1
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Schultze S, Grubmüller H. Bayesian electron density determination from sparse and noisy single-molecule X-ray scattering images. SCIENCE ADVANCES 2024; 10:eadp4425. [PMID: 39454013 PMCID: PMC11506165 DOI: 10.1126/sciadv.adp4425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 09/16/2024] [Indexed: 10/27/2024]
Abstract
Single molecule x-ray scattering experiments using free-electron lasers hold the potential to resolve biomolecular structures and structural ensembles. However, molecular electron density determination has so far not been achieved because of low photon counts, high noise levels, and low hit rates. Most approaches therefore focus on large specimen like entire viruses, which scatter sufficiently many photons to allow orientation determination of each image. Small specimens like proteins, however, scatter too few photons for the molecular orientations to be determined. Here, we present a rigorous Bayesian approach to overcome these limitations, additionally taking into account intensity fluctuations, beam polarization, irregular detector shapes, incoherent scattering, and background scattering. We demonstrate using synthetic scattering images that electron density determination of small proteins is possible in this extreme high noise Poisson regime. Tests on published virus data achieved the detector-limited resolution of 9 nm, using only 0.01% of the available photons per image.
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Affiliation(s)
- Steffen Schultze
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Germany
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2
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Yang Y, Hu X, Wu L, Wang Z, Li X, Zhou S, Wang Z, Guo F, He L, Luo S, Zhang D, Wang J, Chen X, Wu Y, Wang C, Ding D. Extraction of Molecular-Frame Electron-Ion Differential Scattering Cross Sections Based on Elliptical Laser-Induced Electron Diffraction. PHYSICAL REVIEW LETTERS 2024; 133:113203. [PMID: 39331986 DOI: 10.1103/physrevlett.133.113203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/08/2024] [Accepted: 08/06/2024] [Indexed: 09/29/2024]
Abstract
We extracted the molecular-frame elastic differential cross sections (MFDCSs) for electrons scattering from N_{2}^{+} based on elliptical laser-induced electron diffraction (ELIED), wherein the structural evolution is initialized by the same tunneling ionization and probed by incident angle-resolved laser-induced electron diffraction imaging. To establish ELIED, an intuitive interpretation of the ellipticity-dependent rescattering electron momentum distributions was first provided by analyzing the transverse momentum distribution. It was shown that the incident angle of the laser-induced returning electrons could be tuned within 20° by varying the ellipticity and handedness of the driving laser pulses. Accordingly, the incident angle-resolved DCSs of returning electrons for spherically symmetric targets (Xe^{+} and Ar^{+}) were successfully extracted as a proof-of-principle for ELIED. The MFDCSs for N_{2}^{+} were experimentally obtained at incident angles of 4° and 7°, which were well reproduced by the simulations. The ELIED approach is the only successful method so far for obtaining incident angle-resolved ionic MFDCS, which provides a new sensitive observable for the transient structure retrieval of N_{2}^{+}. Our results suggest that the ELIED has the potential to extract the structural tomographic information of polyatomic molecules with femtosecond and subangstrom spatiotemporal resolutions that can enable the visualization of the nuclear motions in complex chemical reactions as well as chiral recognition.
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3
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Jiao Z, Geng Z, Ding W. A predicted model-aided one-step classification-multireconstruction algorithm for X-ray free-electron laser single-particle imaging. IUCRJ 2024; 11:891-900. [PMID: 39194258 PMCID: PMC11364030 DOI: 10.1107/s2052252524007851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024]
Abstract
Ultrafast, high-intensity X-ray free-electron lasers can perform diffraction imaging of single protein molecules. Various algorithms have been developed to determine the orientation of each single-particle diffraction pattern and reconstruct the 3D diffraction intensity. Most of these algorithms rely on the premise that all diffraction patterns originate from identical protein molecules. However, in actual experiments, diffraction patterns from multiple different molecules may be collected simultaneously. Here, we propose a predicted model-aided one-step classification-multireconstruction algorithm that can handle mixed diffraction patterns from various molecules. The algorithm uses predicted structures of different protein molecules as templates to classify diffraction patterns based on correlation coefficients and determines orientations using a correlation maximization method. Tests on simulated data demonstrated high accuracy and efficiency in classification and reconstruction.
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Affiliation(s)
- Zhichao Jiao
- Laboratory of Soft Matter Physics, Institute of PhysicsChinese Academy of SciencesBeijing100190People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Zhi Geng
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Wei Ding
- Laboratory of Soft Matter Physics, Institute of PhysicsChinese Academy of SciencesBeijing100190People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
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4
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Moon J, Lee Y, Ihee H. Time-resolved serial femtosecond crystallography for investigating structural dynamics of chemical systems. Chem Commun (Camb) 2024; 60:9472-9482. [PMID: 39118495 DOI: 10.1039/d4cc03185g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Time-resolved serial femtosecond crystallography (TR-SFX) has emerged as a crucial tool for studying the structural dynamics of proteins. In principle, TR-SFX has the potential to be a powerful tool not only for studying proteins but also for investigating chemical reactions. However, non-protein systems generally face challenges in indexing due to sparse Bragg spots and encounter difficulties in effectively exciting target molecules. Nevertheless, successful TR-SFX studies on chemical systems have been recently reported in a few instances, boding well for the application of TR-SFX to study chemical reactions in the future. In this context, we review the static SFX and TR-SFX studies conducted on chemical systems reported to date and suggest prospects for future research directions.
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Affiliation(s)
- Jungho Moon
- Center for Advanced Reaction Dynamics (CARD), Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Yunbeom Lee
- Center for Advanced Reaction Dynamics (CARD), Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Hyotcherl Ihee
- Center for Advanced Reaction Dynamics (CARD), Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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5
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Jiao Z, He Y, Fu X, Zhang X, Geng Z, Ding W. A predicted model-aided reconstruction algorithm for X-ray free-electron laser single-particle imaging. IUCRJ 2024; 11:602-619. [PMID: 38904548 PMCID: PMC11220885 DOI: 10.1107/s2052252524004858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Ultra-intense, ultra-fast X-ray free-electron lasers (XFELs) enable the imaging of single protein molecules under ambient temperature and pressure. A crucial aspect of structure reconstruction involves determining the relative orientations of each diffraction pattern and recovering the missing phase information. In this paper, we introduce a predicted model-aided algorithm for orientation determination and phase retrieval, which has been tested on various simulated datasets and has shown significant improvements in the success rate, accuracy and efficiency of XFEL data reconstruction.
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Affiliation(s)
- Zhichao Jiao
- Laboratory of Soft Matter PhysicsInstitute of Physics, Chinese Academy of SciencesBeijing100190People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Yao He
- Research Instrument ScientistNew York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Xingke Fu
- Laboratory of Soft Matter PhysicsInstitute of Physics, Chinese Academy of SciencesBeijing100190People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Xin Zhang
- The University of Hong KongHong Kong SARPeople’s Republic of China
| | - Zhi Geng
- Beijing Synchrotron Radiation FacilityInstitute of High Energy Physics, Chinese Academy of SciencesBeijing100049People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Wei Ding
- Laboratory of Soft Matter PhysicsInstitute of Physics, Chinese Academy of SciencesBeijing100190People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
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6
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Adams P, Greaves TL, Martin AV. Crystal structure via fluctuation scattering. IUCRJ 2024; 11:538-555. [PMID: 38842120 PMCID: PMC11220891 DOI: 10.1107/s2052252524003932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/30/2024] [Indexed: 06/07/2024]
Abstract
Crystallography is a quintessential method for determining the atomic structure of crystals. The most common implementation of crystallography uses single crystals that must be of sufficient size, typically tens of micrometres or larger, depending on the complexity of the crystal structure. The emergence of serial data-collection methods in crystallography, particularly for time-resolved experiments, opens up opportunities to develop new routes to structure determination for nanocrystals and ensembles of crystals. Fluctuation X-ray scattering is a correlation-based approach for single-particle imaging from ensembles of identical particles, but has yet to be applied to crystal structure determination. Here, an iterative algorithm is presented that recovers crystal structure-factor intensities from fluctuation X-ray scattering correlations. The capabilities of this algorithm are demonstrated by recovering the structure of three small-molecule crystals and a protein crystal from simulated fluctuation X-ray scattering correlations. This method could facilitate the recovery of structure-factor intensities from crystals in serial crystallography experiments and relax sample requirements for crystallography experiments.
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7
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Mous S, Poitevin F, Hunter MS, Asthagiri DN, Beck TL. Structural biology in the age of X-ray free-electron lasers and exascale computing. Curr Opin Struct Biol 2024; 86:102808. [PMID: 38547555 DOI: 10.1016/j.sbi.2024.102808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 03/07/2024] [Indexed: 05/19/2024]
Abstract
Serial femtosecond X-ray crystallography has emerged as a powerful method for investigating biomolecular structure and dynamics. With the new generation of X-ray free-electron lasers, which generate ultrabright X-ray pulses at megahertz repetition rates, we can now rapidly probe ultrafast conformational changes and charge movement in biomolecules. Over the last year, another innovation has been the deployment of Frontier, the world's first exascale supercomputer. Synergizing extremely high repetition rate X-ray light sources and exascale computing has the potential to accelerate discovery in biomolecular sciences. Here we outline our perspective on each of these remarkable innovations individually, and the opportunities and challenges in yoking them within an integrated research infrastructure.
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Affiliation(s)
- Sandra Mous
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, 94025, CA, USA.
| | - Dilipkumar N Asthagiri
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, 37830-6012, TN, USA
| | - Thomas L Beck
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, 37830-6012, TN, USA.
