Welcome to NanED news page where you can find out about the Nan ED project's progress as well as events, and related news at a national and international level.
A SOF structure solved with an electron diffractometer.
A new paper which is a collaboration between the IIT group and the Eldico Scientific NanED partner, came out recently on Acta Crystallographica B! The paper describes the structure determination of a novel mechanochemically synthesized supramolecular organic framework (SOF) with 3D ED data collected on an the Eldico ED-1 electron diffractometer. This is one of the first structures solved with this new innovative instrument. The authors were able to solve the structure of the SOF and to refine it dynamically. The dynamical refinement was carried out simultaneously on multiple data sets (three) and delivered two partially occupied molecule positions of the residual solvent (benzyl alcohol) trapped in the pores. 12 out of 16 independent hydrogens can be directly seen in different Fourier maps.
TRPX: a new algorithm for compression and decompression of diffraction and cryo-EM data
A second paper from Senik Matinyan, NanED PhD student, came out recently on Acta Crystallographica A! The paper introduces TERSE/PROLIX (TRPX), a novel lossless compression algorithm specifically designed for diffraction data in high-throughput crystallography, addressing the challenges posed by the significant increase in data volume. TRPX outperforms established algorithms like gzip, bzip2, CBF (crystallographic binary file), Zstandard(zstd), LZ4 and HDF5 with gzip, LZF and bitshuffle+LZ4 filters in terms of speed and compression rate, being 60 times faster than bzip2 and three times faster than LZ4. It compresses data to at least 15% of the original size and can handle up to 2000 electron diffraction frames per second using a single core on an Apple's M1 Max processor. The algorithm mitigates storage and transmission concerns and facilitates more efficient data analysis and interpretation. The TRPX compression/decompression code, custom TIFF library, and an ImageJ/Fiji Java plugin are open-sourced on GitHub and Zenodo under the MIT license.
A new error model for 3D ED diffraction intesities
A new paper from FZU group, came out recently on Acta Crystallographica A! The paper describes a proper way to correctly estimate the error to assign to each integrated reflection of a 3D ED experiment. In fact, in the case of electron diffraction, the complexity of electron scattering that includes also dynamical effects, hampers a simple estimation of the integration error of the reflections based only on the standard Poisson statistics. The authors demonstrate that if the estimate of the standard deviation is modified in order to obtain a proper normal distribution of the integration errors, two goals are simultaneously achieved: the number of observed reflections is maximized and the refined structures are more accurate. At the same time a proper error model allows to identify which reflections can be considered as outliers to be excluded from data set. As test structures natrolite, L-alanine and (S)-(+)-ibuprofen have been chosen.
The 1.25 Million CSD structure is a NanED one!
The Cambridge Crystallographic Data Centre (CCDC) has announced that the Cambridge Structure Database (CSD) has passed the milestone of 1.25 million expert-curated experimental crystal structures! This structure is a structure solved and refined with 3D ED by a NanED research team! It is the crystal structure of ibuprofen (CSD Entry: JEKNOC16) published in Acta Crystallographica A by Malak Khouchen, Lukas Palatinus et al. Among the other authors together with the NanED supervisor Lukas Palatinus, we can find also our ESRs Chintakindi Hrushikesh (in the picture together with Lukas and Paul Klar) and Ashwin Suresh. Lukas commented this achievement in an interview for CCDC:
“It is an unexpected privilege and pleasure to have helped to achieve such an important milestone for CSD and for the whole crystallographic community. I always illustrate the importance of crystallography to my students by reminding them that the number of published structures grows with the pace of about one structure every 10 minutes, day and night, 24/7. 1.25 million published structures is an amazing number, and I want to congratulate the whole team behind the CSD as well as to all fellow crystallographers who made this possible. I think it is also symptomatic that the 1.25 millionth CSD structure is a structure determined by 3D electron diffraction. I believe that the number of structures determined by 3D ED in the CSD will quickly grow in the near future.”
To this we can add that for sure 3D ED is one of the forefronts of crystallography and we are proud as NanED to be part of its development.
