1
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Round A, Jungcheng E, Fortmann-Grote C, Giewekemeyer K, Graceffa R, Kim C, Kirkwood H, Mills G, Round E, Sato T, Pascarelli S, Mancuso A. Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:141-162. [PMID: 38507205 DOI: 10.1007/978-3-031-52193-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.
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Affiliation(s)
| | | | | | | | | | - Chan Kim
- European XFEL, Schenefeld, Germany
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2
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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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3
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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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4
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Powell JA, Summers AM, Liu Q, Robatjazi SJ, Rupp P, Stierle J, Trallero-Herrero C, Kling MF, Rudenko A. Interplay of pulse duration, peak intensity, and particle size in laser-driven electron emission from silica nanospheres. OPTICS EXPRESS 2019; 27:27124-27135. [PMID: 31674579 DOI: 10.1364/oe.27.027124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
We present the results of a systematic study of photoelectron emission from isolated dielectric nanoparticles (SiO2) irradiated by intense 25 fs, 780 nm linearly polarized laser pulses as a function of particle size (20 nm to 750 nm in diameter) and laser intensity. We also introduce an experimental technique to reduce the effects of focal volume averaging. The highest photoelectron energies show a strong size dependence, increasing by a factor of six over the range of particles sizes studied at a fixed intensity. For smaller particle sizes (up to 200 nm), our findings agree well with earlier results obtained with few-cycle, ∼4 fs pulses. For large nanoparticles, which exhibit stronger near-field localization due to field-propagation effects, we observe the emission of much more energetic electrons, reaching energies up to ∼200 times the ponderomotive energy. This strong deviation in maximum photoelectron energy is attributed to the increase in ionization and charge interaction for many-cycle pulses at similar intensities.
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5
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Klimešová E, Kulyk O, Gu Y, Dittrich L, Korn G, Hajdu J, Krikunova M, Andreasson J. Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector. Sci Rep 2019; 9:8851. [PMID: 31221980 PMCID: PMC6586673 DOI: 10.1038/s41598-019-45120-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/22/2019] [Indexed: 11/30/2022] Open
Abstract
Aerosol nanoparticle injectors are fundamentally important for experiments where container-free sample handling is needed to study isolated nanoparticles. The injector consists of a nebuliser, a differential pumping unit, and an aerodynamic lens to create and deliver a focused particle beam to the interaction point inside a vacuum chamber. The tightest focus of the particle beam is close to the injector tip. The density of the focusing carrier gas is high at this point. We show here how this gas interacts with a near infrared laser pulse (800 nm wavelength, 120 fs pulse duration) at intensities approaching 1016 Wcm-2. We observe acceleration of gas ions to kinetic energies of 100s eV and study their energies as a function of the carrier gas density. Our results indicate that field ionisation by the intense near-infrared laser pulse opens up a plasma channel behind the laser pulse. The observations can be understood in terms of a Coulomb explosion of the created underdense plasma channel. The results can be used to estimate gas background in experiments with the injector and they open up opportunities for a new class of studies on electron and ion dynamics in nanoparticles surrounded by a low-density gas.
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Affiliation(s)
- Eva Klimešová
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic.
| | - Olena Kulyk
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Yanjun Gu
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Laura Dittrich
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
- Technische Universität Berlin, Institut für Optik und Atomare Physik, ER 1-1, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Georg Korn
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Janos Hajdu
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Maria Krikunova
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
- Technische Universität Berlin, Institut für Optik und Atomare Physik, ER 1-1, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Jakob Andreasson
- ELI Beamlines, Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
- Chalmers University of Technology, Department of Physics, Göteborg, Sweden
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6
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Mancuso AP, Aquila A, Batchelor L, Bean RJ, Bielecki J, Borchers G, Doerner K, Giewekemeyer K, Graceffa R, Kelsey OD, Kim Y, Kirkwood HJ, Legrand A, Letrun R, Manning B, Lopez Morillo L, Messerschmidt M, Mills G, Raabe S, Reimers N, Round A, Sato T, Schulz J, Signe Takem C, Sikorski M, Stern S, Thute P, Vagovič P, Weinhausen B, Tschentscher T. The Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography instrument of the European XFEL: initial installation. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:660-676. [PMID: 31074429 PMCID: PMC6510195 DOI: 10.1107/s1600577519003308] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/07/2019] [Indexed: 05/22/2023]
Abstract
The European X-ray Free-Electron Laser (FEL) became the first operational high-repetition-rate hard X-ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X-ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X-ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time-resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X-ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward-scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation - in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described.
