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1. ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science

Author: Johannes P. Blaschke, Robert Bolotovsky, Aaron S. Brewster, Jeffrey Donatelli, Antoine DuJardin, Wu-chun Feng, Vidya Ganapati, Wilko Kroeger, Derek Mendez, Peter McCorquodale, Seema Mirchandaney, Christopher P. O'Grady, Daniel W. Paley, Amedeo Perazzo, Frederic P. Poitevin, Billy K. Poon, Vinay B. Ramakrishnaiah, Nicholas K. Sauter, Niteya Shah, Elliott Slaughter, Christine Sweeney, Daniel Tchoń, Monarin Uervirojnangkoorn, Felix Wittwer, Michael E. Wall, Chun Hong Yoon, and Iris D. Young
Subjects: exascale, Single Particle Imaging, Serial Femtosecond Crystallography, hardware acceleration, data-intensive, interfacility, Computer software, QA76.75-76.765
Abstract: ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) and Los Alamos National Laboratory. ExaFEL supports real-time data analysis via a cross-facility workflow spanning LCLS and HPC centers such as NERSC and OLCF. Our work therefore constitutes initial path-finding for the US Department of Energy's (DOE) Integrated Research Infrastructure (IRI) program. We present the ExaFEL team's 7 years of experience in developing real-time XFEL data analysis software for the DOE's exascale supercomputers. We present our experiences and lessons learned with the Perlmutter and Frontier supercomputers. Furthermore we outline essential data center services (and the implications for institutional policy) required for real-time data analysis. Finally we summarize our software and performance engineering approaches and our experiences with NERSC's Perlmutter and OLCF's Frontier systems. This work is intended to be a practical blueprint for similar efforts in integrating exascale compute resources into other cross-facility workflows.
Published: 2024
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2. De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Author: Guillaume Tetreau, Michael R. Sawaya, Elke De Zitter, Elena A. Andreeva, Anne-Sophie Banneville, Natalie A. Schibrowsky, Nicolas Coquelle, Aaron S. Brewster, Marie Luise Grünbein, Gabriela Nass Kovacs, Mark S. Hunter, Marco Kloos, Raymond G. Sierra, Giorgio Schiro, Pei Qiao, Myriam Stricker, Dennis Bideshi, Iris D. Young, Ninon Zala, Sylvain Engilberge, Alexander Gorel, Luca Signor, Jean-Marie Teulon, Mario Hilpert, Lutz Foucar, Johan Bielecki, Richard Bean, Raphael de Wijn, Tokushi Sato, Henry Kirkwood, Romain Letrun, Alexander Batyuk, Irina Snigireva, Daphna Fenel, Robin Schubert, Ethan J. Canfield, Mario M. Alba, Frédéric Laporte, Laurence Després, Maria Bacia, Amandine Roux, Christian Chapelle, François Riobé, Olivier Maury, Wai Li Ling, Sébastien Boutet, Adrian Mancuso, Irina Gutsche, Eric Girard, Thomas R. M. Barends, Jean-Luc Pellequer, Hyun-Woo Park, Arthur D. Laganowsky, Jose Rodriguez, Manfred Burghammer, Robert L. Shoeman, R. Bruce Doak, Martin Weik, Nicholas K. Sauter, Brian Federici, Duilio Cascio, Ilme Schlichting, and Jacques-Philippe Colletier
Subjects: Science
Abstract: An environmentally safe means of mosquito control is the application of Bacillus thuringiensis israelensis, which produces a cocktail of four naturally crystalline proteins exclusively toxic to mosquito. Here the authors report the atomic-resolution structures of Bti Cry11Aa and related Btj Cry11Ba solved de novo through Serial Femtosecond Crystallography on naturally-occurring nanocrystals.
Published: 2022
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3. Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I

Author: Stephen M. Keable, Adrian Kölsch, Philipp S. Simon, Medhanjali Dasgupta, Ruchira Chatterjee, Senthil Kumar Subramanian, Rana Hussein, Mohamed Ibrahim, In-Sik Kim, Isabel Bogacz, Hiroki Makita, Cindy C. Pham, Franklin D. Fuller, Sheraz Gul, Daniel Paley, Louise Lassalle, Kyle D. Sutherlin, Asmit Bhowmick, Nigel W. Moriarty, Iris D. Young, Johannes P. Blaschke, Casper de Lichtenberg, Petko Chernev, Mun Hon Cheah, Sehan Park, Gisu Park, Jangwoo Kim, Sang Jae Lee, Jaehyun Park, Kensuke Tono, Shigeki Owada, Mark S. Hunter, Alexander Batyuk, Roland Oggenfuss, Mathias Sander, Serhane Zerdane, Dmitry Ozerov, Karol Nass, Henrik Lemke, Roman Mankowsky, Aaron S. Brewster, Johannes Messinger, Nicholas K. Sauter, Vittal K. Yachandra, Junko Yano, Athina Zouni, and Jan Kern
Subjects: Medicine, Science
Abstract: Abstract Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A1A and A1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.
Published: 2021
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4. Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition

Author: Rana Hussein, Mohamed Ibrahim, Asmit Bhowmick, Philipp S. Simon, Ruchira Chatterjee, Louise Lassalle, Margaret Doyle, Isabel Bogacz, In-Sik Kim, Mun Hon Cheah, Sheraz Gul, Casper de Lichtenberg, Petko Chernev, Cindy C. Pham, Iris D. Young, Sergio Carbajo, Franklin D. Fuller, Roberto Alonso-Mori, Alex Batyuk, Kyle D. Sutherlin, Aaron S. Brewster, Robert Bolotovsky, Derek Mendez, James M. Holton, Nigel W. Moriarty, Paul D. Adams, Uwe Bergmann, Nicholas K. Sauter, Holger Dobbek, Johannes Messinger, Athina Zouni, Jan Kern, Vittal K. Yachandra, and Junko Yano
Subjects: Science
Abstract: The oxygen-evolving complex in Photosystem II (PSII) catalyzes the light-driven oxidation of water to oxygen and it is still under debate how the water reaches the active site. Here, the authors analyse time-resolved XFEL-based crystal structures of PSII that were determined at room temperature and report the structures of the waters in the putative channels surrounding the active site at various time-points during the reaction cycle and conclude that the O1 channel is the likely water intake pathway and the Cl1 channel the likely proton release pathway.
Published: 2021
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5. Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade

Author: Guillaume Tetreau, Anne-Sophie Banneville, Elena A. Andreeva, Aaron S. Brewster, Mark S. Hunter, Raymond G. Sierra, Jean-Marie Teulon, Iris D. Young, Niamh Burke, Tilman A. Grünewald, Joël Beaudouin, Irina Snigireva, Maria Teresa Fernandez-Luna, Alister Burt, Hyun-Woo Park, Luca Signor, Jayesh A. Bafna, Rabia Sadir, Daphna Fenel, Elisabetta Boeri-Erba, Maria Bacia, Ninon Zala, Frédéric Laporte, Laurence Després, Martin Weik, Sébastien Boutet, Martin Rosenthal, Nicolas Coquelle, Manfred Burghammer, Duilio Cascio, Michael R. Sawaya, Mathias Winterhalter, Enrico Gratton, Irina Gutsche, Brian Federici, Jean-Luc Pellequer, Nicholas K. Sauter, and Jacques-Philippe Colletier
Subjects: Science
Abstract: Bacillus thuringiensis israelensis (Bti) produces the naturally-crystalline proteinaceous toxin Cyt1Aa that is toxic to mosquito larvae. Here the authors grow recombinant nanocrystals of the Cyt1Aa protoxin in vivo and use serial femtosecond crystallography to determine its structure at different redox and pH conditions and by combining their structural data with further biochemical, toxicological and biophysical analyses provide mechanistic insights into the Cyt1Aa bioactivation cascade.
Published: 2020
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6. Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

Author: Alexander M. Wolff, Iris D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T. Biel, Sergio Carbajo, Aina E. Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D. Koralek, Minoru Kubo, Tomas S. Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M. Thompson, Henry van den Bedem, Rahel A. Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sebastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James S. Fraser, and Michael C. Thompson
Subjects: microcrystals, batch crystallization, serial crystallography, microed, Crystallography, QD901-999
Abstract: Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.
Published: 2020
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7. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Author: Kaitlyn Tsai, Vanja Stojković, Lianet Noda-Garcia, Iris D Young, Alexander G Myasnikov, Jordan Kleinman, Ali Palla, Stephen N Floor, Adam Frost, James S Fraser, Dan S Tawfik, and Danica Galonić Fujimori
Subjects: Cfr, directed evolution, antibiotic resistance, RNA modifications, peptidyl transferase center, cryoEM, Medicine, Science, Biology (General), QH301-705.5
Abstract: Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition of cfr results in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant that achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-electron microscopy structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr.
Published: 2022
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8. Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I

Author: Aaron S. Brewster, Dmitry Ozerov, Henrik T. Lemke, Sheraz Gul, Roman Mankowsky, Jangwoo Kim, Petko Chernev, Iris D. Young, Johannes Messinger, Sehan Park, Ruchira Chatterjee, Cindy C. Pham, Shigeki Owada, Nigel W. Moriarty, Louise Lassalle, Kensuke Tono, Jaehyun Park, Philipp S. Simon, Mun Hon Cheah, Rana Hussein, Roland Alex Oggenfuss, Nicholas K. Sauter, Asmit Bhowmick, Daniel W. Paley, Johannes Blaschke, Adrian Kölsch, Mathias Sander, Vittal K. Yachandra, Junko Yano, Isabel Bogacz, Mark S. Hunter, Karol Nass, Senthil Kumar Subramanian, In-Sik Kim, Alexander Batyuk, Casper de Lichtenberg, Franklin D. Fuller, Stephen Keable, Sang Jae Lee, Serhane Zerdane, Kyle D. Sutherlin, Hiroki Makita, Mohamed Ibrahim, M. Dasgupta, Jan Kern, Athina Zouni, and Gisu Park
Subjects: Photosynthetic reaction centre, Materials science, media_common.quotation_subject, Science, Thermosynechococcus, Bioenergetics, Crystallography, X-Ray, Photosystem I, Biochemistry, Molecular physics, Asymmetry, Article, Secondary electrons, Electron transfer, Symmetry breaking, Photosynthesis, media_common, Multidisciplinary, Photosystem I Protein Complex, Temperature, Free-electron laser, Biochemistry and Molecular Biology, Vitamin K 1, Protein Structure, Tertiary, Femtosecond, Medicine, Structural biology, Biokemi och molekylärbiologi
Abstract: Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A1A and A1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.
Published: 2021

9. Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-ray Crystallography

Author: Alexander M. Wolff, Eriko Nango, Iris D. Young, Aaron S. Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A. Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James M. Holton, Dohyun Im, Lee J. O’Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G. Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas K. Sauter, James S. Fraser, and Michael C. Thompson
Abstract: Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to trigger conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the sub-millisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature-jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.
Published: 2022

10. Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism

Author: Nigel W. Moriarty, Nicholas R Saichek, Derek Mendez, Nicholas K. Sauter, Holger Dobbek, James M. Holton, Allen M. Orville, Paul D. Adams, Cindy C. Pham, Kensuke Tono, Johannes Messinger, Louise Lassalle, Rana Hussein, Ruchira Chatterjee, Uwe Bergmann, Roberto Alonso-Mori, In-Sik Kim, Alexander Batyuk, Petko Chernev, Vittal K. Yachandra, Junko Yano, Iris D. Young, Casper de Lichtenberg, Kyle D. Sutherlin, Sheraz Gul, Philipp S. Simon, Sergio Carbajo, Asmit Bhowmick, Robert Bolotovsky, Shigeki Owada, Aaron S. Brewster, Mun Hon Cheah, Thomas Fransson, Isabel Bogacz, Franklin D. Fuller, Jan Kern, Athina Zouni, Trent R. Northen, and Mohamed Ibrahim
Subjects: 0301 basic medicine, Photosystem II, Oxygen-evolving complex, 010402 general chemistry, Physical Chemistry, 01 natural sciences, Redox, 03 medical and health sciences, Oxidation state, Molecule, Intermediate state, Magnesium, oxygen-evolving complex, Fysikalisk kemi, chemistry.chemical_classification, Photons, photosynthesis, Multidisciplinary, 030102 biochemistry & molecular biology, Ligand, Quinones, Water, Photosystem II Protein Complex, photosystem II, Biological Sciences, Electron acceptor, 0104 chemical sciences, Oxygen, X-ray free electron laser, Biophysics and Computational Biology, Crystallography, water oxidation, chemistry, Physical Sciences, Oxidation-Reduction, Hydrogen
Abstract: Significance A new bridging oxygen ligand is incorporated between one of the Mn atoms and Ca in the Mn4Ca cluster during the transition from the one-photon induced S2 intermediate state to the two-photon induced S3 state in the catalytic water oxidation reaction in photosystem II. However, the sequence of events leading to this change is not known. Here we report an X-ray crystallography and spectroscopy study at room temperature using an X-ray free electron laser to collect a “molecular movie” of the structural and oxidation state change steps leading to the insertion of this new oxygen bridge, in the 50 µs to 200 ms time scales after photon absorption, which triggers the S2 → S3 state transition., In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a “water wheel”-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.
Published: 2020

11. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Author: Adam Frost, Iris D. Young, Kleinman J, James S. Fraser, Stojković, Stephen N. Floor, K. Tsai, Dan S. Tawfik, Danica Galonić Fujimori, Palla A, Alexander G. Myasnikov, and Lianet Noda-García
Subjects: Peptidyl transferase, Adenosine, antibiotic resistance, Structural Biology and Molecular Biophysics, Antibiotics, Drug Resistance, Ribosome, Microbial, structural biology, directed evolution, Biology (General), Genetics, biology, Escherichia coli Proteins, General Neuroscience, Drug Resistance, Microbial, Methylation, General Medicine, Anti-Bacterial Agents, peptidyl transferase center, cryoEM, Infectious Diseases, Medicine, Infection, Research Article, Cfr, medicine.drug_class, QH301-705.5, Science, chemical biology, RRNA methylation, General Biochemistry, Genetics and Molecular Biology, Vaccine Related, Antibiotic resistance, RNA modifications, Biochemistry and Chemical Biology, molecular biophysics, medicine, Escherichia coli, biochemistry, Ribosomal, Binding Sites, General Immunology and Microbiology, E. coli, Methyltransferases, Ribosomal RNA, biology.organism_classification, coli, RNA, Ribosomal, biology.protein, RNA, Biochemistry and Cell Biology, Antimicrobial Resistance, Directed Molecular Evolution, Bacteria
Abstract: Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition of cfr results in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant that achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-electron microscopy structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr., eLife digest Antibiotics treat or prevent infections by killing bacteria or slowing down their growth. A large proportion of these drugs do this by disrupting an essential piece of cellular machinery called the ribosome which the bacteria need to make proteins. However, over the course of the treatment, some bacteria may gain genetic alterations that allow them to resist the effects of the antibiotic. Antibiotic resistance is a major threat to global health, and understanding how it emerges and spreads is an important area of research. Recent studies have discovered populations of resistant bacteria carrying a gene for a protein named chloramphenicol-florfenicol resistance, or Cfr for short. Cfr inserts a small modification in to the ribosome that prevents antibiotics from inhibiting the production of proteins, making them ineffective against the infection. To date, Cfr has been found to cause resistance to eight different classes of antibiotics. Identifying which mutations enhance its activity and protect bacteria is vital for designing strategies that fight antibiotic resistance. To investigate how the gene for Cfr could mutate and make bacteria more resistant, Tsai et al. performed a laboratory technique called directed evolution, a cyclic process which mimics natural selection. Genetic changes were randomly introduced in the gene for the Cfr protein and bacteria carrying these mutations were treated with tiamulin, an antibiotic rendered ineffective by the modification Cfr introduces into the ribosome. Bacteria that survived were then selected and had more mutations inserted. By repeating this process several times, Tsai et al. identified ‘super’ variants of the Cfr protein that lead to greater resistance. The experiments showed that these variants boosted resistance by increasing the proportion of ribosomes that contained the protective modification. This process was facilitated by mutations that enabled higher levels of Cfr protein to accumulate in the cell. In addition, the current study allowed, for the first time, direct visualization of how the Cfr modification disrupts the effect antibiotics have on the ribosome. These findings will make it easier for clinics to look out for bacteria that carry these ‘super’ resistant mutations. They could also help researchers design a new generation of antibiotics that can overcome resistance caused by the Cfr protein.
Published: 2022

12. Photoreversible interconversion of a phytochrome photosensory module in the crystalline state

Author: Miller, Pierre Aller, Allen M. Orville, Cindy C. Pham, Jason E. Koglin, Sheraz Gul, Aaron S. Brewster, Jonathan A. Clinger, Nicholas K. Sauter, In-Sik Kim, Iris D. Young, Richard D. Vierstra, Hunter, J.V. Heinemann, George N. Phillips, Franklin D. Fuller, A. Batyuk, E.S. Burgie, A. Butryn, Aina E. Cohen, Kyle D. Sutherlin, L. ORiordan, Jan Kern, Asmit Bhowmick, Vittal K. Yachandra, Junko Yano, and Roberto Alonso-Mori
Subjects: Models, Molecular, Light, Protein Conformation, Thermosynechococcus, Crystal structure, Crystallography, X-Ray, Cyanobacteria, 010402 general chemistry, Biochemistry, 01 natural sciences, Autocatalysis, 03 medical and health sciences, chemistry.chemical_compound, Protein Domains, Phycocyanobilin, Models, Phycobilins, Photoreceptor Cells, Cyclic GMP, X-ray crystallography, 030304 developmental biology, phytochrome, 0303 health sciences, Crystallography, Multidisciplinary, Phytochrome, Phosphoric Diester Hydrolases, Resolution (electron density), Phycocyanin, Molecular, Biological Sciences, photoreceptor, 0104 chemical sciences, Biophysics and Computational Biology, chemistry, Physical Sciences, Trans-Activators, X-Ray, Cyanobacteriochrome, Single crystal, Adenylyl Cyclases
Abstract: Significance A major hurdle in structurally defining the sequence of events that underpin the photointerconversion of phytochromes between their dark-adapted and photoactivated states has been the lack of crystals that undergo these transitions. Here, we describe a crystalline form of the GAF domain from Thermosynechococcus elongatus PixJ within the cyanobacteriochrome subfamily that undergoes reversible photointerconversion and thermal reversion back to the dark-adapted state. Preliminary cryocrystallography of irradiated crystals detected movements of the phycoviolobilin chromophore indicative of a D pyrrole ring rotation. However, X-ray hypersensitivity of both absorbing states might complicate interpretation. Fortunately, we found that PixJ is amenable to serial femtosecond X-ray diffraction methods, which we used to generate a 1.55-Å-resolution model of the dark-adapted state at room temperature., A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ in Thermosynechococcus elongatus assembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs − Fobs difference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-Å resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion.
Published: 2019

13. De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Author: Guillaume Tetreau, Michael R. Sawaya, Elke De Zitter, Elena A. Andreeva, Anne-Sophie Banneville, Natalie Schibrowsky, Nicolas Coquelle, Aaron S. Brewster, Marie Luise Grünbein, Gabriela Nass Kovacs, Mark S. Hunter, Marco Kloos, Raymond G. Sierra, Giorgio Schiro, Pei Qiao, Myriam Stricker, Dennis Bideshi, Iris D. Young, Ninon Zala, Sylvain Engilberge, Alexander Gorel, Luca Signor, Jean-Marie Teulon, Mario Hilpert, Lutz Foucar, Johan Bielecki, Richard Bean, Raphael de Wijn, Tokushi Sato, Henry Kirkwood, Romain Letrun, Alexander Batyuk, Irina Snigireva, Daphna Fenel, Robin Schubert, Ethan J. Canfield, Mario M. Alba, Frédéric Laporte, Laurence Després, Maria Bacia, Amandine Roux, Christian Chapelle, François Riobé, Olivier Maury, Wai Li Ling, Sébastien Boutet, Adrian Mancuso, Irina Gutsche, Eric Girard, Thomas R. M. Barends, Jean-Luc Pellequer, Hyun-Woo Park, Arthur D. Laganowsky, Jose Rodriguez, Manfred Burghammer, Robert L. Shoeman, R. Bruce Doak, Martin Weik, Nicholas K. Sauter, Brian Federici, Duilio Cascio, Ilme Schlichting, and Jacques-Philippe Colletier
Abstract: Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.
Published: 2021