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8
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Stransky M, E J, Jurek Z, Santra R, Bean R, Ziaja B, Mancuso AP. Computational study of diffraction image formation from XFEL irradiated single ribosome molecule. Sci Rep 2024; 14:10617. [PMID: 38720133 PMCID: PMC11078940 DOI: 10.1038/s41598-024-61314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-ray free-electron lasers. Such a capability would create great opportunity within the biological sciences, as high-resolution structural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we report on a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule, containing over one hundred thousand non-hydrogen atoms. For this study, we use a dedicated simulation framework, SIMEX, available at the European XFEL facility. Our results demonstrate the full feasibility of computational single-particle imaging studies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be used for simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for these experiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, making the best use of the resource-intensive XFEL operation.
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Affiliation(s)
- Michal Stransky
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Krakow, Poland.
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21, Prague 8, Czech Republic.
| | - Juncheng E
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Zoltan Jurek
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestr. 9-11, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Beata Ziaja
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Krakow, Poland
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK.
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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9
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Ishikawa T, Takeo Y, Sakurai K, Yoshinaga K, Furuya N, Inubushi Y, Tono K, Joti Y, Yabashi M, Kimura T, Yoshimi K. Sub-photon accuracy noise reduction of a single shot coherent diffraction pattern with an atomic model trained autoencoder. OPTICS EXPRESS 2024; 32:18301-18316. [PMID: 38858990 DOI: 10.1364/oe.523999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/17/2024] [Indexed: 06/12/2024]
Abstract
Single-shot imaging with femtosecond X-ray lasers is a powerful measurement technique that can achieve both high spatial and temporal resolution. However, its accuracy has been severely limited by the difficulty of applying conventional noise-reduction processing. This study uses deep learning to validate noise reduction techniques, with autoencoders serving as the learning model. Focusing on the diffraction patterns of nanoparticles, we simulated a large dataset treating the nanoparticles as composed of many independent atoms. Three neural network architectures are investigated: neural network, convolutional neural network and U-net, with U-net showing superior performance in noise reduction and subphoton reproduction. We also extended our models to apply to diffraction patterns of particle shapes different from those in the simulated data. We then applied the U-net model to a coherent diffractive imaging study, wherein a nanoparticle in a microfluidic device is exposed to a single X-ray free-electron laser pulse. After noise reduction, the reconstructed nanoparticle image improved significantly even though the nanoparticle shape was different from the training data, highlighting the importance of transfer learning.
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10
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Hwang J, Kim S, Lee SY, Park E, Shin J, Lee JH, Kim MJ, Kim S, Park SY, Jang D, Eom I, Kim S, Song C, Kim KS, Nam D. Development of the multiplex imaging chamber at PAL-XFEL. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:469-477. [PMID: 38517754 DOI: 10.1107/s1600577524001218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 03/24/2024]
Abstract
Various X-ray techniques are employed to investigate specimens in diverse fields. Generally, scattering and absorption/emission processes occur due to the interaction of X-rays with matter. The output signals from these processes contain structural information and the electronic structure of specimens, respectively. The combination of complementary X-ray techniques improves the understanding of complex systems holistically. In this context, we introduce a multiplex imaging instrument that can collect small-/wide-angle X-ray diffraction and X-ray emission spectra simultaneously to investigate morphological information with nanoscale resolution, crystal arrangement at the atomic scale and the electronic structure of specimens.
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Affiliation(s)
- Junha Hwang
- Photon Science Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sejin Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sung Yun Lee
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Eunyoung Park
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jaeyong Shin
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jae Hyuk Lee
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Myong Jin Kim
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Seonghan Kim
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sang Youn Park
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Dogeun Jang
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Intae Eom
- Photon Science Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sangsoo Kim
- XFEL Beamline Department, Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Changyong Song
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Kyung Sook Kim
- Photon Science Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Daewoong Nam
- Photon Science Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
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11
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Berberich TB, Molodtsov SL, Kurta RP. A workflow for single-particle structure determination via iterative phasing of rotational invariants in fluctuation X-ray scattering. J Appl Crystallogr 2024; 57:324-343. [PMID: 38596737 PMCID: PMC11001396 DOI: 10.1107/s1600576724000992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/29/2024] [Indexed: 04/11/2024] Open
Abstract
Fluctuation X-ray scattering (FXS) offers a complementary approach for nano- and bioparticle imaging with an X-ray free-electron laser (XFEL), by extracting structural information from correlations in scattered XFEL pulses. Here a workflow is presented for single-particle structure determination using FXS. The workflow includes procedures for extracting the rotational invariants from FXS patterns, performing structure reconstructions via iterative phasing of the invariants, and aligning and averaging multiple reconstructions. The reconstruction pipeline is implemented in the open-source software xFrame and its functionality is demonstrated on several simulated structures.
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Affiliation(s)
- Tim B. Berberich
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- I. Institute of Theoretical Physics, University of Hamburg, Notkestraße 9-11, 22607 Hamburg, Germany
| | - Serguei L. Molodtsov
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger Straße 23, 09599 Freiberg, Germany
- Center for Efficient High Temperature Processes and Materials Conversion (ZeHS), TU Bergakademie Freiberg, Winklerstrasse 5, 09599 Freiberg, Germany
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12
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Wollter A, De Santis E, Ekeberg T, Marklund EG, Caleman C. Enhanced EMC-Advantages of partially known orientations in x-ray single particle imaging. J Chem Phys 2024; 160:114108. [PMID: 38506290 DOI: 10.1063/5.0188772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/28/2024] [Indexed: 03/21/2024] Open
Abstract
Single particle imaging of proteins in the gas phase with x-ray free-electron lasers holds great potential to study fast protein dynamics, but is currently limited by weak and noisy data. A further challenge is to discover the proteins' orientation as each protein is randomly oriented when exposed to x-rays. Algorithms such as the expand, maximize, and compress (EMC) exist that can solve the orientation problem and reconstruct the three-dimensional diffraction intensity space, given sufficient measurements. If information about orientation were known, for example, by using an electric field to orient the particles, the reconstruction would benefit and potentially reach better results. We used simulated diffraction experiments to test how the reconstructions from EMC improve with particles' orientation to a preferred axis. Our reconstructions converged to correct maps of the three-dimensional diffraction space with fewer measurements if biased orientation information was considered. Even for a moderate bias, there was still significant improvement. Biased orientations also substantially improved the results in the case of missing central information, in particular in the case of small datasets. The effects were even more significant when adding a background with 50% the strength of the averaged diffraction signal photons to the diffraction patterns, sometimes reducing the data requirement for convergence by a factor of 10. This demonstrates the usefulness of having biased orientation information in single particle imaging experiments, even for a weaker bias than what was previously known. This could be a key component in overcoming the problems with background noise that currently plague these experiments.
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Affiliation(s)
- August Wollter
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Husargatan 3, 75124 Uppsala, Sweden
| | - Emiliano De Santis
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Tomas Ekeberg
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Husargatan 3, 75124 Uppsala, Sweden
| | - Erik G Marklund
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, DE-22607 Hamburg, Germany
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13
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Rafie-Zinedine S, Varma Yenupuri T, Worbs L, Maia FRNC, Heymann M, Schulz J, Bielecki J. Enhancing electrospray ionization efficiency for particle transmission through an aerodynamic lens stack. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:222-232. [PMID: 38306300 PMCID: PMC10914161 DOI: 10.1107/s1600577524000158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/05/2024] [Indexed: 02/04/2024]
Abstract
This work investigates the performance of the electrospray aerosol generator at the European X-ray Free Electron Laser (EuXFEL). This generator is, together with an aerodynamic lens stack that transports the particles into the X-ray interaction vacuum chamber, the method of choice to deliver particles for single-particle coherent diffractive imaging (SPI) experiments at the EuXFEL. For these experiments to be successful, it is necessary to achieve high transmission of particles from solution into the vacuum interaction region. Particle transmission is highly dependent on efficient neutralization of the charged aerosol generated by the electrospray mechanism as well as the geometry in the vicinity of the Taylor cone. We report absolute particle transmission values for different neutralizers and geometries while keeping the conditions suitable for SPI experiments. Our findings reveal that a vacuum ultraviolet ionizer demonstrates a transmission efficiency approximately seven times greater than the soft X-ray ionizer used previously. Combined with an optimized orifice size on the counter electrode, we achieve >40% particle transmission from solution into the X-ray interaction region. These findings offer valuable insights for optimizing electrospray aerosol generator configurations and data rates for SPI experiments.
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Affiliation(s)
- Safi Rafie-Zinedine
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Tej Varma Yenupuri
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), 75124 Uppsala, Sweden
| | - Lena Worbs
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), 75124 Uppsala, Sweden
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), 75124 Uppsala, Sweden
| | - Michael Heymann
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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14
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Yenupuri TV, Rafie-Zinedine S, Worbs L, Heymann M, Schulz J, Bielecki J, Maia FRNC. Helium-electrospray improves sample delivery in X-ray single-particle imaging experiments. Sci Rep 2024; 14:4401. [PMID: 38388562 PMCID: PMC10883998 DOI: 10.1038/s41598-024-54605-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
Imaging the structure and observing the dynamics of isolated proteins using single-particle X-ray diffractive imaging (SPI) is one of the potential applications of X-ray free-electron lasers (XFELs). Currently, SPI experiments on isolated proteins are limited by three factors: low signal strength, limited data and high background from gas scattering. The last two factors are largely due to the shortcomings of the aerosol sample delivery methods in use. Here we present our modified electrospray ionization (ESI) source, which we dubbed helium-ESI (He-ESI). With it, we increased particle delivery into the interaction region by a factor of 10, for 26 nm-sized biological particles, and decreased the gas load in the interaction chamber corresponding to an 80% reduction in gas scattering when compared to the original ESI. These improvements have the potential to significantly increase the quality and quantity of SPI diffraction patterns in future experiments using He-ESI, resulting in higher-resolution structures.
