Biography
Filip Leonarski studied Theoretical Chemistry and Computer Science at the University of Warsaw and the University of Arizona, he has graduated with Master degrees in Chemistry from both universities. He has done his graduate studies in Theoretical Chemistry at the University of Warsaw under supervision of Prof. Joanna Trylska - thesis title: "Coarse-grained models for molecular dynamics of RNA. Evolutionary algorithm optimization of the potential energy function parameters". Later he received 2-year scholarship Mobility Plus scholarship from the Polish Ministry of Science to work in IBMC, Strasbourg under supervision of Dr Pascal Auffinger on classification and validation of Mg2+ binding site to RNA.
From 2016 he was a postdoctoral research at the Paul Scherrer Institute under supervision of Dr Meitian Wang, where he work on JUNGFRAU detector applications for macromolecular crystallography. From 2020 he is a beamline data scientist at the Paul Scherrer Institute. He is a principle investigator on the "NextGenDCU high data rate acquisition system for X-ray detectors in structural biology applications" innovation project supported by Innosuisse and realized together with DECTRIS (2023-2025).
Research interests
Working on design and implementation of IT solutions for handling and on-the-fly processing of data from cutting-edge X-ray detectors, with expected throughput up to 50 GB/s, for macromolecular crystallography and beyond.
Supports data intensive experiments at macromolecular crystallography at SLS, with special interest for serial synchrotron crystallography.
Interested in edge computing, internet-of-things, machine learning, modern computing architectures and theory of X-ray protein diffraction.
Experienced in programming aiming at high performance on heterogeneous platforms - including field programming gate arrays (FPGAs) and general purpose graphical processing units.
Selected publications
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          Appel C, Schmeltz M, Rodriguez-Fernandez I, Anschuetz L, Nielsen LC, Panepucci E, et al.
 Fast small-angle X-ray scattering tensor tomography: an outlook into future applications in life sciences
 Small Methods. 2025. https://doi.org/10.1002/smtd.202500162
 DORA PSI
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          Leonarski F, Henning-Knechtel A, Kirmizialtin S, Ennifar E, Auffinger P
 Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg2+
 Nucleic Acids Research. 2025; 53(1): gkae1148 (21 pp.). https://doi.org/10.1093/nar/gkae1148
 DORA PSI
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          Gasparotto P, Barba L, Stadler HC, Assmann G, Mendonça H, Ashton AW, et al.
 TORO Indexer: a PyTorch-based indexing algorithm for kilohertz serial crystallography
 Journal of Applied Crystallography. 2024; 57(4): 931-944. https://doi.org/10.1107/S1600576724003182
 DORA PSI
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          Glover H, Saßmannshausen T, Bertrand Q, Trabuco M, Slavov C, Bacchin A, et al.
 Photoswitch dissociation from a G protein-coupled receptor resolved by time-resolved serial crystallography
 Nature Communications. 2024; 15(1): 10837 (13 pp.). https://doi.org/10.1038/s41467-024-55109-w
 DORA PSI
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          Leonarski F, Brückner M, Lopez-Cuenca C, Mozzanica A, Stadler H-C, Matěj Z, et al.
 Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors
 Journal of Synchrotron Radiation. 2023; 30: 227-234. https://doi.org/10.1107/S1600577522010268
 DORA PSI
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          Leonarski F, Nan J, Matej Z, Bertrand Q, Furrer A, Gorgisyan I, et al.
 Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source
 IUCrJ. 2023; 10(6): 729-737. https://doi.org/10.1107/S2052252523008618
 DORA PSI
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          Huang C-Y, Aumonier S, Engilberge S, Eris D, Smith KML, Leonarski F, et al.
 Probing ligand binding of endothiapepsin by 'temperature-resolved' macromolecular crystallography
 Acta Crystallographica Section D: Structural Biology. 2022; 78: 964-974. https://doi.org/10.1107/S205979832200612X
 DORA PSI
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          Ashton A, Augustin S, Babic A, Celcer T, Ebner SG, Egli S, et al.
 Conceptual design report on controls and science IT for the SLS 2.0 upgrade project
 Villigen PSI, Switzerland: Paul Scherrer Institut; 2021. PSI Bericht: 21-03.
 DORA PSI
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          Bernstein HJ, Förster A, Bhowmick A, Brewster AS, Brockhauser S, Gelisio L, et al.
 Gold standard for macromolecular crystallography diffraction data
 IUCrJ. 2020; 7(5): 784-792. https://doi.org/10.1107/S2052252520008672
 DORA PSI
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          Görlich S, Samuel AJ, Best RJ, Seidel R, Vacelet J, Leonarski FK, et al.
 Natural hybrid silica/protein superstructure at atomic resolution
 Proceedings of the National Academy of Sciences of the United States of America PNAS. 2020; 117(49): 31088-31093. https://doi.org/10.1073/pnas.2019140117
 DORA PSI
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          Leonarski F, Mozzanica A, Brückner M, Lopez-Cuenca C, Redford S, Sala L, et al.
 JUNGFRAU detector for brighter x-ray sources: solutions for IT and data science challenges in macromolecular crystallography
 Structural Dynamics. 2020; 7(1): 014305 (13 pp.). https://doi.org/10.1063/1.5143480
 DORA PSI
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          Martiel I, Mozzanica A, Opara NL, Panepucci E, Leonarski F, Redford S, et al.
 X-ray fluorescence detection for serial macromolecular crystallography using a JUNGFRAU pixel detector
 Journal of Synchrotron Radiation. 2020; 27: 329-339. https://doi.org/10.1107/S1600577519016758
 DORA PSI
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          Nass K, Cheng R, Vera L, Mozzanica A, Redford S, Ozerov D, et al.
 Advances in long-wavelength native phasing at X-ray free-electron lasers
 IUCrJ. 2020; 7: 965-975. https://doi.org/10.1107/S2052252520011379
 DORA PSI
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          Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, et al.
 Long-wavelength native-SAD phasing: opportunities and challenges
 IUCrJ. 2019; 6(3): 1-14. https://doi.org/10.1107/S2052252519002756
 DORA PSI
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          Leonarski F, D’Ascenzo L, Auffinger P
 Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders - a critical PDB survey
 RNA. 2019; 25(11): 173-192. https://doi.org/10.1261/rna.068437.118
 DORA PSI
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          Leonarski F, Redford S, Mozzanica A, Lopez-Cuenca C, Panepucci E, Nass K, et al.
 Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector
 Nature Methods. 2018; 15(10): 799-804. https://doi.org/10.1038/s41592-018-0143-7
 DORA PSI
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          Mozzanica A, Andrä M, Barten R, Bergamaschi A, Chiriotti S, Brückner M, et al.
 The JUNGFRAU detector for applications at synchrotron light sources and XFELs
 Synchrotron Radiation News. 2018; 31(6): 16-20. https://doi.org/10.1080/08940886.2018.1528429
 DORA PSI
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          Redford S, Andrä M, Barten R, Bergamaschi A, Brückner M, Chiriotti S, et al.
 Operation and performance of the JUNGFRAU photon detector during first FEL and synchrotron experiments
 Journal of Instrumentation. 2018; 13(11): C11006 (9 pp.). https://doi.org/10.1088/1748-0221/13/11/C11006
 DORA PSI
