Article
Chemistry, Multidisciplinary
Hoyoung Jang, Hiroki Ueda, Hyeong-Do Kim, Minseok Kim, Kwang Woo Shin, Kee Hoon Kim, Sang-Youn Park, Hee Jun Shin, Pavel Borisov, Matthew J. Rosseinsky, Dogeun Jang, Hyeongi Choi, Intae Eom, Urs Staub, Sae Hwan Chun
Summary: Ultrafast optical manipulation of magnetic phenomena expands our knowledge of functional nonequilibrium states and reveals the creation mechanism of nonthermal effective magnetic fields. The study demonstrates the impact of photoexcitation on ultrafast field formation through 3D trajectory analysis of AFM magnons, and also shows the photomagnetic coupling control of ferroelectricity in multiferroics.
ADVANCED MATERIALS
(2023)
Article
Optics
Yin Kang, Zhen Wang, Kaiqing Zhang, Chao Feng
Summary: A novel X-ray free-electron laser based light source is proposed in this paper to generate synchronized high-powered X-ray and tunable coherent THz pulses. The technique utilizes a frequency beating laser modulated electron bunch to produce X-ray and THz pulses in two different undulator sections. The results show that the technique can generate synchronized 4 nm X-ray radiation with a peak power of 1.89 GW and narrow-band THz radiation with a pulse energy of 1.62 mJ, with tunable frequency from 0.1 to 40 THz. This technique can be used for dynamic research on the interaction between THz pulses and matter on a femtosecond time scale.
Article
Chemistry, Multidisciplinary
Sungwon Kim, Youngsam Kim, Jaeseung Kim, Sungwook Choi, Kyuseok Yun, Dongjin Kim, Soo Yeon Lim, Sunam Kim, Sae Hwan Chun, Jaeku Park, Intae Eom, Kyung Sook Kim, Tae-Yeong Koo, Yunbo Ou, Ferhat Katmis, Haidan Wen, Anthony DiChiara, Donald A. Walko, Eric C. Landahl, Hyeonsik Cheong, Eunji Sim, Jagadeesh Moodera, Hyunjung Kim
Summary: Our study on ultrafast carrier-induced lattice contractions and interlayer modulations in Bi2Se3 thin films sheds light on the topological phase control by light-induced structural change on ultrafast time scales. The lattice contraction depends on carrier concentration and is followed by interlayer expansion, providing insights into topological phase transition modulation.
Article
Chemistry, Multidisciplinary
Keondo Lee, Donghyeon Lee, Sangwon Baek, Jihan Kim, Jaehyun Park, Sang Jae Lee, Sehan Park, Jangwoo Kim, Jong-Lam Lee, Wan Kyun Chung, Yunje Cho, Ki Hyun Nam
Summary: This study investigated the radiation damage caused by an XFEL to PDMS and PI materials, commonly used in sample delivery devices. The results showed different structural damages in PDMS and PI films, providing insights for developing applications of these materials in XFEL studies.
APPLIED SCIENCES-BASEL
(2022)
Article
Nuclear Science & Technology
Jia-Dong Fan, Ya-Jun Tong, Yong-Gan Nie, Zi-Chen Gao, Bo He, Hui Luan, Dong-Hao Lu, Jian-Hua Zhang, Di-Fei Zhang, Xin-Ye Yuan, Jia-Hua Chen, Zhi Guo, Tao Liu, Meng Zhang, Chao Feng, Hai-Xiao Deng, Bo Liu, Zhen-Tang Zhao, Zhi Liu, Huai-Dong Jiang
Summary: The Shanghai soft X-ray free-electron laser (SXFEL) user facility project aims to deliver ultra-intense coherent femtosecond X-ray pulses for ultrafast X-ray science. The first commissioned endstation, coherent scattering and imaging (CSI), focuses on high-resolution single-shot imaging and the study of ultrafast dynamic processes. Results show excellent coherence and high peak power of the SXFEL.
NUCLEAR SCIENCE AND TECHNIQUES
(2022)
Editorial Material
Pharmacology & Pharmacy
Eric Hovestreydt
Summary: Electron Diffraction (ED) is being increasingly used in science and industry, particularly in the fields of chemical, pharmaceutical, and advanced materials research. Applying ED for nanocrystallography is a disruptive innovation that offers fascinating new perspectives for organic compounds.
