1
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Sanchez del Rio M, Celestre R, Reyes-Herrera J. X-ray lens figure errors retrieved by deep learning from several beam intensity images. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:1001-1009. [PMID: 39042577 PMCID: PMC11371063 DOI: 10.1107/s1600577524004958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/26/2024] [Indexed: 07/25/2024]
Abstract
The phase problem in the context of focusing synchrotron beams with X-ray lenses is addressed. The feasibility of retrieving the surface error of a lens system by using only the intensity of the propagated beam at several distances is demonstrated. A neural network, trained with a few thousand simulations using random errors, can predict accurately the lens error profile that accounts for all aberrations. It demonstrates the feasibility of routinely measuring the aberrations induced by an X-ray lens, or another optical system, using only a few intensity images.
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Affiliation(s)
| | - Rafael Celestre
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000Grenoble, France
| | - Juan Reyes-Herrera
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000Grenoble, France
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2
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Siano M, Geloni G, Paroli B, Butti D, Lefèvre T, Mazzoni S, Trad G, Iriso U, Nosych AA, Torino L, Potenza MAC. FOCUS: fast Monte Carlo approach to coherence of undulator sources. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:217-226. [PMID: 36601940 PMCID: PMC9814064 DOI: 10.1107/s1600577522010748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
FOCUS (Fast Monte CarlO approach to Coherence of Undulator Sources) is a new GPU-based simulation code to compute the transverse coherence of undulator radiation from ultra-relativistic electrons. The core structure of the code, which is written in the language C++ accelerated with CUDA, combines an analytical description of the emitted electric fields and massively parallel computations on GPUs. The combination is rigorously justified by a statistical description of synchrotron radiation based on a Fourier optics approach. FOCUS is validated by direct comparison with multi-electron Synchrotron Radiation Workshop (SRW) simulations, evidencing a reduction in computation times by up to five orders of magnitude on a consumer laptop. FOCUS is then applied to systematically study the transverse coherence in typical third- and fourth-generation facilities, highlighting peculiar features of undulator sources close to the diffraction limit. FOCUS is aimed at fast evaluation of the transverse coherence of undulator radiation as a function of the electron beam parameters, to support and help prepare more advanced and detailed numerical simulations with traditional codes like SRW.
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Affiliation(s)
- M. Siano
- Dipartimento di Fisica, Università degli Studi di Milano, INFN Sezione di Milano, and CIMAINA, via G. Celoria 16, 20133 Milan, Italy
| | - G. Geloni
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - B. Paroli
- Dipartimento di Fisica, Università degli Studi di Milano, INFN Sezione di Milano, and CIMAINA, via G. Celoria 16, 20133 Milan, Italy
| | - D. Butti
- CERN, CH-1211 Geneva, Switzerland
| | | | | | - G. Trad
- CERN, CH-1211 Geneva, Switzerland
| | - U. Iriso
- ALBA-CELLS Synchrotron Radiation Facility, Carrer de la Llum 2-26, 08290 Cerdanyola del Valles, Barcelona, Spain
| | - A. A. Nosych
- ALBA-CELLS Synchrotron Radiation Facility, Carrer de la Llum 2-26, 08290 Cerdanyola del Valles, Barcelona, Spain
| | - L. Torino
- ALBA-CELLS Synchrotron Radiation Facility, Carrer de la Llum 2-26, 08290 Cerdanyola del Valles, Barcelona, Spain
| | - M. A. C. Potenza
- Dipartimento di Fisica, Università degli Studi di Milano, INFN Sezione di Milano, and CIMAINA, via G. Celoria 16, 20133 Milan, Italy
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3
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Lyubomirskiy M, Wittwer F, Kahnt M, Koch F, Kubec A, Falch KV, Garrevoet J, Seyrich M, David C, Schroer CG. Multi-beam X-ray ptychography using coded probes for rapid non-destructive high resolution imaging of extended samples. Sci Rep 2022; 12:6203. [PMID: 35418587 PMCID: PMC9008058 DOI: 10.1038/s41598-022-09466-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
Imaging large areas of a sample non-destructively and with high resolution is of great interest for both science and industry. For scanning coherent X-ray diffraction microscopy, i. e., ptychography, the achievable scan area at a given spatial resolution is limited by the coherent photon flux of modern X-ray sources. Multibeam X-ray ptychography can improve the scanning speed by scanning the sample with several parallel mutually incoherent beams, e. g., generated by illuminating multiple focusing optics in parallel by a partially coherent beam. The main difficulty with this scheme is the robust separation of the superimposed signals from the different beams, especially when the beams and the illuminated sample areas are quite similar. We overcome this difficulty by encoding each of the probing beams with its own X-ray phase plate. This helps the algorithm to robustly reconstruct the multibeam data. We compare the coded multibeam scans to uncoded multibeam and single beam scans, demonstrating the enhanced performance on a microchip sample with regular and repeating structures.
