Article
Chemistry, Multidisciplinary
Kiyofumi Takaba, Saori Maki-Yonekura, Ichiro Inoue, Kensuke Tono, Tasuku Hamaguchi, Keisuke Kawakami, Hisashi Naitow, Tetsuya Ishikawa, Makina Yabashi, Koji Yonekura
Summary: The structure analysis of small crystals is vital in various fields, including synthetic organic chemistry, pharmaceutical and material sciences, where large crystals cannot be obtained. In this study, the structure of an organic molecule, rhodamine6G, was characterized in detail using an X-ray free-electron laser (XFEL) with a resolution of 0.82 A. A direct comparison between the XFEL and electron crystallography methods revealed that both techniques can accurately determine the position of some hydrogen atoms based on the type of chemical bond involved. The variations in distances measured by XFEL and electron diffraction were attributed to the expected differences in X-ray and electron scatterings.
Review
Physics, Multidisciplinary
A. Ghaith, M. -E. Couprie, D. Oumbarek-Espinos, I. A. Andriyash, F. Massimo, J. A. Clarke, M. Courthold, V. Bayliss, A. Bernhard, M. Trunk, M. Valleau, O. Marcouille, A. Chance, S. Licciardi, V. Malka, F. Nguyen, G. Dattoli
Summary: The paper explores the implications of LPA on undulator design, starting with the concept and state-of-art of LPA, discussing the scaling laws, and analyzing different types of compact undulators for LPA-based FEL applications. Examples of experiments and future prospects in transport beamline and spontaneous emission characteristics are also presented.
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS
(2021)
Article
Optics
P. Pongchalee, B. W. J. Mceil
Summary: In this paper, the combination of two unaveraged simulation codes enables the modelling of cavity-based free electron lasers at the sub-wavelength scale, allowing for the investigation of novel modes of operation. The study demonstrates that a cavity FEL can selectively lase at the third harmonic of the fundamental wavelength for small sub-wavelength cavity detunings. This opens up new possibilities for cavity-based FEL operation and further exploration of potentially useful modes.
Article
Chemistry, Multidisciplinary
Andrea Doria
Summary: The present study analyzes a hybrid free electron laser scheme that utilizes a radiation source and slow-wave guiding structure for the oscillator, inducing strong radiation emission. With proper control and design in a magnetic undulator, this effect can be achieved in the far infrared region of the spectrum.
APPLIED SCIENCES-BASEL
(2021)
Article
Chemistry, Multidisciplinary
Haiyun Dong, Chunhuan Zhang, Wu Zhou, Jiannian Yao, Yong Sheng Zhao
Summary: This study proposes a method for fabricating independent photonic structures using a differential polymer chain scission strategy. By one-step electron-beam direct writing on polymer bilayers, the direct formation of suspended optical microcavities is achieved. The technique features high materials compatibility and design flexibility, expanding the application scope of optical microcavities.
ADVANCED MATERIALS
(2022)
Article
Business
Tadhg O. Laoghaire
Summary: This paper presents a distinctive account of corporations' positive duties towards the global poor, based on the concepts of dependence and meeting core needs. It also explores the weighting of assistance claims and the limits of demands that can be placed on corporations. The author concludes by discussing a challenge related to attributing duties to the worst-off among the global poor.