Scanning Precession Electron Tomography
A new paper from Sara Passuti, NanED PhD student, came out recently in Symmetry! The paper describes a new method of collecting 3D ED along a line for mapping fine structural variations with high spatial resolution. A method that the authors named SPET: Scanning Precession Electron Tomography. The method has been tested on a 35 nm thick perovskite 𝑃𝑟𝑉𝑂3(PVO) film deposited on a 𝑆𝑟𝑇𝑖𝑂3 (STO) substrate. As a proofs of concept, the authors wanted like to see if it was possible to monitor the thin film relaxation as a function of the distance from the substrate. The results are extremely encouraging. Tiny unit cell variations and structure deformations could be detected and they are in line with the expected phenomena inside the film. Remarkably the structure modification could be mapped with a spatial resolution between 2 and 5 nm!
NanED @IUCr2023 in Melbourne
Workshops IIT UA FZU CNRS JGU
A strong participation of NanED to the IUCr2023 in Melbourne the most important conference on crystallography of the entire world. There has been talks by our supervisors: Xiaodong Zou on “Probing defects and disorders in nanoporous materials by electron crystallography”, Joke Hadermann on “In situ 3D ED in gas and liquid environments for following structural evolution during reactions”, Lukas Palatinus “Net atomic charges by dynamical kappa refinement against 3D ED data”. A fantastic talk by our PhD Erica Cordero-Oyonarte on ” Diffraction tomography for structural analysis of nanoparticles: a study of minimal size ad associated dynamical effects”. Plus several posters: one from our PhD Amirhossein Hajizadeh on “In situ 3D ED in liquid to study the structural transformation of functional materials during electrochemical reactions: challenges and progress”, one from our PhD Chintakindi Hrushikesh on “Analyzing the frame scaling in the presence of appreciable dynamical diffraction effects of 3D ED data”, and one from our PhD Angelina Vypritskaia on “ Deep learning-driven approach for crystal selection in serial electron diffraction”. Our coordinator, Mauro Gemmi, presented, for the entire project, the results of NanED 3D ED Round Robin on a poster titled “Round Robin results of 3D electron diffraction data on inorganic and organic compounds”. Finally our supervisor Hongyi Xu was one of the organizers of the satellite electron crystallography school in which several of NanED researchers were involved as teachers.
AI in single molecule electron diffraction
A new paper from Senik Matinyan, NanED PhD student, came out recently on Acta Crystallographica A! The paper describes a new way to identify single molecule electron diffraction patterns. While the study of a protein in a TEM is usually confined to single-particle analysis, single molecule electron diffraction has a better signal-to noise ratio and the potential to increase the resolution of protein models with respect to other techniques. However only a minority of the collected electron diffraction data are useful, since the chance of hitting the protein of interest with a narrow beam is very low. This calls for a selection method that is able to recognize which ED patterns carry the sought information and which ones instead should be discarded. Senik and coworkers proposed to use specific machine learning algorithms for this purpose. As proof of concept, they were successful in efficiently distinguishing between the diffraction coming from the amorphous ice and from the carbon support. Although limited to a simple case, this approach exploits inherent characteristics of narrow electron beam diffraction patterns and can be extended for protein data classification and feature extraction.
Rhine-Knee Regional Meeting on X-ray Crystallography of Biomacromolecules
NanED is partner of the Rhine-Knee Regional Meeting on X-ray Crystallography of Biomacromolecules ("Regio Meeting"), which has been a valuable platform for young scientists to engage in discussions with experts in the field of structural biology since its initiation in 1987 by Profs. J.N. Jansonius, G.E. Schulz, and D. Moras. Over the past 25 years, the meeting has maintained its informal and personal character while growing into an international event that showcases new macromolecular structures and innovative methods at a high level.
This year's Regio Meeting will be held from October 10th to 12th, 2023, at Seminarhotel Rigi in Weggis, Switzerland.
NanED researchers at the Electron Crystallography Workshop
From the 30th to the 31st May 2023 at the UAntwerpen was organized by the Special Interest Group on Electron Crystallography (SIG04) of the European Crystallography Association (ECA) a workshop on Electron Crystallography to present the most recent advances in the field.
Most of NanED PhD students and researchers attended to the meeting and present their work in accepted oral communication. Here is the list of their oral communications:
- Hrushikesh Chintakindi: Analysing the frame scaling in the presence of appreciable dynamical diffraction effects of 3D ED data.
- Erica Cordero Oyonarte: Challenges for 3D ED applied to small nanoparticles (below 10 nm).