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Affiliation(s)
- 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, Victoria 3086, Australia
| | - Andrew Aquila
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | | | | | | | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | | | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Steffen Raabe
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | - Nadja Reimers
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Adam Round
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
| | | | | | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Prasad Thute
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Patrik Vagovič
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany
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7
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Shi Y, Yin K, Tai X, DeMirci H, Hosseinizadeh A, Hogue BG, Li H, Ourmazd A, Schwander P, Vartanyants IA, Yoon CH, Aquila A, Liu H. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data. IUCRJ 2019; 6:331-340. [PMID: 30867930 PMCID: PMC6400180 DOI: 10.1107/s2052252519001854] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/31/2019] [Indexed: 05/22/2023]
Abstract
Using X-ray free-electron lasers (XFELs), it is possible to determine three-dimensional structures of nanoscale particles using single-particle imaging methods. Classification algorithms are needed to sort out the single-particle diffraction patterns from the large amount of XFEL experimental data. However, different methods often yield inconsistent results. This study compared the performance of three classification algorithms: convolutional neural network, graph cut and diffusion map manifold embedding methods. The identified single-particle diffraction data of the PR772 virus particles were assembled in the three-dimensional Fourier space for real-space model reconstruction. The comparison showed that these three classification methods lead to different datasets and subsequently result in different electron density maps of the reconstructed models. Interestingly, the common dataset selected by these three methods improved the quality of the merged diffraction volume, as well as the resolutions of the reconstructed maps.
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Affiliation(s)
- Yingchen Shi
- Department of Engineering Physics, Tsinghua University, 30 Shuangqing Rd, Haidian, Beijing 100084, People’s Republic of China
- Complex Systems Division, Beijing Computational Science Research Centre, 8 E Xibeiwang Rd, Haidian, Beijing 100193, People’s Republic of China
| | - Ke Yin
- Center for Mathematical Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, People’s Republic of China
| | - Xuecheng Tai
- Department of Mathematics, University of Bergen, PO Box 7800, Bergen, 5020, Norway
| | - Hasan DeMirci
- Biosciences Division, 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
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin USA
| | - Brenda G. Hogue
- Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute at Arizona State University, Tempe, 85287, USA
| | - Haoyuan Li
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Physics, Stanford University, 450 Serra Mall, Stanford, CA 94305, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin USA
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow, 115409, Russian Federation
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Centre, 8 E Xibeiwang Rd, Haidian, Beijing 100193, People’s Republic of China
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8
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Liu J, van der Schot G, Engblom S. Supervised classification methods for flash X-ray single particle diffraction imaging. OPTICS EXPRESS 2019; 27:3884-3899. [PMID: 30876013 DOI: 10.1364/oe.27.003884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
Current Flash X-ray single-particle diffraction Imaging (FXI) experiments, which operate on modern X-ray Free Electron Lasers (XFELs), can record millions of interpretable diffraction patterns from individual biomolecules per day. Due to the practical limitations with the FXI technology, those patterns will to a varying degree include scatterings from contaminated samples. Also, the heterogeneity of the sample biomolecules is unavoidable and complicates data processing. Reducing the data volumes and selecting high-quality single-molecule patterns are therefore critical steps in the experimental setup. In this paper, we present two supervised template-based learning methods for classifying FXI patterns. Our Eigen-Image and Log-Likelihood classifier can find the best-matched template for a single-molecule pattern within a few milliseconds. It is also straightforward to parallelize them so as to match the XFEL repetition rate fully, thereby enabling processing at site. The methods perform in a stable way on various kinds of synthetic data. As a practical example we tested our methods on a real mimivirus dataset, obtaining a convincing classification accuracy of 0.9.