14. Author response: Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

Author: Kaitlyn Tsai, Vanja Stojković, Lianet Noda-Garcia, Iris D Young, Alexander G Myasnikov, Jordan Kleinman, Ali Palla, Stephen N Floor, Adam Frost, James S Fraser, Dan S Tawfik, and Danica Galonić Fujimori
Published: 2021

15. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

Author: Alexander S. Mankin, K. Tsai, Iris D. Young, James S. Fraser, Nora Vázquez-Laslop, Teresa Szal, Vanja Stojković, Danica Galonić Fujimori, and D. John Lee
Subjects: chemistry.chemical_classification, Alanine, Peptidyl transferase, biology, medicine.drug_class, Stereochemistry, Antibiotics, Translation (biology), Ribosome, chemistry.chemical_compound, Enzyme, chemistry, 5.1 Pharmaceuticals, Linezolid, medicine, biology.protein, Peptide bond, Antimicrobial Resistance, Development of treatments and therapeutic interventions, Infection
Abstract: The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain. In this study, we determined that the second-generation oxazolidinone radezolid also induces stalling with alanine at the penultimate position. However, the molecular basis for context-specificity of these inhibitors has not been elucidated. In this study, we determined high-resolution cryo-EM structures of both linezolid and radezolid-stalled ribosome complexes. These structures reveal that the alanine side chain fits within a small hydrophobic crevice created by oxazolidinone, resulting in improved ribosome binding. Modification of the ribosome by the antibiotic resistance enzyme Cfr disrupts stalling by forcing the antibiotic to adopt a conformation that narrows the hydrophobic alanine pocket. Together, the structural and biochemical findings presented in this work provide molecular understanding of context-specific inhibition of translation by clinically important oxazolidinone antibiotics.
Published: 2021

16. X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis

Author: Pierre Aller, Allen M. Orville, Kensuke Tono, Jos J. A. G. Kamps, Patrick Rabe, Sheraz Gul, In-Sik Kim, Christopher J. Schofield, Denis Shutin, Alexander Batyuk, L. ORiordan, Asmit Bhowmick, Mun Hon Cheah, Hiroki Makita, Cindy C. Pham, Iris D. Young, Ilaria Pettinati, Robin L. Owen, Jürgen Brem, Pauline A. Lang, Uwe Bergmann, James D. S. Linyard, Margaret Doyle, Michael A. McDonough, Shigeki Owada, Ian J. Clifton, Mark S. Hunter, Timothy D. W. Claridge, Yasumasa Joti, Jan Kern, Aaron S. Brewster, Carol V. Robinson, Thomas M. Leissing, Vittal K. Yachandra, Roberto Alonso-Mori, Junko Yano, Nicholas K. Sauter, Franklin D. Fuller, Kyle D. Sutherlin, A. Butryn, and Thomas Fransson
Subjects: Stereochemistry, Isopenicillin N synthase, Electrons, Penicillins, Crystallography, X-Ray, Physical Chemistry, Ferric Compounds, Catalysis, Substrate Specificity, chemistry.chemical_compound, Catalytic Domain, polycyclic compounds, Humans, Research Articles, Fysikalisk kemi, chemistry.chemical_classification, Crystallography, Multidisciplinary, biology, Superoxide, Protein dynamics, Lasers, X-ray, Active site, SciAdv r-articles, Optics, Oxygen, Enzyme, chemistry, Yield (chemistry), X-Ray, biology.protein, Oxidoreductases, Research Article
Abstract: Complementary XFEL methods reveal O2 reaction intermediates and global protein dynamics during Isopenicillin N synthase catalysis., Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.
Published: 2021

17. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics

Author: Kaitlyn Tsai, Vanja Stojković, D. John Lee, Iris D. Young, Teresa Szal, Dorota Klepacki, Nora Vázquez-Laslop, Alexander S. Mankin, James S. Fraser, and Danica Galonić Fujimori
Subjects: Models, Molecular, Biophysics, Medical and Health Sciences, Article, RNA, Transfer, Models, Structural Biology, Molecular Biology, Oxazolidinones, Ribosomal, Alanine, Binding Sites, Cryoelectron Microscopy, Linezolid, Molecular, Biological Sciences, Anti-Bacterial Agents, Transfer, 5.1 Pharmaceuticals, RNA, Ribosomal, Protein Biosynthesis, Chemical Sciences, Peptidyl Transferases, RNA, Development of treatments and therapeutic interventions, Infection, Ribosomes, Developmental Biology
Abstract: The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain. However, the molecular basis for context-specificity has not been elucidated. Here we show that the second-generation oxazolidinone radezolid also induces stalling with a penultimate alanine, and we determine high-resolution cryo-EM structures of linezolid- and radezolid-stalled ribosome complexes to explain their mechanism of action. These structures reveal that the alanine side chain fits within a small hydrophobic crevice created by oxazolidinone, resulting in improved ribosome binding. Modification of the ribosome by the antibiotic resistance enzyme Cfr disrupts stalling due to repositioning of the modified nucleotide. Together, our findings provide molecular understanding for the context-specificity of oxazolidinones.
Published: 2021

18. Structural isomers of the S 2 state in photosystem II: do they exist at room temperature and are they important for function?

Author: Louise Lassalle, Sheraz Gul, Ruchira Chatterjee, Casper de Lichtenberg, Vittal K. Yachandra, Junko Yano, Iris D. Young, Franklin D. Fuller, Mun Hon Cheah, Johannes Messinger, Athina Zouni, Jan Kern, and Mohamed Ibrahim
Subjects: 0106 biological sciences, 0301 basic medicine, X-ray absorption spectroscopy, Photosystem II, Physiology, Chemistry, food and beverages, macromolecular substances, Cell Biology, Plant Science, General Medicine, Photochemistry, 01 natural sciences, Redox, 03 medical and health sciences, Pigment, 030104 developmental biology, Structural biology, visual_art, Genetics, Structural isomer, visual_art.visual_art_medium, Biological sciences, Function (biology), 010606 plant biology & botany
Abstract: In nature, an oxo‐bridged Mn4CaO5 cluster embedded in photosystem II (PSII), a membrane‐bound multi‐subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light‐i ...
Published: 2019

19. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes

Author: Jessica K. Peters, Natalia Jura, Aye C. Thwin, Mehdi Bouhaddou, Fei Li, Jocelyne Lopez, Yang Li, Kuei-Ho Chen, Erron W. Titus, Huong T. Kratochvil, Victor L Lam, Christian B. Billesbølle, Tristan W. Owens, Raphael Trenker, Axel F. Brilot, Danielle L. Swaney, Ursula Schulze-Gahmen, Feng Wang, Gregory E. Merz, Jen Chen, Amy Diallo, Yang Zhang, Adam Frost, Soumya G. Remesh, Junrui Li, Edmond Linossi, Fengbo Zhou, Maliheh Safari, Yifan Cheng, Henry C. Nguyen, Andrea Fossati, Devan Diwanji, Evelyn Hernandez, Aashish Manglik, Nevan J. Krogan, Iris D. Young, Jianhua Zhao, Kyle E. Lopez, Alexandrea N. Rizo, Megan Lo, Thomas H. Pospiech, Gwendolyn M. Jang, Y. Li, Sergei Pourmal, Yuan Zhou, Miles Sasha Dickinson, Un Seng Chio, Kaihua Zhang, Caleigh M. Azumaya, Michael D Paul, Oren S. Rosenberg, Yanxin Liu, Tsz Kin Martin Tsui, Carlos Nowotny, Kate Kim, Kliment A. Verba, Loan Doan, Zanlin Yu, Adrian Pelin, Mariano C Tabios, Lorena Zuliani-Alvarez, Daniel R. Southworth, Melody G. Campbell, Ming Sun, Adamo Mancino, Kaitlin Schaefer, Frank R. Moss, Daniel Asarnow, Meghna Gupta, James S. Fraser, Komal Ishwar Pawar, Amber M. Smith, Robert M. Stroud, Tanja Kortemme, Cristina Puchades, Michelle Moritz, Nadia Herrera, Eric Tse, Mingliang Jin, and David A. Agard
Subjects: drug design, 1.1 Normal biological development and functioning, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viruses, Mutant, Computational biology, medicine.disease_cause, Article, Vaccine Related, Eukaryotic translation, Underpinning research, Transcription (biology), Biodefense, medicine, 2.1 Biological and endogenous factors, Functional studies, Aetiology, Lung, Coronavirus, SARS-CoV-2, Host (biology), Chemistry, Prevention, RNA, virus diseases, Pneumonia, biochemical phenomena, metabolism, and nutrition, proteins, Infectious Diseases, Emerging Infectious Diseases, Pneumonia & Influenza, Generic health relevance, Infection
Abstract: The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.
Published: 2021

20. Review of: 'Improving SARS-CoV-2 structures: Peer review by early coordinate release

Author: Iris D Young and James S Fraser
Abstract: Our review of an earlier version of what was eventually published as: - title: "Improving SARS-CoV-2 structures: Peer review by early coordinate release." - citation: "Croll TI, Williams CJ, Chen VB, Richardson DC, Richardson JS. *Biophysical Journal.* 2021." - pmid: 33460600 &nbsp
Published: 2021
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21. Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition

Author: Mun Hon Cheah, Cindy C. Pham, Mohamed Ibrahim, James M. Holton, Athina Zouni, Sheraz Gul, Kyle D. Sutherlin, Paul D. Adams, Louise Lassalle, A. Batyuk, Iris D. Young, Jan Kern, Nicholas K. Sauter, Roberto Alonso-Mori, Ruchira Chatterjee, Aaron S. Brewster, In-Sik Kim, Sergio Carbajo, Margaret Doyle, Rana Hussein, Johannes Messinger, Philipp S. Simon, Isabel Bogacz, Derek Mendez, Petko Chernev, Uwe Bergmann, Casper de Lichtenberg, Franklin D. Fuller, Asmit Bhowmick, Nigel W. Moriarty, Holger Dobbek, Vittal K. Yachandra, Junko Yano, and Robert Bolotovsky
Subjects: Proton, Photosystem II, Science, General Physics and Astronomy, chemistry.chemical_element, macromolecular substances, Bioenergetics, Photochemistry, Redox, Oxygen, General Biochemistry, Genetics and Molecular Biology, Article, Proton transport, X-ray crystallography, Organisk kemi, Multidisciplinary, biology, Electrolysis of water, Organic Chemistry, Biochemistry and Molecular Biology, Photosystem II Protein Complex, Water, Active site, Substrate (chemistry), Hydrogen Bonding, General Chemistry, chemistry, biology.protein, Protons, Structural biology, Biokemi och molekylärbiologi
Abstract: Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons., The oxygen-evolving complex in Photosystem II (PSII) catalyzes the light-driven oxidation of water to oxygen and it is still under debate how the water reaches the active site. Here, the authors analyse time-resolved XFEL-based crystal structures of PSII that were determined at room temperature and report the structures of the waters in the putative channels surrounding the active site at various time-points during the reaction cycle and conclude that the O1 channel is the likely water intake pathway and the Cl1 channel the likely proton release pathway.
Published: 2021

22. Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade

Author: Martin Rosenthal, Maria Bacia, Maria Teresa Fernandez-Luna, Luca Signor, Guillaume Tetreau, Jayesh Arun Bafna, Enrico Gratton, Anne-Sophie Banneville, Iris D. Young, Mathias Winterhalter, Frederic Laporte, Aaron S. Brewster, Raymond G. Sierra, Manfred Burghammer, Mark S. Hunter, Sébastien Boutet, Elisabetta Boeri-Erba, Elena A. Andreeva, Ninon Zala, Jacques-Philippe Colletier, Tilman A. Grünewald, Irina Gutsche, Nicolas Coquelle, Niamh Burke, Duilio Cascio, Laurence Després, Irina Snigireva, Daphna Fenel, Alister Burt, Jean-Marie Teulon, Rabia Sadir, Nicholas K. Sauter, Jean-Luc Pellequer, Martin Weik, Brian A. Federici, Joël Beaudouin, Hyun-Woo Park, Michael R. Sawaya, Groupe Dynamique et Cinétique des processus moléculaires (IBS-DYNAMOP), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, European Synchrotron Radiation Facility (ESRF), Department of Entomology [Riverside], University of California [Riverside] (UCR), University of California-University of California, California Baptist University (CBU), Jacobs University [Bremen], Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut Laue-Langevin (ILL), ILL, UCLA/DOE Institute for Genomics and Proteomics, University of California [Los Angeles] (UCLA), Laboratory for Fluorescence Dynamics [Irvine], University of California [Irvine] (UCI), AFM platform, Grenoble Instruct-ERIC center (ISBG, UMS 3518 CNRS-CEA-UGAEMBL), ANR-17-CE11-0018,X-in-vivo,Cristallisation in vivo: une nouvelle stratégie pour étudier la structure et la dynamique des protéines dans les lasers à électrons libres et les synchrotrons.(2017), ANR-18-CE11-0005,DynOCP,Investigation du mécanisme de photo-activation de l'OCP par spectroscopie optique ultrarapide et cristallographie sérielle temps-résolue.(2018), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Université Grenoble Alpes (UGA), University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), and University of California [Irvine] (UC Irvine)
Subjects: 0301 basic medicine, Insecticides, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Protein Conformation, General Physics and Astronomy, Crystallography, X-Ray, Microscopy, Atomic Force, Atomic force microscopy, Hemolysin Proteins, Mice, 0302 clinical medicine, Sf9 Cells, Disulfides, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Microscopy, Crystallography, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Nanocrystallography, Chemistry, Atomic Force, Limiting, Hydrogen-Ion Concentration, Bacillus thuringiensis israelensis, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Femtosecond, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Science, Mechanism of action, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Bacterial Proteins, In vivo, parasitic diseases, Animals, Humans, Bacillus thuringiensis Toxins, Cell Membrane, fungi, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Chemistry, Endotoxins, HEK293 Cells, 030104 developmental biology, Yield (chemistry), X-Ray, NIH 3T3 Cells, lcsh:Q, 030217 neurology & neurosurgery
Abstract: Cyt1Aa is the one of four crystalline protoxins produced by mosquitocidal bacterium Bacillus thuringiensis israelensis (Bti) that has been shown to delay the evolution of insect resistance in the field. Limiting our understanding of Bti efficacy and the path to improved toxicity and spectrum has been ignorance of how Cyt1Aa crystallizes in vivo and of its mechanism of toxicity. Here, we use serial femtosecond crystallography to determine the Cyt1Aa protoxin structure from sub-micron-sized crystals produced in Bti. Structures determined under various pH/redox conditions illuminate the role played by previously uncharacterized disulfide-bridge and domain-swapped interfaces from crystal formation in Bti to dissolution in the larval mosquito midgut. Biochemical, toxicological and biophysical methods enable the deconvolution of key steps in the Cyt1Aa bioactivation cascade. We additionally show that the size, shape, production yield, pH sensitivity and toxicity of Cyt1Aa crystals grown in Bti can be controlled by single atom substitution., Bacillus thuringiensis israelensis (Bti) produces the naturally-crystalline proteinaceous toxin Cyt1Aa that is toxic to mosquito larvae. Here the authors grow recombinant nanocrystals of the Cyt1Aa protoxin in vivo and use serial femtosecond crystallography to determine its structure at different redox and pH conditions and by combining their structural data with further biochemical, toxicological and biophysical analyses provide mechanistic insights into the Cyt1Aa bioactivation cascade.
Published: 2020

23. Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit

Author: Vanja Stojković, James S. Fraser, Iris D. Young, Danica Galonić Fujimori, Alexander G. Myasnikov, and Adam Frost
Subjects: Models, Molecular, Static Electricity, Ribosome biogenesis, Ribosome Subunits, Large, Bacterial, Computational biology, Biology, Ribosome, 03 medical and health sciences, 0302 clinical medicine, Structural Biology, 23S ribosomal RNA, Models, Information and Computing Sciences, Escherichia coli, Ribosome Subunits, Genetics, Nucleic acid structure, 030304 developmental biology, 50S, 0303 health sciences, Nucleotides, Cryoelectron Microscopy, Bacterial, RNA, Reproducibility of Results, Molecular, Ribosomal RNA, Biological Sciences, Peptidyl Transferases, Solvents, Large, Generic health relevance, Peptides, Infection, 030217 neurology & neurosurgery, Environmental Sciences, Developmental Biology
Abstract: Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides’ positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.
Published: 2020

24. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

Author: Sergey Koroidov, George N. Phillips, Hugo Lebrette, Thomas Fransson, Martin Högbom, Silke Nelson, Claudiu A. Stan, Louise Lassalle, Roberto Alonso-Mori, Vivek Srinivas, Richard D. Vierstra, Franklin D. Fuller, Thomas Kroll, Christopher J. Pollock, Muhamed Amin, Jonathan A. Clinger, Athina Zouni, Aaron S. Brewster, Iris D. Young, Babak Andi, Amie K. Boal, Diling Zhu, Sanghoon Song, Marc Allaire, Nicholas K. Sauter, Tara Michels-Clark, Pierre Aller, E. Sethe Burgie, Uwe Bergmann, Allen M. Orville, Casper de Lichtenberg, James M. Glownia, Philipp Bräuer, Miao Zhang, Ernest Pastor, Christian G. Roessler, Matthieu Chollet, Dimosthenis Sokaras, Ruchira Chatterjee, Mohamed Ibrahim, Carsten Krebs, Rana Hussein, Sheraz Gul, Mengning Liang, Jan Kern, Clemens Weninger, Markus Kubin, Jason E. Koglin, P. T. Docker, Vittal K. Yachandra, Junko Yano, Johannes Messinger, J. Martin Bollinger, Raymond G. Sierra, Henrik T. Lemke, and Mitchell D. Miller
Subjects: 0301 basic medicine, Free electron model, Materials science, Drop (liquid), X-ray, Nanotechnology, Cell Biology, 010402 general chemistry, Laser, 01 natural sciences, Biochemistry, 0104 chemical sciences, law.invention, 03 medical and health sciences, 030104 developmental biology, law, Others, On demand, Molecular Biology, Biotechnology
Abstract: X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniq ...
Published: 2017

25. Biomaterials in non-integer dimensions

Author: Iris D. Young and James S. Fraser
Subjects: Discrete mathematics, Fractal, Fractals, 010405 organic chemistry, Chemistry, General Chemical Engineering, Biocompatible Materials, General Chemistry, 010402 general chemistry, 01 natural sciences, Computer Science::Distributed, Parallel, and Cluster Computing, 0104 chemical sciences, Integer (computer science)
Abstract: Nature harnesses fractal geometry to create structures with unusual surface-to-volume ratios. Now, a new design approach enables the reversible assembly of functional enzymes into arboreal patterns with fractal geometry.
Published: 2019

26. Structural isomers of the S

Author: Ruchira, Chatterjee, Louise, Lassalle, Sheraz, Gul, Franklin D, Fuller, Iris D, Young, Mohamed, Ibrahim, Casper, de Lichtenberg, Mun Hon, Cheah, Athina, Zouni, Johannes, Messinger, Vittal K, Yachandra, Jan, Kern, and Junko, Yano
Subjects: Crystallography, X-Ray Absorption Spectroscopy, Electron Spin Resonance Spectroscopy, Temperature, Photosystem II Protein Complex, Article
Abstract: In nature, an oxo-bridged Mn(4)CaO(5) cluster embedded in Photosystem II (PSII), a membrane-bound multi-subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light-induced charge separations in the reaction center of PSII. The Mn(4)CaO(5) cluster accumulates four oxidizing equivalents to enable the four-electron four-proton catalysis of two water molecules to one dioxygen molecule and cycles through five intermediate S-states, S(0) – S(4) in the Kok cycle. One important question related to the catalytic mechanism of the oxygen-evolving complex (OEC) that remains is, whether structural isomers are present in some of the intermediate S-states and if such equilibria are essential for the mechanism of the O-O bond formation. Here we compare results from electron paramagnetic resonance (EPR) and X-ray absorption spectroscopy (XAS) obtained at cryogenic temperatures for the S(2) state of PSII with structural data collected of the S(1), S(2) and S(3) states by serial crystallography at neutral pH (~6.5) using an X-ray free electron laser at room temperature. While the cryogenic data demonstrate the presence of at least two structural forms of the S(2) state, the room temperature crystallography data can be well-described by just one S(2) structure. We discuss the deviating results and outline experimental strategies for clarifying this mechanistically important question.
Published: 2018

27. Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs

Author: E. Goggins, T-C Weng, K. Nagaya, Tetsuo Katayama, Dimosthenis Sokaras, B. A. McClure, Kazuki Asa, Nicholas K. Sauter, Roberto Alonso-Mori, Walter W. Weare, Kiyoshi Ueda, Sheraz Gul, Tadashi Togashi, Vittal K. Yachandra, Junko Yano, Toshiyuki Nishiyama, Thomas Kroll, Mohamed Ibrahim, Iris D. Young, Claudio Saracini, Yoshiaki Kumagai, Ruchira Chatterjee, Johannes Messinger, Franklin D. Fuller, Tsukasa Takanashi, Athina Zouni, Koji Motomura, Aaron S. Brewster, Y. Sato, Heinz Frei, D. Iablonskyi, Uwe Bergmann, Hironobu Fukuzawa, Jan Kern, Jason K. Cooper, and Makina Yabashi
Subjects: Free electron model, Astrophysics::High Energy Astrophysical Phenomena, Electrons, Nanotechnology, Crystallography, X-Ray, 010402 general chemistry, 01 natural sciences, Catalysis, Article, law.invention, law, 0103 physical sciences, Artificial systems, Physical and Theoretical Chemistry, 010306 general physics, Physics, Crystallography, Chemical Physics, Lasers, X-Rays, Laser, 0104 chemical sciences, Characterization (materials science), Excited state, Chemical Sciences, Femtosecond, X-Ray
Abstract: This journal is © The Royal Society of Chemistry. The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.
Published: 2016

28. Structures of the intermediates of Kok’s photosynthetic water oxidation clock

Author: Aaron S. Brewster, James M. Holton, Paul D. Adams, Pierre Aller, Ina Seuffert, Allen M. Orville, Holger Dobbek, Ernest Pastor, Roberto Alonso-Mori, Nicholas K. Sauter, Ruchira Chatterjee, J. Wersig, Louise Lassalle, Casper de Lichtenberg, Sergio Carbajo, Rana Hussein, Vittal K. Yachandra, Junko Yano, Jan Kern, Nigel W. Moriarty, Dmitriy Shevela, A. Butryn, Iris D. Young, Mohamed Ibrahim, Thomas Kroll, Raymond G. Sierra, Sébastien Boutet, Uwe Bergmann, Dimosthenis Sokaras, Franklin D. Fuller, Sheraz Gul, Athina Zouni, Clemens Weninger, Johannes Messinger, Miao Zhang, Mun Hon Cheah, Thomas Fransson, Alexander Batyuk, Lacey Douthit, Jason E. Koglin, and Mengning Liang
Subjects: Models, Molecular, Photosystem II, Plastoquinone, 02 engineering and technology, 010402 general chemistry, Photochemistry, Photosynthesis, Crystallography, X-Ray, Cyanobacteria, 01 natural sciences, Article, Biological sciences, Manganese, Multidisciplinary, Chemistry, Oxygen metabolism, Lasers, Oxygen evolution, Photosystem II Protein Complex, Water, Oxidation reduction, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Photosynthetic water oxidation, Oxygen, Water chemistry, Calcium, 0210 nano-technology, Oxidation-Reduction
Abstract: Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok’s S-state clock or cycle(1,2). The model comprises four (meta)stable intermediates (S(0), S(1), S(2) and S(3)) and one transient S(4) state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn(4)CaO(5)) cluster in the oxygen-evolving complex(3–7). This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone Q(B) at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok’s cycle as high-resolution structures (2.04–2.08 Å). In addition, we report structures of two transient states at 150 and 400 μs, revealing notable structural changes including the binding of one additional ‘water’, Ox, during the S(2)→S(3) state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S(3) state between Ca and Mn1 supports O–O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O(2) release. Thus, our results exclude peroxo-bond formation in the S(3) state, and the nucleophilic attack of W3 onto W2 is unlikely.
Published: 2018

29. Improving signal strength in serial crystallography with DIALS geometry refinement

Author: L. ORiordan, Iris D. Young, Gwyndaf Evans, Graeme Winter, Aaron S. Brewster, James M. Parkhurst, David G. Waterman, Richard J. Gildea, Nicholas K. Sauter, and Junko Yano
Subjects: 0301 basic medicine, Diffraction, sparse algebra, Thermolysin, Physics::Optics, Bacillus, Bioengineering, 02 engineering and technology, Crystallography, X-Ray, Signal, Crystal, 03 medical and health sciences, Computer-Assisted, X-Ray Diffraction, Structural Biology, Position (vector), Humans, refinement, Physics, Crystallography, Orientation (computer vision), XFEL, Detector, Radiographic Image Interpretation, 021001 nanoscience & nanotechnology, Metrology, Nonlinear system, 030104 developmental biology, metrology, DIALS, X-Ray, Radiographic Image Interpretation, Computer-Assisted, 0210 nano-technology, Algorithms, Software
Abstract: © 2018 International Union of Crystallography. The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, and detector geometry, that are most consistent with the observed positions of Bragg spots. These parameters can be refined by nonlinear least squares fitting. In previous work, it has been challenging to refine both the positions of the sensors (metrology) on multipanel imaging detectors such as the CSPAD and the orientations of all of the crystals studied. Since the optimal models for metrology and crystal orientation are interdependent, alternate cycles of panel refinement and crystal refinement have been required. To simplify the process, a sparse linear algebra technique for solving the normal equations was implemented, allowing the detector panels to be refined simultaneously against the diffraction from thousands of crystals with excellent computational performance. Separately, it is shown how to refine the metrology of a second CSPAD detector, positioned at a distance of 2.5 m from the crystal, used for recording low-angle reflections. With the ability to jointly refine the detector position against the ensemble of all crystals used for structure determination, it is shown that ensemble refinement greatly reduces the apparent nonisomorphism that is often observed in the unit-cell distributions from still-shot serial crystallography. In addition, it is shown that batching the images by timestamp and re-refining the detector position can realistically model small, time-dependent variations in detector position relative to the sample, and thereby improve the integrated structure-factor intensity signal and heavy-atom anomalous peak heights.
Published: 2018

30. DIALS: Implementation and evaluation of a new integration package

Author: Iris D. Young, Gwyndaf Evans, Nicholas K. Sauter, Melanie Vollmar, Richard J. Gildea, Tara Michels-Clark, Aaron S. Brewster, Luis Fuentes-Montero, James M. Parkhurst, David G. Waterman, Graeme Winter, and Markus Gerstel
Subjects: 0301 basic medicine, methods development, Engineering drawing, Computer science, Thermolysin, Biophysics, 010402 general chemistry, Crystallography, X-Ray, 01 natural sciences, 03 medical and health sciences, Software, Light source, Computer-Assisted, Bacterial Proteins, Structural Biology, Structure (mathematical logic), Data processing, Electronic Data Processing, Software suite, Crystallography, business.industry, Electronic data processing, Search engine indexing, Radiographic Image Interpretation, Biological Sciences, Research Papers, 0104 chemical sciences, X-ray diffraction, Repressor Proteins, 030104 developmental biology, DIALS, Physical Sciences, Chemical Sciences, Data analysis, X-Ray, Radiographic Image Interpretation, Computer-Assisted, business, Algorithms, data processing
Abstract: A new X-ray diffraction data-analysis package is presented with a description of the algorithms and examples of its application to biological and chemical crystallography., The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.
Published: 2018

31. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II

Author: Elia A Junco, Hartawan Laksmono, S. Michael Soltis, Tara Michels-Clark, Christina Y. Hampton, Mengning Liang, Claudiu A. Stan, Iris D. Young, Aaron S. Brewster, Raymond G. Sierra, Franklin D. Fuller, Hasan DeMirci, Michael J. Bogan, Ruchira Chatterjee, Sheraz Gul, Brandon Hayes, Nicholas K. Sauter, Mark S. Hunter, Sébastien Boutet, Jason E. Koglin, Andrew Aquila, Vittal K. Yachandra, Junko Yano, Joseph D. Puglisi, Cornelius Gati, Mohamed Ibrahim, Elisabetta Viani Puglisi, E. Han Dao, Jan Kern, and Athina Zouni
Subjects: Models, Molecular, 0301 basic medicine, Technology, Materials science, Photosystem II, macromolecular substances, ambient temperature crystallography, Medical and Health Sciences, Biochemistry, Ribosome, Article, law.invention, 03 medical and health sciences, Electrokinetic phenomena, Models, Thermolysin, law, antibiotic, SFX, Geobacillus stearothermophilus, Mother liquor, Molecular Biology, electrospinning, concentric-flow, Crystallography, biology, photosystem II, Photosystem II Protein Complex, Molecular, Cell Biology, Injector, Biological Sciences, Thermus thermophilus, biology.organism_classification, 030104 developmental biology, ribosome, bacteria, Ribosomes, Developmental Biology, Biotechnology
Abstract: In this work, a concentric-flow electrokinetic injector delivered microcrystals of Geobacillus stearothermophilus thermolysin (2.2 Å structure), Thermosynechococcus elongatus photosystem II (< 3 Å diffraction) and Thermus thermophilus small ribosomal subunit (3.4 Å structure). The first ambient-temperature X-ray crystal structure of the 30S subunit bound to the antibiotic paromomycin was obtained in its native mother liquor. Compared to previous cryo-cooled structures, this new structure showed that paromomycin binds to the decoding center in a different conformation.
Published: 2015

32. High-speed fixed-target serial virus crystallography

Author: Elizabeth E. Fry, Roberto Alonso-Mori, Pontus Fischer, Tara Michels-Clark, Bernd Reime, David J. Rowlands, J. Kelly, Geoff Sutton, Jingshan Ren, Aaron S. Brewster, Ramona Duman, Helen M. Ginn, Philip Roedig, Iris D. Young, Karl Harlos, Ismo Vartiainen, Thomas S. Walter, Armin Wagner, Nicholas K. Sauter, Silke Nelson, David I. Stuart, Marcin Sikorsky, Tim Pakendorf, Christian David, Daniel S. Damiani, Alke Meents, Martin Warmer, Abhay Kotecha, and Jan Meyer
Subjects: 0301 basic medicine, Technology, 030103 biophysics, Materials science, business.operation, Synchronizing, Crystallography, X-Ray, Medical and Health Sciences, Biochemistry, Sensitivity and Specificity, Article, Imaging, law.invention, 03 medical and health sciences, Computer-Assisted, Imaging, Three-Dimensional, law, ddc:570, Image Interpretation, Computer-Assisted, Image Interpretation, Molecular Biology, Throughput (business), Crystallography, Reproducibility of Results, Cell Biology, Biological Sciences, Laser, Image Enhancement, Sample (graphics), 030104 developmental biology, Roadrunner, Sample size determination, Goniometer, Sample Size, Three-Dimensional, Femtosecond, Viruses, X-Ray, Infection, business, Algorithms, Developmental Biology, Biotechnology
Abstract: © 2017 Nature America, Inc., part of Springer Nature. All rights reserved. We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.
Published: 2017