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Affiliation(s)
- Tej Varma Yenupuri
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 75124, Uppsala, Sweden
| | - Safi Rafie-Zinedine
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, 70569, Germany
| | - Lena Worbs
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 75124, Uppsala, Sweden
| | - Michael Heymann
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, Stuttgart, 70569, Germany
| | | | - Johan Bielecki
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 75124, Uppsala, Sweden.
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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15
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Wang G, Dijkstal P, Reiche S, Schnorr K, Prat E. Millijoule Femtosecond X-Ray Pulses from an Efficient Fresh-Slice Multistage Free-Electron Laser. PHYSICAL REVIEW LETTERS 2024; 132:035002. [PMID: 38307082 DOI: 10.1103/physrevlett.132.035002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
We present the generation of x-ray pulses with average pulse energies up to one millijoule and rms pulse durations down to the femtosecond level. We have produced these intense and short pulses by employing the fresh-slice multistage amplification scheme with a transversely tilted electron beam in a free-electron laser. In this scheme, a short pulse is produced in the first stage and later amplified by fresh parts of the electron bunch in up to a total of four stages of amplification. Our implementation is efficient, since practically the full electron beam contributes to produce the x-ray pulse. Our implementation is also compact, utilizing only 32 m of undulator. The demonstration was done at Athos, the soft x-ray beamline of SwissFEL, which was designed with high flexibility to take full advantage of the multistage amplification scheme. It opens the door for scientific opportunities following ultrafast dynamics using nonlinear x-ray spectroscopy techniques or avoiding electronic damage when capturing structures with a single intense pulse via single-particle imaging.
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Affiliation(s)
- Guanglei Wang
- Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | | | - Sven Reiche
- Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
| | | | - Eduard Prat
- Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland
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16
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Robinson MS, Küpper J. Unraveling the ultrafast dynamics of thermal-energy chemical reactions. Phys Chem Chem Phys 2024; 26:1587-1601. [PMID: 38131437 DOI: 10.1039/d3cp03954d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In this perspective, we discuss how one can initiate, image, and disentangle the ultrafast elementary steps of thermal-energy chemical dynamics, building upon advances in technology and scientific insight. We propose that combinations of ultrashort mid-infrared laser pulses, controlled molecular species in the gas phase, and forefront imaging techniques allow to unravel the elementary steps of general-chemistry reaction processes in real time. We detail, for prototypical first reaction systems, experimental methods enabling these investigations, how to sufficiently prepare and promote gas-phase samples to thermal-energy reactive states with contemporary ultrashort mid-infrared laser systems, and how to image the initiated ultrafast chemical dynamics. The results of such experiments will clearly further our understanding of general-chemistry reaction dynamics.
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Affiliation(s)
- Matthew S Robinson
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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17
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Abbasi E, Jafari S. Chaotic dynamics in X-ray free-electron lasers with an optical undulator. Sci Rep 2024; 14:1341. [PMID: 38228742 PMCID: PMC10791656 DOI: 10.1038/s41598-024-51891-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/10/2024] [Indexed: 01/18/2024] Open
Abstract
In this work, the chaotic motions of relativistic electrons in X-ray free-electron lasers are investigated using an optical undulator in the presence of a magnetized ion-channel background. To miniaturize X-ray light sources, the optical undulator is a promising concept. The optical undulator provides higher optical gain than conventional magnetostatic undulators due to its micrometer wavelength. In addition, it reduces the required electron beam energy from several GeV to the multi-MeV range to produce X-ray pulses. The interaction of an optical undulator with an intense relativistic electron beam is a highly non-linear phenomenon that can lead to chaotic dynamics. At synchrotron radiation sources, the possibility of chaos control for X-ray FELs can be critical for certain classes of experimental studies. The equations of motion for a relativistic electron propagating through the optical undulator in the presence of a magnetized ion-channel can be derived from the Hamiltonian of the interaction region. Simulation results revealed that the intensity of the perturbation route from orderly behavior to chaos depends on the beam density, axial magnetic field strength, ion-channel density parameter, and pump laser undulator. Specific values of parameters were obtained for the transition from regular to chaotic paths. Bifurcation diagrams of the system were plotted to demonstrate the origin of chaos at a critical point, and Poincaré maps were created to distinguish between chaotic and orderly motions of electrons. The proposed new scheme can help to improve X-ray FELs, which have potential usages in basic sciences, medicine, and industry.
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Affiliation(s)
- E Abbasi
- Department of Physics, Faculty of Science, University of Guilan, Rasht, 41335-1914, Iran
| | - S Jafari
- Department of Physics, Faculty of Science, University of Guilan, Rasht, 41335-1914, Iran.
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18
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Chen Z, Zheng S, Wang W, Song J, Yuan X. Temporal structured illumination and vision-transformer enables large field-of-view binary snapshot ptychography. OPTICS EXPRESS 2024; 32:1540-1551. [PMID: 38297703 DOI: 10.1364/oe.504721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024]
Abstract
Ptychography, a widely used computational imaging method, generates images by processing coherent interference patterns scattered from an object of interest. In order to capture scenes with large field-of-view (FoV) and high spatial resolution simultaneously in a single shot, we propose a temporal-compressive structured-light Ptychography system. A novel three-step reconstruction algorithm composed of multi-frame spectra reconstruction, phase retrieval, and multi-frame image stitching is developed, where we employ the emerging Transformer-based network in the first step. Experimental results demonstrate that our system can expand the FoV by 20× without losing spatial resolution. Our results offer huge potential for enabling lensless imaging of molecules with large FoV as well as high spatial-temporal resolutions. We also notice that due to the loss of low-intensity information caused by the compressed sensing process, our method so far is only applicable to binary targets.
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19
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Ekeberg T, Assalauova D, Bielecki J, Boll R, Daurer BJ, Eichacker LA, Franken LE, Galli DE, Gelisio L, Gumprecht L, Gunn LH, Hajdu J, Hartmann R, Hasse D, Ignatenko A, Koliyadu J, Kulyk O, Kurta R, Kuster M, Lugmayr W, Lübke J, Mancuso AP, Mazza T, Nettelblad C, Ovcharenko Y, Rivas DE, Rose M, Samanta AK, Schmidt P, Sobolev E, Timneanu N, Usenko S, Westphal D, Wollweber T, Worbs L, Xavier PL, Yousef H, Ayyer K, Chapman HN, Sellberg JA, Seuring C, Vartanyants IA, Küpper J, Meyer M, Maia FRNC. Observation of a single protein by ultrafast X-ray diffraction. LIGHT, SCIENCE & APPLICATIONS 2024; 13:15. [PMID: 38216563 PMCID: PMC10786860 DOI: 10.1038/s41377-023-01352-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.
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Affiliation(s)
- Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Dameli Assalauova
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Rebecca Boll
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Benedikt J Daurer
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK
| | - Lutz A Eichacker
- University of Stavanger, Centre Organelle Research, Richard-Johnsensgate 4, 4021, Stavanger, Norway
| | - Linda E Franken
- Leibniz Institute for Experimental Virology (HPI), Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany
| | - Davide E Galli
- Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, via Celoria 16, 20133, Milano, Italy
| | - Luca Gelisio
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | - Laura H Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | | | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Alexandr Ignatenko
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jayanath Koliyadu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Olena Kulyk
- ELI Beamlines/IoP Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Ruslan Kurta
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Kuster
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Wolfgang Lugmayr
- Multi-User CryoEM Facility, Centre for Structural Systems Biology, Notkestr.85, 22607, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Jannik Lübke
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Tommaso Mazza
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carl Nettelblad
- Division of Scientific Computing, Science for Life Laboratory, Department of Information Technology, Uppsala University, Box 337, SE-75105, Uppsala, Sweden
| | | | | | - Max Rose
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Amit K Samanta
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | | | - Egor Sobolev
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala, Sweden
| | - Sergey Usenko
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Tamme Wollweber
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lena Worbs
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Paul Lourdu Xavier
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Kartik Ayyer
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jonas A Sellberg
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Carolin Seuring
- Multi-User CryoEM Facility, Centre for Structural Systems Biology, Notkestr.85, 22607, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, 20146, Hamburg, Germany
| | - Ivan A Vartanyants
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Michael Meyer
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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20
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Takayama Y, Nakasako M. Similarity score for screening phase-retrieved maps in X-ray diffraction imaging - characterization in reciprocal space. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:95-112. [PMID: 38054944 PMCID: PMC10833420 DOI: 10.1107/s1600577523009827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]
Abstract
X-ray diffraction imaging (XDI) is utilized for visualizing the structures of non-crystalline particles in material sciences and biology. In the structural analysis, phase-retrieval (PR) algorithms are applied to the diffraction amplitude data alone to reconstruct the electron density map of a specimen particle projected along the direction of the incident X-rays. However, PR calculations may not lead to good convergence because of a lack of diffraction patterns in small-angle regions and Poisson noise in X-ray detection. Therefore, the PR calculation is still a bottleneck for the efficient application of XDI in the structural analyses of non-crystalline particles. For screening maps from hundreds of trial PR calculations, we have been using a score and measuring the similarity between a pair of retrieved maps. Empirically, probable maps approximating the particle structures gave a score smaller than a threshold value, but the reasons for the effectiveness of the score are still unclear. In this study, the score is characterized in terms of the phase differences between the structure factors of the retrieved maps, the usefulness of the score in screening the maps retrieved from experimental diffraction patterns is demonstrated, and the effective resolution of similarity-score-selected maps is discussed.