JOURNAL OF BUSINESS ETHICS
(2023)
Article
Chemistry, Multidisciplinary
Xiao-Ming Jiang, Shu-Juan Lin, Chao He, Bin-Wen Liu, Guo-Cong Guo
Summary: This study explores the NLO functional motif of LiB3O5 under different laser conditions, identifying the NLO functional motif as [B3O5](-). The research extracts the NLO functional motif of a NLO material experimentally for the first time and highlights the crucial role of in situ electron density analysis in studying NLO mechanisms.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Satoshi Abe, Junko Tanaka, Mariko Kojima, Shuji Kanamaru, Kunio Hirata, Keitaro Yamashita, Ayako Kobayashi, Takafumi Ueno
Summary: The CFPC method enables direct protein crystallization without the need for protein purification, expanding the potential for high-throughput structure determination of challenging proteins. The technique has successfully been applied to crystallize and determine the structures of nano-sized polyhedra crystals and nanocrystals at high resolutions.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Takayasu Kawasaki, Koichi Tsukiyama, Phuong H. Nguyen
Summary: Amyloid fibrils, which are composed of rigid beta-sheet stacking conformation, can cause serious amyloidosis. In this study, we used infrared free electron laser (IR-FEL) irradiation to disassemble amyloid fibrils by selectively exciting the vibrational modes. By tuning the irradiation to specific wavelengths, we observed a decrease in beta-sheet abundance and an increase in alpha-helix abundance in different types of amyloid fibrils. This research suggests that IR-FEL has potential applications in amyloid research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Multidisciplinary
A. M. Kalitenko
Summary: This paper presents a technique for building a neural network to analyze parameters of free electron lasers (FELs). By collecting numerical simulation data and finding the optimal architecture, a neural network was trained to analyze multiple configurations of FELs based on undulator and electron beam parameters quickly. This technique is capable of simulating more complex systems and can be applied to facility optimization.
Article
Chemistry, Physical
Huijeong Hwang, Taehyun Kim, Hyunchae Cynn, Thomas Vogt, Rachel J. Husband, Karen Appel, Carsten Baehtz, Orianna B. Ball, Marzena A. Baron, Richard Briggs, Maxim Bykov, Elena Bykova, Valerio Cerantola, Julien Chantel, Amy L. Coleman, Dana Dattlebaum, Leora E. Dresselhaus-Marais, Jon H. Eggert, Lars Ehm, William J. Evans, Guillaume Fiquet, Mungo Frost, Konstantin Glazyrin, Alexander F. Goncharov, Zsolt Jenei, Jaeyong Kim, Zuzana Konopkova, Jona Mainberger, Mikako Makita, Hauke Marquardt, Emma E. McBride, James D. McHardy, Sebastien Merkel, Guillaume Morard, Earl F. O'Bannon, Christoph Otzen, Edward J. Pace, Alexander Pelka, Charles M. Pepin, Jeffrey S. Pigott, Vitali B. Prakapenka, Clemens Prescher, Ronald Redmer, Sergio Speziale, Georg Spiekermann, Cornelius Strohm, Blake T. Sturtevant, Nenad Velisavljevic, Max Wilke, Choong-Shik Yoo, Ulf Zastrau, Hanns-Peter Liermann, Malcolm McMahon, R. Stewart McWilliams, Yongjae Lee
Summary: The ultrafast synthesis of epsilon-Fe3N1+x from Fe and N-2 under high pressure using XFEL was observed, demonstrating the exploration of time-dependence of reactions under high-pressure conditions by coupling intense X-ray exposures with the source time structure.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Physics, Multidisciplinary
Laura Di Lucchio, Paul Gibbon
Summary: This paper determines the energy gain of attosecond electron bunches emitted during the interaction of intense, few-cycle linearly polarized lasers with nanoscale spherical clusters. An analytical model for focused light waves interacting with compact, overdense electron bunches in vacuum is derived, and compared with three-dimensional PIC simulations to determine the effective increase in bunch energy under realistic conditions.
Article
Chemistry, Multidisciplinary
Haoran Xu, Petr M. Anisimov, Bruce E. Carlsten, Leanne D. Duffy, Quinn R. Marksteiner, River R. Robles
Summary: We present a complete model of our accelerator lattice design using a laser-assisted bunch compression (LABC) scheme in an X-ray free electron laser (XFEL). The lattice utilizes a two-stage bunch compression scheme, with the first stage compressing the beam current from 20 A to 500 A at 750 MeV, and the second stage achieving compression by modulating the beam with a 1-μm wavelength laser and compressing the modulated beam into microbunches with 3-kA current spikes. The LABC architecture is based on enhanced self-amplified spontaneous emission (ESASE) scheme, but operates in different parameters.