DRUG DISCOVERY TODAY
(2022)
Article
Chemistry, Multidisciplinary
Dan Pan, Jiadong Fan, Zhenzhen Nie, Zhibin Sun, Jianhua Zhang, Yajun Tong, Bo He, Changyong Song, Yoshiki Kohmura, Makina Yabashi, Tetsuya Ishikawa, Yuequan Shen, Huaidong Jiang
Summary: This article introduces a clustering algorithm named ConvRe based on deep learning, which is used to accurately reconstruct images of biomaterials from noisy diffraction patterns. Through CDI experiments and application of different radiation doses, the impact of X-ray radiation on mitochondrial structure was investigated.
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
Materials Science, Multidisciplinary
Argha Dutta, Apu Sarkar, P. Mukherjee, N. Gayathri, Santu Dey, S. Neogy, Archna Sagdeo
Summary: The microstructural evolution and mechanical property changes of proton irradiated Nb-1Zr-0.1C alloy were studied as a function of irradiation dose. It was observed that dislocation density increased and saturated at the highest dose, while the hardness of the alloy increased continuously with dose. The findings suggest that alloying additions, especially carbon, play a significant role in governing the irradiation behavior of the alloy.
JOURNAL OF NUCLEAR MATERIALS
(2021)
Article
Optics
Inhyuk Nam, Chang-Ki Min, Bonggi Oh, Gyujin Kim, Donghyun Na, Young Jin Suh, Haeryong Yang, Myung Hoon Cho, Changbum Kim, Min-Jae Kim, Chi Hyun Shim, Jun Ho Ko, Hoon Heo, Jaehyun Park, Jangwoo Kim, Sehan Park, Gisu Park, Seonghan Kim, Sae Hwan Chun, HyoJung Hyun, Jae Hyuk Lee, Kyung Sook Kim, Intae Eom, Seungyu Rah, Deming Shu, Kwang-Je Kim, Sergey Terentyev, Vladimir Blank, Yuri Shvyd'ko, Sang Jae Lee, Heung-Sik Kang
Summary: The hard X-ray self-seeded X-ray free-electron laser at the Pohang Accelerator Laboratory offers high peak brightness and stability, providing superior data quality compared to SASE mode.
Article
Chemistry, Multidisciplinary
Linda Young, Emily T. Nienhuis, Dimitris Koulentianos, Gilles Doumy, Anne Marie March, Stephen H. Southworth, Sue B. Clark, Thomas M. Orlando, Jay A. LaVerne, Carolyn I. Pearce
Summary: Understanding the origin of reactive species following ionization in aqueous systems is crucial for studying radiation-matter interactions. Tunable ultrafast X-ray free-electron pulses provide a new window to probe events occurring on the sub-picosecond timescale, aiding in capturing chemical processes with better time resolution. Ultimately, these methods can be applied to understanding radiation effects in complex aqueous solutions.
APPLIED SCIENCES-BASEL
(2021)
Article
Physics, Multidisciplinary
Xiaofan Wang, Chao Feng, Bart Faatz, Weiqing Zhang, Zhentang Zhao
Summary: This paper presents a novel technique that utilizes a long modulator as a platform for laser amplification and electron modulation, reducing the required seed laser power and increasing the repetition rate of a seeded FEL. Simulation results demonstrate that this technique enables the realization of fully coherent EUV and soft x-ray FELs with a repetition rate of MHz and an average power of about 100 W.
NEW JOURNAL OF PHYSICS
(2022)
Article
Multidisciplinary Sciences
Marie Luise Grunbein, Alexander Gorel, Lutz Foucar, Sergio Carbajo, William Colocho, Sasha Gilevich, Elisabeth Hartmann, Mario Hilpert, Mark Hunter, Marco Kloos, Jason E. Koglin, Thomas J. Lane, Jim Lewandowski, Alberto Lutman, Karol Nass, Gabriela Nass Kovacs, Christopher M. Roome, John Sheppard, Robert L. Shoeman, Miriam Stricker, Tim van Driel, Sharon Vetter, R. Bruce Doak, Sebastien Boutet, Andrew Aquila, Franz Josef Decker, Thomas R. M. Barends, Claudiu Andrei Stan, Ilme Schlichting
Summary: X-ray free-electron lasers (XFELs) enable novel insights in structural biology, but challenges arise in time-resolved crystallography experiments due to possible sample damage. Authors performed an experiment mimicking the 4.5MHz data collection mode and observed structural changes and decreased diffraction data quality in crystals.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Adham Aleid, Khalid Alhussaini, Mohammad Nisar
Summary: This study investigated the impact of varying positions of different materials in an X-ray target on its coherent scatter pattern using the scatter imaging technique. The results showed that the position of materials affects the scatter patterns, and the coherent scatter imaging technique can be used to determine the position of materials in composite targets.