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Affiliation(s)
- Yuki Takayama
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Sayo-gun, Hyogo 679-5148, Japan
- Synchrotron Radiation Research Center, Hyogo Science and Technology Association, 1-490-2 Kouto, Shingu, Tatsuno, Hyogo 679-5148, Japan
- International Center for Synchrotron Radiation Innovation Smart, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Masayoshi Nakasako
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Sayo-gun, Hyogo 679-5148, Japan
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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21
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Zhao W, Miyashita O, Nakano M, Tama F. Structure determination using high-order spatial correlations in single-particle X-ray scattering. IUCRJ 2024; 11:92-108. [PMID: 38096036 PMCID: PMC10833384 DOI: 10.1107/s2052252523009831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/10/2023] [Indexed: 01/10/2024]
Abstract
Single-particle imaging using X-ray free-electron lasers (XFELs) is a promising technique for observing nanoscale biological samples under near-physiological conditions. However, as the sample's orientation in each diffraction pattern is unknown, advanced algorithms are required to reconstruct the 3D diffraction intensity volume and subsequently the sample's density model. While most approaches perform 3D reconstruction via determining the orientation of each diffraction pattern, a correlation-based approach utilizes the averaged spatial correlations of diffraction intensities over all patterns, making it well suited for processing experimental data with a poor signal-to-noise ratio of individual patterns. Here, a method is proposed to determine the 3D structure of a sample by analyzing the double, triple and quadruple spatial correlations in diffraction patterns. This ab initio method can reconstruct the basic shape of an irregular unsymmetric 3D sample without requiring any prior knowledge of the sample. The impact of background and noise on correlations is investigated and corrected to ensure the success of reconstruction under simulated experimental conditions. Additionally, the feasibility of using the correlation-based approach to process incomplete partial diffraction patterns is demonstrated. The proposed method is a variable addition to existing algorithms for 3D reconstruction and will further promote the development and adoption of XFEL single-particle imaging techniques.
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Affiliation(s)
- Wenyang Zhao
- Computational Structural Biology Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Osamu Miyashita
- Computational Structural Biology Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Miki Nakano
- Computational Structural Biology Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Florence Tama
- Computational Structural Biology Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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22
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Yoshida S, Harada K, Uezu S, Takayama Y, Nakasako M. Protocol using similarity score and improved shrink-wrap algorithm for better convergence of phase-retrieval calculation in X-ray diffraction imaging. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:113-128. [PMID: 38054945 PMCID: PMC10833425 DOI: 10.1107/s1600577523009864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023]
Abstract
In X-ray diffraction imaging (XDI), electron density maps of a targeted particle are reconstructed computationally from the diffraction pattern alone using phase-retrieval (PR) algorithms. However, the PR calculations sometimes fail to yield realistic electron density maps that approximate the structure of the particle. This occurs due to the absence of structure amplitudes at and near the zero-scattering angle and the presence of Poisson noise in weak diffraction patterns. Consequently, the PR calculation becomes a bottleneck for XDI structure analyses. Here, a protocol to efficiently yield realistic maps is proposed. The protocol is based on the empirical observation that realistic maps tend to yield low similarity scores, as suggested in our prior study [Sekiguchi et al. (2017), J. Synchrotron Rad. 24, 1024-1038]. Among independently and concurrently executed PR calculations, the protocol modifies all maps using the electron-density maps exhibiting low similarity scores. This approach, along with a new protocol for estimating particle shape, improved the probability of obtaining realistic maps for diffraction patterns from various aggregates of colloidal gold particles, as compared with PR calculations performed without the protocol. Consequently, the protocol has the potential to reduce computational costs in PR calculations and enable efficient XDI structure analysis of non-crystalline particles using synchrotron X-rays and X-ray free-electron laser pulses.
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Affiliation(s)
- Syouyo Yoshida
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
| | - Kosei Harada
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
| | - So Uezu
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
| | - Yuki Takayama
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
- International Center for Synchrotron Radiation Innovation Smart, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- RIKEN Spring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayogun, Hyogo, Japan
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23
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Cao M, Wang Y, Wang L, Zhang K, Guan Y, Guo Y, Chen C. In situ label-free X-ray imaging for visualizing the localization of nanomedicines and subcellular architecture in intact single cells. Nat Protoc 2024; 19:30-59. [PMID: 37957402 DOI: 10.1038/s41596-023-00902-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 08/10/2023] [Indexed: 11/15/2023]
Abstract
Understanding the intracellular behaviors of nanomedicines and morphology variation of subcellular architecture impacted by nanomaterial-biology (nano-bio) interactions could help guide the safe-by-design, manufacturing and evaluation of nanomedicines for clinical translation. The in situ and label-free analysis of nano-bio interactions in intact single cells at nanoscale remains challenging. We developed an approach based on X-ray microscopy to directly visualize the 2D or 3D intracellular distribution without labeling at nanometer resolution and analyze the chemical transformation of nanomedicines in situ. Here, we describe an optimized workflow for cell sample preparation, beamline selection, data acquisition and analysis. With several model bionanomaterials as examples, we analyze the localization of nanomedicines in various primary blood cells, macrophages, dendritic cells, monocytes and cancer cells, as well as the morphology of some organelles with soft and hard X-rays. Our protocol has been successfully implemented at three beamline facilities: 4W1A of Beijing Synchrotron Radiation Facility, BL08U1A of Shanghai Synchrotron Radiation Facility and BL07W of the National Synchrotron Radiation Laboratory. This protocol can be completed in ~2-5 d, depending on the cell types, their incubation times with nanomaterials and the selected X-ray beamline. The protocol enables the in situ analysis of the varieties of metal-containing nanomaterials, visualization of intracellular endocytosis, distribution and excretion and corresponding subcellular morphological variation influenced by nanomedicines in cell lines or primary cells by using this universal and robust platform. The results facilitate the understanding of the true principle and mechanism underlying the nano-bio interaction.
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Affiliation(s)
- Mingjing Cao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Yaling Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Liming Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Kai Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Yuecong Guo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China.
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
- GBA National Institute for Nanotechnology Innovation, Guangzhou, China.
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24
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Choi TK, Park J, Kim G, Jang H, Park SY, Sohn JH, Cho BI, Kim H, Kim KS, Nam I, Chun SH. Resonant X-ray emission spectroscopy using self-seeded hard X-ray pulses at PAL-XFEL. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:1038-1047. [PMID: 37738032 PMCID: PMC10624040 DOI: 10.1107/s1600577523007312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
Self-seeded hard X-ray pulses at PAL-XFEL were used to commission a resonant X-ray emission spectroscopy experiment with a von Hamos spectrometer. The self-seeded beam, generated through forward Bragg diffraction of the [202] peak in a 100 µm-thick diamond crystal, exhibited an average bandwidth of 0.54 eV at 11.223 keV. A coordinated scanning scheme of electron bunch energy, diamond crystal angle and silicon monochromator allowed us to map the Ir Lβ2 X-ray emission lines of IrO2 powder across the Ir L3-absorption edge, from 11.212 to 11.242 keV with an energy step of 0.3 eV. This work provides a reference for hard X-ray emission spectroscopy experiments utilizing self-seeded pulses with a narrow bandwidth, eventually applicable for pump-probe studies in solid-state and diluted systems.
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Affiliation(s)
- Tae-Kyu Choi
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jaeku Park
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyujin Kim
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hoyoung Jang
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
- Photon Science Center, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sang-Youn Park
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jang Hyeob Sohn
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Byoung Ick Cho
- Department of Physics and Photon Science, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hyunjung Kim
- Department of Physics, Sogang University, Seoul 04107, Republic of Korea
| | - Kyung Sook Kim
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Inhyuk Nam
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sae Hwan Chun
- XFEL Division, Pohang Accelerator Laboratory, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
- Photon Science Center, POSTECH, Pohang, Gyeongbuk 37673, Republic of Korea
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25
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E J, Stransky M, Shen Z, Jurek Z, Fortmann-Grote C, Bean R, Santra R, Ziaja B, Mancuso AP. Water layer and radiation damage effects on the orientation recovery of proteins in single-particle imaging at an X-ray free-electron laser. Sci Rep 2023; 13:16359. [PMID: 37773512 PMCID: PMC10541445 DOI: 10.1038/s41598-023-43298-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/21/2023] [Indexed: 10/01/2023] Open
Abstract
The noise caused by sample heterogeneity (including sample solvent) has been identified as one of the determinant factors for a successful X-ray single-particle imaging experiment. It influences both the radiation damage process that occurs during illumination as well as the scattering patterns captured by the detector. Here, we investigate the impact of water layer thickness and radiation damage on orientation recovery from diffraction patterns of the nitrogenase iron protein. Orientation recovery is a critical step for single-particle imaging. It enables to sort a set of diffraction patterns scattered by identical particles placed at unknown orientations and assemble them into a 3D reciprocal space volume. The recovery quality is characterized by a "disconcurrence" metric. Our results show that while a water layer mitigates protein damage, the noise generated by the scattering from it can introduce challenges for orientation recovery and is anticipated to cause problems in the phase retrieval process to extract the desired protein structure. Compared to these disadvantageous effects due to the thick water layer, the effects of radiation damage on the orientation recovery are relatively small. Therefore, minimizing the amount of residual sample solvent should be considered a crucial step in improving the fidelity and resolution of X-ray single-particle imaging experiments.
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Affiliation(s)
- Juncheng E
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Michal Stransky
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Kraków, Poland
| | - Zhou Shen
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Zoltan Jurek
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | | | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestr. 9-11, 22607, Hamburg, Germany
| | - Beata Ziaja
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342, Kraków, Poland
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK.