APPLIED SCIENCES-BASEL
(2023)
Article
Chemistry, Physical
Natalia Gelfand, Francoise Remacle, Raphael D. Levine
Summary: Charge migration in LiH, LiD, and LiT molecules, including non-adiabatic effects of nuclear motions, were studied using quantum dynamics. Mass-independent charge migration was observed between the ground and first excited sigma states upon excitation by an ultrafast UV pulse. The opposite polarity of these states and a small energy gap allowed for charge oscillation within 2 fs after the pulse. A mass-dependent revival of coherence was computed with periods of 80, 107, and 123 fs for LiH, LiD, and LiT, respectively.
CHEMICAL PHYSICS LETTERS
(2023)
Article
Optics
P. Cinquegrana, A. Demidovich, G. Kurdi, I Nikolov, P. Sigalotti, P. Susnjar, M. B. Danailov
Summary: An important trend in recent years has been the use of an external laser as seeding to improve the coherence and stability of free-electron laser pulses, with high-gain harmonic generation seeding technique achieving high coherence and stability at FERMI. The seed laser also plays a crucial role in pump-probe experiments at FERMI, helping achieve record-low timing jitter.
HIGH POWER LASER SCIENCE AND ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Graeme Winter, James Beilsten-Edmands, Nicholas Devenish, Markus Gerstel, Richard J. Gildea, David McDonagh, Elena Pascal, David G. Waterman, Benjamin H. Williams, Gwyndaf Evans
Summary: The DIALS software is introduced as a toolkit for processing X-ray diffraction data, emphasizing its usage as a toolkit for data processing, with support for automated systems and command-line usage, and the ability to write new tools using the API for bespoke analysis. In addition to macromolecular X-ray crystallography, DIALS can also be applied to techniques outside of this field.
Article
Biochemistry & Molecular Biology
Matthew Herdman, Andriko von Kugelgen, Danguole Kureisaite-Ciziene, Ramona Duman, Kamel El Omari, Elspeth F. Garman, Andreas Kjaer, Dimitrios Kolokouris, Jan Lowe, Armin Wagner, Phillip J. Stansfeld, Tanmay A. M. Bharat
Summary: In this study, the role of metal ions in the formation of Caulobacter crescentus S-layer was investigated. It was found that calcium ions facilitate S-layer lattice formation and cell-surface binding, and that bound metal ions are crucial for the S-layer lattice. The positions of metal ions in the S-layer were also mapped using advanced imaging techniques. These findings contribute to the understanding of S-layer formation and have implications for synthetic biology.
Article
Biochemistry & Molecular Biology
Matthew J. Rodrigues, Nitai Giri, Antoine Royant, Yang Zhang, Rachel Bolton, Gwyndaf Evans, Steve E. Ealick, Tadhg Begley, Ivo Tews
Summary: The Pdx1 enzyme catalyzes the formation of pyridoxal 5-phosphate (PLP) through an imine relay mechanism, involving stereoselective deprotonation and substrate-assisted phosphate elimination. The I-333 intermediate, characterized by structural, UV-vis absorption spectroscopy and mass spectrometry analyses, plays a central role in PLP biosynthesis.
RSC CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Paola Lanzoni-Mangutchi, Oishik Banerji, Jason Wilson, Anna Barwinska-Sendra, Joseph A. Kirk, Filipa Vaz, Shauna O'Beirne, Arnaud Basle, Kamel El Omari, Armin Wagner, Neil F. Fairweather, Gillian R. Douce, Per A. Bullough, Robert P. Fagan, Paula S. Salgado
Summary: S-layers are two-dimensional protein arrays that cover the surface of bacteria and archaea, playing important roles in cell physiology. In this study, the crystal structure of the main S-layer protein SIpA from the bacterial pathogen Clostridioides difficile was determined, and the organization and assembly mechanism of the S-layer was studied using electron microscopy. The compact and tightly-packed array of triangular prisms in the crystal lattice mimics the assembly of the S-layer in the cell, and the flexible ridges on the surface of the array were found to be dispensable for overall structure and assembly.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Guillaume Tetreau, Michael R. Sawaya, Elke De Zitter, Elena A. Andreeva, Anne-Sophie Banneville, Natalie A. Schibrowsky, Nicolas Coquelle, Aaron S. Brewster, Marie Luise Gruenbein, 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, Frederic Laporte, Laurence Despres, Maria Bacia, Amandine Roux, Christian Chapelle, Francois Riobe, Olivier Maury, Wai Li Ling, Sebastien 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, Jacques-Philippe Colletier
