04) and the MPI as an MPI fellow. S.V.A. and S.B. acknowledge financial support from the Research Foundation-Flanders (FWO, grant no. G0A7723N). S.M.J.R. and V.V.S. acknowledge funding from the Research Board of Ghent University (BOF). The computational resources and services used in this work were provided by the VSC (Flemish Supercomputer Center), funded by the Research Foundation- Flanders (FWO) and the Flemish Government�department EWI.; KU Leuven, iBOF-21-085 PERsist ; Universiteit Antwerpen, iBOF-21-085 PERsist ; Universiteit Gent, iBOF-21-085 PERsist ; Vlaamse regering, CASAS2, Meth/15/04 ; Fonds Wetenschappelijk Onderzoek, G.0B39.15 G098319N G.0B49.15 1SC1319 12T3522N ZW15 09-GOH6316 G0A7723N 1275521N S004322N S002019N ;			Approved	Most recent IF: 3.7; 2023 IF: 4.536
	Call Number	EMAT @ emat @c:irua:202124			Serial	8985
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	Author	Lobato, I.; Friedrich, T.; Van Aert, S.
	Title	Deep convolutional neural networks to restore single-shot electron microscopy images			Type	A1 Journal Article
	Year	2024	Publication	npj Computational Materials	Abbreviated Journal	npj Comput Mater
	Volume	10	Issue	1	Pages	10
	Keywords	A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
	Abstract	Advanced electron microscopy techniques, including scanning electron microscopes (SEM), scanning transmission electron microscopes (STEM), and transmission electron microscopes (TEM), have revolutionized imaging capabilities. However, achieving high-quality experimental images remains a challenge due to various distortions stemming from the instrumentation and external factors. These distortions, introduced at different stages of imaging, hinder the extraction of reliable quantitative insights. In this paper, we will discuss the main sources of distortion in TEM and S(T)EM images, develop models to describe them, and propose a method to correct these distortions using a convolutional neural network. We validate the effectiveness of our method on a range of simulated and experimental images, demonstrating its ability to significantly enhance the signal-to-noise ratio. This improvement leads to a more reliable extraction of quantitative structural information from the images. In summary, our findings offer a robust framework to enhance the quality of electron microscopy images, which in turn supports progress in structural analysis and quantification in materials science and biology.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001138183000001	Publication Date	2024-01-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2057-3960	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor		Times cited		Open Access
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A.). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N and EOS 40007495). S.V.A. acknowledges funding from the University of Antwerp Research Fund (BOF). The authors thank Lukas Grünewald for data acquisition and support for Fig. 7.			Approved	Most recent IF: NA
	Call Number	EMAT @ emat @c:irua:202714			Serial	8994
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	Author	Hugenschmidt, M.; Jannis, D.; Kadu, A.A.; Grünewald, L.; De Marchi, S.; Perez-Juste, J.; Verbeeck, J.; Van Aert, S.; Bals, S.
	Title	Low-dose 4D-STEM tomography for beam-sensitive nanocomposites			Type	A1 Journal article
	Year	2023	Publication	ACS materials letters	Abbreviated Journal
	Volume	6	Issue	1	Pages	165-173
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Electron tomography is essential for investigating the three-dimensional (3D) structure of nanomaterials. However, many of these materials, such as metal-organic frameworks (MOFs), are extremely sensitive to electron radiation, making it difficult to acquire a series of projection images for electron tomography without inducing electron-beam damage. Another significant challenge is the high contrast in high-angle annular dark field scanning transmission electron microscopy that can be expected for nanocomposites composed of a metal nanoparticle and an MOF. This strong contrast leads to so-called metal artifacts in the 3D reconstruction. To overcome these limitations, we here present low-dose electron tomography based on four-dimensional scanning transmission electron microscopy (4D-STEM) data sets, collected using an ultrafast and highly sensitive direct electron detector. As a proof of concept, we demonstrate the applicability of the method for an Au nanostar embedded in a ZIF-8 MOF, which is of great interest for applications in various fields, including drug delivery.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001141178500001	Publication Date	2023-12-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2639-4979	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor		Times cited		Open Access
	Notes	This work was supported by the European Research Council (Grant 815128 REALNANO to S.B., Grant 770887 PICOMETRICS to S.V.A.). J.P.-J. and S.M. acknowledge financial support from the MCIN/AEI/10.13039/501100011033 (Grants No. PID2019-108954RB-I00) and EU Horizon 2020 research and innovation program under grant agreement no. 883390 (SERSing). J.V., S.B., S.V.A., and L.G. acknowledge funding from the Flemish government (iBOF-21-085 PERsist).			Approved	no
	Call Number	UA @ admin @ c:irua:202771			Serial	9053
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	Author	Grünewald, L.; Chezganov, D.; De Meyer, R.; Orekhov, A.; Van Aert, S.; Bogaerts, A.; Bals, S.; Verbeeck, J.