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Affiliation(s)
- Mikhail Lyubomirskiy
- Center for X-ray and Nano Science CXNS, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
| | - Felix Wittwer
- Center for X-ray and Nano Science CXNS, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Maik Kahnt
- MAX IV Laboratory, Lund University, Box 118, 221 00, Lund, Sweden
| | - Frieder Koch
- Paul-Scherrer-Institut (PSI), Forschungsstr. 111, 5232, Villigen, Switzerland.,GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, 64291, Darmstadt, Germany
| | - Adam Kubec
- Paul-Scherrer-Institut (PSI), Forschungsstr. 111, 5232, Villigen, Switzerland.,XRnanotech GmbH, Forschungsstr. 111,ODRA 117, 5232, Villigen, Switzerland
| | - Ken Vidar Falch
- Center for X-ray and Nano Science CXNS, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jan Garrevoet
- Center for X-ray and Nano Science CXNS, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Martin Seyrich
- Center for X-ray and Nano Science CXNS, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Christian David
- Paul-Scherrer-Institut (PSI), Forschungsstr. 111, 5232, Villigen, Switzerland
| | - Christian G Schroer
- Center for X-ray and Nano Science CXNS, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.,Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Helmholtz Imaging Platform, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
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4
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Sanchez-Cano C, Alvarez-Puebla RA, Abendroth JM, Beck T, Blick R, Cao Y, Caruso F, Chakraborty I, Chapman HN, Chen C, Cohen BE, Conceição ALC, Cormode DP, Cui D, Dawson KA, Falkenberg G, Fan C, Feliu N, Gao M, Gargioni E, Glüer CC, Grüner F, Hassan M, Hu Y, Huang Y, Huber S, Huse N, Kang Y, Khademhosseini A, Keller TF, Körnig C, Kotov NA, Koziej D, Liang XJ, Liu B, Liu S, Liu Y, Liu Z, Liz-Marzán LM, Ma X, Machicote A, Maison W, Mancuso AP, Megahed S, Nickel B, Otto F, Palencia C, Pascarelli S, Pearson A, Peñate-Medina O, Qi B, Rädler J, Richardson JJ, Rosenhahn A, Rothkamm K, Rübhausen M, Sanyal MK, Schaak RE, Schlemmer HP, Schmidt M, Schmutzler O, Schotten T, Schulz F, Sood AK, Spiers KM, Staufer T, Stemer DM, Stierle A, Sun X, Tsakanova G, Weiss PS, Weller H, Westermeier F, Xu M, Yan H, Zeng Y, Zhao Y, Zhao Y, Zhu D, Zhu Y, Parak WJ. X-ray-Based Techniques to Study the Nano-Bio Interface. ACS NANO 2021; 15:3754-3807. [PMID: 33650433 PMCID: PMC7992135 DOI: 10.1021/acsnano.0c09563] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/25/2021] [Indexed: 05/03/2023]
Abstract
X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.