Summary: In this study, the structures of two toxins produced by mosquitocidal Bacillus thuringiensis were determined using serial femtosecond crystallography. The toxins exhibit a novel in vivo crystallization pattern, which provides insights into their toxicity and potential for mosquito control.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
V. U. Chukhutsina, J. M. Baxter, A. Fadini, R. M. Morgan, M. A. Pope, K. Maghlaoui, C. M. Orr, A. Wagner, J. J. van Thor
Summary: This study provides insights into the photo-sensing mechanism of Orange Carotenoid protein (OCP), revealing the involvement of single bond isomerization and structural changes. The findings contribute to a better understanding of OCP's role in light-harvesting.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Sarah A. E. Barwell, Ramona Duman, Armin Wagner, Todd Holyoak
Summary: Phosphoenolpyruvate carboxykinase (PEPCK) is an enzyme involved in glucose metabolism, catalyzing a key step in gluconeogenesis. The preferential synthesis of phosphoenolpyruvate (PEP) from oxaloacetic acid (OAA) catalyzed by PEPCK in vivo is facilitated by anion-mediated enzyme inhibition. The binding of ubiquitous anions like chloride restricts the enzyme to function in the direction of PEP synthesis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Michael W. W. Martynowycz, Anna Shiriaeva, Max T. B. Clabbers, William J. J. Nicolas, Sara J. J. Weaver, Johan Hattne, Tamir Gonen
Summary: In this study, the authors demonstrate a method for milling vitrified biological material and collecting MicroED data for the adenosine receptor. They use an integrated fluorescence light microscope inside a focused ion beam and scanning electron microscope to identify and mill fluorescently labeled GPCR crystals. Plasma ion-beam milling is shown to be a powerful tool for preparing biological lamellae.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Jon Agirre, Mihaela Atanasova, Haroldas Bagdonas, Charles B. Ballard, Arnaud Basle, James Beilsten-Edmands, Rafael J. Borges, David G. Brown, J. Javier Burgos-Marmol, John M. Berrisford, Paul S. Bond, Iracema Caballero, Lucrezia Catapano, Grzegorz Chojnowski, Atlanta G. Cook, Kevin D. Cowtan, Tristan I. Croll, Judit E. Debreczeni, Nicholas E. Devenish, Eleanor J. Dodson, Tarik R. Drevon, Paul Emsley, Gwyndaf Evans, Phil R. Evans, Maria Fando, James Foadi, Luis Fuentes-Montero, Elspeth F. Garman, Markus Gerstel, Richard J. Gildea, Kaushik Hatti, Maarten L. Hekkelman, Philipp Heuser, Soon Wen Hoh, Michael A. Hough, Huw T. Jenkins, Elisabet Jimenez, Robbie P. Joosten, Ronan M. Keegan, Nicholas Keep, Eugene B. Krissinel, Petr Kolenko, Oleg Kovalevskiy, Victor S. Lamzin, David M. Lawson, Andrey A. Lebedev, Andrew G. W. Leslie, Bernhard Lohkamp, Fei Long, Martin Maly, Airlie J. McCoy, Stuart J. McNicholas, Ana Medina, Claudia Millan, James W. Murray, Garib N. Murshudov, Robert A. Nicholls, Martin E. M. Noble, Robert Oeffner, Navraj S. Pannu, James M. Parkhurst, Nicholas Pearce, Joana Pereira, Anastassis Perrakis, Harold R. Powell, Randy J. Read, Daniel J. Rigden, William Rochira, Massimo Sammito, Filomeno Sanchez Rodriguez, George M. Sheldrick, Kathryn L. Shelley, Felix Simkovic, Adam J. Simpkin, Pavol Skubak, Egor Sobolev, Roberto A. Steiner, Kyle Stevenson, Ivo Tews, Jens M. H. Thomas, Andrea Thorn, Josep Trivino Valls, Ville Uski, Isabel Uson, Alexei Vagin, Sameer Velankar, Melanie Vollmar, Helen Walden, David Waterman, Keith S. Wilson, Martyn D. Winn, Graeme Winter, Marcin Wojdyr, Keitaro Yamashita