33. Overview of the JET results in support to ITER

Author: Alfredo Pironti, J. Simpson-Hutchinson, Sean Conroy, J. Uljanovs, D. Middleton-Gear, G. Possnert, C. Angioni, R. McAdams, Nicholas Watkins, E. Fortuna-Zalesna, A. Garcia-Carrasco, K. Gałązka, D. Nodwell, Pasquale Gaudio, R.A. Pitts, Svetlana V. Ratynskaia, Seppo Koivuranta, O. J. Kwon, C. Boyd, A. Boboc, M. Reinhart, Igor Lengar, Jarrod Leddy, Hiroyasu Utoh, J. H. Ahn, A. Stevens, J. Lönnroth, U. Kruezi, C. Guillemaut, N. Fonnesu, W. Studholme, Marek Rubel, P. Cahyna, O. McCormack, A. S. Jacobsen, D. Mazon, Gunta Kizane, N. Ashikawa, William Tang, J. Goff, F. Nespoli, Thomas Giegerich, G. Petravich, Angela Busse, Corneliu Porosnicu, M. Bigi, M. Wheatley, Christopher N. Bowman, J. Zacks, Ivan Calvo, U. Losada, H. Weisen, B. Bauvir, Stanislas Pamela, Sylvain Brémond, M.F. Stamp, Scott W. McIntosh, A. Rakha, S. Glöggler, V. Braic, C. Bottereau, S. Murphy, S. Knott, Luigi Fortuna, P. Bunting, N. Vora, S. D. Scott, A. Lazaros, R. Dejarnac, P. Buratti, H.R. Strauss, Gabriele Croci, M. Nocente, A. Hollingsworth, S. Reynolds, D. J. Wilson, D. D. Brown, T.C. Luce, S. Zoletnik, E. Nilsson, L. Laguardia, O. Marchuk, F.P. Orsitto, E. Cecil, V. Huber, J. B. Girardo, Stylianos Varoutis, M. D. Axton, Hyun-Tae Kim, E. Safi, Ch. Day, S. Arshad, J. Rzadkiewicz, P. Prior, A. Meigs, S. Esquembri, P. Gohil, K. Purahoo, Torbjörn Hellsten, N. Tipton, R. Guirlet, E. Joffrin, V. Aldred, Calin Besliu, M. Valentinuzzi, G. T. Jones, J. Edwards, Giuseppe Ambrosino, Laurent Marot, N. Lam, F. Crisanti, G. Verona Rinati, R. Marshal, Michael L. Brown, D. Frigione, D. Chandra, Michaele Freisinger, R. Olney, Jari Varje, S. Whetham, F. Parra Diaz, M. R. Hough, P. Dinca, F. Salzedas, A. Goodyear, R. Gowland, J. A. Wilson, J. Horacek, D. King, K. Flinders, I. R. Merrigan, M. Ghate, R. Michling, F. Saint-Laurent, G. Kocsis, D. Van Eester, C. Young, R. O. Dendy, A. Meakins, N. Pace, C. L. Hunter, D. Alegre, S. Foster, V. Riccardo, M. Bulman, C. Jeong, Marek Szawlowski, B. D. Whitehead, Vasily Kiptily, James Harrison, Hiroshi Tojo, G. T. A. Huijsmans, J. W. Coenen, X. Litaudon, Justin Williams, C. Hidalgo, S. Lesnoj, I.E. Day, A. W. Morris, R. Mooney, Yann Corre, S. Brezinsek, B. Gonçalves, M. Kresina, D. Coombs, F. Köchl, J. L. Gardarein, W. Davis, Aqsa Shabbir, Kanti M. Aggarwal, L. Colas, A. B. Kukushkin, Seppo Sipilä, Elisabeth Rachlew, Leena Aho-Mantila, O. G. Pompilian, E. Viezzer, Shane Cooper, Fabio Villone, P. Blanchard, Patrick Tamain, P. Camp, T. Szabolics, C. Luna, Kalle Heinola, H. G. Esser, V. Bobkov, James Buchanan, Andrew West, Hajime Urano, Roberta Lima Gomes, J.P. Coad, Th. Pütterich, A. Sinha, S. Hollis, R. D. Wood, G. D. Ewart, F. S. Griph, T. Kobuchi, X. Lefebvre, S. Warder, A.J. Thornton, S. Peschanyi, B. Graham, Giuseppe Telesca, M. Kempenaars, J. Bernardo, M. Hughes, Eva Belonohy, S. Schmuck, Kai Nordlund, T. J. Smith, P. Hertout, K. D. Lawson, M. Brix, Matthew Sibbald, Grégoire Hornung, C. Tame, Matthew Carr, S. Wray, P. T. Doyle, A. Somers, Giuseppe Chitarin, D. C. Campling, Mitul Abhangi, I. Jepu, David A. Wood, J. Miettunen, A. Sopplesa, Raffaele Fresa, S. Saarelma, M. Bacharis, J. Pozzi, P. Vallejos Olivares, Teddy Craciunescu, Raffaele Albanese, S. Knipe, Jason P. Byrne, A. C. C. Sips, S. Hazel, V. Kazantzidis, G. Stankūnas, A. Kundu, J. Mailloux, C. Guerard, Pramit Dutta, J. E. Boom, Eduardo Alves, P. Grazier, Saskia Mordijck, V.S. Neverov, Kazuo Hoshino, A. P. Vadgama, P. D. Brennan, P. Innocente, Piergiorgio Sonato, M. Irishkin, M. Berry, D. W. Robson, Dieter Leichtle, Fabio Pisano, P. McCullen, T. M. Huddleston, Kensaku Kamiya, D. Pacella, Tommy Ahlgren, A. Kirschner, B. Magesh, A. Ash, J. Mlynář, C. Castaldo, C. Marchetto, D. L. Hillis, M. Incelli, B. Viola, R. J. Robins, E. Andersson Sundén, G. Ramogida, Matthew Reinke, Gerd Meisl, Yannis Kominis, R. Proudfoot, C. Noble, N. J. Conway, V. P. Lo Schiavo, Jorge Luis Rodriguez, Hugo Bufferand, C. H. A. Hogben, B. Evans, R. Sartori, H. Greuner, M. G. Dunne, K. Schöpf, M. I. K. Santala, E. Giovannozzi, A. E. Shevelev, C. Gil, P. Boulting, P. Sagar, A.E. Shumack, P. A. Coates, C. Ayres, R. Prakash, C. Giroud, M. Parsons, J. C. Giacalone, S. Meshchaninov, A. Peackoc, G. De Temmerman, A.C.A. Figueiredo, D. Gallart, P. Santa, Sergey Popovichev, Ivan Lupelli, M. Valovic, Thomas Johnson, Y. Martynova, M. Rack, Olivier Sauter, J. Garcia, P. Siren, I. Balboa, S. Lee, Hans Nordman, R. Roccella, M. Faitsch, Julien Hillairet, Patrick J. McCarthy, C. Reux, Irena Ivanova-Stanik, V. Coccorese, Ye. O. Kazakov, R. El-Jorf, C. Hamlyn-Harris, Matthias Weiszflog, C. F. Maggi, Panagiotis Tolias, N. C. Hawkes, E. Clark, Bruno Santos, B. Sieglin, R. Rodionov, Roch Kwiatkowski, P. Denner, C. Woodley, Hugh Summers, Francesco Pizzo, G. Pucella, D. Croft, F. Di Maio, M. Tomes, D. Molina, A. Fernades, L. Amicucci, Marco Cecconello, A. Bisoffi, Z. Ul-Abidin, J. Wilkinson, H. Maier, S. Rowe, M. Beckers, P.J. Knight, E. Pajuste, Choong-Seock Chang, K. Deakin, M. Enachescu, A. Cobalt, D. Tskhakaya Jun, Michela Gelfusa, Rémy Nouailletas, R. Ragona, N. Bonanomi, D. A. Homfray, K. Riddle, Yann Camenen, J. D. Thomas, R.P. Doerner, Timothy P. Robinson, Y. Miyoshi, Ph. Jacquet, H. T. Lambertz, D. Pulley, A. Bécoulet, E. Tholerus, O. Bogar, M. Peterka, R. Crowe, C. Sommariva, A. R. Talbot, N. K. Butler, N. Reid, R. Zagórski, Gerald Pintsuk, Juri Romazanov, Andre Neto, G. L. Ravera, Paolo Arena, A. Manning, F. Durodié, Maryna Chernyshova, D. Karkinsky, Štefan Matejčík, J. P. Thomas, A. Wilson, L. Joita, R. Naish, P. Strand, M. Balden, M. Kaufman, T. Powell, V. Schmidt, D. Barnes, José Vicente, S. Doswon, Daniel F. Valcarcel, Claudia Corradino, R. Warren, Annette M. Hynes, J. D. Strachan, A. M. Messiaen, M. Kovari, O. Omolayo, D. M. Witts, R. C. Felton, C. Fleming, C. A. Marren, Patrick Maget, J. Galdon-Quiroga, H. R. Koslowski, Bruce Lipschultz, Ana Elisa Bauer de Camargo Silva, J. Waterhouse, R. J. Dumont, M. Schneider, Sara Moradi, K. J. Nicholls, M. Beldishevski, Benedikt Geiger, A. Jardin, A. Ekedahl, A. Lyssoivan, C. Waldon, Davide Galassi, F. Jaulmes, A. Kirk, Yannick Marandet, F. Hasenbeck, Gabor Szepesi, R. C. Pereira, J. Juul Rasmussen, Nobuyuki Aiba, Michelle E. Walker, Gábor Cseh, Scott W. Mosher, R. Bastow, A. Di Siena, E. Lazzaro, M. Curuia, C. D. Challis, Z. Ghani, J. Deane, João M. C. Sousa, Henrik Sjöstrand, T. O'Gorman, H. R. Wilson, P. Devynck, M. Price, C. A. Thompson, Daniele Marocco, A. Cullen, M. Clark, M. Lennholm, D. Carralero, N. Balshaw, Roland Sabot, I. Stepanov, N. Petrella, Filippo Sartori, L. W. Packer, P. Thomas, M. Lungu, A. V. Krasilnikov, R. Young, Jonathan Graves, J. C. Hillesheim, Mǎdǎlina Vlad, Duccio Testa, Pierre Dumortier, Paulo Carvalho, M. Gosk, Yong-Su Na, M. Buckley, Carlos A. Silva, V. Fuchs, K. Vasava, P. A. Tigwell, B. Wakeling, M. Medland, M. Bellinger, K. Gal, Petter Ström, E. Veshchev, F. Nabais, A. Wynn, L. Lauro Taroni, B. Beckett, L. Gil, M. Towndrow, Brian Grierson, Harry M. Meyer, V. Philipps, A. de Castro, D. Kinna, D. Conka, Göran Ericsson, L. Piron, J. Hawkins, D. Cooper, Kenneth Hammond, V.V. Parail, Cristian Ruset, G.J. van Rooij, M. N. A. Beurskens, N. Fawlk, G. Evison, M. Van De Mortel, N. Marcenko, B. Slade, Th. Franke, Simone Peruzzo, N. den Harder, D. Baião, A. Martin de Aguilera, Frederic Imbeaux, Carlo Sozzi, J.L. de Pablos, J. Svensson, A. Withycombe, Ane Lasa, H. Sheikh, V.A. Yavorskij, Nick Walkden, E. Lerche, C. S. Gibson, Roberto Zanino, Y. Peysson, David Hatch, B. Bazylev, E. de la Cal, S. Hacquin, T. D. V. Haupt, S. A. Silburn, T.T.C. Jones, Maria Teresa Porfiri, Walid Helou, S. E. Sharapov, M. Zerbini, Ken W Bell, Marco Marinelli, Kyriakos Hizanidis, J. M. Fontdecaba, N. Teplova, K. K. Kirov, S. Vartanian, W. W. Pires de Sa, T. C. Hender, J. K. Blackburn, I. Monakhov, H. Patten, P. A. Simmons, Y. Austin, J. Regana, Stefano Coda, Amanda J. Page, D. Fuller, António J.N. Batista, A. Horton, P. Heesterman, S. Cramp, J. Hobirk, F. Clairet, A. Burckhart, M. Allinson, Larry R. Baylor, W. Leysen, D. B. Gin, P. Nielsen, A. Kantor, Yueqiang Liu, A.V. Stephen, Jose Ramon Martin-Solis, P. Mantica, B. C. Regan, Aleksander Drenik, A. Lukin, L. Thorne, G. Nemtsev, J. Denis, M. E. Graham, D. Rigamonti, W. Van Renterghem, M. Tardocchi, M. Koubiti, A. Malaquias, M. Tsalas, A. Cufar, Giuseppe Prestopino, D. Kogut, N. Pomaro, J. Keep, Jochen Linke, Shimpei Futatani, Boris Breizman, A. Sirinelli, M. Chandler, M. Fortune, F. Degli Agostini, I. Jenkins, T. Spelzini, G. Calabrò, O. N. Kent, A. Lunniss, Etienne Hodille, Z. Vizvary, Volker Naulin, T. Eich, F. Mink, A. Alkseev, P. W. Haydon, Massimo Angelone, Norberto Catarino, J. Lapins, Roberto Pasqualotto, R. Lawless, T. Schlummer, F. Bonelli, M. Wischmeier, Stéphane Devaux, G. Saibene, Dirk Reiser, Y. R. Martin, H. Bergsåker, Jon Godwin, Alessia Santucci, C. Lane, Justyna Grzonka, Ph. Mertens, Claudio Verona, David Moulton, E. Delabie, Anna Salmi, P. G. Smith, T. Bolzonella, Silvio Ceccuzzi, Ulrich Fischer, G. Liu, M. A. Henderson, M. Marinucci, T. Suzuki, Jakub Bielecki, João Figueiredo, M. Afzal, J. Cane, Robert Hager, Luciano Bertalot, M. Firdaouss, G. Tvalashvili, D. Hepple, D. Esteve, M. De Bock, Y. Baranov, R. D'Inca, G. De Tommasi, Ch. Linsmeier, T. Nicolas, I. J. Pearson, P. Finburg, Ireneusz Książek, S. Talebzadeh, A. Czarnecka, A. Botrugno, M. Gethins, Bohdan Bieg, R. Baughan, I. Borodkina, B. Kos, A. Muraro, T. Vasilopoulou, G. Hermon, S.J. Wukitch, Jari Likonen, D. P. Coster, Guglielmo Rubinacci, I. H. Coffey, Justine M. Kent, S. E. Dorling, J. Dankowski, Geert Verdoolaege, Daisuke Nishijima, R. Clarkson, E. R. Solano, M. Stephen, A. Lescinskis, P. Staniec, Karl Schmid, M. Mayer, Peter Lang, T. Franklin, M.I. Williams, C. G. Elsmore, F. Maviglia, C. Di Troia, C. Penot, A. Zarins, Pierre Manas, D. F. Gear, Yu Gao, Philipp Drews, E. Letellier, A. S. Thompson, L. Forsythe, I. Zychor, E. Khilkevich, A. Manzanares, T. Nakano, Paulo Rodrigues, J. Edmond, Sebastián Dormido-Canto, R. Dux, C. Appelbee, L. Moser, Angelo Cenedese, D. Fagan, N. Richardson, Giuseppe Gorini, V. Rohde, R. Paprok, João P. S. Bizarro, P. Aleynikov, M. Sertoli, Ł. Świderski, Simone Palazzo, O. W. Davies, D. Douai, N. Macdonald, M. Baruzzo, J. López-Razola, M. Lungaroni, D. Clatworthy, R. Bravanec, J. Lovell, Ambrogio Fasoli, S.-P. Pehkonen, M. E. Puiatti, P. Papp, G. Bodnar, V. Aslanyan, A. Weckmann, K. A. Taylor, R. Henriques, I. T. Chapman, Ewa Pawelec, Miles M. Turner, Steven J. Meitner, M. Bernert, Ph. Maquet, R. C. Meadows, A. Shaw, N. Vianello, L. Barrera Orte, Tomas Markovic, A. Fil, A. S. Couchman, Inessa Bolshakova, J. Fyvie, Konstantina Mergia, J. Gallagher, R.V. Budny, Frank Leipold, C. J. Rapson, R. C. Lobel, Gennady V. Miloshevsky, K.-D. Zastrow, Ph. Duckworth, Gianluca Rubino, G. Withenshaw, S. Maruyama, S. P. Hallworth Cook, M. Newman, Jérôme Bucalossi, P. Drewelow, Nuno Cruz, D. Iglesias, I. Nedzelski, T. Donne, P. Leichuer, R. Cesario, M. D. J. Bright, T. Boyce, N. Imazawa, Per Petersson, R. King, A. Loving, L. Garzotti, Jorge Ferreira, G. Corrigan, D. Sandiford, B. Tal, P. Puglia, Daniel Tegnered, J. Karhunen, James S. Wright, Tom Wauters, J. McKehon, K. Rathod, Olivier Février, Alessandro Formisano, Petra Bilkova, M. Groth, Ricardo Magnus Osorio Galvao, F. Medina, S. Collins, H. J. Boyer, Elena Bruno, Horacio Fernandes, M. J. Stead, R. Paccagnella, J. Kaniewski, Ion E. Stamatelatos, F. Causa, M. F. F. Nave, A. Patel, D. C. McDonald, L. Moreira, Mariano Ruiz, K. Dylst, Raymond A. Shaw, A. Brett, Jane Johnston, P. P. Pereira Puglia, J. Ongena, N. A. Benterman, V. N. Amosov, Christian Grisolia, J. Simpson, C. Perez von Thun, Jan Weiland, P. Tonner, F. Belli, T. Odupitan, T. Dittmar, Edmund Highcock, Taina Kurki-Suonio, I. Uytdenhouwen, Estelle Gauthier, M. Oberkofler, B. Alper, Iris D. Young, S. Soare, Yuji Hatano, D. Reece, D. Borodin, M. Moneti, W. Yanling, S. Mianowski, K. Fenton, Stephen J. Bailey, R. Coelho, Sandra C. Chapman, E. Łaszyńska, A. R. Field, F.J. Martínez, Anders Nielsen, M. Smithies, M. J. Mantsinen, A. J. Capel, N. D. Smith, A. Pires dos Reis, M.-L. Mayoral, T. Loarer, P. Carman, N. Grazier, S. Breton, J. M. A. Bradshaw, Alexandre C. Pereira, Fulvio Auriemma, Fulvio Militello, Barbara Cannas, D. Ulyatt, A. Kappatou, P. Blatchford, R. Scannell, B. I. Oswuigwe, Darren Price, Robert E. Grove, D. Guard, M. Leyland, G. Stubbs, J. W. Banks, V.V. Plyusnin, M. S. J. Rainford, Andrea Murari, Sanjeev Ranjan, A. Huber, V. Krasilnikov, C. Bower, H. Leggate, S. Abduallev, P. Tsavalas, G. Giruzzi, K. Maczewa, Colin Roach, P. Beaumont, R. P. Johnson, Anna Widdowson, L. A. Kogan, A. Baron Wiechec, Markus Airila, J. Morris, Robert Skilton, Katarzyna Słabkowska, M. A. Barnard, Jean-Paul Booth, Alessandro Pau, R. Price, R. Bament, M. Tokitani, I. Turner, T. Vu, P. Huynh, S.N. Gerasimov, D. I. Refy, Yunfeng Liang, Anders Hjalmarsson, S. Dalley, Roberto Ambrosino, O. Hemming, T. R. Blackman, Y. Zhou, Vasile Zoita, P. Vincenzi, A. Loarte, C. Rayner, Martin Imrisek, M. Tripsky, C. Mazzotta, A. Uccello, V. Basiuk, Lide Yao, V. Goloborod'ko, S. Villari, B. P. Duval, N. Bulmer, W. Zhang, L. Hackett, D. N. Borba, M. Halitovs, Mario Pillon, H. Arnichand, Alberto Alfier, A. Lawson, A. Masiello, T. Makkonen, A. Vitins, D. Rendell, D. Paton, L. Avotina, A. Krivska, M. Maslov, Richard Verhoeven, Marc Goniche, A. Broslawski, Marica Rebai, E. de la Luna, E. Militello-Asp, V. Cocilovo, L. Carraro, Michael Fitzgerald, Bernardo B. Carvalho, D. Young, C.G. Lowry, F. J. Casson, L.-G. Eriksson, T. M. Biewer, B. Esposito, F.G. Rimini, J. Fessey, G. Kaveney, S. Hall, Robin Barnsley, Michael Lehnen, N. Bekris, L. F. Ruchko, P. Batistoni, E. Alessi, M. G. O'Mullane, D. S. Darrow, C. N. Grundy, N. Hayter, Ivo S. Carvalho, M. Brombin, Enrico Zilli, M. Valisa, M. Reich, S. Panja, C. Gurl, Charles Harrington, Emmanuele Peluso, M. Porton, Michael Walsh, D. Falie, A. Reed, Jacob Eriksson, P. Macheta, J. M. Faustin, S. Cortes, S. Fietz, P. Piovesan, D. Ciric, Eric Nardon, R. Neu, Bojiang Ding, G.A. Rattá, F. Reimold, R. Craven, M. Cox, J. Orszagh, Aaro Järvinen, A. S. Thrysøe, A. Shepherd, I. Ďuran, Andrew M. Edwards, A. Kinch, J. Beal, M. Gherendi, Martin Köppen, D. Samaddar, P. Dalgliesh, I. Vinyar, J. Jansons, Nengchao Wang, J. Wu, John Wright, S. Wiesen, C. King, Alessandra Fanni, L. D. Horton, N. Krawczyk, J. Buch, K. Krieger, Václav Petržílka, D. Schworer, C. Watts, T. Keenan, Andrea Malizia, B. D. Stevens, P. Trimble, C. P. Lungu, V. Prajapati, Marco Ariola, C. Wellstood, S. Gilligan, Mirko Salewski, Michael Barnes, Florin Spineanu, H. Doerk, C. Kennedy, S. Jachmich, J. Caumont, Isabel L. Nunes, A. Petre, A. Kallenbach, M. Anghel, B. Lomanowski, Marco Riva, M. Romanelli, G. De Masi, T. May-Smith, T. Xu, A. Goussarov, S. Romanelli, M. Okabayashi, A. Baker, R. Salmon, T. Tala, Nicolas Fedorczak, S. Lanthaler, Giuliana Sias, J. Risner, Clarisse Bourdelle, M. E. Manso, Fabio Moro, R. Lucock, M. Bassan, M. T. Ogawa, V. Thompson, A. M. Whitehead, S. D. A. Reyes Cortes, Igor Bykov, Gennady Sergienko, E. Stefanikova, Mattia Frasca, H. Dabirikhah, Lorenzo Frassinetti, N. Dzysiuk, D. L. Keeling, Juan Manuel López, M. Turnyanskiy, Daniel Dunai, David Taylor, Arturo Buscarino, Carolina Björkas, A. Baciero, S. Meigh, M. Garcia-Munoz, Massimiliano Mattei, M. Hill, Gwyndaf Evans, S. Minucci, Xiang Gao, A. V. Chankin, Francesco Romanelli, A. Lahtinen, L. Giacomelli, A. Owen, Jesús Vega, Jonathan Citrin, Antti Hakola, Petr Vondracek, Sehyun Kwak, P. Abreu, L. Meneses, S. S. Medley, G. Gervasini, Surya K. Pathak, Kristel Crombé, M. Cleverly, H.S. Kim, C. Stan-Sion, Nobuyuki Asakura, E. Wang, A. Cardinali, L. Fazendeiro, R. Cavazzana, P. J. Lomas, J. Hawes, G. Stables, Silvia Spagnolo, S. P. Hotchin, N. R. Green, Slawomir Jednorog, Ewa Kowalska-Strzęciwilk, A. Martin, Linwei Li, Rajnikant Makwana, Richard Goulding, I. Voitsekhovitch, M. Bowden, I. Kodeli, Peter Hawkins, S. S. Henderson, Ondrej Ficker, Carl Hellesen, D. Yadikin, Fabio Subba, Luka Snoj, Anthony Laing, N. Ben Ayed, Mario Cavinato, M. Goodliffe, C. Clements, D. Kenny, Axel Klix, S. Gee, R. J. E. Smith, P. de Vries, L. Fittill, Min-Gu Yoo, S. Menmuir, K. Cave-Ayland, S. Potzel, D. Grist, K. Blackman, S. A. Robinson, Rodney Walker, David Pfefferlé, W. Broeckx, D. Harting, S. G. J. Tyrrell, F. Binda, L. Horvath, Davide Flammini, P. V. Edappala, Raul Moreno, G. M. D. Hogeweij, P. Card, A. Hagar, Ion Tiseanu, Rita Lorenzini, L. Appel, Jet Contributors, J. Flanagan, C. Paz Soldan, U. Samm, Otto Asunta, F. Eriksson, C. Taliercio, F. S. Zaitsev, G. F. Matthews, Tuomas Koskela, P. J. Howarth, D. Terranova, M. Skiba, Amanda Hubbard, R. Otin, K. G. McClements, M. Park, R. McKean, C. Christopher Klepper, I. Karnowska, Peter J. Pool, G. Ciraolo, Jennifer M. Lehmann, Institut de Mécanique des Fluides et des Solides (IMFS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), VTT Technical Research Centre of Finland (VTT), Association EURATOM-TEKES, Association EURATOM-TEKES, Helsinki University of Technology, Finland, Assoc. Euratom-ENEA-CREATE, Universita Mediterranea of Reggio Calabria [Reggio Calabria], EURATOM/CCFE Fusion Association, Culham Science Centre [Abingdon], Instituto Tecnológico e Nuclear (ITN), ITN, University of Naples Federico II = Università degli studi di Napoli Federico II, Max-Planck-Institut für Plasmaphysik [Garching] (IPP), Università degli studi di Catania = University of Catania (Unict), National Institute for Fusion Science (NIFS), Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), ITER organization (ITER), Karlsruhe Institute of Technology (KIT), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche sur la Fusion par confinement Magnétique (IRFM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), European Fusion Development Agreement [Garching bei München] ( EFDA-CSU), Institut d'ophtalmologie Hédi-Rais de Tunis, Service Cardiologie [CHU Toulouse], Pôle Cardiovasculaire et Métabolique [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), H. Niewodniczanski Institute of Nuclear Physics, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Laboratoire de recherche en Hydrodynamique, Énergétique et Environnement Atmosphérique (LHEEA), École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Euratom/UKAEA Fusion Assoc., Magnetic Sensor laboratory [Lviv] (MSL), National Polytechnic University of Lviv (LPNU), The National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) [Moscow, Russia], Institute of Energy and Climate Research - Plasma Physics (IEK-4), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Institute for Problems of Material Science, National Academy of Sciences of Ukraine (NASU), Institute of Plasma Physics [Praha], Czech Academy of Sciences [Prague] (CAS), Physique des interactions ioniques et moléculaires (PIIM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Département Méthodes et Modèles Mathématiques pour l'Industrie (3MI-ENSMSE), École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre G2I, Department of Hydraulics, Transportations and Roads, Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Metallurgical & Materials Engineering Department (MS 388), University of Nevada [Reno], AUTRES, Institute of Plasma Physics and Laser Microfusion [Warsaw] (IPPLM), Culham Centre for Fusion Energy (CCFE), Astrophysics Research Centre [Belfast] (ARC), Queen's University [Belfast] (QUB), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), School of Mathematics [Cardiff], Cardiff University, Associazone EURATOM ENEA sulla Fusione, EURATOM, Laboratoire de physique des plasmas de l'ERM, Laboratorium voor plasmafysica van de KMS (LPP ERM KMS), Ecole Royale Militaire / Koninklijke Militaire School (ERM KMS), Paul-Drude-Institut für Festkörperelektronik (PDI), Institut für Physik, University of Basel (Unibas), Dutch Institute for Fundamental Energy Research [Nieuwegein] (DIFFER), Dutch Institute for Fundamental Energy Research [Eindhoven] (DIFFER), Institut Jean Lamour (IJL), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), CEA Cadarache, Dipartimento di Energia [Milano], Politecnico di Milano [Milan] (POLIMI), Laboratoire de Mécanique, Modélisation et Procédés Propres (M2P2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Lille économie management - UMR 9221 (LEM), Université d'Artois (UA)-Université catholique de Lille (UCL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Euratom research and training programme 633053, Institut de Mécanique des Fluides et des Solides ( IMFS ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), VTT Technical Research Centre of Finland ( VTT ), Univ. Mediterranea RC, Culham Science Centre, Instituto Tecnológico e Nuclear ( ITN ), Università degli studi di Napoli Federico II, Max-Planck-Institut für Plasmaphysik [Garching] ( IPP ), Università degli studi di Catania [Catania], National Institute for Fusion Science, National Institutes of Natural Sciences, Laboratoire de Physique Nucléaire et de Hautes Énergies ( LPNHE ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), School of Geography, Earth and Environmental Sciences, ITER Organization, Karlsruhe Institute of Technology ( KIT ), Laboratoire de Nanotechnologie et d'Instrumentation Optique ( LNIO ), Institut Charles Delaunay ( ICD ), Université de Technologie de Troyes ( UTT ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Technologie de Troyes ( UTT ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Chimie des Substances Naturelles ( ICSN ), Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche sur la Fusion par confinement Magnétique ( IRFM ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), European Fusion Development Agreement [Garching bei München] ( EFDA-CSU ), Service de cardiologie [Toulouse], Université Paul Sabatier - Toulouse 3 ( UPS ) -CHU Toulouse [Toulouse]-Hôpital de Rangueil, ITER [St. Paul-lez-Durance], ITER, Polska Akademia Nauk ( PAN ), Laboratoire de recherche en Hydrodynamique, Énergétique et Environnement Atmosphérique ( LHEEA ), École Centrale de Nantes ( ECN ) -Centre National de la Recherche Scientifique ( CNRS ), MSL, Lviv Polytechnic National University ( MSL ), Lviv Polytechnic National University, Centre d'études et de recherches appliquées à la gestion ( CERAG ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Centre National de la Recherche Scientifique ( CNRS ), Institute of Energy and Climate Research - Plasma Physics ( IEK-4 ), Forschungszentrum Jülich GmbH, National Academy of Sciences of Ukraine ( NASU ), Lille - Economie et Management ( LEM ), Université catholique de Lille ( UCL ) -Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Czech Academy of Sciences [Prague] ( ASCR ), Physique des interactions ioniques et moléculaires ( PIIM ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Département Méthodes et Modèles Mathématiques pour l'Industrie ( 3MI-ENSMSE ), École des Mines de Saint-Étienne ( Mines Saint-Étienne MSE ), Institut Mines-Télécom [Paris]-Institut Mines-Télécom [Paris]-Centre G2I, Laboratoire de microbiologie et génétique moléculaires ( LMGM ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), University of Nevada, Institute of Plasma Physics and Laser Microfusion [Warsaw] ( IPPLM ), UCL Department of Space and Climate Physics, University College of London [London] ( UCL ), Astrophysics Research Centre [Belfast] ( ARC ), Queen's University [Belfast] ( QUB ), Laboratoire d'Electronique et des Technologies de l'Information ( CEA-LETI ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes [Saint Martin d'Hères], Cardiff School of Mathematics, Laboratoire de physique des plasmas de l'ERM, Laboratorium voor plasmafysica van de KMS ( LPP ERM KMS ), Ecole Royale Militaire / Koninklijke Militaire School ( ERM KMS ), Paul-Drude-Institut für Festkörperelektronik, University of Basel ( Unibas ), Dutch Institute for Fundamental Energy Research [Nieuwegein] ( DIFFER ), Dutch Institute for Fundamental Energy Research [Eindhoven] ( DIFFER ), Institut Jean Lamour ( IJL ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Lorraine ( UL ), Dipartimento di Energia, Politecnico di Milano [Milan], Max Planck Institute for Plasma Physics, Laboratoire de Mécanique, Modélisation et Procédés Propres ( M2P2 ), Aix Marseille Université ( AMU ) -Ecole Centrale de Marseille ( ECM ) -Centre National de la Recherche Scientifique ( CNRS ), Universitat Politècnica de Catalunya. Departament de Física, Universitat Politècnica de Catalunya. ANT - Advanced Nuclear Technologies Research Group, JET Contributors, Litaudon, X, Abduallev, S, Abhangi, M, Abreu, P, Afzal, M, Aggarwal, K, Ahlgren, T, Ahn, J, Aho Mantila, L, Aiba, N, Airila, M, Albanese, R, Aldred, V, Alegre, D, Alessi, E, Aleynikov, P, Alfier, A, Alkseev, A, Allinson, M, Alper, B, Alves, E, Ambrosino, G, Ambrosino, R, Amicucci, L, Amosov, V, Andersson SundÃ©n, E, Angelone, M, Anghel, M, Angioni, C, Appel, L, Appelbee, C, Arena, P, Ariola, M, Arnichand, H, Arshad, S, Ash, A, Ashikawa, N, Aslanyan, V, Asunta, O, Auriemma, F, Austin, Y, Avotina, L, Axton, M, Ayres, C, Bacharis, M, Baciero, A, Baiã¡o, D, Bailey, S, Baker, A, Balboa, I, Balden, M, Balshaw, N, Bament, R, Banks, J, Baranov, Y, Barnard, M, Barnes, D, Barnes, M, Barnsley, R, Baron Wiechec, A, Barrera Orte, L, Baruzzo, M, Basiuk, V, Bassan, M, Bastow, R, Batista, A, Batistoni, P, Baughan, R, Bauvir, B, Baylor, L, Bazylev, B, Beal, J, Beaumont, P, Beckers, M, Beckett, B, Becoulet, A, Bekris, N, Beldishevski, M, Bell, K, Belli, F, Bellinger, M, Belonohy, Ã, Ben Ayed, N, Benterman, N, Bergsã¥ker, H, Bernardo, J, Bernert, M, Berry, M, Bertalot, L, Besliu, C, Beurskens, M, Bieg, B, Bielecki, J, Biewer, T, Bigi, M, Bãlkovã¡, P, Binda, F, Bisoffi, A, Bizarro, J, Bjã¶rkas, C, Blackburn, J, Blackman, K, Blackman, T, Blanchard, P, Blatchford, P, Bobkov, V, Boboc, A, Bodnã¡r, G, Bogar, O, Bolshakova, I, Bolzonella, T, Bonanomi, N, Bonelli, F, Boom, J, Booth, J, Borba, D, Borodin, D, Borodkina, I, Botrugno, A, Bottereau, C, Boulting, P, Bourdelle, C, Bowden, M, Bower, C, Bowman, C, Boyce, T, Boyd, C, Boyer, H, Bradshaw, J, Braic, V, Bravanec, R, Breizman, B, Bremond, S, Brennan, P, Breton, S, Brett, A, Brezinsek, S, Bright, M, Brix, M, Broeckx, W, Brombin, M, Broså‚awski, A, Brown, D, Brown, M, Bruno, E, Bucalossi, J, Buch, J, Buchanan, J, Buckley, M, Budny, R, Bufferand, H, Bulman, M, Bulmer, N, Bunting, P, Buratti, P, Burckhart, A, Buscarino, A, Busse, A, Butler, N, Bykov, I, Byrne, J, Cahyna, P, Calabrã², G, Calvo, I, Camenen, Y, Camp, P, Campling, D, Cane, J, Cannas, B, Capel, A, Card, P, Cardinali, A, Carman, P, Carr, M, Carralero, D, Carraro, L, Carvalho, B, Carvalho, I, Carvalho, P, Casson, F, Castaldo, C, Catarino, N, Caumont, J, Causa, F, Cavazzana, R, Cave Ayland, K, Cavinato, M, Cecconello, M, Ceccuzzi, S, Cecil, E, Cenedese, A, Cesario, R, Challis, C, Chandler, M, Chandra, D, Chang, C, Chankin, A, Chapman, I, Chapman, S, Chernyshova, M, Chitarin, G, Ciraolo, G, Ciric, D, Citrin, J, Clairet, F, Clark, E, Clark, M, Clarkson, R, Clatworthy, D, Clements, C, Cleverly, M, Coad, J, Coates, P, Cobalt, A, Coccorese, V, Cocilovo, V, Coda, S, Coelho, R, Coenen, J, Coffey, I, Colas, L, Collins, S, Conka, D, Conroy, S, Conway, N, Coombs, D, Cooper, D, Cooper, S, Corradino, C, Corre, Y, Corrigan, G, Cortes, S, Coster, D, Couchman, A, Cox, M, Craciunescu, T, Cramp, S, Craven, R, Crisanti, F, Croci, G, Croft, D, Crombã©, K, Crowe, R, Cruz, N, Cseh, G, Cufar, A, Cullen, A, Curuia, M, Czarnecka, A, Dabirikhah, H, Dalgliesh, P, Dalley, S, Dankowski, J, Darrow, D, Davies, O, Davis, W, Day, C, Day, I, De Bock, M, De Castro, A, De La Cal, E, De La Luna, E, De Masi, G, De Pablos, J, De Temmerman, G, De Tommasi, G, De Vries, P, Deakin, K, Deane, J, Degli Agostini, F, Dejarnac, R, Delabie, E, Den Harder, N, Dendy, R, Denis, J, Denner, P, Devaux, S, Devynck, P, Di Maio, F, Di Siena, A, Di Troia, C, Dinca, P, D'Inca, R, Ding, B, Dittmar, T, Doerk, H, Doerner, R, Donnã©, T, Dorling, S, Dormido Canto, S, Doswon, S, Douai, D, Doyle, P, Drenik, A, Drewelow, P, Drews, P, Duckworth, P, Dumont, R, Dumortier, P, Dunai, D, Dunne, M, Äžuran, I, Durodiã©, F, Dutta, P, Duval, B, Dux, R, Dylst, K, Dzysiuk, N, Edappala, P, Edmond, J, Edwards, A, Edwards, J, Eich, T, Ekedahl, A, El Jorf, R, Elsmore, C, Enachescu, M, Ericsson, G, Eriksson, F, Eriksson, J, Eriksson, L, Esposito, B, Esquembri, S, Esser, H, Esteve, D, Evans, B, Evans, G, Evison, G, Ewart, G, Fagan, D, Faitsch, M, Falie, D, Fanni, A, Fasoli, A, Faustin, J, Fawlk, N, Fazendeiro, L, Fedorczak, N, Felton, R, Fenton, K, Fernades, A, Fernandes, H, Ferreira, J, Fessey, J, Fã©vrier, O, Ficker, O, Field, A, Fietz, S, Figueiredo, A, Figueiredo, J, Fil, A, Finburg, P, Firdaouss, M, Fischer, U, Fittill, L, Fitzgerald, M, Flammini, D, Flanagan, J, Fleming, C, Flinders, K, Fonnesu, N, Fontdecaba, J, Formisano, A, Forsythe, L, Fortuna, L, Fortuna Zalesna, E, Fortune, M, Foster, S, Franke, T, Franklin, T, Frasca, M, Frassinetti, L, Freisinger, M, Fresa, R, Frigione, D, Fuchs, V, Fuller, D, Futatani, S, Fyvie, J, Gã¡l, K, Galassi, D, Gaå‚azka, K, Galdon Quiroga, J, Gallagher, J, Gallart, D, Galvã¡o, R, Gao, X, Gao, Y, Garcia, J, Garcia Carrasco, A, GarcÃa MuÃ±oz, M, Gardarein, J, Garzotti, L, Gaudio, P, Gauthier, E, Gear, D, Gee, S, Geiger, B, Gelfusa, M, Gerasimov, S, Gervasini, G, Gethins, M, Ghani, Z, Ghate, M, Gherendi, M, Giacalone, J, Giacomelli, L, Gibson, C, Giegerich, T, Gil, C, Gil, L, Gilligan, S, Gin, D, 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W., Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Hôpital de Rangueil, CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lorraine (UL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Energia [Milano] (DENG), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Research Centre Julich (FZJ), Institute for Plasma Research, Instituto Superior Tecnico Lisboa, Queen's University Belfast, University of Helsinki, CEA, Department of Applied Physics, School services, SCI, National Institutes for Quantum and Radiological Science and Technology, VTT, University of Naples Federico II, Universidad Nacional de Educacion a Distancia, CNR, Russian Research Centre Kurchatov Institute, Universita degli Studi di Napoli Parthenope, Ente Per Le Nuove Tecnologie L'energia e l'ambiente, Troitsk Institute for Innovation and Fusion Research, Uppsala University, National Institute for Cryogenics and Isotopic Technology, Max-Planck-Institut fur Plasmaphysik, University of Catania, Fusion for Energy Joint Undertaking, National Institutes of Natural Sciences - National Institute for Fusion Science, Massachusetts Institute of Technology, University of Latvia, Imperial College London, CIEMAT, University of Oxford, EUROfusion Programme Management Unit, Oak Ridge National Laboratory, Karlsruhe Institute of Technology KIT, University of York, Royal Institute of Technology, Maritime University of Szczecin, H. Niewodniczanski Institute of Nuclear Physics of the Polish Academy of Sciences, Czech Academy of Sciences, University of Trento, Ecole Polytechnique Federale de Lausanne (EPFL), Wigner Research Centre for Physics, Comenius University, University of Milan - Bicocca, National Institute for Optoelectronics, Fourth State Research, University of Texas at Austin, Belgian Nuclear Research Center, National Centre for Nuclear Research (NCBJ), Princeton University, CNRS, University of Cagliari, University of Warwick, Soltan Institute for Nuclear Studies, FOM Institute DIFFER, National Institute for Laser, Plasma and Radiation Physics, Ghent University, J. Stefan Institute, Universite de Lorraine, CAS - Institute of Plasma Physics, University of California at San Diego, Koninklijke Militaire School - Ecole Royale Militaire, Horia Hulubei National Institute of Physics and Nuclear Engineering, Chalmers University of Technology, School services, ELEC, Department of Signal Processing and Acoustics, Automaatio- ja systeemitekniik, Universidad Politecnica de Madrid, Second University of Naples, Warsaw University of Technology, Universita della Basilicata, Barcelona Supercomp. Center, Universidad de Sevilla, Centro Brasileiro de Pesquisas Fisicas, Department of Electrical Engineering and Automation, Sähkötekniikan laitos, University of Rome Tor Vergata, RAS - Ioffe Physico Technical Institute, General Atomics, University of Innsbruck, Fusion and Plasma Physics, University of Toyama, University of Strathclyde, National Technical University of Athens, Universita della Tuscia, Technical University of Denmark, Korea Advanced Institute of Science and Technology, Seoul National University, University College Cork, Vienna University of Technology, University of Opole, Daegu University, National Fusion Research Institute, Dublin City University, Universidad Politécnica de Madrid, PELIN LLC, Arizona State University, Universidad Complutense, University of Basel, Universidad Carlos III de Madrid, Consorzio CREATE, Demokritos National Centre for Scientific Research, Purdue University, Universite Libre de Bruxelles, School Services, ARTS, Department of Design, University of California Office of the President, Universidade de Sao Paulo, School Services, BIZ, Department of Information and Service Management, Lithuanian Energy Institute, HRS Fusion, Politecnico di Torino, University of Cassino, University of Electronic Science and Technology of China, Department of Electronics and Nanoengineering, Aalto-yliopisto, Aalto University, and Faculdade de Engenharia
Subjects: Technology, fusion, Física [Ciências exactas e naturais], Tokamak, Nuclear engineering, DIAGNOSTICS, 01 natural sciences, ILW, 010305 fluids & plasmas, law.invention, Ilw, [SPI.MECA.MEFL]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph], Plasma, H-Mode Plasmas, law, ITER, Disruption Prediction, COLLISIONALITY, EDGE LOCALIZED MODES, Diagnostics, Operation, JET, plasma, Nuclear and High Energy Physics, Condensed Matter Physics, Physics, Jet (fluid), JET, plasma, fusion, ITER, Divertor, Settore FIS/01 - Fisica Sperimentale, Fusion, Plasma and Space Physics, DENSITY PEAKING, Carbon Wall, H-MODE PLASMAS, [ SPI.MECA.MEFL ] Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph], Density Peaking, Neutron transport, Facing Components, Collisionality, 114 Physical sciences, Física, Física, Nuclear physics, Physical sciences [Natural sciences], Fusion, plasma och rymdfysik, Pedestal, 0103 physical sciences, Nuclear fusion, ddc:530, Neutron, 010306 general physics, Fusion, Physics, Physical sciences, Nuclear and High Energy Physic, Edge Localized Modes, QC717, Física [Àrees temàtiques de la UPC], Reactors de fusió, Física, FACING COMPONENTS, Fusion reactors, Jet, CARBON WALL, DISRUPTION PREDICTION, OPERATION, ddc:600
Abstract: The 2014–2016 JET results are reviewed in the light of their significance for optimising the ITER research plan for the active and non-active operation. More than 60 h of plasma operation with ITER first wall materials successfully took place since its installation in 2011. New multi-machine scaling of the type I-ELM divertor energy flux density to ITER is supported by first principle modelling. ITER relevant disruption experiments and first principle modelling are reported with a set of three disruption mitigation valves mimicking the ITER setup. Insights of the L–H power threshold in Deuterium and Hydrogen are given, stressing the importance of the magnetic configurations and the recent measurements of fine-scale structures in the edge radial electric. Dimensionless scans of the core and pedestal confinement provide new information to elucidate the importance of the first wall material on the fusion performance. H-mode plasmas at ITER triangularity (H = 1 at ßN ~ 1.8 and n/nGW ~ 0.6) have been sustained at 2 MA during 5 s. The ITER neutronics codes have been validated on high performance experiments. Prospects for the coming D–T campaign and 14 MeV neutron calibration strategy are reviewed. This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014–2018 under grant agreement No 633053. Peer Reviewed Article signat per 1.173 autors/es: X. Litaudon35, S. Abduallev39, M. Abhangi46, P. Abreu53, M. Afzal7, K.M. Aggarwal29, T. Ahlgren101, J.H. Ahn8, L. Aho-Mantila112, N. Aiba69, M. Airila112, R. Albanese105, V. Aldred7, D. Alegre93, E. Alessi45, P. Aleynikov55, A. Alfier12, A. Alkseev72, M. Allinson7, B. Alper7, E. Alves53, G. Ambrosino105, R. Ambrosino106, L. Amicucci90, V. Amosov88, E. Andersson Sundén22, M. Angelone90, M. Anghel85, C. Angioni62, L. Appel7, C. Appelbee7, P. Arena30, M. Ariola106, H. Arnichand8, S. Arshad41, A. Ash7, N. Ashikawa68, V. Aslanyan64, O. Asunta1, F. Auriemma12, Y. Austin7, L. Avotina103, M.D. Axton7, C. Ayres7, M. Bacharis24, A. Baciero57, D. Baião53, S. Bailey7, A. Baker7, I. Balboa7, M. Balden62, N. Balshaw7, R. Bament7, J.W. Banks7, Y.F. Baranov7, M.A. Barnard7, D. Barnes7, M. Barnes27, R. Barnsley55, A. Baron Wiechec7, L. Barrera Orte34, M. Baruzzo12, V. Basiuk8, M. Bassan55, R. Bastow7, A. Batista53, P. Batistoni90, R. Baughan7, B. Bauvir55, L. Baylor73, B. Bazylev56, J. Beal110, P.S. Beaumont7, M. Beckers39, B. Beckett7, A. Becoulet8, N. Bekris35, M. Beldishevski7, K. Bell7, F. Belli90, M. Bellinger7, É. Belonohy62, N. Ben Ayed7, N.A. Benterman7, H. Bergsåker42, J. Bernardo53, M. Bernert62, M. Berry7, L. Bertalot55, C. Besliu7, M. Beurskens63, B. Bieg61, J. Bielecki47, T. Biewer73, M. Bigi12, P. Bílková50, F. Binda22, A. Bisoffi31, J.P.S. Bizarro53, C. Björkas101, J. Blackburn7, K. Blackman7, T.R. Blackman7, P. Blanchard33, P. Blatchford7, V. Bobkov62, A. Boboc7, G. Bodnár113, O. Bogar18, I. Bolshakova60, T. Bolzonella12, N. Bonanomi97, F. Bonelli56, J. Boom62, J. Booth7, D. Borba35,53, D. Borodin39, I. Borodkina39, A. Botrugno90, C. Bottereau8, P. Boulting7, C. Bourdelle8, M. Bowden7, C. Bower7, C. Bowman110, T. Boyce7, C. Boyd7, H.J. Boyer7, J.M.A. Bradshaw7, V. Braic87, R. Bravanec40, B. Breizman107, S. Bremond8, P.D. Brennan7, S. Breton8, A. Brett7, S. Brezinsek39, M.D.J. Bright7, M. Brix7, W. Broeckx78, M. Brombin12, A. Brosławski65, D.P.D. Brown7, M. Brown7, E. Bruno55, J. Bucalossi8, J. Buch46, J. Buchanan7, M.A. Buckley7, R. Budny76, H. Bufferand8, M. Bulman7, N. Bulmer7, P. Bunting7, P. Buratti90, A. Burckhart62, A. Buscarino30, A. Busse7, N.K. Butler7, I. Bykov42, J. Byrne7, P. Cahyna50, G. Calabrò90, I. Calvo57, Y. Camenen4, P. Camp7, D.C. Campling7, J. Cane7, B. Cannas17, A.J. Capel7, P.J. Card7, A. Cardinali90, P. Carman7, M. Carr7, D. Carralero62, L. Carraro12, B.B. Carvalho53, I. Carvalho53, P. Carvalho53, F.J. Casson7, C. Castaldo90, N. Catarino53, J. Caumont7, F. Causa90, R. Cavazzana12, K. Cave-Ayland7, M. Cavinato12, M. Cecconello22, S. Ceccuzzi90, E. Cecil76, A. Cenedese12, R. Cesario90, C.D. Challis7, M. Chandler7, D. Chandra46, C.S. Chang76, A. Chankin62, I.T. Chapman7, S.C. Chapman28, M. Chernyshova49, G. Chitarin12, G. Ciraolo8, D. Ciric7, J. Citrin38, F. Clairet8, E. Clark7, M. Clark7, R. Clarkson7, D. Clatworthy7, C. Clements7, M. Cleverly7, J.P. Coad7, P.A. Coates7, A. Cobalt7, V. Coccorese105, V. Cocilovo90, S. Coda33, R. Coelho53, J.W. Coenen39, I. Coffey29, L. Colas8, S. Collins7, D. Conka103, S. Conroy22, N. Conway7, D. Coombs7, D. Cooper7, S.R. Cooper7, C. Corradino30, Y. Corre8, G. Corrigan7, S. Cortes53, D. Coster62, A.S. Couchman7, M.P. Cox7, T. Craciunescu86, S. Cramp7, R. Craven7, F. Crisanti90, G. Croci97, D. Croft7, K. Crombé15, R. Crowe7, N. Cruz53, G. Cseh113, A. Cufar81, A. Cullen7, M. Curuia85, A. Czarnecka49, H. Dabirikhah7, P. Dalgliesh7, S. Dalley7, J. Dankowski47, D. Darrow76, O. Davies7, W. Davis55,76, C. Day56, I.E. Day7, M. De