Article
Crystallography
Fiacre Kabayiza, Sarah B. Woodruff, William J. Bauer
Summary: Gamification in education has been proven to be an effective strategy for engaging learners and increasing their interest and knowledge in complex and advanced fields. The XFEL Crystal Blaster game provides a simple and accessible platform for middle and high school students to learn about XFELs and X-ray crystallography, and enhances their interest in these fields.
Article
Computer Science, Theory & Methods
Paul Scheffler, Florian Zaruba, Fabian Schuiki, Torsten Hoefler, Luca Benini
Summary: Sparse linear algebra is important in many application domains, but it is challenging to handle efficiently. In this research, an existing memory-streaming RISC-V ISA extension was enhanced to accelerate the operations of sparse tensors, achieving higher speedups and efficiency.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2023)
Article
Mathematics, Applied
Erin Carson, Noaman Khan
Summary: This paper investigates the use of sparse approximate inverse preconditioners in GMRES iterative refinement and analyzes the computation of sparse approximate inverses and the constraints for achieving user-specified stopping criteria. It also analyzes the behavior and convergence constraints of a five-precision GMRES-based iterative refinement scheme that uses sparse approximate inverse preconditioning, called SPAI-GMRES-IR. The numerical experiments confirm the theoretical analysis and illustrate the tradeoffs between preconditioner sparsity and GMRES-IR convergence rate.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2023)
Article
Mathematics, Applied
Zhenyue Zhang, Zheng Zhai, Limin Li
Summary: This research proposes a novel method, called Simultaneously Low-rank and Sparse Approximation (SLSA), for graph refinement by imposing strict sparse and low-rank assumptions on the underlying group structures. Experimental results show that SLSA performs better than other methods on both synthetic and real-world data sets.
SIAM JOURNAL ON SCIENTIFIC COMPUTING
(2022)
Article
Multidisciplinary Sciences
Stefano Maffessanti, Karsten Hansen, Stefan Aschauer, Andrea Castoldi, Florian Erdinger, Carlo Fiorini, Peter Fischer, Pradeep Kalavakuru, Helmut Klaer, Massimo Manghisoni, Christian Reckleben, Lothar Strueder, Matteo Porro
Summary: This paper summarizes the functionality and properties of the 64k pixel DEPFET module, a key sensitive component of the DEPFET Sensor with Signal Compression (DSSC) used for capturing and measuring soft X-rays at the European XFEL. The module features low input capacitance and signal compression capability, and has been calibrated and evaluated in a laboratory testbench. The pixel sensors provide excellent energy resolution and can meet the specifications of the DSSC project.
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Information Systems
Paul Burkhardt
Summary: The popularity of algebraic methods for graph algorithms has increased due to the development of the GraphBLAS library and other sparse matrix methods. Researchers have introduced a new optimal algebraic BFS algorithm for sparse graphs, achieving significant improvements and addressing a gap in existing literature.
ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA
(2021)
Article
Chemistry, Multidisciplinary
Mariya Aleksich, Daniel W. Paley, Elyse A. Schriber, Will Linthicum, Vanessa Oklejas, David W. Mittan-Moreau, Ryan P. Kelly, Patience A. Kotei, Anita Ghodsi, Raymond G. Sierra, Andrew Aquila, Freideiric Poitevin, Johannes P. Blaschke, Mohammad Vakili, Christopher J. Milne, Fabio Dall'Antonia, Dmitry Khakhulin, Fernando Ardana-Lamas, Frederico Lima, Joana Valerio, Huijong Han, Tamires Gallo, Hazem Yousef, Oleksii Turkot, Ivette J. Bermudez J. Macias, Thomas Kluyver, Philipp Schmidt, Luca Gelisio, Adam R. Round, Yifeng Jiang, Doriana Vinci, Yohei Uemura, Marco Kloos, Mark Hunter, Adrian P. Mancuso, Bryan D. Huey, Lucas R. Parent, Nicholas K. Sauter, Aaron S. Brewster, J. Nathan Hohman
Summary: In this study, smSFX method was used to successfully characterize the structure of silver n-alkanethiolates at atomic resolution, resolving long-standing controversies regarding atomic connectivity and odd-even effects of layer stacking. This method allows for high-quality crystal structures directly from the powder of unknown samples, which is particularly useful for systems with small or defective crystals.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Computer Science, Hardware & Architecture
Chao Zhang, Maximilian Bremer, C. Y. Chan, John Shalf, Xiaochen Guo
Summary: Sparse linear algebra is crucial in many applications. The column-wise SpGEMM algorithm has good locality but the sparse accumulation (SPA) step remains a performance bottleneck. This work proposes the ASA architecture to overcome the challenges of SPA and achieves significant speedup.
