Real-time data processing for serial crystallography experiments

Authors: Thomas White, Tim Schoof, Sergey Yakubov, Aleksandra Tolstikova, Philipp Middendorf, Mikhail Karnevskiy, Valerio Mariani, Alessandra Henkel, Bjarne Klopprogge, Juergen Hannappel, Dominik Oberthuer, Ivan De Gennaro Aquino, Dmitry Egorov, Anna Munke, Janina Sprenger, Guillaume Pompidor, Helena Taberman, Andrey Gruzinov, Jan Meyer, Johanna Hakanpää, Martin Gasthuber

Source: IUCrJ, Vol 12, Iss 1, Pp 97-108 (2025)

Subject Terms: macromolecular crystallography, serial crystallography, x-ray crystallography, real-time data processing, Crystallography, QD901-999

File Description: electronic resource

Relation: https://journals.iucr.org/paper?S2052252524011837; https://doaj.org/toc/2052-2525

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End-to-end deep learning pipeline for real-time Bragg peak segmentation: from training to large-scale deployment

Authors: Cong Wang, Valerio Mariani, Frédéric Poitevin, Matthew Avaylon, Jana Thayer

Source: Frontiers in High Performance Computing, Vol 3 (2025)

Subject Terms: deep learning in crystallography, real-time Bragg peak finding, model distillation, producer-consumer architecture, X-ray free electron lasers, Computer software, QA76.75-76.765

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fhpcp.2025.1536471/full; https://doaj.org/toc/2813-7337

Access URL: https://doaj.org/article/1e5e7f3376e64efc9118a5c2f1459bf4

Biofilm-mediated antibiotic tolerance in Staphylococcus aureus from spinal cord stimulation device-related infections

Authors: Francesca Sivori, Ilaria Cavallo, Mauro Truglio, Lorella Pelagalli, Valerio Mariani, Giorgia Fabrizio, Elva Abril, Iolanda Santino, Piera Assunta Fradiani, Mariacarmela Solmone, Fulvia Pimpinelli, Luigi Toma, Roberto Arcioni, Roberto Alberto De Blasi, Enea Gino Di Domenico

Source: Microbiology Spectrum, Vol 12, Iss 12 (2024)

Subject Terms: biofilm, spinal cord stimulation, Staphylococcus aureus, vancomycin, oxacillin, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2165-0497

Access URL: https://doaj.org/article/de6b5b6e6031439b80197a697d433bae

Optimal mixture design for organic Rankine cycle using machine learning algorithm

Authors: Valerio Mariani, Saverio Ottaviano, Davide Scampamorte, Andrea De Pascale, Giulio Cazzoli, Lisa Branchini, Gian Marco Bianchi

Source: Energy Conversion and Management: X, Vol 24, Iss , Pp 100733- (2024)

Subject Terms: Engineering (General). Civil engineering (General), TA1-2040

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2590174524002113; https://doaj.org/toc/2590-1745

Access URL: https://doaj.org/article/48aac6a6abbe4a7da405bc65fc798a50

Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam

Authors: Tek Narsingh Malla, Kara Zielinski, Luis Aldama, Sasa Bajt, Denisse Feliz, Brendon Hayes, Mark Hunter, Christopher Kupitz, Stella Lisova, Juraj Knoska, Jose Manuel Martin-Garcia, Valerio Mariani, Suraj Pandey, Ishwor Poudyal, Raymond G. Sierra, Alexandra Tolstikova, Oleksandr Yefanov, Chung Hong Yoon, Abbas Ourmazd, Petra Fromme, Peter Schwander, Anton Barty, Henry N. Chapman, Emina A. Stojkovic, Alexander Batyuk, Sébastien Boutet, George N. Phillips, Lois Pollack, Marius Schmidt

Source: Nature Communications, Vol 14, Iss 1, Pp 1-15 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/50042ef4cec14678ac809352eb19f238

CFD Methodology to Capture the Combustion Behavior of a Conventional Diesel Engine Retrofitted to Operate in Gasoline Compression Ignition Mode