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9
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Ab initio structure determination from experimental fluctuation X-ray scattering data. Proc Natl Acad Sci U S A 2018; 115:11772-11777. [PMID: 30373827 PMCID: PMC6243272 DOI: 10.1073/pnas.1812064115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Fluctuation X-ray scattering is a biophysical structural characterization technique that overcomes low data-to-parameter ratios encountered in traditional X-ray methods used for studying noncrystalline samples. By collecting a series of ultrashort X-ray exposures on an ensemble of particles at a free-electron laser, information-dense experimental data can be extracted that ultimately result in structures with a greater level of detail than can be obtained using traditional X-ray scattering methods. In this article we demonstrate the practical feasibility of this technique by introducing data-processing techniques and advanced noise-filtering methods that reduce the required data collection time to less than a few minutes. This will ultimately allow one to visualize details of structural dynamics that may be inaccessible through traditional methods. Fluctuation X-ray scattering (FXS) is an emerging experimental technique in which X-ray solution scattering data are collected from particles in solution using ultrashort X-ray exposures generated by a free-electron laser (FEL). FXS experiments overcome the low data-to-parameter ratios associated with traditional solution scattering measurements by providing several orders of magnitude more information in the final processed data. Here we demonstrate the practical feasibility of FEL-based FXS on a biological multiple-particle system and describe data-processing techniques required to extract robust FXS data and significantly reduce the required number of snapshots needed by introducing an iterative noise-filtering technique. We showcase a successful ab initio electron density reconstruction from such an experiment, studying the Paramecium bursaria Chlorella virus (PBCV-1).
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10
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Östlin C, Tîmneanu N, Jönsson HO, Ekeberg T, Martin AV, Caleman C. Reproducibility of single protein explosions induced by X-ray lasers. Phys Chem Chem Phys 2018; 20:12381-12389. [PMID: 29488514 DOI: 10.1039/c7cp07267h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems - four polypeptides with different amounts of surface bound water - were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.
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Affiliation(s)
- Christofer Östlin
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
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11
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Current Status of Single Particle Imaging with X-ray Lasers. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8010132] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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Jönsson HO, Caleman C, Andreasson J, Tîmneanu N. Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission. IUCRJ 2017; 4:778-784. [PMID: 29123680 PMCID: PMC5668863 DOI: 10.1107/s2052252517014154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/02/2017] [Indexed: 05/31/2023]
Abstract
Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.
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Affiliation(s)
- H. Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-226 07 Hamburg, Germany
| | - Jakob Andreasson
- ELI Beamlines, Institute of Physics, Czech Academy of Science, Na Slovance 2, CZ-182 21 Prague, Czech Republic
- Condensed Matter Physics, Department of Physics, Chalmers University of Technology, SE-412 96, Göteborg, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Nicuşor Tîmneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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13
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Kurta RP, Donatelli JJ, Yoon CH, Berntsen P, Bielecki J, Daurer BJ, DeMirci H, Fromme P, Hantke MF, Maia FRNC, Munke A, Nettelblad C, Pande K, Reddy HKN, Sellberg JA, Sierra RG, Svenda M, van der Schot G, Vartanyants IA, Williams GJ, Xavier PL, Aquila A, Zwart PH, Mancuso AP. Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses. PHYSICAL REVIEW LETTERS 2017; 119:158102. [PMID: 29077445 PMCID: PMC5757528 DOI: 10.1103/physrevlett.119.158102] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Indexed: 05/19/2023]
Abstract
We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.