ACM TRANSACTIONS ON ARCHITECTURE AND CODE OPTIMIZATION
(2022)
Article
Chemistry, Multidisciplinary
Intae Eom, Sae Hwan Chun, Jae Hyuk Lee, Daewoong Nam, Rory Ma, Jaehyun Park, Sehan Park, Sang Han Park, Haeryong Yang, Inhyuk Nam, Myung Hoon Cho, Chi Hyun Shim, Gyujin Kim, Chang-Ki Min, Hoon Heo, Heung-Sik Kang, Changbum Kim
Summary: Since its opening to users in 2017, the X-ray free-electron laser (PAL-XFEL) at the Pohang Accelerator Laboratory has made significant progress in operation and beamline experiments. The PAL-XFEL has achieved increased pulse and photon energy, self-seeding FEL generation, and trials of two-color operation, resulting in excellent scientific results through efficient user experiments.
APPLIED SCIENCES-BASEL
(2022)
Article
Engineering, Multidisciplinary
Peng Wenju, Xiao Yongshun
Summary: X-ray computed tomography (CT) is a common technique in non-destructive testing and an important method in dimensional measurement. This paper proposes a method for simultaneous measurement of geometric errors based on a priori information, which can achieve a high level of accuracy in sparse view projections.
MEASUREMENT SCIENCE AND TECHNOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Mawussi Zounon, Nicholas J. Higham, Craig Lucas, Francoise Tisseur
Summary: Reduced precision arithmetic is commonly used to speed up the solution of dense linear systems, but its efficiency in parallel solvers for sparse linear systems remains unclear. Single precision arithmetic can provide performance benefits in some cases when solving double precision sparse linear systems using multiple cores, but may not be suitable for all problems.
PEERJ COMPUTER SCIENCE
(2022)
Review
Optics
Tetsuya Ishikawa
Summary: The SACLA is a small-scale, low-cost X-ray free-electron laser that generates coherent light in the wavelength region of 0.1 nm. It was constructed after a period of slow progress and became the second light source in this wavelength region, following the LCLS in the United States. This paper reviews the history of SACLA and describes the preparatory stage and construction/commissioning of SACLA.
Article
Engineering, Electrical & Electronic
Kun Li, Yujie Wang, Xinchen Ye, Chenggang Yan, Jingyu Yang
Summary: This paper proposes an intrinsic decomposition method from a single RGB-D image, utilizing sparsity term regularization and bilateral kernel to address the ill-conditioned problem. The proposed method outperforms state-of-the-art methods and can integrate existing depth estimation methods.
SIGNAL PROCESSING-IMAGE COMMUNICATION
(2021)
Review
Chemistry, Multidisciplinary
Sarah Milliken, Alyxandra N. Thiessen, I. Teng Cheong, Kevin M. O'Connor, Ziqi Li, Riley W. Hooper, Christopher Jay T. Robidillo, Jonathan G. C. Veinot
Summary: Preparation of silicon nanoparticles presents challenges in determining size, crystallinity, composition, and surface chemistry, with controlling these parameters essential for realizing their full potential in areas such as alternative energy, sensors, and medical imaging. Numerous teams have explored innovative synthesis methods and surface functionalization protocols, while substantial effort has been made to understand how these parameters influence material properties. Opportunities for future studies on silicon nanoparticles are highlighted, including tailoring optical and electronic properties through structure and composition definition.