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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26
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Wang C, Florin E, Chang HY, Thayer J, Yoon CH. SpeckleNN: a unified embedding for real-time speckle pattern classification in X-ray single-particle imaging with limited labeled examples. IUCRJ 2023; 10:568-578. [PMID: 37458190 PMCID: PMC10478515 DOI: 10.1107/s2052252523006115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/10/2023] [Indexed: 09/06/2023]
Abstract
With X-ray free-electron lasers (XFELs), it is possible to determine the three-dimensional structure of noncrystalline nanoscale particles using X-ray single-particle imaging (SPI) techniques at room temperature. Classifying SPI scattering patterns, or `speckles', to extract single-hits that are needed for real-time vetoing and three-dimensional reconstruction poses a challenge for high-data-rate facilities like the European XFEL and LCLS-II-HE. Here, we introduce SpeckleNN, a unified embedding model for real-time speckle pattern classification with limited labeled examples that can scale linearly with dataset size. Trained with twin neural networks, SpeckleNN maps speckle patterns to a unified embedding vector space, where similarity is measured by Euclidean distance. We highlight its few-shot classification capability on new never-seen samples and its robust performance despite having only tens of labels per classification category even in the presence of substantial missing detector areas. Without the need for excessive manual labeling or even a full detector image, our classification method offers a great solution for real-time high-throughput SPI experiments.
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Affiliation(s)
- Cong Wang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Eric Florin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hsing-Yin Chang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jana Thayer
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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27
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Zhang L, Li Z, Liu D, Wu C, Xu H, Li Z. Entangled X-Ray Photon Pair Generation by Free-Electron Lasers. PHYSICAL REVIEW LETTERS 2023; 131:073601. [PMID: 37656859 DOI: 10.1103/physrevlett.131.073601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/06/2023] [Accepted: 07/14/2023] [Indexed: 09/03/2023]
Abstract
We investigate entangled x-ray photon pair emissions in a free-electron laser (FEL) and establish a quantum electrodynamical theory for coherently amplified entangled photon pair emission from microbunched electron pulses in the undulator. We provide a scheme to generate highly entangled x-ray photon pairs and numerically demonstrate the properties of entangled emission, which is of great importance in x-ray quantum optics. Our work shows a unique advantage of FELs in entangled x-ray photon pair generation.
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Affiliation(s)
- Linfeng Zhang
- State Key Laboratory for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Zunqi Li
- State Key Laboratory for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Dongyu Liu
- State Key Laboratory for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Physics Department, Stanford University, California 94305, USA
| | - Chengyin Wu
- State Key Laboratory for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
| | - Haitan Xu
- School of Materials Science and Intelligent Engineering, Nanjing University, Suzhou, Jiangsu 215163, China
- Shishan Laboratory, Nanjing University, Suzhou, Jiangsu 215163, China
- School of Physical Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zheng Li
- State Key Laboratory for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
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28
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Shao Z, Schnitzer N, Ruf J, Gorobtsov OY, Dai C, Goodge BH, Yang T, Nair H, Stoica VA, Freeland JW, Ruff JP, Chen LQ, Schlom DG, Shen KM, Kourkoutis LF, Singer A. Real-space imaging of periodic nanotextures in thin films via phasing of diffraction data. Proc Natl Acad Sci U S A 2023; 120:e2303312120. [PMID: 37410867 PMCID: PMC10334741 DOI: 10.1073/pnas.2303312120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/11/2023] [Indexed: 07/08/2023] Open
Abstract
New properties and exotic quantum phenomena can form due to periodic nanotextures, including Moire patterns, ferroic domains, and topologically protected magnetization and polarization textures. Despite the availability of powerful tools to characterize the atomic crystal structure, the visualization of nanoscale strain-modulated structural motifs remains challenging. Here, we develop nondestructive real-space imaging of periodic lattice distortions in thin epitaxial films and report an emergent periodic nanotexture in a Mott insulator. Specifically, we combine iterative phase retrieval with unsupervised machine learning to invert the diffuse scattering pattern from conventional X-ray reciprocal-space maps into real-space images of crystalline displacements. Our imaging in PbTiO3/SrTiO3 superlattices exhibiting checkerboard strain modulation substantiates published phase-field model calculations. Furthermore, the imaging of biaxially strained Mott insulator Ca2RuO4 reveals a strain-induced nanotexture comprised of nanometer-thin metallic-structure wires separated by nanometer-thin Mott-insulating-structure walls, as confirmed by cryogenic scanning transmission electron microscopy (cryo-STEM). The nanotexture in Ca2RuO4 film is induced by the metal-to-insulator transition and has not been reported in bulk crystals. We expect the phasing of diffuse X-ray scattering from thin crystalline films in combination with cryo-STEM to open a powerful avenue for discovering, visualizing, and quantifying the periodic strain-modulated structures in quantum materials.
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Affiliation(s)
- Ziming Shao
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY14853
| | - Noah Schnitzer
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY14853
| | - Jacob Ruf
- Department of Physics, Cornell University, Ithaca, NY14853
| | - Oleg Yu. Gorobtsov
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY14853
| | - Cheng Dai
- Department of Materials Science and Engineering, Pennsylvania State University, University Park, PA16802
| | - Berit H. Goodge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY14853
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY14853
| | - Tiannan Yang
- Department of Materials Science and Engineering, Pennsylvania State University, University Park, PA16802
| | - Hari Nair
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY14853
| | - Vlad A. Stoica
- Department of Materials Science and Engineering, Pennsylvania State University, University Park, PA16802
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL60439
| | - John W. Freeland
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL60439
| | - Jacob P. Ruff
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY14853
| | - Long-Qing Chen
- Department of Materials Science and Engineering, Pennsylvania State University, University Park, PA16802
| | - Darrell G. Schlom
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY14853
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY14853
- Leibniz-Institut für Kristallzüchtung, Berlin12489, Germany
| | - Kyle M. Shen
- Department of Physics, Cornell University, Ithaca, NY14853
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY14853
| | - Lena F. Kourkoutis
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY14853
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY14853
| | - Andrej Singer
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY14853
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29
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Trost F, Ayyer K, Prasciolu M, Fleckenstein H, Barthelmess M, Yefanov O, Dresselhaus JL, Li C, Bajt S, Carnis J, Wollweber T, Mall A, Shen Z, Zhuang Y, Richter S, Karl S, Cardoch S, Patra KK, Möller J, Zozulya A, Shayduk R, Lu W, Brauße F, Friedrich B, Boesenberg U, Petrov I, Tomin S, Guetg M, Madsen A, Timneanu N, Caleman C, Röhlsberger R, von Zanthier J, Chapman HN. Imaging via Correlation of X-Ray Fluorescence Photons. PHYSICAL REVIEW LETTERS 2023; 130:173201. [PMID: 37172237 DOI: 10.1103/physrevlett.130.173201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/01/2023] [Accepted: 03/08/2023] [Indexed: 05/14/2023]
Abstract
We demonstrate that x-ray fluorescence emission, which cannot maintain a stationary interference pattern, can be used to obtain images of structures by recording photon-photon correlations in the manner of the stellar intensity interferometry of Hanbury Brown and Twiss. This is achieved utilizing femtosecond-duration pulses of a hard x-ray free-electron laser to generate the emission in exposures comparable to the coherence time of the fluorescence. Iterative phasing of the photon correlation map generated a model-free real-space image of the structure of the emitters. Since fluorescence can dominate coherent scattering, this may enable imaging uncrystallised macromolecules.
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Affiliation(s)
- Fabian Trost
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Kartik Ayyer
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Mauro Prasciolu
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - J Lukas Dresselhaus
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jerome Carnis
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Tamme Wollweber
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
| | - Zhou Shen
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
| | - Yulong Zhuang
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
| | - Stefan Richter
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 1, 91058 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander Universität Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052, Erlangen, Germany
| | - Sebastian Karl
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 1, 91058 Erlangen, Germany
| | - Sebastian Cardoch
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
| | - Kajwal Kumar Patra
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Alexey Zozulya
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Roman Shayduk
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Wei Lu
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Felix Brauße
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Bertram Friedrich
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Ulrike Boesenberg
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Ilia Petrov
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Sergey Tomin
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marc Guetg
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anders Madsen
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
| | - Carl Caleman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
| | - Ralf Röhlsberger
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Helmholtz-Institut Jena, Fröbelstieg 3, 07743 Jena, Germany
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, 62491 Jena, Germany
- Institut für Optik und Quantenelektronik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - Joachim von Zanthier
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 1, 91058 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander Universität Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052, Erlangen, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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30
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Colombo A, Dold S, Kolb P, Bernhardt N, Behrens P, Correa J, Düsterer S, Erk B, Hecht L, Heilrath A, Irsig R, Iwe N, Jordan J, Kruse B, Langbehn B, Manschwetus B, Martinez F, Meiwes-Broer KH, Oldenburg K, Passow C, Peltz C, Sauppe M, Seel F, Tanyag RMP, Treusch R, Ulmer A, Walz S, Fennel T, Barke I, Möller T, von Issendorff B, Rupp D. Three-dimensional femtosecond snapshots of isolated faceted nanostructures. SCIENCE ADVANCES 2023; 9:eade5839. [PMID: 36812315 PMCID: PMC9946342 DOI: 10.1126/sciadv.ade5839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The structure and dynamics of isolated nanosamples in free flight can be directly visualized via single-shot coherent diffractive imaging using the intense and short pulses of x-ray free-electron lasers. Wide-angle scattering images encode three-dimensional (3D) morphological information of the samples, but its retrieval remains a challenge. Up to now, effective 3D morphology reconstructions from single shots were only achieved via fitting with highly constrained models, requiring a priori knowledge about possible geometries. Here, we present a much more generic imaging approach. Relying on a model that allows for any sample morphology described by a convex polyhedron, we reconstruct wide-angle diffraction patterns from individual silver nanoparticles. In addition to known structural motives with high symmetries, we retrieve imperfect shapes and agglomerates that were not previously accessible. Our results open unexplored routes toward true 3D structure determination of single nanoparticles and, ultimately, 3D movies of ultrafast nanoscale dynamics.