Bock55, A. de Castro57, E. de la Cal57, E. de la Luna57, G. De Masi12, J. L. de Pablos57, G. De Temmerman55, G. De Tommasi105, P. de Vries55, K. Deakin7, J. Deane7, F. Degli Agostini12, R. Dejarnac50, E. Delabie73, N. den Harder38, R.O. Dendy7, J. Denis8, P. Denner39, S. Devaux62,104, P. Devynck8, F. Di Maio55, A. Di Siena62, C. Di Troia90, P. Dinca86, R. D’Inca62, B. Ding51, T. Dittmar39, H. Doerk62, R.P. Doerner9, T. Donné34, S.E. Dorling7, S. Dormido-Canto93, S. Doswon7, D. Douai8, P.T. Doyle7, A. Drenik62,81, P. Drewelow63, P. Drews39, Ph. Duckworth55, R. Dumont8, P. Dumortier58, D. Dunai113, M. Dunne62, I. Ďuran50, F. Durodié58, P. Dutta46, B. P. Duval33, R. Dux62, K. Dylst78, N. Dzysiuk22, P.V. Edappala46, J. Edmond7, A.M. Edwards7, J. Edwards7, Th. Eich62, A. Ekedahl8, R. El-Jorf7, C.G. Elsmore7, M. Enachescu84, G. Ericsson22, F. Eriksson16, J. Eriksson22, L.G. Eriksson36, B. Esposito90, S. Esquembri94, H.G. Esser39, D. Esteve8, B. Evans7, G.E. Evans7, G. Evison7, G.D. Ewart7, D. Fagan7, M. Faitsch62, D. Falie86, A. Fanni17, A. Fasoli33, J. M. Faustin33, N. Fawlk7, L. Fazendeiro53, N. Fedorczak8, R.C. Felton7, K. Fenton7, A. Fernades53, H. Fernandes53, J. Ferreira53, J.A. Fessey7, O. Février8, O. Ficker50, A. Field7, S. Fietz62, A. Figueiredo53, J. Figueiredo53,35, A. Fil8, P. Finburg7, M. Firdaouss8, U. Fischer56, L. Fittill7, M. Fitzgerald7, D. Flammini90, J. Flanagan7, C. Fleming7, K. Flinders7, N. Fonnesu90, J. M. Fontdecaba57, A. Formisano79, L. Forsythe7, L. Fortuna30, E. Fortuna-Zalesna19, M. Fortune7, S. Foster7, T. Franke34, T. Franklin7, M. Frasca30, L. Frassinetti42, M. Freisinger39, R. Fresa98, D. Frigione90, V. Fuchs50, D. Fuller35, S. Futatani6, J. Fyvie7, K. Gál34,62, D. Galassi2, K. Gałązka49, J. Galdon-Quiroga92, J. Gallagher7, D. Gallart6, R. Galvão10, X. Gao51, Y. Gao39, J. Garcia8, A. Garcia-Carrasco42, M. García-Muñoz92, J.-L. Gardarein3, L. Garzotti7, P. Gaudio95, E. Gauthier8, D.F. Gear7, S.J. Gee7, B. Geiger62, M. Gelfusa95, S. Gerasimov7, G. Gervasini45, M. Gethins7, Z. Ghani7, M. Ghate46, M. Gherendi86, J.C. Giacalone8, L. Giacomelli45, C.S. Gibson7, T. Giegerich56, C. Gil8, L. Gil53, S. Gilligan7, D. Gin54, E. Giovannozzi90, J.B. Girardo8, C. Giroud7, G. Giruzzi8, S. Glöggler62, J. Godwin7, J. Goff7, P. Gohil43, V. Goloborod’ko102, R. Gomes53, B. Gonçalves53, M. Goniche8, M. Goodliffe7, A. Goodyear7, G. Gorini97, M. Gosk65, R. Goulding76, A. Goussarov78, R. Gowland7, B. Graham7, M.E. Graham7, J. P. Graves33, N. Grazier7, P. Grazier7, N.R. Green7, H. Greuner62, B. Grierson76, F.S. Griph7, C. Grisolia8, D. Grist7, M. Groth1, R. Grove73, C.N. Grundy7, J. Grzonka19, D. Guard7, C. Guérard34, C. Guillemaut8,53, R. Guirlet8, C. Gurl7, H.H. Utoh69, L.J. Hackett7, S. Hacquin8,35, A. Hagar7, R. Hager76, A. Hakola112, M. Halitovs103, S.J. Hall7, S.P. Hallworth Cook7, C. Hamlyn-Harris7, K. 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Jachmich58,35, A.S. Jacobsen83, P. Jacquet7, J. Jansons103, A. Jardin8, A. Järvinen1, F. Jaulmes38, S. Jednoróg49, I. Jenkins7, C. Jeong20, I. Jepu86, E. Joffrin8, R. Johnson7, T. Johnson42, Jane Johnston7, L. Joita7, G. Jones7, T.T.C. Jones7, K.K. Hoshino69, A. Kallenbach62, K. Kamiya69, J. Kaniewski7, A. Kantor7, A. Kappatou62, J. Karhunen1, D. Karkinsky7, I. Karnowska7, M. Kaufman73, G. Kaveney7, Y. Kazakov58, V. Kazantzidis70, D.L. Keeling7, T. Keenan7, J. Keep7, M. Kempenaars7, C. Kennedy7, D. Kenny7, J. Kent7, O.N. Kent7, E. Khilkevich54, H.T. Kim35, H.S. Kim80, A. Kinch7, C. king7, D. King7, R.F. King7, D.J. Kinna7, V. Kiptily7, A. Kirk7, K. Kirov7, A. Kirschner39, G. Kizane103, C. Klepper73, A. Klix56, P. Knight7, S.J. Knipe7, S. Knott96, T. Kobuchi69, F. Köchl111, G. Kocsis113, I. Kodeli81, L. Kogan7, D. Kogut8, S. Koivuranta112, Y. Kominis70, M. Köppen39, B. Kos81, T. Koskela1, H.R. Koslowski39, M. Koubiti4, M. Kovari7, E. Kowalska-Strzęciwilk49, A. Krasilnikov88, V. 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Porton7, G. Possnert22, S. Potzel62, T. Powell7, J. Pozzi7, V. Prajapati46, R. Prakash46, G. Prestopino95, D. Price7, M. Price7, R. Price7, P. Prior7, R. Proudfoot7, G. Pucella90, P. Puglia52, M.E. Puiatti12, D. Pulley7, K. Purahoo7, Th. Pütterich62, E. Rachlew25, M. Rack39, R. Ragona58, M.S.J. Rainford7, A. Rakha6, G. Ramogida90, S. Ranjan46, C.J. Rapson62, J.J. Rasmussen83, K. Rathod46, G. Rattá57, S. Ratynskaia82, G. Ravera90, C. Rayner7, M. Rebai97, D. Reece7, A. Reed7, D. Réfy113, B. Regan7, J. Regaña34, M. Reich62, N. Reid7, F. Reimold39, M. Reinhart34, M. Reinke110,73, D. Reiser39, D. Rendell7, C. Reux8, S.D.A. Reyes Cortes53, S. Reynolds7, V. Riccardo7, N. Richardson7, K. Riddle7, D. Rigamonti97, F.G. Rimini7, J. Risner73, M. Riva90, C. Roach7, R.J. Robins7, S.A. Robinson7, T. Robinson7, D.W. Robson7, R. Roccella55, R. Rodionov88, P. Rodrigues53, J. Rodriguez7, V. Rohde62, F. Romanelli90, M. Romanelli7, S. Romanelli7, J. Romazanov39, S. Rowe7, M. Rubel42, G. Rubinacci105, G. Rubino12, L. Ruchko52, M. Ruiz94, C. Ruset86, J. Rzadkiewicz65, S. Saarelma7, R. Sabot8, E. Safi101, P. Sagar7, G. Saibene41, F. Saint-Laurent8, M. Salewski83, A. Salmi112, R. Salmon7, F. Salzedas53, D. Samaddar7, U. Samm39, D. Sandiford7, P. Santa46, M.I.K. Santala1, B. Santos53, A. Santucci90, F. Sartori41, R. Sartori41, O. Sauter33, R. Scannell7, T. Schlummer39, K. Schmid62, V. Schmidt12, S. Schmuck7, M. Schneider8, K. Schöpf102, D. Schwörer32, S.D. Scott76, G. Sergienko39, M. Sertoli62, A. Shabbir15, S.E. Sharapov7, A. Shaw7, R. Shaw7, H. Sheikh7, A. Shepherd7, A. Shevelev54, A. Shumack38, G. Sias17, M. Sibbald7, B. Sieglin62, S. Silburn7, A. Silva53, C. Silva53, P.A. Simmons7, J. Simpson7, J. Simpson-Hutchinson7, A. Sinha46, S.K. Sipilä1, A.C.C. Sips36, P. Sirén112, A. Sirinelli55, H. Sjöstrand22, M. Skiba22, R. Skilton7, K. Slabkowska49, B. Slade7, N. Smith7, P.G. Smith7, R. Smith7, T.J. Smith7, M. Smithies110, L. Snoj81, S. Soare85, E. R. Solano35,57, A. Somers32, C. Sommariva8, P. Sonato12, A. Sopplesa12, J. Sousa53, C. Sozzi45, S. Spagnolo12, T. Spelzini7, F. Spineanu86, G. Stables7, I. Stamatelatos71, M.F. Stamp7, P. Staniec7, G. Stankūnas59, C. Stan-Sion84, M.J. Stead7, E. Stefanikova42, I. Stepanov58, A.V. Stephen7, M. Stephen46, A. Stevens7, B.D. Stevens7, J. Strachan76, P. Strand16, H.R. Strauss44, P. Ström42, G. Stubbs7, W. Studholme7, F. Subba75, H.P. Summers21, J. Svensson63, Ł. Świderski65, T. Szabolics113, M. Szawlowski49, G. Szepesi7, T.T. Suzuki69, B. Tál113, T. Tala112, A.R. Talbot7, S. Talebzadeh95, C. Taliercio12, P. Tamain8, C. Tame7, W. Tang76, M. Tardocchi45, L. Taroni12, D. Taylor7, K.A. Taylor7, D. Tegnered16, G. Telesca15, N. Teplova54, D. Terranova12, D. Testa33, E. Tholerus42, J. Thomas7, J.D. Thomas7, P. Thomas55, A. Thompson7, C.-A. Thompson7, V.K. Thompson7, L. Thorne7, A. Thornton7, A.S. Thrysøe83, P.A. Tigwell7, N. Tipton7, I. Tiseanu86, H. Tojo69, M. Tokitani67, P. Tolias82, M. Tomeš50, P. Tonner7, M. Towndrow7, P. Trimble7, M. Tripsky58, M. Tsalas38, P. Tsavalas71, D. Tskhakaya jun102, I. Turner7, M.M. Turner32, M. Turnyanskiy34, G. Tvalashvili7, S.G.J. Tyrrell7, A. Uccello45, Z. Ul-Abidin7, J. Uljanovs1, D. Ulyatt7, H. Urano69, I. Uytdenhouwen78, A.P. Vadgama7, D. Valcarcel7, M. Valentinuzzi8, M. Valisa12, P. Vallejos Olivares42, M. Valovic7, M. Van De Mortel7, D. Van Eester58, W. Van Renterghem78, G.J. van Rooij38, J. Varje1, S. Varoutis56, S. Vartanian8, K. Vasava46, T. Vasilopoulou71, J. Vega57, G. Verdoolaege58, R. Verhoeven7, C. Verona95, G. Verona Rinati95, E. Veshchev55, N. Vianello45, J. Vicente53, E. Viezzer62,92, S. Villari90, F. Villone100, P. Vincenzi12, I. Vinyar74, B. Viola90, A. Vitins103, Z. Vizvary7, M. Vlad86, I. Voitsekhovitch34, P. Vondráček50, N. Vora7, T. Vu8, W.W. Pires de Sa52, B. Wakeling7, C.W.F. Waldon7, N. Walkden7, M. Walker7, R. Walker7, M. Walsh55, E. Wang39, N. Wang39, S. Warder7, R.J. Warren7, J. Waterhouse7, N.W. Watkins28, C. Watts55, T. Wauters58, A. Weckmann42, J. Weiland23, H. Weisen33, M. Weiszflog22, C. Wellstood7, A.T. West7, M.R. Wheatley7, S. Whetham7, A.M. Whitehead7, B.D. Whitehead7, A.M. Widdowson7, S. Wiesen39, J. Wilkinson7, J. Williams7, M. Williams7, A.R. Wilson7, D.J. Wilson7, H.R. Wilson110, J. Wilson7, M. Wischmeier62, G. Withenshaw7, A. Withycombe7, D.M. Witts7, D. Wood7, R. Wood7, C. Woodley7, S. Wray7, J. Wright7, J.C. Wright64, J. Wu89, S. Wukitch64, A. Wynn110, T. Xu7, D. Yadikin16, W. Yanling39, L. Yao89, V. Yavorskij102, M.G. Yoo80, C. Young7, D. Young7, I.D. Young7, R. Young7, J. Zacks7, R. Zagorski49, F.S. Zaitsev18, R. Zanino75, A. Zarins103, K.D. Zastrow7, M. Zerbini90, W. Zhang62, Y. Zhou42, E. Zilli12, V. Zoita86, S. Zoletnik113, I. Zychor65 and JET Contributorsa // EUROfusion Consortium JET, Culham Science Centre, Abingdon, OX14 3DB, United Kingdom / 1 Aalto University, PO Box 14100, FIN-00076 Aalto, Finland / 2 Aix Marseille Université, CNRS, Centrale Marseille, M2P2 UMR 7340, 13451, Marseille, France / 3 Aix-Marseille Université, CNRS, IUSTI UMR 7343, 13013 Marseille, France / 4 Aix-Marseille Université, CNRS, PIIM, UMR 7345, 13013 Marseille, France / 5 Arizona State University, Tempe, AZ, United States of America / 6 Barcelona Supercomputing Center, Barcelona, Spain / 7 CCFE, Culham Science Centre, Abingdon, Oxon, OX14 3DB, United Kingdom / 8 CEA, IRFM, F-13108 Saint Paul Lez Durance, France / 9 Center for Energy Research, University of California at San Diego, La Jolla, CA 92093, United States of America / 10 Centro Brasileiro de Pesquisas Fisicas, Rua Xavier Sigaud, 160, Rio de Janeiro CEP 22290-180, Brazil / 11 Consorzio CREATE, Via Claudio 21, 80125 Napoli, Italy / 12 Consorzio RFX, corso Stati Uniti 4, 35127 Padova, Italy / 13 Daegu University, Jillyang, Gyeongsan, Gyeongbuk 712-174, Republic of Korea / 14 Departamento de Física, Universidad Carlos III de Madrid, 28911 Leganés, Madrid, Spain / 15 Department of Applied Physics UG (Ghent University) St-Pietersnieuwstraat 41 B-9000 Ghent, Belgium / 16 Department of Earth and Space Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden / 17 Department of Electrical and Electronic Engineering, University of Cagliari, Piazza d’Armi 09123, Cagliari, Italy / 18 Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics Comenius University Mlynska dolina F2, 84248 Bratislava, Slovakia / 19 Department of Materials Science, Warsaw University of Technology, PL-01-152 Warsaw, Poland / 20 Department of Nuclear and Quantum Engineering, KAIST, Daejeon 34141, Korea / 21 Department of Physics and Applied Physics, University of Strathclyde, Glasgow, G4 ONG, United Kingdom / 22 Department of Physics and Astronomy, Uppsala University, SE-75120 Uppsala, Sweden / 23 Department of Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden / 24 Department of Physics, Imperial College London, London, SW7 2AZ, United Kingdom / 25 Department of Physics, SCI, KTH, SE-10691 Stockholm, Sweden / 26 Department of Physics, University of Basel, Basel, Switzerland / 27 Department of Physics, University of Oxford, Oxford, OX1 2JD, United Kingdom / 28 Department of Physics, University of Warwick, Coventry, CV4 7AL, United Kingdom / 29 Department of Pure and Applied Physics, Queens University, Belfast, BT7 1NN, United Kingdom / 30 Dipartimento di Ingegneria Elettrica Elettronica e Informatica, Università degli Studi di Catania, 95125 Catania, Italy / 31 Dipartimento di Ingegneria Industriale, University of Trento, Trento, Italy / 32 Dublin City University (DCU), Dublin, Ireland / 33 Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Plasma Center (SPC), CH-1015 Lausanne, Switzerland / 34 EUROfusion Programme Management Unit, Boltzmannstr. 2, 85748 Garching, Germany / 35 EUROfusion Programme Management Unit, Culham Science Centre, Culham, OX14 3DB, United Kingdom / 36 European Commission, B-1049 Brussels, Belgium / 37 Fluid and Plasma Dynamics, ULB—Campus Plaine—CP 231 Boulevard du Triomphe, 1050 Bruxelles, Belgium / 38 FOM Institute DIFFER, Eindhoven, Netherlands / 39 Forschungszentrum Jülich GmbH, Institut für Energie- und Klimaforschung—Plasmaphysik, 52425 Jülich, Germany / 40 Fourth State Research, 503 Lockhart Dr, Austin, TX, United States of America / 41 Fusion for Energy Joint Undertaking, Josep Pl. 2, Torres Diagonal Litoral B3, 08019, Barcelona, Spain / 42 Fusion Plasma Physics, EES, KTH, SE-10044 Stockholm, Sweden / 43 General Atomics, PO Box 85608, San Diego, CA 92186-5608, United States of America / 44 HRS Fusion, West Orange, NJ, United States of America / 45 IFP-CNR, via R. Cozzi 53, 20125 Milano, Italy / 46 Institute for Plasma Research, Bhat, Gandhinagar-382 428, Gujarat State, India / 47 Institute of Nuclear Physics, Radzikowskiego 152, 31-342 Kraków, Poland / 48 Institute of Physics, Opole University, Oleska 48, 45-052 Opole, Poland / 49 Institute of Plasma Physics and Laser Microfusion, Hery 23, 01-497 Warsaw, Poland / 50 Institute of Plasma Physics AS CR, Za Slovankou 1782/3, 182 00 Praha 8, Czechia / 51 Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, People’s Republic of China / 52 Instituto de Física, Universidade de São Paulo, Rua do Matão Travessa R Nr.187 CEP 05508-090 Cidade Universitária, São Paulo, Brasil / 53 Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal / 54 Ioffe Physico-Technical Institute, 26 Politekhnicheskaya, St Petersburg 194021, Russian Federation / 55 ITER Organization, Route de Vinon, CS 90 046, 13067 Saint Paul Lez Durance, France / 56 Karlsruhe Institute of Technology, PO Box 3640, D-76021 Karlsruhe, Germany / 57 Laboratorio Nacional de Fusión, CIEMAT, Madrid, Spain / 58 Laboratory for Plasma Physics Koninklijke Militaire School—Ecole Royale Militaire, Renaissancelaan 30 Avenue de la Renaissance B-1000, Brussels, Belgium / 59 Lithuanian energy institute, Breslaujos g. 3, LT-44403, Kaunas, Lithuania / 60 Magnetic Sensor Laboratory, Lviv Polytechnic National University, Lviv, Ukraine / 61 Maritime University of Szczecin, Waly Chrobrego 1-2, 70-500 Szczecin, Poland / 62 Max-Planck-Institut für Plasmaphysik, D-85748 Garching, Germany / 63 Max-Planck-Institut für Plasmaphysik, Teilinsitut Greifswald, D-17491 Greifswald, Germany / 64 MIT Plasma Science and Fusion Centre, Cambridge, MA 02139, United States of America / 65 National Centre for Nuclear Research (NCBJ), 05-400 Otwock-Świerk, Poland / 66 National Fusion Research Institute (NFRI), 169-148 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea / 67 National Institute for Fusion Science, Oroshi, Toki, Gifu 509-5292, Japan / 68 National Institute for Fusion Science, Toki, 509-5292, Japan / 69 National Institutes for Quantum and Radiological Science and Technology, Naka, Ibaraki 311-0193, Japan / 70 National Technical University of Athens, Iroon Politechniou 9, 157 73 Zografou, Athens, Greece / 71 NCSR ‘Demokritos’, 153 10, Agia Paraskevi Attikis, Greece / 72 NRC Kurchatov Institute, 1 Kurchatov Square, Moscow 123182, Russian Federation / 73 Oak Ridge National Laboratory, Oak Ridge, TN 37831-6169, United States of America / 74 PELIN LLC, 27a, Gzhatskaya Ulitsa, Saint Petersburg, 195220, Russian Federation / 75 Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy / 76 Princeton Plasma Physics Laboratory, James Forrestal Campus, Princeton, NJ 08543, United States of America / 77 Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, United States of America / 78 SCK-CEN, Nuclear Research Centre, 2400 Mol, Belgium / 79 Second University of Napoli, Consorzio CREATE, Via Claudio 21, 80125 Napoli, Italy / 80 Seoul National University, Shilim-Dong, Gwanak-Gu, Republic of Korea / 81 Slovenian Fusion Association (SFA), Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia / 82 Space and Plasma Physics, EES, KTH SE-100 44 Stockholm, Sweden / 83 Technical University of Denmark, Department of Physics, Bldg 309, DK-2800 Kgs Lyngby, Denmark / 84 The ‘Horia Hulubei’ National Institute for Physics and Nuclear Engineering, Magurele-Bucharest, Romania / 85 The National Institute for Cryogenics and Isotopic Technology, Ramnicu Valcea, Romania / 86 The National Institute for Laser, Plasma and Radiation Physics, Magurele-Bucharest, Romania / 87 The National Institute for Optoelectronics, Magurele-Bucharest, Romania / 88 Troitsk Insitute of Innovating and Thermonuclear Research (TRINITI), Troitsk 142190, Moscow Region, Russian Federation / 89 University of Electronic Science and Technology of China, Chengdu, People’s Republic of China / 90 Unità Tecnica Fusione, ENEA C. R. Frascati, via E. Fermi 45, 00044 Frascati (Roma), Italy / 91 Universidad Complutense de Madrid, Madrid, Spain / 92 Universidad de Sevilla, Sevilla, Spain / 93 Universidad Nacional de Educación a Distancia, Madrid, Spain / 94 Universidad Politécnica de Madrid, Grupo I2A2, Madrid, Spain / 95 Università di Roma Tor Vergata, Via del Politecnico 1, Roma, Italy / 96 University College Cork (UCC), Ireland / 97 University Milano-Bicocca, piazza della Scienza 3, 20126 Milano, Italy / 98 University of Basilicata, Consorzio CREATE, Via Claudio 21, 80125 Napoli, Italy / 99 University of California, 1111 Franklin St., Oakland, CA 94607, United States of America / 100 University of Cassino, Consorzio CREATE, Via Claudio 21, 80125 Napoli, Italy / 101 University of Helsinki, PO Box 43, FI-00014 University of Helsinki, Finland / 102 University of Innsbruck, Fusion@Österreichische Akademie der Wissenschaften (ÖAW), Innsbruck, Austria / 103 University of Latvia, 19 Raina Blvd., Riga, LV 1586, Latvia / 104 University of Lorraine, CNRS, UMR7198, YIJL, Nancy, France / 105 University of Napoli ‘Federico II’, Consorzio CREATE, Via Claudio 21, 80125 Napoli, Italy / 106 University of Napoli Parthenope, Consorzio CREATE, Via Claudio 21, 80125 Napoli, Italy / 107 University of Texas at Austin, Institute for Fusion Studies, Austin, TX 78712, United States of America / 108 University of Toyama, Toyama, 930-8555, Japan / 109 University of Tuscia, DEIM, Via del Paradiso 47, 01100 Viterbo, Italy / 110 University of York, Heslington, York YO10 5DD, United Kingdom / 111 Vienna University of Technology, Fusion@Österreichische Akademie der Wissenschaften (ÖAW), Austria / 112 VTT Technical Research Centre of Finland, PO Box 1000, FIN-02044 VTT, Finland / 113 Wigner Research Centre for Physics, PO Box 49, H-1525 Budapest, Hungary
Published: 2017