	Title	Supplementary Information for “In-situ Plasma Studies using a Direct Current Microplasma in a Scanning Electron Microscope”			Type	Dataset
	Year	2023	Publication		Abbreviated Journal
	Volume		Issue		Pages
	Keywords	Dataset; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Supplementary information for the article “In-situ Plasma Studies using a Direct Current Microplasma in a Scanning Electron Microscope” containing the videos of in-situ SEM imaging (mp4 files), raw data/images, and Jupyter notebooks (ipynb files) for data treatment and plots. Link to the preprint: https://doi.org/10.48550/arXiv.2308.15123 Explanation of the data files can be found in the Information.pdf file. The Videos folder contains the in-situ SEM image series mentioned in the paper. If there are any questions/bugs, feel free to contact me at lukas.grunewaldatuantwerpen.be
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	no
	Call Number	UA @ admin @ c:irua:203389			Serial	9100
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	Author	Zhang, Z.; Lobato, I.; Brown, H.; Jannis, D.; Verbeeck, J.; Van Aert, S.; Nellist, P.
	Title	Generalised oscillator strength for core-shell electron excitation by fast electrons based on Dirac solutions			Type	Dataset
	Year	2023	Publication		Abbreviated Journal
	Volume		Issue		Pages
	Keywords	Dataset; Electron microscopy for materials research (EMAT)
	Abstract	Inelastic excitation as exploited in Electron Energy Loss Spectroscopy (EELS) contains a rich source of information that is revealed in the scattering process. To accurately quantify core-loss EELS, it is common practice to fit the observed spectrum with scattering cross-sections calculated using experimental parameters and a Generalized Oscillator Strength (GOS) database [1]. The GOS is computed using Fermi’s Golden Rule and orbitals of bound and excited states. Previously, the GOS was based on Hartree-Fock solutions [2], but more recently Density Functional Theory (DFT) has been used [3]. In this work, we have chosen to use the Dirac equation to incorporate relativistic effects and have performed calculations using Flexible Atomic Code (FAC) [4]. This repository contains a tabulated GOS database based on Dirac solutions for computing double differential cross-sections under experimental conditions. We hope the Dirac-based GOS database can benefit the EELS community for both academic use and industry integration. Database Details: – Covers all elements (Z: 1-108) and all edges – Large energy range: 0.01 – 4000 eV – Large momentum range: 0.05 -50 Å-1 – Fine log sampling: 128 points for energy and 256 points for momentum – Data format: GOSH [3] Calculation Details: – Single atoms only; solid-state effects are not considered – Unoccupied states before continuum states of ionization are not considered; no fine structure – Plane Wave Born Approximation – Frozen Core Approximation is employed; electrostatic potential remains unchanged for orthogonal states when – core-shell electron is excited – Self-consistent Dirac–Fock–Slater iteration is used for Dirac calculations; Local Density Approximation is assumed for electron exchange interactions; continuum states are normalized against asymptotic form at large distances – Both large and small component contributions of Dirac solutions are included in GOS – Final state contributions are included until the contribution of the previous three states falls below 0.1%. A convergence log is provided for reference. Version 1.1 release note: – Update to be consistent with GOSH data format [3], all the edges are now within a single hdf5 file. A notable change in particular, the sampling in momentum is in 1/m, instead of previously in 1/Å. Great thanks to Gulio Guzzinati for his suggestions and sending conversion script. Version 1.2 release note: – Add “File Type / File version” information [1] Verbeeck, J., and S. Van Aert. Ultramicroscopy 101.2-4 (2004): 207-224. [2] Leapman, R. D., P. Rez, and D. F. Mayers. The Journal of Chemical Physics 72.2 (1980): 1232-1243. [3] Segger, L, Guzzinati, G, & Kohl, H. Zenodo (2023). doi:10.5281/zenodo.7645765 [4] Gu, M. F. Canadian Journal of Physics 86(5) (2008): 675-689.