- Ashwin Suresh: Charge density analysis from 3D ED data.
- Lukas Palatinus: New features in PETS2: how to make the most of your data.
- Mauro Gemmi: 3D ED on beam sensitive materials: organics and MOF.
- Joke Hadermann: Progress and hurdles for in situ 3DED in gas and liquid environments.
- Sara Passuti: SPET as a tool to investigate nanodomains in functionals materials.
NanED Workshop III - TEM imaging and Spectroscopy
The workshop main goal was to teach to NanED PhD students how to use the state of art TEM imaging techniques and how to combine them with the most sophisticated analytical methods available in a TEM. International experts of the EMAT institute (Prof. Thomas Altanzis, Prof. Hosni Idrissi) were explaining how nowadays it can be reached sub atomic resolution in both TEM and STEM imaging. Specific subjects like ptycography (Prof. Timothy Pennycook), image tomography at the atomic resolution and image quantification (Prof. Annick De Backer) were discussed in details. For the analytical part an introduction to TEM spectroscopy was delivered by Prof. Jo Verbeeck.
The students could also learn which are the best strategies and techniques to write a project grant. This lecture was delivered by Prof. Joke Hadermann one of NanED supervisors.
Several local students and researches joined the school making the lectures and the discussions very participated.
Sara’s Poster Prize at IWT2023
Sara Passuti won the Poster Prize at the International Workshop on Thermoelectrics Materials IWT2023 that took place in Caen (FR)
She presented her work about "3D Scanning Precession Electron Diffraction Tomography of nanodomains in thermoelectrics".
Starting from the results obtained by 3D ED on interconnected Enargite-Stannite Cu2+xMn1-xGeS4 nanocomposites that we find in the recent publication of Pavan Kumar V. et al (2022), she explored the possibilites for a more detailed analysis of these thermoelectric samples by combining scanning electron diffraction techniques, such as orientation mapping and Scanning Precession Electron diffraction Tomography (SPET). In particular, by means of this last technique, she's investigating the possibility of an accurate structure solution of different nanodomains in the sample with a single acquisition.
The data were acquired with the TEM facilities at Crismat (JEOL F200 200 kV), and in collaboration with TESCAN with the new TENSOR 100 kV Analytical 4D-STEM
Lei Wang takes his secondment at AstraZeneca @AstraZeneca
Lei Wang, NanED PhD student (ESR 10), is taking his first secondment at AstraZeneca, Göteborg. This secondment aims to study protein-ligand interactions and experience the real life of an industrial company.
In AstraZeneca, Lei Wang learned how to do drug soaking, crystal fishing and ligand refinement based on large crystals and synchrotron data under the supervisor of Helena Käck. A new protein crystallization method developed by SU was also employed to make small protein crystals in the lab, and MicroED data was collected.
Life in AstraZeneca is pleasant. The working time is usually effective and people in AstraZeneca have a good balance between work and leisure.
Thanks to Helena’s kind help, everything worked out well!
Moussa Faye wins second best poster prize @GE3C2023
Moussa Faye, NanED PhD student working at IIT in Pontedera, Italy on electron nanocrystallography of heterometallic MOF, won the second-best poster prize at GE3C XXX Simposio in Benidorm, Spain! Moussa’s poster was about “Structure determination of Metal-Organic Frameworks using 3D Electron Diffraction (3D ED)" and describes a dedicated procedure of 3DED data collection on beam sensitive MOF and the successful structure solution of two new MOF, one monometallic and one heterometallic, using this technique. The poster is a collaboration between IIT, the University of Parma, and the group of Prof. Carlos Martì-Gastaldo of ICMol Spain. Well done, Moussa!
2022 News Archive
NanED Workshop II - Imperfect crystals, complementarity with PXRD, intellectual property and patent in Science
From the 6th to the 8th of December 2022, the NanED project had its second workshop, held in Mainz at the Johannes Guthenberg University.