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Affiliation(s)
- Carlos Sanchez-Cano
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
| | - Ramon A. Alvarez-Puebla
- Universitat
Rovira i Virgili, 43007 Tarragona, Spain
- ICREA, Passeig Lluís
Companys 23, 08010 Barcelona, Spain
| | - John M. Abendroth
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
| | - Tobias Beck
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Robert Blick
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yuan Cao
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Frank Caruso
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology
and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Indranath Chakraborty
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Henry N. Chapman
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Centre
for Ultrafast Imaging, Universität
Hamburg, 22761 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Chunying Chen
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Bruce E. Cohen
- The
Molecular Foundry and Division of Molecular Biophysics and Integrated
Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - David P. Cormode
- Radiology
Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daxiang Cui
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Gerald Falkenberg
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Chunhai Fan
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Neus Feliu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- CAN, Fraunhofer Institut, 20146 Hamburg, Germany
| | - Mingyuan Gao
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Elisabetta Gargioni
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Claus-C. Glüer
- Section
Biomedical Imaging, Department of Radiology and Neuroradiology, University Medical Clinic Schleswig-Holstein and Christian-Albrechts-University
Kiel, 24105 Kiel, Germany
| | - Florian Grüner
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Moustapha Hassan
- Karolinska University Hospital, Huddinge, and Karolinska
Institutet, 17177 Stockholm, Sweden
| | - Yong Hu
- College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Yalan Huang
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Samuel Huber
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nils Huse
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yanan Kang
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation, Los Angeles, California 90049, United States
| | - Thomas F. Keller
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Christian Körnig
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Nicholas A. Kotov
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Michigan
Institute for Translational Nanotechnology (MITRAN), Ypsilanti, Michigan 48198, United States
| | - Dorota Koziej
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Xing-Jie Liang
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Beibei Liu
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 China
| | - Yang Liu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ziyao Liu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Luis M. Liz-Marzán
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Centro de Investigación Biomédica
en Red de Bioingeniería,
Biomateriales y Nanomedicina (CIBER-BBN), Paseo de Miramon 182, 20014 Donostia-San Sebastián, Spain
| | - Xiaowei Ma
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Andres Machicote
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wolfgang Maison
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La
Trobe Institute for Molecular
Science, La Trobe University, Melbourne 3086, Victoria, Australia
| | - Saad Megahed
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Bert Nickel
- Sektion Physik, Ludwig Maximilians Universität
München, 80539 München, Germany
| | - Ferdinand Otto
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Cristina Palencia
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | | | - Arwen Pearson
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Oula Peñate-Medina
- Section
Biomedical Imaging, Department of Radiology and Neuroradiology, University Medical Clinic Schleswig-Holstein and Christian-Albrechts-University
Kiel, 24105 Kiel, Germany
| | - Bing Qi
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Joachim Rädler
- Sektion Physik, Ludwig Maximilians Universität
München, 80539 München, Germany
| | - Joseph J. Richardson
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology
and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Axel Rosenhahn
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kai Rothkamm
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Michael Rübhausen
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | | | - Raymond E. Schaak
- Department of Chemistry, Department of Chemical Engineering,
and
Materials Research Institute, The Pennsylvania
State University, University Park, Pensylvania 16802, United States
| | - Heinz-Peter Schlemmer
- Department of Radiology, German Cancer
Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marius Schmidt
- Department of Physics, University
of Wisconsin-Milwaukee, 3135 N. Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Oliver Schmutzler
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Florian Schulz
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - A. K. Sood
- Department of Physics, Indian Institute
of Science, Bangalore 560012, India
| | - Kathryn M. Spiers
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Theresa Staufer
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dominik M. Stemer
- California NanoSystems Institute, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Andreas Stierle
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Xing Sun
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Molecular Science and Biomedicine Laboratory (MBL) State
Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Gohar Tsakanova
- Institute of Molecular Biology of National
Academy of Sciences of
Republic of Armenia, 7 Hasratyan str., 0014 Yerevan, Armenia
- CANDLE Synchrotron Research Institute, 31 Acharyan str., 0040 Yerevan, Armenia
| | - Paul S. Weiss
- California NanoSystems Institute, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Horst Weller
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- CAN, Fraunhofer Institut, 20146 Hamburg, Germany
| | - Fabian Westermeier
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 China
| | - Huijie Yan
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yuan Zeng
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ying Zhao
- Karolinska University Hospital, Huddinge, and Karolinska
Institutet, 17177 Stockholm, Sweden
| | - Yuliang Zhao
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Dingcheng Zhu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ying Zhu
- Bioimaging Center, Shanghai Synchrotron Radiation Facility,
Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Division of Physical Biology, CAS Key Laboratory
of Interfacial
Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Wolfgang J. Parak
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Hu L, Sutter JP, Wang H. Fast convolution-based performance estimation method for diffraction-limited source with imperfect X-ray optics. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1539-1552. [PMID: 33147179 PMCID: PMC7642962 DOI: 10.1107/s1600577520012825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Although optical element error analysis is always an important part of beamline design for highly coherent synchrotron radiation or free-electron laser sources, the usual wave optics simulation can be very time-consuming, which limits its application at the early stage of the beamline design. In this work, a new theoretical approach has been proposed for quick evaluations of the optical performance degradation due to optical element error. In this way, time-consuming detailed simulations can be applied only when truly necessary. This approach treats the imperfections as perturbations that convolve with the ideal performance. For simplicity, but not by necessity, the Gaussian Schell-model has been used to show the application of this theoretical approach. The influences of the finite aperture size and height error of a focusing mirror are analysed using the proposed theory. The physical explanation of the performance degradation acquired from the presented approach helps to give a better definition of the critical range of error spatial frequencies that most affect the performance of a mirror. An example comparing two mirror surface errors with identical power spectral density functions is given. These two types of mirror surface errors result in very different intensity profiles. The approach presented in this work could help beamline designers specify the error tolerances on general optical elements more accurately.