34. Structure of photosystem II and substrate binding at room temperature

Author: Holger Dobbek, Pierre Aller, Allen M. Orville, Mengning Liang, Ernest Pastor, Sergey Koroidov, Raymond G. Sierra, Athina Zouni, Pavel V. Afonine, Markus Kubin, Monarin Uervirojnangkoorn, Joseph Robinson, Tara Michels-Clark, Clemens Weninger, Dimosthenis Sokaras, Dorothee Liebschner, Louise Lassalle, Thomas Fransson, Petrus H. Zwart, Philippe Wernet, Ruchira Chatterjee, Sheraz Gul, P. T. Docker, Thomas Kroll, Mark S. Hunter, Sébastien Boutet, Franklin D. Fuller, Nicholas K. Sauter, Gwyndaf Evans, Casper de Lichtenberg, Vittal K. Yachandra, Junko Yano, William I. Weis, Aaron S. Brewster, Jan Kern, Lacey Douthit, Rosalie Tran, Mohamed Ibrahim, James M. Glownia, Nigel W. Moriarty, Miao Zhang, Artem Y. Lyubimov, Babak Andi, Jason E. Koglin, Andrew Aquila, David G. Waterman, Paul D. Adams, Hartawan Laksmono, Uwe Bergmann, Philipp Bräuer, Marcin Sikorski, Mackenzie A. Bean, Rana Hussein, Dmitriy Shevela, Iris D. Young, Claudiu A. Stan, Thomas J. Lane, Roberto Alonso-Mori, Mun Hon Cheah, Johannes Messinger, Tsu-Chien Weng, Long Vo Pham, Axel T. Brunger, Claudio Saracini, Diling Zhu, Silke Nelson, Ina Seuffert, and Håkan Nilsson
Subjects: Models, Molecular, Photosystem II, General Science & Technology, chemistry.chemical_element, Electrons, 02 engineering and technology, 010402 general chemistry, Photosynthesis, Photochemistry, Cyanobacteria, 01 natural sciences, Oxygen, Redox, Article, Catalysis, Substrate Specificity, Bacterial Proteins, Ammonia, Models, Manganese, Multidisciplinary, Binding Sites, Lasers, Temperature, Substrate (chemistry), Water, Photosystem II Protein Complex, Molecular, 021001 nanoscience & nanotechnology, Electron transport chain, 0104 chemical sciences, Crystallography, chemistry, Generic Health Relevance, 0210 nano-technology, Crystallization, Biophysical chemistry
Abstract: © 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn 4 CaO 5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S 0 to S 4), in which S 1 is the dark-stable state and S 3 is the last semi-stable state before O-O bond formation and O 2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S 1), two-flash illuminated (2F; S 3 -enriched), and ammonia-bound two-flash illuminated (2F-NH 3; S 3 -enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S 1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn 4 CaO 5 cluster in the S 2 and S 3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.
Published: 2016

35. Optimizing and evaluating protein microcrystallography experiments: strengths and weaknesses of X-rays and electrons

Author: N. S. Sauter, Michihiro Sugahara, Rie Tanaka, Iris D. Young, Erin M. Thompson, Michael C. Thompson, So Iwata, Avi J. Samelson, Rahel A. Woldeyes, S.V. Cortez, Kensuke Tono, Wei Zhao, Michael W. Martynowycz, K. Ito, Eriko Nango, Tamir Gonen, Raymond G. Sierra, Sébastien Boutet, Takanori Nakane, Jake Koralek, Aaron S. Brewster, Fumiaki Yumoto, Andrew Aquila, H. van den Bedem, Alexander M. Wolff, Justin T Biel, and James S. Fraser
Subjects: Inorganic Chemistry, Physics, Structural Biology, General Materials Science, Electron, Physical and Theoretical Chemistry, Condensed Matter Physics, Biochemistry, Strengths and weaknesses, Computational physics
Abstract: Recently, significant technological innovations have enabled the measurement of both X-ray and electron diffraction from protein microcrystals. These new microcrystallography experiments are useful when large crystals cannot be obtained, but also in other cases, such as when large crystals suffer from long-range disorder, or when uniform perturbations need to be applied rapidly to the entire crystal volume. Optimizing the preparation of protein microcrystals for this new class of experiments presents new challenges for crystallographers, who have traditionally sought to grow large, single crystals. To better understand these new challenges, we optimized the production of microcrystalline samples of cyclophilin A (CypA), starting from conditions that produced millimeter scale crystals. Next, we used these microcrystals to determine CypA structures by serial femtosecond crystallography (SFX) at two XFEL lightsources, and by microcrystal electron diffraction (microED) in an electron cryomicroscope. Here, I will present our optimization strategy for protein microcrystallization, and compare the results of X-ray and electron microcrystallography experiments with CypA. I will focus on the unique caveats of sample delivery for each method, and compare the resulting structures. The goal will be to provide insight into which microcrystallography experiment is most appropriate for which types of samples, and to share our experience with sample preparation and delivery for each type of experiment.
Published: 2019

36. Turning up the heat on dynamic proteins: observing molecular motion in real time with temperature-jump X-ray crystallography

Author: Takashi Tanaka, Aaron S. Brewster, Takehiko Tosha, James S. Fraser, Fumiaki Yumoto, Rie Tanaka, Sébastien Boutet, Nicholas K. Sauter, So Iwata, Andrew Aquila, Raymond G. Sierra, Takashi Nomura, Iris D. Young, Alexander M. Wolff, Dohyun Im, Shigeki Owada, Michael C. Thompson, K. Ito, Minoru Kubo, Kensuke Tono, Ayumi Yamashita, Eriko Nango, Takanori Nakane, Tomoya Hino, Sergio Carbajo, F. Luo, Michihiro Sugahara, and Jake Koralek
Subjects: Inorganic Chemistry, Materials science, Structural Biology, Temperature jump, X-ray crystallography, Molecular motion, General Materials Science, Physical and Theoretical Chemistry, Condensed Matter Physics, Biochemistry, Molecular physics
Published: 2019

37. Structure of intermediates of the water oxidation reaction in photosystem II

Author: Louise Lassalle, Kyle D. Sutherlin, Aaron S. Brewster, Asmit Bhowmick, Nicholas K. Sauter, Sheraz Gul, Jan Kern, Vittal K. Yachandra, A. Zouni, Rana Hussein, Ruchira Chatterjee, Johannes Messinger, Franklin D. Fuller, Mohamed Ibrahim, Junko Yano, and Iris D. Young
Subjects: Photosystem II, Electrolysis of water, Chemistry, Electron, Oxygen-evolving complex, Condensed Matter Physics, Photochemistry, Biochemistry, Redox, Inorganic Chemistry, Structural Biology, Cluster (physics), Light driven, General Materials Science, Physical and Theoretical Chemistry
Abstract: Photosystem II (PSII) catalyzes the light driven oxidation of water into dioxygen, protons and electrons. This reaction takes place at the oxygen evolving complex (OEC) a Mn4CaO5 cluster, through f ...
Published: 2019

38. Further observations on LKB1/STK11 status and cancer risk in Peutz-Jeghers syndrome

Author: R C Macdonald, I. P. M. Tomlinson, Robin Kenneth Stewart Phillips, Iris D. Young, Shirley Hodgson, W Lim, Diana Eccles, E. T. Swarbrick, D Alderson, A.G. Lim, A G Holbrook, P.W. Lee, N Hearle, B J Stoodley, Bindiya Shah, Ian C. Talbot, A A M Lewis, Martin Robinson, Anneke Lucassen, Victoria Murday, Alan Donaldson, J. O'Donohue, S Vyas, K Neale, and Richard S. Houlston
Subjects: Oncology, Adult, Male, congenital, hereditary, and neonatal diseases and abnormalities, Cancer Research, medicine.medical_specialty, Pathology, Genotype, STK11, Peutz-Jeghers Syndrome, Peutz–Jeghers syndrome, Breast Neoplasms, Biology, cancer risk, Protein Serine-Threonine Kinases, Germline, Breast cancer, Germline mutation, AMP-Activated Protein Kinase Kinases, Risk Factors, Internal medicine, medicine, Humans, Genetic Predisposition to Disease, skin and connective tissue diseases, Germ-Line Mutation, Aged, Gastrointestinal Neoplasms, Genetic heterogeneity, Absolute risk reduction, Cancer, Genetics and Genomics, Middle Aged, medicine.disease, Phenotype, LKB1/STK11, Female, mutation, Follow-Up Studies
Abstract: Germline mutations in the LKB1/STK11 tumour suppressor gene cause Peutz-Jeghers syndrome (PJS), a rare dominant disorder. In addition to typical hamartomatous gastrointestinal polyps and pigmented perioral lesions, PJS is associated with an increased risk of tumours at multiple sites. Follow-up information on carriers is limited and genetic heterogeneity makes counselling and management in PJS difficult. Here we report the analysis of the LKB1/STK11 locus in a series of 33 PJS families, and estimation of cancer risks in carriers and noncarriers. Germline mutations of LKB1/STK11 were identified in 52% of cases. This observation reinforces the hypothesis of a second PJS locus. In carriers of LKB1/STK11 mutations, the risk of cancer was markedly elevated. The risk of developing any cancer in carriers by age 65 years was 47% (95% CI: 27-73%) with elevated risks of both gastrointestinal and breast cancer. PJS with germline mutations in LKB1/STK11 are at a very high relative and absolute risk of multiple gastrointestinal and nongastrointestinal cancers. To obtain precise estimates of risk associated with PJS requires further studies of genotype-phenotype especially with respect to LKB1/STK11 negative cases, as this group is likely to be heterogeneous.
Published: 2016

39. Insights into the oxygen-evolving mechanism of photosynthesis using XFELs

Author: Nicholas K. Sauter, Iris D. Young, Ruchira Chatterjee, Mohamed Ibrahim, Sheraz Gul, Vittal K. Yachandra, Junko Yano, Jan Kern, Aaron S. Brewster, and Franklin D. Fuller
Subjects: Inorganic Chemistry, Structural Biology, Chemistry, Biophysics, chemistry.chemical_element, General Materials Science, Physical and Theoretical Chemistry, Condensed Matter Physics, Photosynthesis, Biochemistry, Oxygen, Mechanism (sociology)
Published: 2017

40. X-ray crystallography and spectroscopy of metalloenzymes using drop-on-tape method

Author: Nicholas K. Sauter, Franklin D. Fuller, Sheraz Gul, Jan Kern, Allen M. Orville, Aaron S. Brewster, Vittal K. Yachandra, Junko Yano, Ruchira Chatterjee, and Iris D. Young
Subjects: Inorganic Chemistry, Crystallography, Materials science, Structural Biology, Drop (liquid), X-ray crystallography, General Materials Science, Physical and Theoretical Chemistry, Condensed Matter Physics, Spectroscopy, Biochemistry
Published: 2017

41. Exploring the dynamic of PSII at room temperature by simultaneous femtosecond X-ray spectroscopy and dffraction

Author: Louise Lassalle, Ernest Pastor, Ruchira Chatterjee, Franklin D. Fuller, Aaron S. Brewster, Athina Zouni, Lacey Douthit, Nicholas K. Sauter, Vittal K. Yachandra, Junko Yano, Mohamed Ibrahim, Sheraz Gul, Jan Kern, and Iris D. Young
Subjects: Inorganic Chemistry, X-ray spectroscopy, Materials science, Structural Biology, Femtosecond, Analytical chemistry, General Materials Science, Physical and Theoretical Chemistry, Condensed Matter Physics, Biochemistry
Published: 2017

42. Processing XFEL still shots and merging multi-crystal data

Author: Nicholas K. Sauter, Aaron S. Brewster, and Iris D. Young
Subjects: Inorganic Chemistry, Diffraction, Crystallography, Optics, Materials science, Structural Biology, business.industry, Crystal data, General Materials Science, Physical and Theoretical Chemistry, Condensed Matter Physics, business, Biochemistry
Published: 2016

43. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

Author: Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, and James S Fraser
Subjects: enzyme, chitin, lung, Medicine, Science, Biology (General), QH301-705.5
Abstract: Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high-resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.
Published: 2024
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44. Deep neural networks for plasma tomography with applications to JET and COMPASS