Authors: Davide Viscione, Vittorio Ravaglioli, Valerio Mariani, Giacomo Silvagni, Gian Marco Bianchi

Source: Energies, Vol 17, Iss 16, p 4061 (2024)

Subject Terms: gasoline compression ignition, injection strategy, computational fluid dynamics, low-temperature combustion, emissions, Technology

File Description: electronic resource

Relation: https://www.mdpi.com/1996-1073/17/16/4061; https://doaj.org/toc/1996-1073

Access URL: https://doaj.org/article/a6a8a60e8988488784942caf81d16252

Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive

Authors: Kara A Zielinski, Andreas Prester, Hina Andaleeb, Soi Bui, Oleksandr Yefanov, Lucrezia Catapano, Alessandra Henkel, Max O. Wiedorn, Olga Lorbeer, Eva Crosas, Jan Meyer, Valerio Mariani, Martin Domaracky, Thomas A. White, Holger Fleckenstein, Iosifina Sarrou, Nadine Werner, Christian Betzel, Holger Rohde, Martin Aepfelbacher, Henry N. Chapman, Markus Perbandt, Roberto A. Steiner, Dominik Oberthuer

Source: IUCrJ, Vol 9, Iss 6, Pp 778-791 (2022)

Subject Terms: serial crystallography, partial reflections, protein structures, sample delivery, room temperature, cfel tapedrive, k. pneumoniae ctx-m-14, n. haematococca gh11 xylanase, a. flavus urate oxidase, Crystallography, QD901-999

File Description: electronic resource

Relation: http://scripts.iucr.org/cgi-bin/paper?S2052252522010193; https://doaj.org/toc/2052-2525

Access URL: https://doaj.org/article/1a539044df7442e893cbada6b50b1d5b

FDIP—A Fast Diffraction Image Processing Library for X-ray Crystallography Experiments

Authors: Yaroslav Gevorkov, Marina Galchenkova, Valerio Mariani, Anton Barty, Thomas A. White, Henry N. Chapman, Oleksandr Yefanov

Source: Crystals, Vol 14, Iss 2, p 164 (2024)

Subject Terms: serial crystallography, masking artefacts, peak finding algorithm, real-time feedback, Crystallography, QD901-999

File Description: electronic resource

Relation: https://www.mdpi.com/2073-4352/14/2/164; https://doaj.org/toc/2073-4352

Access URL: https://doaj.org/article/454c66b102d04065b6b252a7f1bd06fa

Comparison between Conventional and Non-Conventional Computer Methods to Define Antiknock Properties of Fuel Mixtures

Authors: Leonardo Pulga, Diego Lacrimini, Claudio Forte, Valerio Mariani, Stefania Falfari, Gian Marco Bianchi

Source: Fuels, Vol 3, Iss 2, Pp 217-231 (2022)

Subject Terms: antiknock properties, RON calculation, machine learning, engine thermodynamics, chemical kinetics simulation, Fuel, TP315-360

File Description: electronic resource

Relation: https://www.mdpi.com/2673-3994/3/2/14; https://doaj.org/toc/2673-3994

Access URL: https://doaj.org/article/41ab80e0377141f8bc6c4401bea36299

Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Authors: Esra Ayan, Busra Yuksel, Ebru Destan, Fatma Betul Ertem, Gunseli Yildirim, Meryem Eren, Oleksandr M. Yefanov, Anton Barty, Alexandra Tolstikova, Gihan K. Ketawala, Sabine Botha, E. Han Dao, Brandon Hayes, Mengning Liang, Matthew H. Seaberg, Mark S. Hunter, Alexander Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Aina Cohen, Tzanko Doukov, Raymond G. Sierra, Çağdaş Dağ, Hasan DeMirci

Source: Communications Biology, Vol 5, Iss 1, Pp 1-13 (2022)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/ce08830956e641dd939e81eeed58b63b

Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography

Authors: Suraj Pandey, George Calvey, Andrea M. Katz, Tek Narsingh Malla, Faisal H. M. Koua, Jose M. Martin-Garcia, Ishwor Poudyal, Jay-How Yang, Mohammad Vakili, Oleksandr Yefanov, Kara A. Zielinski, Sasa Bajt, Salah Awel, Katarina Doerner, Matthias Frank, Luca Gelisio, Rebecca Jernigan, Henry Kirkwood, Marco Kloos, Jayanath Koliyadu, Valerio Mariani, Mitchell D. Miller, Grant Mills, Garrett Nelson, Jose L. Olmos Jr, Alireza Sadri, Tokushi Sato, Alexandra Tolstikova, Weijun Xu, Abbas Ourmazd, John C. H. Spence, Peter Schwander, Anton Barty, Henry N. Chapman, Petra Fromme, Adrian P. Mancuso, George N. Phillips Jr, Richard Bean, Lois Pollack, Marius Schmidt

Source: IUCrJ, Vol 8, Iss 6, Pp 878-895 (2021)

Subject Terms: substrate diffusion in crystals, antibiotic resistance, β-lactamases, enzyme kinetics, irreversible inhibition, mix-and-inject serial crystallography, serial femtosecond crystallography, european x-ray free-electron laser, megahertz pulse-repetition rate, protein structure determination, drug discovery, ceftriaxone, sulbactam, x-ray crystallography, enzyme mechanisms, Crystallography, QD901-999

File Description: electronic resource

Relation: http://scripts.iucr.org/cgi-bin/paper?S2052252521008125; https://doaj.org/toc/2052-2525

Access URL: https://doaj.org/article/fbdbd2a5c401447a974071c858ead28e

Electrically stimulated droplet injector for reduced sample consumption in serial crystallography

Authors: Mukul Sonker, Diandra Doppler, Ana Egatz-Gomez, Sahba Zaare, Mohammad T. Rabbani, Abhik Manna, Jorvani Cruz Villarreal, Garrett Nelson, Gihan K. Ketawala, Konstantinos Karpos, Roberto C. Alvarez, Reza Nazari, Darren Thifault, Rebecca Jernigan, Dominik Oberthür, Huijong Han, Raymond Sierra, Mark S. Hunter, Alexander Batyuk, Christopher J. Kupitz, Robert E. Sublett, Frederic Poitevin, Stella Lisova, Valerio Mariani, Alexandra Tolstikova, Sebastien Boutet, Marc Messerschmidt, J. Domingo Meza-Aguilar, Raimund Fromme, Jose M. Martin-Garcia, Sabine Botha, Petra Fromme, Thomas D. Grant, Richard A. Kirian, Alexandra Ros

Source: Biophysical Reports, Vol 2, Iss 4, Pp 100081- (2022)

Subject Terms: Physics, QC1-999, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667074722000386; https://doaj.org/toc/2667-0747

Access URL: https://doaj.org/article/06f016f7c31f4ce680e6addcce2a3da0

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Authors: Saminathan Ramakrishnan, Jason R. Stagno, Chelsie E. Conrad, Jienyu Ding, Ping Yu, Yuba R. Bhandari, Yun-Tzai Lee, Gary Pauly, Oleksandr Yefanov, Max O. Wiedorn, Juraj Knoska, Dominik Oberthür, Thomas A. White, Anton Barty, Valerio Mariani, Chufeng Li, Wolfgang Brehm, William F. Heinz, Valentin Magidson, Stephen Lockett, Mark S. Hunter, Sébastien Boutet, Nadia A. Zatsepin, Xiaobing Zuo, Thomas D. Grant, Suraj Pandey, Marius Schmidt, John C. H. Spence, Henry N. Chapman, Yun-Xing Wang

Source: Nature Communications, Vol 12, Iss 1, Pp 1-10 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d3c2ae5ddc16425aacc1cbd35314f690