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	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	no
	Call Number	UA @ admin @ c:irua:203392			Serial	9042
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	Author	Van Aert, S.; den Dekker, A.J.; van den Bos, A.; van Dyck, D.
	Title	Statistical experimental design for quantitative atomic resolution transmission electron microscopy			Type	H1 Book chapter
	Year	2004	Publication		Abbreviated Journal	Adv Imag Elect Phys
	Volume		Issue		Pages	1-164
	Keywords	H1 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	Academic Press	Place of Publication	San Diego, Calif.	Editor
	Language		Wos	000223226700001	Publication Date	2011-01-05
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1076-5670;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited	13	Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ lucian @ c:irua:47513			Serial	3156
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	Author	Van Aert, S.; den Dekker, A.J.; van Dyck, D.
	Title	How to optimize the experimental design of quantitative atomic resolution TEM experiments?			Type	A1 Journal article
	Year	2004	Publication	Micron	Abbreviated Journal	Micron
	Volume	35	Issue		Pages	425-429
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000221721000005	Publication Date	2004-03-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0968-4328;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.98	Times cited	14	Open Access
	Notes				Approved	Most recent IF: 1.98; 2004 IF: 1.464
	Call Number	UA @ lucian @ c:irua:47514			Serial	1495
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	Author	van Dyck, D.; Van Aert, S.; den Dekker, A.J.
	Title	Physical limits on atomic resolution			Type	A1 Journal article
	Year	2004	Publication	Microscopy and microanalysis	Abbreviated Journal	Microsc Microanal
	Volume	10	Issue		Pages	153-157
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Cambridge, Mass.	Editor
	Language		Wos	000188882100022	Publication Date	2004-08-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1431-9276;1435-8115;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	1.891	Times cited	14	Open Access
	Notes				Approved	Most recent IF: 1.891; 2004 IF: 2.389
	Call Number	UA @ lucian @ c:irua:47515			Serial	2616
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	Author	van Dyck, D.; Van Aert, S.; den Dekker, A.J.; van den Bos, A.
	Title	Is atomic resolution transmission electron microscopy able to resolve and refine amorphous structures?			Type	A1 Journal article
	Year	2003	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	98	Issue		Pages	27-42
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000186831500003	Publication Date	2003-04-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	26	Open Access
	Notes				Approved	Most recent IF: 2.843; 2003 IF: 1.665
	Call Number	UA @ lucian @ c:irua:47516			Serial	1749
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	Author	Van Aert, S.; den Dekker, A.J.; van Dyck, D.; van den Bos, A.
	Title	Optimal experimental design of STEM measurement of atom column positions			Type	A1 Journal article
	Year	2002	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	90	Issue		Pages	273-289
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000174770900004	Publication Date	2002-07-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	35	Open Access
	Notes				Approved	Most recent IF: 2.843; 2002 IF: 1.772
	Call Number	UA @ lucian @ c:irua:47517			Serial	2483
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	Author	den Dekker, A.J.; Van Aert, S.; van Dyck, D.; van den Bos, A.; Geuens, P.
	Title	Does a monochromator improve the precision in quantitative HRTEM?			Type	A1 Journal article
	Year	2001	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	89	Issue		Pages	275-290
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000172667000004	Publication Date	2002-07-25
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	22	Open Access
	Notes				Approved	Most recent IF: 2.843; 2001 IF: 1.890
	Call Number	UA @ lucian @ c:irua:47518			Serial	746
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