The workshop's main goal was to teach NanED PhD students how to use powder x-ray diffraction (PXRD) as a complementary tool to 3D ED. The students learned how to solve structures using PXRD and how to refine them with the Rietveld method. As a second topic, the workshop dealt with the problem of investigating disordered structures. The students had the possibility to learn how to treat diffuse scattering both in PXRD and 3DED using the most novel PDF approaches. The workshop hosted several external experts in PXRD and diffuse scattering such as R. Dinnebier of MPI Stuttgart, M. U. Schmidt of Frankfurt University, N. Barrier of CNRS Caen, J. Plasier of Elettra Sincrotrone Trieste, R. Nieder of Erlangen University, E. Schmidt of Bremen University, C. Cuocci of Istituto di Cristallografia CNR Bari, S. Plana Ruiz of University Rovira I Virgili Tarragona.
The workshop was designed with theoretical lectures in the morning and practical sessions in the afternoon, where the students could learn how to use the most advanced software for PXRD data analysis and had the opportunity to visit the 3D ED facilities of JGU
In order to expand and improve their soft skills, the students followed a lecture about the intellectual properties and the patent in science held by T. Einfeld of BASF.
NanED was live on Linkedin
During the IIT digital festival “Science is ready” broadcasted live on Linkedin the 21st of October, our coordinator Mauro Gemmi has discussed, together with other two IIT PIs, Annamaria Petrozza and Virgilio Mattoli leading the PERSEPHONE and the 5DNanoprinting projects respectively, about the most recent advances in realizing new materials that may have a great impact on our life. Mauro had the opportunity to explain to a wide audience the targets and the aim of our project with a strong accent on its importance on the formation of a new generation of scientists that will bring forward the development of electron crystallography. The discussion was moderated by Valeria delle Cave, head of the Foreign Press Office and Communication of competitive projects Office at IIT.
NanED at European Researchers’ Night
NanED PhD students Vincentia Agbemeh and Moussa Faye presented their PhD projects to the wide public in an event organized by IIT in Genova for the 2022 European Researchers’ Night.
Vincentia and Moussa had to explain to people from young children to adults what they do, why their work is important and what it will bring to our everyday life. A difficult task that Vincentia and Moussa carried out successfully. For them it was a really rewarding experience. Well done!
Identifying nanodomains in a nanomaterial using 3D ED
The first paper involving the work of one of NanED PhD students is already out! A research group led by CRISMAT-CNRS laboratory synthesized a series of self-doped compounds Cu2+xMn1-xGeS4 through Cu substitution to Mn. Using a combination of powder X-ray diffraction, high resolution transmission electron microscopy and precession-assisted electron diffraction tomography, they evidenced that the materials are composed of interconnected enargite- and stannite-type structures, via the formation of nanodomains with a high density of coherent interfaces. The complex crystal chemistry of such nanocomposites rises the issue of the role of the two structures and of their interfaces in the mechanism governing their electrical and thermal conductivities. Sara Passuti (ESR12 working at CRISMAT CNRS in Caen France) has analyzed and identified the structure of both stannite and enargite nanodomains using 3D ED in these complex intergrown nanocomposites. The paper is just out on Angewandte Chemie. Well done Sara!
Great participation of the NanED team at the 33rd European Crystallographic Meeting (ECM33) held in Versailles France from the 23rd to the 27th of August 2022. Several supervisors were involved in the congress as chairs and speakers in different sessions and NanED PhD students presented 9 posters in different sessions from electron crystallography to metallorganic framework, from organic crystals to macromolecules. Their posters have attracted a lot of interest and discussion. The participation in the congress has been very fruitful with the opening of possible collaboration.
Laura Gemmrich Hernandez wins two poster prizes @ECM33
Laura Gemmrich Hernandez, NanED PhD student working at Johannes Guthenberg University in Mainz on structural investigation of cement hydration mechanism by electron crystallography, won two poster prizes at ECM33! One in the electron crystallography session shared with the other NanED PhD student Sara Passuti offered by Nanomegas and another offered by CHARMAMAT LABEX in the field of advanced and functional materials. Laura’s poster was about "Structure solution using 3DED of beam and vacuum sensitive Metal Organic Frameworks" and describes the structure modification of two new porous metal phosphonates built by an organic acid linker in the TEM vacuum. Thanks to 3D ED it has been possible to determine their structures during the transformation process induced by the TEM vacuum and by the electron beam. Congratulation to Laura!