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Affiliation(s)
- Lingfei Hu
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B Yuquan Road, Shijingshan District, Beijing 100049, People’s Republic of China
| | - John P. Sutter
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Hongchang Wang
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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6
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Dufresne EM, Narayanan S, Reininger R, Sandy AR, Lurio L. Focusing a round coherent beam by spatial filtering the horizontal source. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1528-1538. [PMID: 33147178 PMCID: PMC7842205 DOI: 10.1107/s1600577520012163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
This paper illustrates the use of spatial filtering with a horizontal slit near the source to enlarge the horizontal coherence in an experimental station and produce a diffraction-limited round focus at an insertion device beamline for X-ray photon correlation spectroscopy experiments. Simple expressions are provided to guide the optical layout, and wave propagation simulations confirm their applicability. The two-dimensional focusing performance of Be compound refractive lenses to produce a round diffraction-limited focus at 11 keV capable of generating a high-contrast speckle pattern of an aerogel sample is demonstrated. The coherent scattering patterns have comparable speckle sizes in both horizontal and vertical directions. The focal spot sizes are consistent with hybrid ray-tracing calculations. Producing a two-dimensional focus on the sample can be helpful to resolve speckle patterns with modern pixel array detectors with high visibility. This scheme has now been in use since 2019 for the 8-ID beamline at the Advanced Photon Source, sharing the undulator beam with two separate beamlines, 8-ID-E and 8-ID-I at 7.35 keV, with increased partially coherent flux, reduced horizontal spot sizes on samples, and good speckle contrast.
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Affiliation(s)
- Eric M. Dufresne
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Suresh Narayanan
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ruben Reininger
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Alec R. Sandy
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Larry Lurio
- Department of Physics, Northern Illinois University, DeKalb, IL, USA
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7
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Seiboth F, Brückner D, Kahnt M, Lyubomirskiy M, Wittwer F, Dzhigaev D, Ullsperger T, Nolte S, Koch F, David C, Garrevoet J, Falkenberg G, Schroer CG. Hard X-ray wavefront correction via refractive phase plates made by additive and subtractive fabrication techniques. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1121-1130. [PMID: 32876586 PMCID: PMC7467333 DOI: 10.1107/s1600577520007900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/11/2020] [Indexed: 06/02/2023]
Abstract
Modern subtractive and additive manufacturing techniques present new avenues for X-ray optics with complex shapes and patterns. Refractive phase plates acting as glasses for X-ray optics have been fabricated, and spherical aberration in refractive X-ray lenses made from beryllium has been successfully corrected. A diamond phase plate made by femtosecond laser ablation was found to improve the Strehl ratio of a lens stack with a numerical aperture (NA) of 0.88 × 10-3 at 8.2 keV from 0.1 to 0.7. A polymer phase plate made by additive printing achieved an increase in the Strehl ratio of a lens stack at 35 keV with NA of 0.18 × 10-3 from 0.15 to 0.89, demonstrating diffraction-limited nanofocusing at high X-ray energies.