Author: J. Denis, M. Tardocchi, Kiptily, M. Koubiti, M. Ghate, R. Michling, G. De Masi, T. Tala, M. Bassan, R. McAdams, S. Dowson, Antoine Merle, Seppo Koivuranta, O. J. Kwon, S. Mahesan, P. Sparapani, A. Malaquias, M. Tsalas, Gennady V. Miloshevsky, M. Vecsei, Michal Stano, E. Lerche, Štefan Matejčík, Piergiorgio Sonato, S. D. Pinches, A. Dal Molin, O. McCormack, B. Colling, F. Mink, Ph. Mertens, P. Drewelow, Nuno Cruz, D. Iglesias, Alessandro Zocco, K. Rathod, S. Collins, F. Koechl, James Buchanan, Andrew West, Francesco Maviglia, E. Stefanikova, David Taylor, B. Graham, T. Lunt, S. Meshchaninov, Arturo Buscarino, G. L. Ravera, Maide Bucolo, J. P. Thomas, S. Foley, B. Wakeling, N. Ashikawa, D. W. Robson, N. J. Conway, V. P. Lo Schiavo, Stefan Buller, Sergey Popovichev, M. Saleem, Jorge Luis Rodriguez, M. Wheatley, Gabriele Croci, Hugo Bufferand, J.F. Artaud, R. C. Felton, O. Kovanda, D. Hepple, K. Dylst, Gabor Szepesi, M. Oberkofler, G.J. van Rooij, N. Teplova, Istvan Cziegler, K. K. Kirov, S. Vartanian, Y. Xue, D. Nina, J. Bernardo, Lorenzo Figini, Guglielmo Rubinacci, Peter Lang, R. Scannell, N. C. Hawkes, P. Denner, Istvan Pusztai, D. D. Carvalho, Salvatore Ventre, A. Lescinskis, Afanasev, C. Hamlyn-Harris, Panagiotis Tolias, R. Vale, T. O'Gorman, S. Lesnoj, I.E. Day, Karol Malinowski, D. Carralero, N. Balshaw, Massimo Angelone, Michaele Freisinger, I. Monakhov, Jesús Vega, Jonathan Citrin, Antti Hakola, H. Patten, P. A. Simmons, Y. Austin, Sehyun Kwak, J. Regana, Rohde, T. Eich, A. Alkseev, R. Lawless, C. G. Elsmore, Fusco, S. Hacquin, S. A. Silburn, A. Fernades, Luigi Fortuna, P. Bunting, R. Sartori, Yuji Hatano, D. Borodin, L. Colas, Daniele Marocco, M. Lennholm, Carlo Sozzi, J. J. Rasmussen, P. McCullen, Tommy Ahlgren, A. Kirschner, Thomas Johnson, M. Rack, Göran Ericsson, Hans Nordman, Jakub Bielecki, P. Merriman, M. Cavedon, G. Hermon, Geert Verdoolaege, K. J. Gibson, Daisuke Nishijima, R. Clarkson, Fuchs, M. Tomes, R. Zagórski, Gerald Pintsuk, W. Higginson, Daniel F. Valcarcel, R. Mooney, K. Dawson, A. Tallargio, T.H. Osborne, P. J. Carvalho, M. Gethins, R. Dux, Pierre Dumortier, G. Urbanczyk, Inessa Bolshakova, R. King, B. Tal, Daniel Tegnered, J. W. Coenen, Leena Aho-Mantila, Eva Belonohy, S. Schmuck, Kai Nordlund, Grégoire Hornung, G. Tvalashvili, M. De Bock, Y. Baranov, G. De Tommasi, A. Urban, L. Forsythe, I. Zychor, J. Dobrashian, E. Clark, Paolo Arena, Alessia Santucci, Ivan Lupelli, S. Nowak, M. Curuia, Jonathan Graves, J. C. Hillesheim, Claudio Verona, Zoita, S. Moon, C. Castaldo, A.V. Stephen, Karl Schmid, A. Sahlberg, C. Di Troia, R. Woodley, L. Garzotti, D. Sandiford, Matthew M. Knight, Juho Leppänen, S. Emery, O. G. Pompilian, M. Goniche, C. Luna, M. Mayer, M. Baruzzo, A. Weckmann, M. Kempenaars, S. Hazel, Fabio Pisano, Claudia Corradino, A. G. Meigs, P. Leichauer, S. Potzel, Stéphane Devaux, C. Piron, G. Saibene, David A Rasmussen, Bruce Lipschultz, A. Di Siena, E. Lazzaro, J. Deane, C. Meadowcroft, C. J. Rapson, K.-D. Zastrow, Ph. Duckworth, Tom Wauters, F. Nabais, T. Goerler, D. Brunetti, R. Ellis, David Moulton, L. Jones, E. Delabie, Anna Salmi, Luciano Bertalot, G. Burroughes, B. Kos, Laurent Marot, Daniel Primetzhofer, I Miron, N. Lam, F. Napoli, S. Rowe, E. Pajuste, Choong-Seock Chang, R.P. Doerner, D. Silvagni, C. Guillemaut, S. Warder, A.J. Thornton, Matthew Carr, A. Dempsey, Jorge Morales, Pramit Dutta, J. L. Herfindal, S. Maruyama, P. Camp, X. Lefebvre, Ye. O. Kazakov, Andrea G. Chiariello, Gabriele Manduchi, Andre Neto, T. Powell, J. Griffiths, José Vicente, C. Barcellona, J. Hobirk, F. Clairet, L. Xiang, Dirk Reiser, H. Bergsåker, I. Duran, G. Giacometti, M. Kalsey, David Tskhakaya, A. Martin de Aguilera, T. Dittmar, Edmund Highcock, I. Uytdenhouwen, S. Soare, Giuseppe Prestopino, L. Chôné, W. Davis, G. De Temmerman, Basiuk, G. Learoyd, C. Guerard, A. Klix, M. Incelli, B. Viola, R. J. Robins, A. Burckhart, W. Leysen, Jochen Linke, M. Oberparleiter, A. Murari, M. Sertoli, S. 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Ciric, Eric Nardon, A. Somers, I. Igaune, E. Laszynska, S. Saarelma, A. Cullen, Mǎdǎlina Vlad, D. Nodwell, S. Griph, T. Donne, T. Boyce, M. Tyshchenko, Paulo Carvalho, Elena Bruno, Ion E. Stamatelatos, A. Patel, E. de la Luna, F. Causa, Robin Barnsley, Michael Lehnen, F. Belli, N. Jones, B. Bauvir, M. Tokitani, I. Turner, Y. Zhou, J. Simpson, A. Vitins, D. Rendell, Alberto Milocco, Benjamin P. Brown, F.G. Rimini, C. Lamb, V. Thompson, E. Alessi, S. Arshad, J. Rzadkiewicz, P. Prior, J. Moran, S. D. A. Reyes Cortes, Igor Bykov, M. Weiszflog, Annette M. Hynes, Gennady Sergienko, J. Lönnroth, T. C. Hender, M.-L. Mayoral, Mattia Frasca, R. Coelho, J-J Honore, A. Jackson, A. Sirinelli, M. D. Axton, Hyun-Tae Kim, F. P. Keenan, H. J. Boyer, Elisabeth Rachlew, T. Szabolics, J. Ongena, Braic, Sandra C. Chapman, Anders Nielsen, John E. Marsh, J. Jansons, S. Gloeggler, Nengchao Wang, Naulin, M. Porton, D. Falie, P. Welch, G. T. Jones, N. Fil, M. Vincent, U. Kruezi, R. Pereira, L. Horvath, M. F. F. Nave, Lorella Carraro, N. Fonnesu, Davide Flammini, P. V. Edappala, G. M. D. Hogeweij, K. Krieger, P. Card, G. Poulipoulis, W. Studholme, Didier Mazon, T. Odupitan, D. Young, F. J. Casson, N. Muthusonai, I. Jepu, Olivier Sauter, Dimitri Voltolina, Sara Carcangiu, C. Reux, Irena Ivanova-Stanik, D. Tskhakaya Jun, O. Bogar, E. Viezzer, Shane Cooper, Fabio Villone, Florin Spineanu, H. Doerk, E. Cecil, J. Goff, F. Nespoli, F. Schluck, G. Ciraolo, Jennifer M. Lehmann, Jan Mlynar, H. J. C. Oliver, M. Marinucci, N. Krawczyk, J. Buch, M. Dreval, G. Possnert, C. Angioni, C. P. Lungu, Marco Ariola, S. Breton, Christopher N. Bowman, A. Kundu, J. Mailloux, I. Stepanov, D. Sprada, J. Zacks, G. Ramogida, E. Wolfrum, N.W. Eidietis, A. Pires dos Reis, Barbara Cannas, Robert E. Grove, A. Huber, Giuliana Sias, A. Baron Wiechec, Markus Airila, M. Berry, P. Huynh, R. Kovaldins, R. Bastow, Darren Price, S. Abduallev, P. Tsavalas, N. Aiba, Plyusnin, Ion Tiseanu, James Williams, M. Beckers, M. Weiland, S.N. Gerasimov, Alessandra Fanni, L. D. Horton, T. Xu, L. Joita, N. Reid, D. Zarzoso Fernandez, D. I. Refy, Jerry Hughes, Clarisse Bourdelle, J. E. Boom, G. Hancu, K. M. Aggarwal, F. Crisanti, M. Poradziński, A. Loarte, P. Vallejos Olivares, T. Mrowetz, Teddy Craciunescu, R. Guirlet, M. Valentinuzzi, J. Stephens, J. Stober, Michael Barnes, Isabel L. Nunes, Mario Pillon, P. Batistoni, G. Verona Rinati, Fabio Moro, R. Lucock, R. Olney, Jari Varje, B. Butler, A. Mariani, M. Hamed, Skvara, C. Terry, Larisa Baumane, T. Alarcon, Mike Kotschenreuther, T. M. Biewer, O. Hemming, N. Marcenko, Z. Kollo, B. Slade, J. Garcia, T. R. Blackman, Simone Peruzzo, N. den Harder, S. Ng, P. Siren, K. G. McClements, Rita Lorenzini, Y. Yakovenko, Lorenzo Frassinetti, J. Hawes, A. Kirk, C. Noble, Nicola Bonanomi, Y. Martynova, A.E. Shumack, F. Di Maio, H. R. Koslowski, N. Pomaro, G. Nemtsev, M. I. K. Santala, Richard George, E. Giovannozzi, T. Giegerich, C. Woodley, G. Pucella, D. Hopley, P.J. 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Finburg, Henrik Sjöstrand, Slawomir Jednorog, Ewa Kowalska-Strzęciwilk, A. Martin, R. O. Dendy, B. Lepiavko, D. Croft, Goloborod'ko, A. V. Krasilnikov, M. Wischmeier, K. Gal, R. Ragona, Petter Ström, N. Parsons, G. Calabrò, Jean-Stéphane Joly, A. Capat, Linwei Li, T. Nakano, Paulo Rodrigues, L. Moser, João P. S. Bizarro, L. Piron, K. Pepperell, P. Aleynikov, Ambrogio Fasoli, S.-P. Pehkonen, Giuseppe Gorini, C. Taliercio, M. E. Puiatti, J. Svensson, H. R. Wilson, John Wright, S. Wiesen, O. Asztalos, R.V. Budny, A. Withycombe, P. Piovesan, Jonathan Gaspar, B. D. Stevens, P. Trimble, Vinodh Bandaru, F. S. Zaitsev, H. Sheikh, G. F. Matthews, Daniele Carnevale, K. Schoepf, L. McNamee, A. Czarnecka, P. Blanchard, Erik Fransson, J.P. Coad, Daniel Dunai, Carolina Björkas, A. Manzanares, M. Reich, A. Lahtinen, L. Giacomelli, Mirko Salewski, E. de la Cal, T. D. V. Haupt, T.T.C. Jones, M. Anghel, Kyriakos Hizanidis, J. M. Fontdecaba, Huber, A. Shaw, A. Cufar, A. Muraro, M. Clark, A. Meakins, Roland Sabot, A. Owen, K. Valerii, A. L. Esquisabel, Petr Vondracek, Maria Teresa Porfiri, Walid Helou, S. E. Sharapov, D. Terranova, M. Skiba, Konstantina Mergia, Frank Leipold, Francisco L. Tabarés, M. Zerbini, Ken W Bell, Marco Marinelli, Marco Riva, R. Martone, Bobkov, B. Magesh, A. Ash, Parail, M. Hook, Amanda Hubbard, Silvio Ceccuzzi, Ulrich Fischer, G. Liu, Nick Walkden, R. Otin, P. Santa, P. Abreu, Demerdzhiev, Roberto Zanino, T. Spelzini, António J.N. Batista, P. G. Smith, L. Meneses, S. S. Medley, M. J. Mantsinen, K. Vasava, G. Gervasini, Surya K. Pathak, Kristel Crombé, G. Ellwood, P. Raj, Robert Hager, Ch. Linsmeier, C. Stokes, Petra Bilkova, M. Groth, G. Pautasso, C. R. Nobs, S. Sridhar, P. Chmielewski, David Hatch, Luca Boncagni, I. Balboa, C. Stan-Sion, Nobuyuki Asakura, R. McKean, L. Pigatto, João Figueiredo, Roberto Cavazzana, Juri Romazanov, M. Beurskens, C. Christopher Klepper, Maryna Chernyshova, O. Biletskyi, D. Karkinsky, A. Eksaeva, S. Dalley, Pasquale Gaudio, J. Benayas, J. Dankowski, S. Korolczuk, R. Buckingham, F. Parra Diaz, E. Wang, A. Cardinali, J. Naish, R. O. Pavlichenko, Kalle Heinola, Hiroshi Tojo, Miles M. Turner, Brett Chapman, A. Lyssoivan, F. Militello, E. Matveeva, T. Kobuchi, I. Ksiazek, P. Bohm, Cody Jones, W. Yanling, T. Jackson, P. Gohil, D. Alegre, Tim D. Bohm, F. Jaulmes, L. Zakharov, Peter J. Pool, C.G. Lowry, M. Passeri, D. Testa, Igor Lengar, A. Formisano, C. M. Roach, A. Hjalmarsson, A. Drenik, S. Meiter, William Tang, Carlos B. da Silva, Diogo R. Ferreira, P. J. Lomas, M. McHardy, Gunta Kizane, Angela Busse, S. Jachmich, Corneliu Porosnicu, Stanislas Pamela, Yavorskij, Eduardo Alves, Saskia Mordijck, Boniface Nkonga, J. Morris, Dean A. J. Whittaker, S. Ertmer, A. Hollingsworth, T. Barnard, R. Tatali, S. Reynolds, S. Mistry, Sergio Galeani, Torbjörn Hellsten, V.S. Neverov, David Dickinson, T. M. Huddleston, D. Baiao, F. Salzedas, D. Willoughby, M. Tripsky, Emmanuele Peluso, J. R. Harrison, C. Mazzotta, R. Zarins, M. Maslov, X. Bonnin, T. E. Gebhart, S. Fietz, K. Flinders, C. Hidalgo, Yann Corre, Aqsa Shabbir, A. B. Kukushkin, A. Shepherd, M.L. Walker, R. Clay, T. Vasilopoulou, Paolo Innocente, I. H. Coffey, P. Lalousis, Italo Predebon, R. Bravanec, P. Papp, D. Sytnykov, Ewa Pawelec, M. Bernert, G. Corrigan, Lutsenko, M. Romanelli, Gergely Papp, S. Romanelli, R. Salmon, J. Risner, M. T. Ogawa, A. M. Whitehead, E. Fable, H. Dabirikhah, Juan Manuel López, M. Turnyanskiy, A. Baciero, S. Meigh, M. Garcia-Munoz, Massimiliano Mattei, J.-M. Noterdaeme, N. Hamilton, S. Minucci, I Wilson, A. Muir, A. V. Chankin, C. Clements, Matthias Hoelzl, Francesco Romanelli, S. Gee, R. J. E. Smith, P. de Vries, L. Fittill, S. Menmuir, K. Cave-Ayland, P. Curson, Richard Fridström, D. Grist, S. A. Robinson, Rodney Walker, Michael Loughlin, S. Aleiferis, W. Broeckx, Clayton E. Myers, S. F. Smith, D. Harting, W. Zwingmann, F. Binda, Mark R. Gilbert, Rajnikant Makwana, Richard Goulding, D. Van Eester, I. Voitsekhovitch, M. Bowden, I. Kodeli, Tomasz Czarski, Peter Hawkins, S. S. Henderson, M. Koeppen, D. Ricci, Ondrej Ficker, Carl Hellesen, D. Yadikin, Fabio Subba, Luka Snoj, Anthony Laing, E. R. Solano, M. Stephen, P. Staniec, C. Appelbee, M. Newman, Susan Leerink, M. Nicassio, P. P. Pereira Puglia, M. Brombin, Wouter Tierens, C. Perez von Thun, Cédric Boulbe, Ya. I. Kolesnichenko, Taina Kurki-Suonio, S. Hallworth-Cook, R. P. Johnson, B. B. Carvalho, Anna Widdowson, Alessandro Pau, R. Price, B. Gonçalves, D. L. Keeling, Kazantzidis, Michael Fitzgerald, M. Hughes, K. D. Lawson, M. Brix, Raffaele Fresa, Juha Karhunen, S. Esquembri, K. Purahoo, Matthew Reinke, Gerd Meisl, M. Valovic, J. Horacek, D. King, H. Maier, Philipps, Kenji Tanaka, M. Kresina, M. Valisa, L. Omoregie, Gábor Cseh, Seppo Sipilä, Scott W. Mosher, Filippo Sartori, J. Kaniewski, Jan Weiland, Giuseppe Chitarin, Coccorese, A. R. Field, P. Beaumont, Robert Skilton, D. C. Campling, Mitul Abhangi, S. Villari, Roberta Lima Gomes, G. D. Ewart, S. Wray, A. Broslawski, A. Sinha, Roberto Paccagnella, S. Hollis, R. D. Wood, Albert Gutierrez-Milla, E. Jonasson, L.-G. Eriksson, R. Leach, L. W. Packer, M. Vuksic, H. J. Sun, C. Marchetto, Giuseppe Telesca, Dieter Leichtle, S. Cramp, Blaise Faugeras, M. Allinson, Yannis Kominis, R. Normanton, H. J. Leggate, Francesco Ghezzi, T. Schlummer, Tommaso Bolzonella, Jorge Ferreira, M. J. Walsh, C. Day, Philipp Drews, Steven J. Meitner, M. D. J. Bright, Per Petersson, D. L. Hillis, M. Webb, P. Wright, C. F. Maggi, B. Sieglin, A. Farahani, J. Strachan, M. Muraglia, M. Cecconello, F. Durodié, D. Callaghan, J. Waterhouse, R. J. Dumont, Sara Moradi, Patrick J. McCarthy, S. Feng, M. Balden, M. Kaufman, R. Warren, Brian Grierson, Harry M. Meyer, S.C. Bradnam, D. Kinna, A. Krivska, M. Lungu, E. Suchkov, A. Kantor, D. Conka, C. Penot, A. Zarins, Pierre Manas, D. F. Gear, J. Callaghan, L. Barrera Orte, Tomas Markovic, Yu Gao, A. Lunniss, Z. Vizvary, E. Khilkevich, Th. Puetterich, Dmitry Matveev, E. Perelli Cippo, T. Owen, N. Imazawa, A. Silva, H. P. Summers, Norberto Catarino, Roberto Pasqualotto, P. Muscat, K. Keogh, Ricardo Magnus Osorio Galvao, P. Carman, M. Leyland, E. Veshchev, A. de Castro, M. Gruca, D. C. McDonald, L. Moreira, J. W. Banks, Sanjeev Ranjan, N. Sutton, Iris D. Young, Martin Imrisek, W. Zhang, J. K. Blackburn, Moiseenko, A. Parsloe, T. Loarer, D. N. Borba, S.J. Wukitch, D. P. Coster, J. Penzo, Jose Ramon Martin-Solis, P. Mantica, N. Bekris, M. G. O'Mullane, S. E. Dorling, Yunfeng Liang, S. Gulati, Roberto Ambrosino, J. Schweinzer, Cocilovo, D. Douai, M. A. Henderson, T. Suzuki, Gianluca Rubino, A. Peackoc, Yann Camenen, Y. Miyoshi, Ph. Jacquet, H. T. Lambertz, E. Tholerus, C. Sommariva, Prajapati, Yannick Marandet, F. Hasenbeck, Faa Federico Felici, M. Buckley, Kenneth Hammond, Daniele Milanesio, Cristian Ruset, Katsumichi Hoshino, D. Frigione, D. Chandra, I. Borodkina, P. Dinca, S. Brezinsek, J. Stallard, H. G. Esser, Matthew Sibbald, S. Knipe, Jorge Estrela da Silva, Kensaku Kamiya, P. A. Coates, J. C. Giacalone, Alfredo Pironti, Carvalho, D. D., Ferreira, D. R., Carvalho, P. J., Imrisek, M., Mlynar, J., Fernandes, H., and Formisano, A.
Subjects: Computer science, Feature extraction, Image processing, Computerized Tomography (CT) and Computed Radiography (CR), Plasma diagnostics - interferometry, spectroscopy and imaging, 01 natural sciences, Convolutional neural network, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Compass, Plasma diagnostics-interferometry, spectroscopy and imaging, 0103 physical sciences, Computer vision, Instrumentation, Mathematical Physics, Jet (fluid), Contextual image classification, 010308 nuclear & particles physics, business.industry, Cognitive neuroscience of visual object recognition, Plasma diagnostics - interferometry spectroscopy and imaging, Tomography, Artificial intelligence, business, plasma diagnostics - interferometry, spectroscopy and imaging
Abstract: Convolutional neural networks (CNNs) have found applications in many image processing tasks, such as feature extraction, image classification, and object recognition. It has also been shown that the inverse of CNNs, so- called deconvolutional neural networks, can be used for inverse problems such as plasma tomography. In essence, plasma tomography consists in reconstructing the 2D plasma profile on a poloidal cross-section of a fusion device, based on line-integrated measurements from multiple radiation detectors. Since the reconstruction process is computationally intensive, a deconvolutional neural network trained to produce the same results will yield a significant computational speedup, at the expense of a small error which can be assessed using different metrics. In this work, we discuss the design principles behind such networks, including the use of multiple layers, how they can be stacked, and how their dimensions can be tuned according to the number of detectors and the desired tomographic resolution for a given fusion device. We describe the application of such networks at JET and COMPASS, where at JET we use the bolometer system, and at COMPASS we use the soft X-ray diagnostic based on photodiode arrays.
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