Gold Standard for macromolecular crystallography diffraction data

Authors: Herbert J. Bernstein, Andreas Förster, Asmit Bhowmick, Aaron S. Brewster, Sandor Brockhauser, Luca Gelisio, David R. Hall, Filip Leonarski, Valerio Mariani, Gianluca Santoni, Clemens Vonrhein, Graeme Winter

Source: IUCrJ, Vol 7, Iss 5, Pp 784-792 (2020)

Subject Terms: structural biology, serial crystallography, macromolecular diffraction data format, synchrotrons, xfels, nexus, hdf5, nxmx, cbf, imgcif, Crystallography, QD901-999

File Description: electronic resource

Relation: http://scripts.iucr.org/cgi-bin/paper?S2052252520008672; https://doaj.org/toc/2052-2525

Access URL: https://doaj.org/article/480c9cbf00654de3b0dd4bf579ed9f2e

Segmented flow generator for serial crystallography at the European X-ray free electron laser

Authors: Austin Echelmeier, Jorvani Cruz Villarreal, Marc Messerschmidt, Daihyun Kim, Jesse D. Coe, Darren Thifault, Sabine Botha, Ana Egatz-Gomez, Sahir Gandhi, Gerrit Brehm, Chelsie E. Conrad, Debra T. Hansen, Caleb Madsen, Saša Bajt, J. Domingo Meza-Aguilar, Dominik Oberthür, Max O. Wiedorn, Holger Fleckenstein, Derek Mendez, Juraj Knoška, Jose M. Martin-Garcia, Hao Hu, Stella Lisova, Aschkan Allahgholi, Yaroslav Gevorkov, Kartik Ayyer, Steve Aplin, Helen Mary Ginn, Heinz Graafsma, Andrew J. Morgan, Dominic Greiffenberg, Alexander Klujev, Torsten Laurus, Jennifer Poehlsen, Ulrich Trunk, Davide Mezza, Bernd Schmidt, Manuela Kuhn, Raimund Fromme, Jolanta Sztuk-Dambietz, Natascha Raab, Steffen Hauf, Alessandro Silenzi, Thomas Michelat, Chen Xu, Cyril Danilevski, Andrea Parenti, Leonce Mekinda, Britta Weinhausen, Grant Mills, Patrik Vagovic, Yoonhee Kim, Henry Kirkwood, Richard Bean, Johan Bielecki, Stephan Stern, Klaus Giewekemeyer, Adam R. Round, Joachim Schulz, Katerina Dörner, Thomas D. Grant, Valerio Mariani, Anton Barty, Adrian P. Mancuso, Uwe Weierstall, John C. H. Spence, Henry N. Chapman, Nadia Zatsepin, Petra Fromme, Richard A. Kirian, Alexandra Ros

Source: Nature Communications, Vol 11, Iss 1, Pp 1-10 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/813507b66a6b4fc7a68f618e55926b0f

Improving Visual SLAM by Combining SVO and ORB-SLAM2 with a Complementary Filter to Enhance Indoor Mini-Drone Localization under Varying Conditions

Authors: Amin Basiri, Valerio Mariani, Luigi Glielmo

Source: Drones, Vol 7, Iss 6, p 404 (2023)

Subject Terms: visual SLAM, indoor positioning, mini-drone, Motor vehicles. Aeronautics. Astronautics, TL1-4050

File Description: electronic resource

Relation: https://www.mdpi.com/2504-446X/7/6/404; https://doaj.org/toc/2504-446X

Access URL: https://doaj.org/article/657f792d6de4471a8442f301e85830c1

Hydrogen Application as a Fuel in Internal Combustion Engines

Authors: Stefania Falfari, Giulio Cazzoli, Valerio Mariani, Gian Marco Bianchi

Source: Energies, Vol 16, Iss 6, p 2545 (2023)

Subject Terms: hydrogen, gas injection, under-expanded jets, laminar flame speed, ignition delay time, oil–fuel dilution, Technology

File Description: electronic resource

Relation: https://www.mdpi.com/1996-1073/16/6/2545; https://doaj.org/toc/1996-1073