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Affiliation(s)
- Frank Seiboth
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dennis Brückner
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Maik Kahnt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Felix Wittwer
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dmitry Dzhigaev
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Tobias Ullsperger
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Strasse 15, 07745 Jena, Germany
| | - Stefan Nolte
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Strasse 15, 07745 Jena, Germany
- Fraunhofer Institute for Applied Optics and Precision Engineering, Albert-Einstein-Strasse 7, 07745 Jena, Germany
| | - Frieder Koch
- Laboratory for Micro- and Nanotechnology, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Christian David
- Laboratory for Micro- and Nanotechnology, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jan Garrevoet
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Gerald Falkenberg
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian G. Schroer
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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8
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Schropp A, Döhrmann R, Botta S, Brückner D, Kahnt M, Lyubomirskiy M, Ossig C, Scholz M, Seyrich M, Stuckelberger ME, Wiljes P, Wittwer F, Garrevoet J, Falkenberg G, Fam Y, Sheppard TL, Grunwaldt JD, Schroer CG. PtyNAMi: ptychographic nano-analytical microscope. J Appl Crystallogr 2020; 53:957-971. [PMID: 32788903 PMCID: PMC7401781 DOI: 10.1107/s1600576720008420] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ptychographic X-ray imaging at the highest spatial resolution requires an optimal experimental environment, providing a high coherent flux, excellent mechanical stability and a low background in the measured data. This requires, for example, a stable performance of all optical components along the entire beam path, high temperature stability, a robust sample and optics tracking system, and a scatter-free environment. This contribution summarizes the efforts along these lines to transform the nanoprobe station on beamline P06 (PETRA III) into the ptychographic nano-analytical microscope (PtyNAMi).
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Affiliation(s)
- Andreas Schropp
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Ralph Döhrmann
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Stephan Botta
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Dennis Brückner
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, DE-22761 Hamburg, Germany
| | - Maik Kahnt
- Department Physik, Universität Hamburg, Luruper Chaussee 149, DE-22761 Hamburg, Germany
- MAX IV Laboratory, Fotongatan 2, SE-225 94 Lund, Sweden
| | - Mikhail Lyubomirskiy
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Christina Ossig
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, DE-22761 Hamburg, Germany
| | - Maria Scholz
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, DE-22761 Hamburg, Germany
| | - Martin Seyrich
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, DE-22761 Hamburg, Germany
| | | | - Patrik Wiljes
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Felix Wittwer
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, DE-22761 Hamburg, Germany
| | - Jan Garrevoet
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Gerald Falkenberg
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Yakub Fam
- Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstrasse 20, DE-76131 Karlsruhe, Germany
| | - Thomas L. Sheppard
- Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstrasse 20, DE-76131 Karlsruhe, Germany
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, DE-76344 Eggenstein-Leopoldshafen, Germany
| | - Jan-Dierk Grunwaldt
- Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstrasse 20, DE-76131 Karlsruhe, Germany
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, DE-76344 Eggenstein-Leopoldshafen, Germany
| | - Christian G. Schroer
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, DE-22761 Hamburg, Germany
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9
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Celestre R, Berujon S, Roth T, Sanchez del Rio M, Barrett R. Modelling phase imperfections in compound refractive lenses. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:305-318. [PMID: 32153269 PMCID: PMC7842213 DOI: 10.1107/s1600577519017235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/25/2019] [Indexed: 05/12/2023]
Abstract
A framework based on physical optics for simulating the effect of imperfect compound refractive lenses (CRLs) upon an X-ray beam is described, taking into account measured phase errors obtained from at-wavelength metrology. A CRL stack is modelled, with increasing complexity, as a single thin phase element, then as a more realistic compound element including absorption and thickness effects, and finally adding realistic optical imperfections to the CRL. Coherent and partially coherent simulations using Synchrotron Radiation Workshop (SRW) are used to evaluate the different models, the effects of the phase errors and to check the validity of the design equations and suitability of the figures of merit.
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Affiliation(s)
- Rafael Celestre
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sebastien Berujon
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Thomas Roth
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | - Raymond Barrett
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
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10
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Khubbutdinov R, Menushenkov AP, Vartanyants IA. Coherence properties of the high-energy fourth-generation X-ray synchrotron sources. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:1851-1862. [PMID: 31721727 PMCID: PMC6853378 DOI: 10.1107/s1600577519013079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/23/2019] [Indexed: 05/22/2023]
Abstract
An analysis of the coherence properties of the fourth-generation high-energy storage rings with emittance values of 10 pm rad is performed. It is presently expected that a storage ring with these low emittance values will reach diffraction limit at hard X-rays. Simulations of coherence properties were performed with the XRT software and an analytical approach for different photon energies from 500 eV to 50 keV. It was demonstrated that a minimum photon emittance (diffraction limit) reached at such storage rings is λ/2π. Using mode decomposition it is shown that, for the parameters of the storage ring considered in this work, the diffraction limit will be reached for soft X-ray energies of 500 eV. About ten modes will contribute to the radiation field at 12 keV photon energy and even more modes give a contribution at higher photon energies. Energy spread effects of the electron beam in a low-emittance storage ring were analysed in detail. Simulations were performed at different relative energy spread values from zero to 2 × 10-3. A decrease of the degree of coherence with an increase of the relative energy spread value was observed. This analysis shows that, to reach the diffraction limit for high photon energies, electron beam emittance should go down to 1 pm rad and below.