Review
Physics, Multidisciplinary
R. Xiang, A. Arnold, J. W. Lewellen
Summary: A dependable and consistent electron source is crucial for high-power free electron lasers (FELs). Over the past two decades, photoinjectors based on SRF technology (SRF guns) have shown promise for continuous wave (CW) beam generation. SRF guns combine high accelerating field gradients with low power dissipation, making them suitable for high-brightness, high-current beams required for CW-XFELs. This paper provides an overview of design concepts, important parameters, and the development status of worldwide SRF gun projects.
FRONTIERS IN PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Kaitlyn Tsai, Vanja Stojkovic, D. John Lee, Iris D. Young, Teresa Szal, Dorota Klepacki, Nora Vazquez-Laslop, Alexander S. Mankin, James S. Fraser, Danica Galonic Fujimori
Summary: Linezolid and radezolid are oxazolidinone antibiotics that inhibit bacterial ribosome translation by binding to the peptidyl transferase center in a context-specific manner, leading to stalling when alanine occupies the penultimate position in the nascent chain.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
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 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
Biochemical Research Methods
Richard J. Gildea, James Beilsten-Edmands, Danny Axford, Sam Horrell, Pierre Aller, James Sandy, Juan Sanchez-Weatherby, C. David Owen, Petra Lukacik, Claire Strain-Damerell, Robin L. Owen, Martin A. Walsh, Graeme Winter
Summary: In macromolecular crystallography, data collection from a single crystal is limited by radiation damage. Thus, merging data sets from multiple crystals is necessary. A new program called xia2.multiplex has been developed to facilitate the scaling and merging of multi-crystal data sets, including symmetry analysis and analysis of factors affecting data quality.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Quantum Science & Technology
Trevor Vincent, Lee J. O'Riordan, Mikhail Andrenkov, Jack Brown, Nathan Killoran, Haoyu Qi, Ish Dhand
Summary: We introduce Jet, a new open-source software library that employs task-based parallelism to accelerate classical tensor-network simulations of quantum circuits. The provided speed-ups come from the increased parallelism introduced by mapping the tensor-network simulation to a task-based framework, the novel method of reusing shared work between tensor network contraction tasks, and the concurrent contraction of tensor networks on all available hardware. Benchmarking results against other simulators and theoretical performance estimates for various circuits are provided.
Article
Chemistry, Multidisciplinary
Tarik R. Drevon, David G. Waterman, Eugene Krissinel
Summary: In this paper, the exact solution to the scattering of high-energy electrons by a regular array of light atoms is obtained using the T-matrix formalism. The validity of the forward scattering approximation and the phase grating approximation is discussed, and a new interpretation of multiple scattering is proposed and compared with existing interpretations.
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(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
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
Quantum Science & Technology
Angus Lowe, Matija Medvidovic, Anthony Hayes, Lee J. O'Riordan, Thomas R. Bromley, Juan Miguel Arrazola, Nathan Killoran
Summary: We propose a method to expand a quantum computation by adding random measure-and-prepare channels, enabling large circuits to be expressed as separable states across multiple devices. Our method utilizes randomized measurements with a sample overhead of Oe(4k/s2), where s is the accuracy and k is the number of parallel wires cut to obtain smaller sub-circuits. We demonstrate that circuits in QAOA with p entangling layers can be simulated with an overhead of roughly 2O(ptc) using a fraction of the original qubits' number.
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
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)
Meeting Abstract
Biochemistry & Molecular Biology
Alexander Wolff, Eriko Nango, Iris Young, Aaron Brewster, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Raymond Sierra, Fumiaki Yumoto, Kensuke Tono, So Iwata, Nicholas Sauter, James Fraser, Michael Thompson
Meeting Abstract
Biophysics
Iris D. Young, James S. Fraser
BIOPHYSICAL JOURNAL
(2022)