Sara Passuti wins a poster prize @ECM33
Sara Passuti, NanED PhD student working at CNRS in Caen on electron crystallography of nanodomains in functional materials, won a poster prize at ECM33 in the electron crystallography session offered by Nanomegas! Sara’s poster was about “3D scanning precession electron diffraction analysis of nanodomains in thin films” and describes a procedure about how collect 3D ED data of structure solution quality across a thin film. This procedure should allow to determine the modifications of the crystal structure in different portion of a thin film. Congratulation to Sara!
NanED Workshop I - Data processing and structure refinement
From the 25th to the 27th of May 2022, the NanED project had its first Workshop, held in Prague at the Institute of Physics of the Czech Academy of Sciences.
The workshop's main goal was to teach NanED PhD students how to collect reliable 3D ED data and how to process these data for a successful structure solution and refinement. The workshop was divided into morning theoretical sessions and afternoon practical sessions to learn how to use all the available structure analysis software for 3D ED. Together with most of the NanED supervisors, we had two invited speakers from outside the project, Prof. Tim Gruene from Vienna University a crystallographer expert in the use of SHELX and Dr Gerhard Hofer of Stockholm University a master in protein crystallography. It was the first we gathered together in person and it has been a fantastic experience for all of us.
Cryo measurements started in JGU
Working on beam-sensitive and hydrated samples is a complex process. Therefore, Laura Gemmrich Hernandez (ESR08) is currently focused on optimizing the data acquisition routines and sample preparation to get quality data that can lead to the structure solution of such materials.
Currently, the project is focused on microscope management, cryoEM, and data processing of many different types of challenging, organic as well as inorganic, samples; such as hydrated, beam sensitive, and disordered materials. The cryoEM training has included a visit to the BASF in Ludwigshafen (Germany) to learn and practice the vitrification and cryotransfer procedures for these types of samples.
3D ED on disordered structure: ESR9 work is progressing
Establishing new crystal tracking routines requires a deep understanding of the hardware, software and 3DED technique and its limitations. Due to that, the work of Marco Santucci (NanED ESR9) is focused in mastering the microscope, with a special eye on the “hidden parameters” that allow the microscope to work. This deep knowledge is necessary to figure out how to handle a basic 3DED experiment, translate it in an automated and technically flexible approach by scripting as well as to improve it.
Marco is focused in the management of the machine, the data collection and processing of organic and inorganic samples, due to their intrinsically different beam stability. Regarding the scripting, Marco is learning Python and DigitalMicrograph© in order to be flexible and synchronize every element of our TEM machines during the data acquisition. Thanks to these acquired competences, Marco will develop a routine to set automatically the best eucentric height, a key parameter for sample mechanical stability during our experiments. At the same time, Marco is also learning how to model disordered crystals and simulate their diffuse scattering using DISCUS, thanks to a visit to the Prof. Rheinard Neder at the FAU in Erlangen.
Towards the implementation of Scanning RED experiments
The current objective in the context of Sara Passuti’s (ESR12 @ CNRS) research project is to implement new strategies for diffraction dataset acquisitions for thin films. Differently from a classical Rotation Electron Diffraction (RED) experiment, the beam is scanned across a pre-defined area going from the coating to the substrate of the thin film or vice versa for every tilt angle.
This way, differences in the lattice parameters in distinct areas of the sample could be highlighted and different domains could be identified.
The main issues concern the optimization of the dataset acquisition protocol, making it faster and more efficient, as well as the sorting of the acquired patterns in order to have separated datasets to analyze for different areas of the sample.
2021 News Archive
NanED Joint Initial Meeting
MeetingsOn the 29th and 30th of November 2021 the NanED project had its Joint Initial Meeting (JIM). The meeting should be held in Italy, in Pisa, but due to Covid-19 issues and to the fact that most of the ESRs have not been employed yet, we decided to organize it as an online event. Having the meeting online has allowed all 13 ESRs to participate to the JIM.
NanED PhD students start @Crismat
The PhD students Sara Passuti (left) and Erica Cordero-Oyonarte (right) just started at Crismat in Caen their NanED adventure. Sara will work on the project, “Electron crystallography of nanodomains in functional materials” focusing on materials with amazing properties whose crystallography is extremely difficult due to too small ordered domains. Meanwhile, Erica's project is “Electron crystallography of nanoparticles” which involves studying the limiting size of a 3D ED experiment.