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Affiliation(s)
- R. Khubbutdinov
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow 115409, Russian Federation
| | - A. P. Menushenkov
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow 115409, Russian Federation
| | - I. A. Vartanyants
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow 115409, Russian Federation
- Correspondence e-mail:
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11
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Methods for Determining and Understanding Serpin Structure and Function: X-Ray Crystallography. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1826:9-39. [PMID: 30194591 DOI: 10.1007/978-1-4939-8645-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Deciphering the X-ray crystal structures of serine protease inhibitors (serpins) and serpin complexes has been an integral part of understanding serpin function and inhibitory mechanisms. In addition, high-resolution structural information of serpins derived from the three domains of life (bacteria, archaea, and eukaryotic) and viruses has provided valuable insights into the hereditary and evolutionary history of this unique superfamily of proteins. This chapter will provide an overview of the predominant biophysical method that has yielded this information, X-ray crystallography. In addition, details of up-and-coming methods, such as neutron crystallography, cryo-electron microscopy, and small- and wide-angle solution scattering, and their potential applications to serpin structural biology will be briefly discussed. As serpins remain important both biologically and medicinally, the information provided in this chapter will aid in future experiments to expand our knowledge of this family of proteins.
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12
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Schroer CG, Agapov I, Brefeld W, Brinkmann R, Chae YC, Chao HC, Eriksson M, Keil J, Nuel Gavaldà X, Röhlsberger R, Seeck OH, Sprung M, Tischer M, Wanzenberg R, Weckert E. PETRA IV: the ultralow-emittance source project at DESY. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1277-1290. [PMID: 30179167 PMCID: PMC6140396 DOI: 10.1107/s1600577518008858] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/16/2018] [Indexed: 05/19/2023]
Abstract
The PETRA IV project aims at upgrading the present synchrotron radiation source PETRA III at DESY into an ultralow-emittance source. Being diffraction limited up to X-rays of about 10 keV, PETRA IV will be ideal for three-dimensional X-ray microscopy of biological, chemical and physical processes under realistic conditions at length scales from atomic dimensions to millimetres and time scales down to the sub-nanosecond regime. In this way, it will enable groundbreaking studies in many fields of science and industry, such as health, energy, earth and environment, mobility and information technology. The science case is reviewed and the current state of the conceptual design is summarized, discussing a reference lattice, a hybrid multi-bend achromat with an interleaved sextupole configuration based on the ESRF-EBS design, in more detail as well as alternative lattice concepts.
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Affiliation(s)
- Christian G. Schroer
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ilya Agapov
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Werner Brefeld
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Reinhard Brinkmann
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Yong-Chul Chae
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Hung-Chun Chao
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Mikael Eriksson
- MAX IV Laboratory, Lund University, PO Box 118, SE-221 00 Lund, Sweden
| | - Joachim Keil
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Xavier Nuel Gavaldà
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Ralf Röhlsberger
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oliver H. Seeck
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Markus Tischer
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Rainer Wanzenberg
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Edgar Weckert
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
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13
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Gollwitzer J, Bocklage L, Schlage K, Herlitschke M, Wille HC, Leupold O, Adolff CF, Meier G, Röhlsberger R. Incoherent Nuclear Resonant Scattering from a Standing Spin Wave. Sci Rep 2018; 8:11261. [PMID: 30050130 PMCID: PMC6062533 DOI: 10.1038/s41598-018-29596-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/11/2018] [Indexed: 11/09/2022] Open
Abstract
We introduce a method to study the spatial profiles of standing spin waves in ferromagnetic microstructures. The method relies on Nuclear Resonant Scattering of 57Fe using a microfocused beam of synchrotron radiation, the transverse coherence length of which is smaller than the length scale of lateral variations in the magnetization dynamics. Using this experimental method, the nuclear resonant scattering signal due to a confined spin wave is determined on the basis of an incoherent superposition model. From the fits of the Nuclear Resonant Scattering time spectra, the precessional amplitude profile across the stripe predicted by an analytical model is reconstructed. Our results pave the way for studying non-homogeneous dynamic spin configurations in microstructured magnetic systems using nuclear resonant scattering of synchrotron light.