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Affiliation(s)
- Alessandro Colombo
- Laboratory for Solid State Physics, ETH Zurich, 8093 Zurich, Switzerland
| | - Simon Dold
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Patrice Kolb
- Laboratory for Solid State Physics, ETH Zurich, 8093 Zurich, Switzerland
| | - Nils Bernhardt
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Patrick Behrens
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Jonathan Correa
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Stefan Düsterer
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Benjamin Erk
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Linos Hecht
- Laboratory for Solid State Physics, ETH Zurich, 8093 Zurich, Switzerland
| | - Andrea Heilrath
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Robert Irsig
- Institute of Physics, University of Rostock, 18057 Rostock, Germany
| | - Norman Iwe
- Institute of Physics, University of Rostock, 18057 Rostock, Germany
| | - Jakob Jordan
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Björn Kruse
- Institute of Physics, University of Rostock, 18057 Rostock, Germany
| | - Bruno Langbehn
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | | | | | - Karl-Heinz Meiwes-Broer
- Institute of Physics, University of Rostock, 18057 Rostock, Germany
- Department of Life, Light and Matter, University of Rostock, 18051 Rostock, Germany
| | - Kevin Oldenburg
- Institute of Physics, University of Rostock, 18057 Rostock, Germany
| | | | - Christian Peltz
- Institute of Physics, University of Rostock, 18057 Rostock, Germany
| | - Mario Sauppe
- Laboratory for Solid State Physics, ETH Zurich, 8093 Zurich, Switzerland
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Fabian Seel
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Rico Mayro P. Tanyag
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Rolf Treusch
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Anatoli Ulmer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Saida Walz
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Thomas Fennel
- Institute of Physics, University of Rostock, 18057 Rostock, Germany
| | - Ingo Barke
- Institute of Physics, University of Rostock, 18057 Rostock, Germany
- Department of Life, Light and Matter, University of Rostock, 18051 Rostock, Germany
| | - Thomas Möller
- Institut für Optik und Atomare Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Bernd von Issendorff
- Department of Physics, University of Freiburg, 79104 Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, 79104 Freiburg, Germany
| | - Daniela Rupp
- Laboratory for Solid State Physics, ETH Zurich, 8093 Zurich, Switzerland
- Max Born Institute, 12489 Berlin, Germany
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31
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Zimmermann J, Beguet F, Guthruf D, Langbehn B, Rupp D. Finding the semantic similarity in single-particle diffraction images using self-supervised contrastive projection learning. NPJ COMPUTATIONAL MATERIALS 2023; 9:24. [PMID: 38666059 PMCID: PMC11041688 DOI: 10.1038/s41524-023-00966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/10/2023] [Indexed: 04/28/2024]
Abstract
Single-shot coherent diffraction imaging of isolated nanosized particles has seen remarkable success in recent years, yielding in-situ measurements with ultra-high spatial and temporal resolution. The progress of high-repetition-rate sources for intense X-ray pulses has further enabled recording datasets containing millions of diffraction images, which are needed for the structure determination of specimens with greater structural variety and dynamic experiments. The size of the datasets, however, represents a monumental problem for their analysis. Here, we present an automatized approach for finding semantic similarities in coherent diffraction images without relying on human expert labeling. By introducing the concept of projection learning, we extend self-supervised contrastive learning to the context of coherent diffraction imaging and achieve a dimensionality reduction producing semantically meaningful embeddings that align with physical intuition. The method yields substantial improvements compared to previous approaches, paving the way toward real-time and large-scale analysis of coherent diffraction experiments at X-ray free-electron lasers.
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Affiliation(s)
| | | | | | | | - Daniela Rupp
- ETH Zürich, Zürich, Switzerland
- Max-Born-Institut, Berlin, Germany
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32
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Assalauova D, Vartanyants IA. The structure of tick-borne encephalitis virus determined at X-ray free-electron lasers. Simulations. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:24-34. [PMID: 36601923 PMCID: PMC9814066 DOI: 10.1107/s1600577522011341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
The study of virus structures by X-ray free-electron lasers (XFELs) has attracted increased attention in recent decades. Such experiments are based on the collection of 2D diffraction patterns measured at the detector following the application of femtosecond X-ray pulses to biological samples. To prepare an experiment at the European XFEL, the diffraction data for the tick-borne encephalitis virus (TBEV) was simulated with different parameters and the optimal values were identified. Following the necessary steps of a well established data-processing pipeline, the structure of TBEV was obtained. In the structure determination presented, a priori knowledge of the simulated virus orientations was used. The efficiency of the proposed pipeline was demonstrated.
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Affiliation(s)
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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33
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Kim YY, Khubbutdinov R, Carnis J, Kim S, Nam D, Nam I, Kim G, Shim CH, Yang H, Cho M, Min CK, Kim C, Kang HS, Vartanyants IA. Statistical analysis of hard X-ray radiation at the PAL-XFEL facility performed by Hanbury Brown and Twiss interferometry. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1465-1479. [PMID: 36345755 PMCID: PMC9641567 DOI: 10.1107/s1600577522008773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
A Hanbury Brown and Twiss interferometry experiment based on second-order correlations was performed at the PAL-XFEL facility. The statistical properties of the X-ray radiation were studied within this experiment. Measurements were performed at the NCI beamline at 10 keV photon energy under various operation conditions: self-amplified spontaneous emission (SASE), SASE with a monochromator, and self-seeding regimes at 120 pC, 180 pC and 200 pC electron bunch charge. Statistical analysis showed short average pulse duration from 6 fs to 9 fs depending on the operational conditions. A high spatial degree of coherence of about 70-80% was determined in the spatial domain for the SASE beams with the monochromator and self-seeding regime of operation. The obtained values describe the statistical properties of the beams generated at the PAL-XFEL facility.
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Affiliation(s)
- Young Yong Kim
- Photon Science, Deutsche Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Ruslan Khubbutdinov
- Photon Science, Deutsche Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jerome Carnis
- Photon Science, Deutsche Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Sangsoo Kim
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Daewoong Nam
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
- Photon Science Center, POSTECH, Pohang 37673, Republic of Korea
| | - Inhyuk Nam
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyujin Kim
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Chi Hyun Shim
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Haeryong Yang
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Myunghoon Cho
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Chang-Ki Min
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Changbum Kim
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Heung-Sik Kang
- Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Ivan A. Vartanyants
- Photon Science, Deutsche Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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Abstract
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
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Affiliation(s)
- Ignacio de la Higuera
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
| | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
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35
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Colombo A, Zimmermann J, Langbehn B, Möller T, Peltz C, Sander K, Kruse B, Tümmler P, Barke I, Rupp D, Fennel T. The Scatman: an approximate method for fast wide-angle scattering simulations. J Appl Crystallogr 2022; 55:1232-1246. [PMID: 36249495 PMCID: PMC9533759 DOI: 10.1107/s1600576722008068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
Single-shot coherent diffraction imaging (CDI) is a powerful approach to characterize the structure and dynamics of isolated nanoscale objects such as single viruses, aerosols, nanocrystals and droplets. Using X-ray wavelengths, the diffraction images in CDI experiments usually cover only small scattering angles of a few degrees. These small-angle patterns represent the magnitude of the Fourier transform of the 2D projection of the sample's electron density, which can be reconstructed efficiently but lacks any depth information. In cases where the diffracted signal can be measured up to scattering angles exceeding ∼10°, i.e. in the wide-angle regime, some 3D morphological information of the target is contained in a single-shot diffraction pattern. However, the extraction of the 3D structural information is no longer straightforward and defines the key challenge in wide-angle CDI. So far, the most convenient approach relies on iterative forward fitting of the scattering pattern using scattering simulations. Here the Scatman is presented, an approximate and fast numerical tool for the simulation and iterative fitting of wide-angle scattering images of isolated samples. Furthermore, the open-source software implementation of the Scatman algorithm, PyScatman, is published and described in detail. The Scatman approach, which has already been applied in previous work for forward-fitting-based shape retrieval, adopts the multi-slice Fourier transform method. The effects of optical properties are partially included, yielding quantitative results for small, isolated and weakly interacting samples. PyScatman is capable of computing wide-angle scattering patterns in a few milliseconds even on consumer-level computing hardware, potentially enabling new data analysis schemes for wide-angle coherent diffraction experiments.