Summary: The Collaborative Computational Project No. 4 (CCP4) is an international collective led by the UK, dedicated to the development, testing, distribution, and promotion of software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs, unified by familiar execution routines, common libraries, and graphical interfaces. This article serves as a general literature citation for the use of the CCP4 software suite, providing an overview of its recent changes, new features, and future developments, while also highlighting the individual programs within the suite and providing up-to-date references for crystallographers worldwide.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Jack D. Whitehead, Jonathan M. Grimes, Jeremy R. Keown
Summary: Bornaviruses are RNA viruses that infect a wide range of hosts including mammals, reptiles, and birds. This study presents the structure of the oligomerization domain of the phosphoprotein, which is an important component of the bornavirus replication complex. The findings provide valuable insights into the assembly process of the phosphoprotein and its role in viral replication.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
James M. Parkhurst, Adam D. Crawshaw, C. Alistair Siebert, Maud Dumoux, C. David Owen, Pedro Nunes, David Waterman, Thomas Glen, David I. Stuart, James H. Naismith, Gwyndaf Evans
Summary: Three-dimensional electron diffraction from nanocrystals of biological macromolecules requires the use of very small crystals, typically less than 300 nm-thick. Focused-ion-beam milling has been used to prepare thin samples for this purpose, but little work has been done to quantify the damage caused to delicate biological samples. This study analyzed the effect of plasma FIB milling on lysozyme crystals and compared argon and xenon plasmas with a gallium source. The results showed an upper bound and a lower bound for the depth of the milling damage layer.
Article
Chemistry, Multidisciplinary
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, Michael C. Thompson
Summary: Understanding and controlling protein motion at atomic resolution is a challenge in structural biology. In this study, the combination of solvent-based temperature jump and time-resolved crystallography was used to observe structural motions in lysozyme. Inhibitor binding altered the dynamics by blocking key motions in the enzyme.
Article
Multidisciplinary Sciences
Hugo Lebrette, Vivek Srinivas, Juliane John, Oskar Aurelius, Rohit Kumar, Daniel Lundin, Aaron S. Brewster, Asmit Bhowmick, Abhishek Sirohiwal, In-Sik Kim, Sheraz Gul, Cindy Pham, Kyle D. Sutherlin, Philipp Simon, Agata Butryn, Pierre Aller, Allen M. Orville, Franklin D. Fuller, Roberto Alonso-Mori, Alexander Batyuk, Nicholas K. Sauter, Vittal K. Yachandra, Junko Yano, Ville R. I. Kaila, Britt-Marie Sjoberg, Jan Kern, Katarina Roos, Martin Hogbom
Summary: This study presents a high-resolution room temperature structure of the class Ie R2 protein radical in RNR, revealing conformational reorganization and restructuring of the hydrogen bond network. These findings help explain radical handling and transfer mechanisms in RNR and have implications for radical transfer in proteins more generally.
Article
Multidisciplinary Sciences
Jeremy R. R. Keown, Adam D. D. Crawshaw, Jose Trincao, Loic Carrique, Richard J. J. Gildea, Sam Horrell, Anna J. J. Warren, Danny Axford, Robin Owen, Gwyndaf Evans, Annie Bezier, Peter Metcalf, Jonathan M. M. Grimes
Summary: Infectious protein crystals called occlusion bodies or polyhedra are crucial for the viral lifecycle of certain insect viruses. A study reveals the structure of a polyhedrin from the Nudiviridae family, which was previously thought to lack occlusion bodies. The findings show that the nudivirus occlusion body has a distinct protein structure but shares common principles with occlusion bodies from other viruses.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Max T. B. Clabbers, Michael W. Martynowycz, Johan Hattne, Tamir Gonen
Summary: Microcrystal electron diffraction (MicroED) is a powerful technique for protein structure determination. Recent studies have shown that with high-resolution MicroED data, it is possible to accurately identify over a third of hydrogen atom positions and visualize hydrogen bonding interactions and the charged states of residues.
JOURNAL OF STRUCTURAL BIOLOGY-X
(2022)