RADIATION PHYSICS AND CHEMISTRY
(2023)
Article
Optics
Peco Myint, Miaoqi Chu, Ashish Tripathi, Michael J. Wojcik, JIan Zhou, Mathew J. Cherukara, Suresh Narayanan, Jin Wang, Zhang Jiang
Summary: Surface-sensitive reflection-geometry scattering techniques, such as grazing incident small angle X-ray scattering, are commonly used to study nanostructures on substrates and provide statistical structural information. Coherent surface scattering imaging (CSSI) is a powerful yet non-invasive technique that can probe the absolute three-dimensional structural morphology of the sample. However, conventional CDI reconstruction techniques cannot be directly applied to CSSI due to the dynamical scattering phenomenon near the critical angle of total external reflection. To overcome this, a multislice forward model was developed to simulate the dynamical scattering from surface structures and the underlying substrate, enabling the reconstruction of an elongated 3D pattern from a single shot scattering image in CSSI geometry.
Article
Chemistry, Physical
Ibrahim Eliah Dawod, Nicusor Timneanu, Adrian P. Mancuso, Carl Caleman, Oscar Granas
Summary: X-ray free-electrons lasers have revolutionized imaging biological macromolecules by allowing structural determination of single particles and crystals at room temperature with reduced radiation damage effects. Understanding how radiation damage affects atomic-scale structure is crucial for accurate reconstruction in the presence of damage.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Monika Balint, Balazs Zoltan Zsido, David van der Spoel, Csaba Hetenyi
Summary: The human genome only contains a limited number of druggable proteins, but there is still potential for discovering new drug-binding mechanisms and modes. A new method called NetBinder is introduced in this study for the systematic identification and classification of prerequisite binding sites at atomic resolution. NetBinder is validated using the binding mechanism of blebbistatin to myosin 2, and it shows excellent agreement with experimentally determined binding sites and structural changes. NetBinder provides a new paradigm for drug design by elucidating binding mechanisms at an atomic resolution using a networking framework.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Kara A. Zielinski, Andreas Prester, Hina Andaleeb, Soi Bui, Oleksandr Yefanov, Lucrezia Catapano, Alessandra Henkel, Max O. Wiedorn, Olga Lorbeer, Eva Crosas, Jan Meyer, Valerio Mariani, Martin Domaracky, Thomas A. White, Holger Fleckenstein, Iosifina Sarrou, Nadine Werner, Christian Betzel, Holger Rohde, Martin Aepfelbacher, Henry N. Chapman, Markus Perbandt, Roberto A. Steiner, Dominik Oberthuer
Summary: Serial crystallography at conventional synchrotron light sources allows for routine data collection at room temperature, but currently takes longer than cryo-crystallography. This study demonstrates the potential for high-throughput SSX using a sample delivery system, collecting complete datasets in less than a minute with minimal sample requirements.
Article
Chemistry, Medicinal
Kristian Kriz, Lisa Schmidt, Alfred T. Andersson, Marie-Madeleine Walz, David van der Spoel
Summary: Force fields (FFs) for molecular simulation have been developed for more than half a century. The availability of standardized data sets and benchmarks is crucial for rigorous testing and comparisons of FF models. Currently, there are limited benchmarks for evaluating FFs, and development teams mostly rely on their own sets. This article discusses the potential reuse of quantum chemistry benchmarks for evaluating FFs, the need for new data, and the importance of utilizing experimental data in automated tools for condensed phases.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Alireza Sadri, Marjan Hadian-Jazi, Oleksandr Yefanov, Marina Galchenkova, Henry Kirkwood, Grant Mills, Marcin Sikorski, Romain Letrun, Raphael de Wijn, Mohammad Vakili, Dominik Oberthuer, Dana Komadina, Wolfgang Brehm, Adrian P. Mancuso, Jerome Carnis, Luca Gelisio, Henry N. Chapman
Summary: This paper introduces a methodology and program based on machine learning for generating bad-pixel masks for large-area X-ray pixel detectors. By analyzing routine measurements, the method discriminates normal pixels from abnormal ones and improves the performance of peak finders with a new mask generator.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2022)
Article
Chemistry, Physical
Malin Lueking, David van der Spoel, Johan Elf, Gareth A. A. Tribello
Summary: There are difficult problems in biochemistry that are challenging to study experimentally, but simulation methods provide a direct way to obtain atomic coordinates over time. However, molecular simulations face challenges in system size and time scales. Enhanced sampling algorithms can potentially overcome these limitations. This paper discusses a problem in biochemistry that serves as a benchmark for comparing machine learning approaches, focusing on the transitions of LacI between non-specific and specific DNA binding states.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
A. Najla Hosseini, David van der Spoel
Summary: There is a lack of effective treatment for amyloid diseases due to limited understanding of amyloid formation. Therefore, fundamental research at the molecular level is needed to support drug development.