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Affiliation(s)
- Alessandro Colombo
- Laboratory for Solid State Physics, ETH Zürich, 8093 Zürich, Switzerland
| | - Julian Zimmermann
- Laboratory for Solid State Physics, ETH Zürich, 8093 Zürich, Switzerland
| | - Bruno Langbehn
- Institute for Optics and Atomic Physics, Technical University Berlin, 10623 Berlin, Germany
| | - Thomas Möller
- Institute for Optics and Atomic Physics, Technical University Berlin, 10623 Berlin, Germany
| | - Christian Peltz
- Institute for Physics, University of Rostock, 18059 Rostock, Germany
| | - Katharina Sander
- Institute for Physics, University of Rostock, 18059 Rostock, Germany
| | - Björn Kruse
- Institute for Physics, University of Rostock, 18059 Rostock, Germany
| | - Paul Tümmler
- Institute for Physics, University of Rostock, 18059 Rostock, Germany
| | - Ingo Barke
- Institute for Physics, University of Rostock, 18059 Rostock, Germany
- Department of Life, Light and Matter, University of Rostock, 18059 Rostock, Germany
| | - Daniela Rupp
- Laboratory for Solid State Physics, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Fennel
- Institute for Physics, University of Rostock, 18059 Rostock, Germany
- Department of Life, Light and Matter, University of Rostock, 18059 Rostock, Germany
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36
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Neurotransmitter uptake of synaptic vesicles studied by X-ray diffraction. EUROPEAN BIOPHYSICS JOURNAL 2022; 51:465-482. [PMID: 35904588 PMCID: PMC9463337 DOI: 10.1007/s00249-022-01609-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
The size, polydispersity, and electron density profile of synaptic vesicles (SVs) can be studied by small-angle X-ray scattering (SAXS), i.e. by X-ray diffraction from purified SV suspensions in solution. Here we show that size and shape transformations, as they appear in the functional context of these important synaptic organelles, can also be monitored by SAXS. In particular, we have investigated the active uptake of neurotransmitters, and find a mean vesicle radius increase of about 12% after the uptake of glutamate, which indicates an unusually large extensibility of the vesicle surface, likely to be accompanied by conformational changes of membrane proteins and rearrangements of the bilayer. Changes in the electron density profile (EDP) give first indications for such a rearrangement. Details of the protein structure are screened, however, by SVs polydispersity. To overcome the limitations of large ensemble averages and heterogeneous structures, we therefore propose serial X-ray diffraction by single free electron laser pulses. Using simulated data for realistic parameters, we show that this is in principle feasible, and that even spatial distances between vesicle proteins could be assessed by this approach.
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37
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Asi H, Dasgupta B, Nagai T, Miyashita O, Tama F. A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data. Front Mol Biosci 2022; 9:913860. [PMID: 36660427 PMCID: PMC9846856 DOI: 10.3389/fmolb.2022.913860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/04/2022] [Indexed: 01/06/2023] Open
Abstract
X-ray free-electron laser (XFEL) is the latest generation of the X-ray source that could become an invaluable technique in structural biology. XFEL has ultrashort pulse duration, extreme peak brilliance, and high spatial coherence, which could enable the observation of the biological molecules in near nature state at room temperature without crystallization. However, for biological systems, due to their low diffraction power and complexity of sample delivery, experiments and data analysis are not straightforward, making it extremely challenging to reconstruct three-dimensional (3D) structures from single particle XFEL data. Given the current limitations to the amount and resolution of the data from such XFEL experiments, we propose a new hybrid approach for characterizing biomolecular conformational transitions by using a single 2D low-resolution XFEL diffraction pattern in combination with another known conformation. In our method, we represent the molecular structure with a coarse-grained model, the Gaussian mixture model, to describe large conformational transitions from low-resolution XFEL data. We obtain plausible 3D structural models that are consistent with the XFEL diffraction pattern by deforming an initial structural model to maximize the similarity between the target pattern and the simulated diffraction patterns from the candidate models. We tested the proposed algorithm on two biomolecules of different sizes with different complexities of conformational transitions, adenylate kinase, and elongation factor 2, using synthetic XFEL data. The results show that, with the proposed algorithm, we can successfully describe the conformational transitions by flexibly fitting the coarse-grained model of one conformation to become consistent with an XFEL diffraction pattern simulated from another conformation. In addition, we showed that the incident beam orientation has some effect on the accuracy of the 3D structure modeling and discussed the reasons for the inaccuracies for certain orientations. The proposed method could serve as an alternative approach for retrieving information on 3D conformational transitions from the XFEL diffraction patterns to interpret experimental data. Since the molecules are represented by Gaussian kernels and no atomic structure is needed in principle, such a method could also be used as a tool to seek initial models for 3D reconstruction algorithms.
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Affiliation(s)
- Han Asi
- Department of Physics, Nagoya University, Nagoya, Japan
| | - Bhaskar Dasgupta
- Division of Biological Data Science, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro City, Japan
| | - Tetsuro Nagai
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, Kobe, Japan,*Correspondence: Osamu Miyashita, ; Florence Tama,
| | - Florence Tama
- Department of Physics, Nagoya University, Nagoya, Japan,RIKEN Center for Computational Science, Kobe, Japan,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan,*Correspondence: Osamu Miyashita, ; Florence Tama,
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38
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Cao M, Zhang K, Zhang S, Wang Y, Chen C. Advanced Light Source Analytical Techniques for Exploring the Biological Behavior and Fate of Nanomedicines. ACS CENTRAL SCIENCE 2022; 8:1063-1080. [PMID: 36032763 PMCID: PMC9413437 DOI: 10.1021/acscentsci.2c00680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 05/09/2023]
Abstract
Exploration of the biological behavior and fate of nanoparticles, as affected by the nanomaterial-biology (nano-bio) interaction, has become progressively critical for guiding the rational design and optimization of nanomedicines to minimize adverse effects, support clinical translation, and aid in evaluation by regulatory agencies. Because of the complexity of the biological environment and the dynamic variations in the bioactivity of nanomedicines, in-situ, label-free analysis of the transport and transformation of nanomedicines has remained a challenge. Recent improvements in optics, detectors, and light sources have allowed the expansion of advanced light source (ALS) analytical technologies to dig into the underexplored behavior and fate of nanomedicines in vivo. It is increasingly important to further develop ALS-based analytical technologies with higher spatial and temporal resolution, multimodal data fusion, and intelligent prediction abilities to fully unlock the potential of nanomedicines. In this Outlook, we focus on several selected ALS analytical technologies, including imaging and spectroscopy, and provide an overview of the emerging opportunities for their applications in the exploration of the biological behavior and fate of nanomedicines. We also discuss the challenges and limitations faced by current approaches and tools and the expectations for the future development of advanced light sources and technologies. Improved ALS imaging and spectroscopy techniques will accelerate a profound understanding of the biological behavior of new nanomedicines. Such advancements are expected to inspire new insights into nanomedicine research and promote the development of ALS capabilities and methods more suitable for nanomedicine evaluation with the goal of clinical translation.
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Affiliation(s)
- Mingjing Cao
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Kai Zhang
- Beijing
Synchrotron Radiation Facility, Institute
of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Shuhan Zhang
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Yaling Wang
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- The
GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
| | - Chunying Chen
- CAS
Key Laboratory for Biomedical Effects of Nanomedicines and Nanosafety
& CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- The
GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
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39
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Peck A, Chang HY, Dujardin A, Ramalingam D, Uervirojnangkoorn M, Wang Z, Mancuso A, Poitevin F, Yoon CH. Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules. J Appl Crystallogr 2022; 55:1002-1010. [PMID: 35974743 PMCID: PMC9348890 DOI: 10.1107/s1600576722005994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
X-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.
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Affiliation(s)
- Ariana Peck
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hsing-Yin Chang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Antoine Dujardin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Deeban Ramalingam
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Monarin Uervirojnangkoorn
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Zhaoyou Wang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Adrian Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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40
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Song L, Lam EY. Iterative phase retrieval with a sensor mask. OPTICS EXPRESS 2022; 30:25788-25802. [PMID: 36237101 DOI: 10.1364/oe.461367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/05/2022] [Indexed: 06/16/2023]
Abstract
As an important inverse imaging problem in diffraction optics, Fourier phase retrieval aims at estimating the latent image of the target object only from the magnitude of its Fourier measurement. Although in real applications alternating methods are widely-used for Fourier phase retrieval considering the constraints in the object and Fourier domains, they need a lot of initial guesses and iterations to achieve reasonable results. In this paper, we show that a proper sensor mask directly attached to the Fourier magnitude can improve the efficiency of the iterative phase retrieval algorithms, such as alternating direction method of multipliers (ADMM). Furthermore, we refer to the learning-based method to determine the sensor mask according to the Fourier measurement, and unrolled ADMM is used for phase retrieval. Numerical results show that our method outperforms other existing methods for the Fourier phase retrieval problem.
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41
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Zhao J, Xu W, Yi J, Wang B, Zhang F. Extended coherent modulation imaging for single-shot object retrieval free from illumination artifacts. Ultramicroscopy 2022; 240:113591. [DOI: 10.1016/j.ultramic.2022.113591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/05/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
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42
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Low-dose shift- and rotation-invariant diffraction recognition imaging. Sci Rep 2022; 12:11202. [PMID: 35778504 PMCID: PMC9249920 DOI: 10.1038/s41598-022-15486-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/24/2022] [Indexed: 12/04/2022] Open
Abstract
A low-dose imaging technique which uses recognition rather than recording of a full high-resolution image is proposed. A structural hypothesis is verified by probing the object with only a few particles (photons, electrons). Each scattered particle is detected in the far field and its position on the detector is analysed by applying Bayesian statistics. Already a few detected particles are sufficient to confirm a structural hypothesis at a probability exceeding 95%. As an example, the method is demonstrated as an application in optical character recognition, where a hand-written number is recognized from a set of different written numbers. In other provided examples, the structural hypothesis of a single macromolecule is recognized from a diffraction pattern acquired at an extremely low radiation dose, less than one X-ray photon or electron per Å2, thus leaving the macromolecule practically without any radiation damage. The proposed principle of low-dose recognition can be utilized in various applications, ranging from optical character recognition and optical security elements to recognizing a certain protein or its conformation.