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Affiliation(s)
- Ruslan P Kurta
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - Jeffrey J Donatelli
- Mathematics Department, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Peter Berntsen
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Hasan DeMirci
- Biosciences Division, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Max Felix Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- Division of Scientific Computing, Science for Life Laboratory, Department of Information Technology, Uppsala University, SE-751 05 Uppsala, Sweden
| | - Kanupriya Pande
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Hemanth K N Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Jonas A Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm SE-106 91, Sweden
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Gijs van der Schot
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Ivan A Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, D-22607 Hamburg, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, 115409 Moscow, Russia
| | - Garth J Williams
- NSLS-II, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973, USA
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, 22607 Hamburg, Germany
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Peter H Zwart
- Center for Advanced Mathematics for Energy Research Applications, 1 Cyclotron Road, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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14
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Single molecule imaging using X-ray free electron lasers. Curr Opin Struct Biol 2016; 40:186-194. [DOI: 10.1016/j.sbi.2016.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/21/2016] [Accepted: 11/21/2016] [Indexed: 02/02/2023]
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15
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Foucar L. CFEL-ASG Software Suite ( CASS): usage for free-electron laser experiments with biological focus. J Appl Crystallogr 2016; 49:1336-1346. [PMID: 27504079 PMCID: PMC4970498 DOI: 10.1107/s1600576716009201] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/07/2016] [Indexed: 11/29/2022] Open
Abstract
CASS [Foucar et al. (2012). Comput. Phys. Commun.183, 2207-2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of CASS for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.
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Affiliation(s)
- Lutz Foucar
- Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
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16
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Bobkov SA, Teslyuk AB, Kurta RP, Gorobtsov OY, Yefanov OM, Ilyin VA, Senin RA, Vartanyants IA. Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1345-52. [PMID: 26524297 DOI: 10.1107/s1600577515017348] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/16/2015] [Indexed: 05/22/2023]
Abstract
Modern X-ray free-electron lasers (XFELs) operating at high repetition rates produce a tremendous amount of data. It is a great challenge to classify this information and reduce the initial data set to a manageable size for further analysis. Here an approach for classification of diffraction patterns measured in prototypical diffract-and-destroy single-particle imaging experiments at XFELs is presented. It is proposed that the data are classified on the basis of a set of parameters that take into account the underlying diffraction physics and specific relations between the real-space structure of a particle and its reciprocal-space intensity distribution. The approach is demonstrated by applying principal component analysis and support vector machine algorithms to the simulated and measured X-ray data sets.
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Affiliation(s)
- S A Bobkov
- National Research Centre `Kurchatov Institute', Akademika Kurchatova pl. 1, 123182 Moscow, Russia
| | - A B Teslyuk
- National Research Centre `Kurchatov Institute', Akademika Kurchatova pl. 1, 123182 Moscow, Russia
| | - R P Kurta
- European XFEL GmbH, Albert-Einstein-Ring 19, D-22761 Hamburg, Germany
| | - O Yu Gorobtsov
- National Research Centre `Kurchatov Institute', Akademika Kurchatova pl. 1, 123182 Moscow, Russia
| | - O M Yefanov
- Center for Free-Electron Laser Science, Notkestrasse 85, D-22607 Hamburg, Germany
| | - V A Ilyin
- National Research Centre `Kurchatov Institute', Akademika Kurchatova pl. 1, 123182 Moscow, Russia
| | - R A Senin
- National Research Centre `Kurchatov Institute', Akademika Kurchatova pl. 1, 123182 Moscow, Russia
| | - I A Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
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17
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Rath AD, Timneanu N, Maia FRNC, Bielecki J, Fleckenstein H, Iwan B, Svenda M, Hasse D, Carlsson G, Westphal D, Mühlig K, Hantke M, Ekeberg T, Seibert MM, Zani A, Liang M, Stellato F, Kirian R, Bean R, Barty A, Galli L, Nass K, Barthelmess M, Aquila A, Toleikis S, Treusch R, Roling S, Wöstmann M, Zacharias H, Chapman HN, Bajt S, DePonte D, Hajdu J, Andreasson J. Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser. OPTICS EXPRESS 2014; 22:28914-28925. [PMID: 25402130 DOI: 10.1364/oe.22.028914] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 10¹⁶W/cm² with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.
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