Article
Chemistry, Multidisciplinary
Wolfgang Brehm, Thomas White, Henry N. Chapman
Summary: The recent diversification of macromolecular crystallographic experiments has exposed the limitations of using the Laue equations for diffraction prediction. This article presents a computationally efficient method for calculating approximate crystal diffraction patterns based on different distributions of the incoming beam, crystal shapes, and other hidden parameters. The method models each pixel of a diffraction pattern, improving data processing by enabling the correction of partially recorded reflections. By expressing distributions as weighted sums of Gaussian functions, the approach reduces the number of patterns needed for refining a structure to a given error.
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2023)
Article
Chemistry, Multidisciplinary
Alessandra Henkel, Marina Galchenkova, Julia Maracke, Oleksandr Yefanov, Bjarne Klopprogge, Johanna Hakanpaa, Jeroen R. Mesters, Henry N. Chapman, Dominik Oberthuer
Summary: Macromolecular crystallography is a well-established method in structural biology but is now being developed to investigate protein dynamics through time-resolved methods. This study presents a novel one-step process called JINXED that combines protein crystallization and data collection, avoiding the need for multiple handling steps and potentially enabling time-resolved experiments with crystals containing small solvent channels.
Editorial Material
Chemistry, Multidisciplinary
Henry N. Chapman
Article
Crystallography
Marina Galchenkova, Aida Rahmani Mashhour, Patrick Y. A. Reinke, Sebastian Guenther, Jan Meyer, Henry N. Chapman, Oleksandr M. Yefanov
Summary: Serial crystallography is a rapidly developing method for determining the structure of biomolecules at near-atomic resolution. This paper proposes a strategy to optimize beamtime utilization in serial crystallography experiments, which involves fast scanning of the chip to determine crystal positions and excluding empty positions during data acquisition, resulting in significant savings in beamtime utilization and reduced data volume.
Article
Chemistry, Physical
Lisa Schmidt, David van der Spoel, Marie-Madeleine Walz
Summary: A profound understanding of the physicochemical properties of organic crystals is crucial for various fields, including material science and drug discovery. Molecular dynamics simulations using accurate force fields can provide valuable insights into the structure, dynamics, and thermodynamic properties of materials, including liquids and biomolecules. In this study, the popular AMBER force field was used to investigate the properties of 30 organic crystals, including solid-solid and solid-liquid phase transitions. The results suggest the presence of a phase transition from an ordered to a plastic crystal in many compounds, and the molecular dynamics simulations offer an explanation for the properties of the plastic crystal phase.
ACS PHYSICAL CHEMISTRY AU
(2023)
Article
Physics, Fluids & Plasmas
Sebastian Cardoch, Fabian Trost, Howard A. Scott, Henry N. Chapman, Carl Caleman, Nicusor Timneanu
Summary: Saturable absorption is a nonlinear effect that hinders a material's ability to absorb light due to a high influx of photons and the creation of electron vacancies. This computational study investigates the interaction between femtosecond x rays and copper using nonlocal thermodynamic equilibrium plasma simulations. The results show that copper's saturable absorption reduces the temporal duration of transmitted x-ray laser pulses and leads to changes in opacity and the emergence of resonances. The authors also propose the use of fluorescence induced by the incident beam as an alternative source for achieving shorter x-ray pulses.
Article
Chemistry, Physical
Pamela H. W. Svensson, Lucas Schwob, Oscar Granaes, Isaak Unger, Olle Bjoerneholm, Nicusor Timneanu, Rebecka Lindblad, Anna-Lydia Vieli, Vicente Zamudio-Bayer, Martin Timm, Konstantin Hirsch, Carl Caleman, Marta Berholts
Summary: The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. The experimental results are explained using theoretical simulations based on density functional theory, providing important insights into the properties of these compounds.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