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43
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Walter P, Osipov T, Lin MF, Cryan J, Driver T, Kamalov A, Marinelli A, Robinson J, Seaberg MH, Wolf TJA, Aldrich J, Brown N, Champenois EG, Cheng X, Cocco D, Conder A, Curiel I, Egger A, Glownia JM, Heimann P, Holmes M, Johnson T, Lee L, Li X, Moeller S, Morton DS, Ng ML, Ninh K, O’Neal JT, Obaid R, Pai A, Schlotter W, Shepard J, Shivaram N, Stefan P, Van X, Wang AL, Wang H, Yin J, Yunus S, Fritz D, James J, Castagna JC. The time-resolved atomic, molecular and optical science instrument at the Linac Coherent Light Source. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:957-968. [PMID: 35787561 PMCID: PMC9255571 DOI: 10.1107/s1600577522004283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
The newly constructed time-resolved atomic, molecular and optical science instrument (TMO) is configured to take full advantage of both linear accelerators at SLAC National Accelerator Laboratory, the copper accelerator operating at a repetition rate of 120 Hz providing high per-pulse energy as well as the superconducting accelerator operating at a repetition rate of about 1 MHz providing high average intensity. Both accelerators power a soft X-ray free-electron laser with the new variable-gap undulator section. With this flexible light source, TMO supports many experimental techniques not previously available at LCLS and will have two X-ray beam focus spots in line. Thereby, TMO supports atomic, molecular and optical, strong-field and nonlinear science and will also host a designated new dynamic reaction microscope with a sub-micrometer X-ray focus spot. The flexible instrument design is optimized for studying ultrafast electronic and molecular phenomena and can take full advantage of the sub-femtosecond soft X-ray pulse generation program.
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Affiliation(s)
- Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Timur Osipov
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ming-Fu Lin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - James Cryan
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Taran Driver
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrei Kamalov
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Agostino Marinelli
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Joe Robinson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matthew H. Seaberg
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas J. A. Wolf
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jeff Aldrich
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Nolan Brown
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Elio G. Champenois
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Xinxin Cheng
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniele Cocco
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alan Conder
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ivan Curiel
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Adam Egger
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - James M. Glownia
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Philip Heimann
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael Holmes
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Tyler Johnson
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Lance Lee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Xiang Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Stefan Moeller
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel S. Morton
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - May Ling Ng
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Kayla Ninh
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jordan T. O’Neal
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Razib Obaid
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Allen Pai
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - William Schlotter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jackson Shepard
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Niranjan Shivaram
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Peter Stefan
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Xiong Van
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Anna Li Wang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Hengzi Wang
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jing Yin
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sameen Yunus
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - David Fritz
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Justin James
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jean-Charles Castagna
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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Stransky M, Jurek Z, Santra R, Mancuso AP, Ziaja B. Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN. Molecules 2022; 27:molecules27134206. [PMID: 35807452 PMCID: PMC9267930 DOI: 10.3390/molecules27134206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 12/04/2022] Open
Abstract
In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility. In order to improve the XMDYN performance, we incorporated the existing tree-algorithm based Coulomb solver, PEPC, into the code, and developed a dedicated tree-algorithm based secondary ionization solver, now also included in the XMDYN code. These extensions enable computationally efficient simulations of X-ray irradiated large atomic assemblies, e.g., large protein systems or viruses that are of strong interest for ultrafast X-ray science. The XMDYN-based preparatory simulations can now guide future single-particle-imaging experiments at the free-electron-laser facility, EuXFEL.
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Affiliation(s)
- Michal Stransky
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany;
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland;
- Correspondence: (M.S.); (Z.J.)
| | - Zoltan Jurek
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany;
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Correspondence: (M.S.); (Z.J.)
| | - Robin Santra
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany;
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Notkestr. 9-11, 22607 Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany;
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Beata Ziaja
- Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland;
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany;
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45
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Abstract
SignificanceExcitation of molecules by an ultrashort laser pulse creates rotational wave packets that lead to transient alignment of the molecules along the laser polarization direction. Here, we show that a train of ultrashort laser pulses can be used to enhance the degree of alignment to a high level such that the diffraction from precisely timed ultrashort electron beams may be used to reconstruct the structure of the isolated molecules with atomic resolution through a coherent diffraction imaging technique. Our results mark a great step toward imaging noncrystallized molecules with atomic resolution and pave the way for creation of three-dimensional "molecular movies" at the femtosecond time scale and atomic spatial scale.
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Vakili M, Bielecki J, Knoška J, Otte F, Han H, Kloos M, Schubert R, Delmas E, Mills G, de Wijn R, Letrun R, Dold S, Bean R, Round A, Kim Y, Lima FA, Dörner K, Valerio J, Heymann M, Mancuso AP, Schulz J. 3D printed devices and infrastructure for liquid sample delivery at the European XFEL. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:331-346. [PMID: 35254295 PMCID: PMC8900844 DOI: 10.1107/s1600577521013370] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
The Sample Environment and Characterization (SEC) group of the European X-ray Free-Electron Laser (EuXFEL) develops sample delivery systems for the various scientific instruments, including systems for the injection of liquid samples that enable serial femtosecond X-ray crystallography (SFX) and single-particle imaging (SPI) experiments, among others. For rapid prototyping of various device types and materials, sub-micrometre precision 3D printers are used to address the specific experimental conditions of SFX and SPI by providing a large number of devices with reliable performance. This work presents the current pool of 3D printed liquid sample delivery devices, based on the two-photon polymerization (2PP) technique. These devices encompass gas dynamic virtual nozzles (GDVNs), mixing-GDVNs, high-viscosity extruders (HVEs) and electrospray conical capillary tips (CCTs) with highly reproducible geometric features that are suitable for time-resolved SFX and SPI experiments at XFEL facilities. Liquid sample injection setups and infrastructure on the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument are described, this being the instrument which is designated for biological structure determination at the EuXFEL.
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Affiliation(s)
| | | | - Juraj Knoška
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Florian Otte
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Physics, TU Dortmund, Otto-Hahn-Straße 4, 44221 Dortmund, Germany
| | - Huijong Han
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Elisa Delmas
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Simon Dold
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5AZ, United Kingdom
| | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Joana Valerio
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Michael Heymann
- Institute for Biomaterials and Biomolecular Systems (IBBS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne 3086, Australia
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Bellisario A, Maia FRNC, Ekeberg T. Noise reduction and mask removal neural network for X-ray single-particle imaging. J Appl Crystallogr 2022; 55:122-132. [PMID: 35145358 PMCID: PMC8805166 DOI: 10.1107/s1600576721012371] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/22/2021] [Indexed: 12/03/2022] Open
Abstract
Free-electron lasers could enable X-ray imaging of single biological macromolecules and the study of protein dynamics, paving the way for a powerful new imaging tool in structural biology, but a low signal-to-noise ratio and missing regions in the detectors, colloquially termed 'masks', affect data collection and hamper real-time evaluation of experimental data. In this article, the challenges posed by noise and masks are tackled by introducing a neural network pipeline that aims to restore diffraction intensities. For training and testing of the model, a data set of diffraction patterns was simulated from 10 900 different proteins with molecular weights within the range of 10-100 kDa and collected at a photon energy of 8 keV. The method is compared with a simple low-pass filtering algorithm based on autocorrelation constraints. The results show an improvement in the mean-squared error of roughly two orders of magnitude in the presence of masks compared with the noisy data. The algorithm was also tested at increasing mask width, leading to the conclusion that demasking can achieve good results when the mask is smaller than half of the central speckle of the pattern. The results highlight the competitiveness of this model for data processing and the feasibility of restoring diffraction intensities from unknown structures in real time using deep learning methods. Finally, an example is shown of this preprocessing making orientation recovery more reliable, especially for data sets containing very few patterns, using the expansion-maximization-compression algorithm.
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Affiliation(s)
- Alfredo Bellisario
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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48
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Density functional tight binding approach utilized to study X-ray-induced transitions in solid materials. Sci Rep 2022; 12:1551. [PMID: 35091574 PMCID: PMC8799736 DOI: 10.1038/s41598-022-04775-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/02/2021] [Indexed: 01/17/2023] Open
Abstract
Intense X-ray pulses from free-electron lasers can trigger ultrafast electronic, structural and magnetic transitions in solid materials, within a material volume which can be precisely shaped through adjustment of X-ray beam parameters. This opens unique prospects for material processing with X rays. However, any fundamental and applicational studies are in need of computational tools, able to predict material response to X-ray radiation. Here we present a dedicated computational approach developed to study X-ray induced transitions in a broad range of solid materials, including those of high chemical complexity. The latter becomes possible due to the implementation of the versatile density functional tight binding code DFTB+ to follow band structure evolution in irradiated materials. The outstanding performance of the implementation is demonstrated with a comparative study of XUV induced graphitization in diamond.
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Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene-maleic acid (SMA), diisobutylene-maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
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Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
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50
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In a flash of light: X-ray free electron lasers meet native mass spectrometry. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:89-99. [PMID: 34906329 DOI: 10.1016/j.ddtec.2021.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 06/14/2021] [Accepted: 07/13/2021] [Indexed: 01/02/2023]
Abstract
During the last years, X-ray free electron lasers (XFELs) have emerged as X-ray sources of unparalleled brightness, delivering extreme amounts of photons in femtosecond pulses. As such, they have opened up completely new possibilities in drug discovery and structural biology, including studying high resolution biomolecular structures and their functioning in a time resolved manner, and diffractive imaging of single particles without the need for their crystallization. In this perspective, we briefly review the operation of XFELs, their immediate uses for drug discovery and focus on the potentially revolutionary single particle diffractive imaging technique and the challenges which remain to be overcome to fully realize its potential to provide high resolution structures without the need for crystallization, freezing or the need to keep proteins stable at extreme concentrations for long periods of time. As the issues have been to a large extent sample delivery related, we outline a way for native mass spectrometry to overcome these and enable so far impossible research with a potentially huge impact on structural biology and drug discovery, such as studying structures of transient intermediate species in viral life cycles or during functioning of molecular machines.
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