Access URL: https://doaj.org/article/5f99dcd327814c808797745e3b639ae5

Membrane protein megahertz crystallography at the European XFEL

Authors: Chris Gisriel, Jesse Coe, Romain Letrun, Oleksandr M. Yefanov, Cesar Luna-Chavez, Natasha E. Stander, Stella Lisova, Valerio Mariani, Manuela Kuhn, Steve Aplin, Thomas D. Grant, Katerina Dörner, Tokushi Sato, Austin Echelmeier, Jorvani Cruz Villarreal, Mark S. Hunter, Max O. Wiedorn, Juraj Knoska, Victoria Mazalova, Shatabdi Roy-Chowdhury, Jay-How Yang, Alex Jones, Richard Bean, Johan Bielecki, Yoonhee Kim, Grant Mills, Britta Weinhausen, Jose D. Meza, Nasser Al-Qudami, Saša Bajt, Gerrit Brehm, Sabine Botha, Djelloul Boukhelef, Sandor Brockhauser, Barry D. Bruce, Matthew A. Coleman, Cyril Danilevski, Erin Discianno, Zachary Dobson, Hans Fangohr, Jose M. Martin-Garcia, Yaroslav Gevorkov, Steffen Hauf, Ahmad Hosseinizadeh, Friederike Januschek, Gihan K. Ketawala, Christopher Kupitz, Luis Maia, Maurizio Manetti, Marc Messerschmidt, Thomas Michelat, Jyotirmoy Mondal, Abbas Ourmazd, Gianpietro Previtali, Iosifina Sarrou, Silvan Schön, Peter Schwander, Megan L. Shelby, Alessandro Silenzi, Jolanta Sztuk-Dambietz, Janusz Szuba, Monica Turcato, Thomas A. White, Krzysztof Wrona, Chen Xu, Mohamed H. Abdellatif, James D. Zook, John C. H. Spence, Henry N. Chapman, Anton Barty, Richard A. Kirian, Matthias Frank, Alexandra Ros, Marius Schmidt, Raimund Fromme, Adrian P. Mancuso, Petra Fromme, Nadia A. Zatsepin

Source: Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/e40721fe4c004e8eb6b285872cab2121

On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies

Authors: Julia Lieske, Maximilian Cerv, Stefan Kreida, Dana Komadina, Janine Fischer, Miriam Barthelmess, Pontus Fischer, Tim Pakendorf, Oleksandr Yefanov, Valerio Mariani, Thomas Seine, Breyan H. Ross, Eva Crosas, Olga Lorbeer, Anja Burkhardt, Thomas J. Lane, Sebastian Guenther, Julian Bergtholdt, Silvan Schoen, Susanna Törnroth-Horsefield, Henry N. Chapman, Alke Meents

Source: IUCrJ, Vol 6, Iss 4, Pp 714-728 (2019)

Subject Terms: serial crystallography, silicon chip, fixed-target crystallography, in-situ diffraction, vapor diffusion, ligand binding, ligand soaking, drug discovery, protein structure, X-ray crystallography, Crystallography, QD901-999

File Description: electronic resource

Relation: http://scripts.iucr.org/cgi-bin/paper?S2052252519007395; https://doaj.org/toc/2052-2525

Access URL: https://doaj.org/article/9cf038e492ec4349b8a7aa1396ce04ee

Development of a Control-Oriented Ignition Delay Model for GCI Combustion

Authors: Giacomo Silvagni, Vittorio Ravaglioli, Stefania Falfari, Fabrizio Ponti, Valerio Mariani

Source: Energies, Vol 15, Iss 17, p 6470 (2022)

Subject Terms: LTC, GCI, CO2 reduction, ignition delay, control-oriented model, combustion stability, Technology

File Description: electronic resource

Relation: https://www.mdpi.com/1996-1073/15/17/6470; https://doaj.org/toc/1996-1073

Access URL: https://doaj.org/article/98e342f96f0f4c9c89947623a4dccc88