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Affiliation(s)
- Jakob Gollwitzer
- Institute for Applied Physics, Universität Hamburg, Jungiusstrasse 11, 20355, Hamburg, Germany.
| | - Lars Bocklage
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Kai Schlage
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Marcus Herlitschke
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Olaf Leupold
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christian F Adolff
- Institute for Applied Physics, Universität Hamburg, Jungiusstrasse 11, 20355, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Guido Meier
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Ralf Röhlsberger
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
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14
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The Influence of Photoelectron Escape in Radiation Damage Simulations of Protein Micro-Crystallography. CRYSTALS 2018. [DOI: 10.3390/cryst8070267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Radiation damage represents a fundamental limit in the determination of protein structures via macromolecular crystallography (MX) at third-generation synchrotron sources. Over the past decade, improvements in both source and detector technology have led to MX experiments being performed with smaller and smaller crystals (on the order of a few microns), often using microfocus beams. Under these conditions, photoelectrons (PEs), the primary agents of radiation-damage in MX, may escape the diffraction volume prior to depositing all of their energy. The impact of PE escape is more significant at higher beam energies (>20 keV) as the electron inelastic mean free path (IMFP) is longer, allowing the electrons to deposit their energy over a larger area, extending further from their point of origin. Software such as RADDOSE-3D has been used extensively to predict the dose (energy absorbed per unit mass) that a crystal will absorb under a given set of experimental parameters and is an important component in planning a successful MX experiment. At the time this study was undertaken, dose predictions made using RADDOSE-3D were spatially-resolved, but did not yet account for the propagation of PEs through the diffraction volume. Hence, in the case of microfocus crystallography, it is anticipated that deviations may occur between the predicted and actual dose absorbed due to the influence of PEs. To explore this effect, we conducted a series of simulations of the dose absorbed by micron-sized crystals during microfocus MX experiments. Our simulations spanned beam and crystal sizes ranging from 1μm to 5μm for beam energies between 9 keV and 30 keV. Our simulations were spatially and temporarily resolved and accounted for the escape of PEs from the diffraction volume. The spatially-resolved dose maps produced by these simulations were used to predict the rate of intensity loss in a Bragg spot, a key metric for tracking global radiation damage. Our results were compared to predictions obtained using a recent version of RADDOSE-3D that did not account for PE escape; the predicted crystal lifetimes are shown to differ significantly for the smallest crystals and for high-energy beams, when PE escape is included in the simulations.
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15
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Westfahl H, Lordano Luiz SA, Meyer BC, Meneau F. The coherent radiation fraction of low-emittance synchrotrons. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:566-575. [PMID: 28452747 DOI: 10.1107/s1600577517003058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/23/2017] [Indexed: 05/22/2023]
Abstract
In this work the coherence properties of the synchrotron radiation beam from an X-ray undulator in a fourth-generation storage ring are analyzed. A slightly focused X-ray beam is simulated using a wavefront propagation through a non-redundant array of slits and the mutual coherence function is directly obtained and compared with the Gaussian-Schell approximation. The numerical wave propagation and the approximate analytical approaches are shown to agree qualitatively, and it is also shown that, when the coherent fraction is selected by a finite aperture before the focusing element, even achromatic focusing systems like total reflection mirrors become slightly chromatic. This effect is also well accounted for in the Gaussian-Schell model. The wavefront propagation simulation through the non-redundant array was repeated with an imperfect mirror demonstrating that, although the wavefront is distorted, its coherent length is practically unchanged.
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Affiliation(s)
- Harry Westfahl
- Brazilian Synchrotron Light Laboratory - LNLS, CNPEM, CP 6192, 13083-970 Campinas, SP, Brazil
| | - Sérgio A Lordano Luiz
- Brazilian Synchrotron Light Laboratory - LNLS, CNPEM, CP 6192, 13083-970 Campinas, SP, Brazil
| | - Bernd C Meyer
- Brazilian Synchrotron Light Laboratory - LNLS, CNPEM, CP 6192, 13083-970 Campinas, SP, Brazil
| | - Florian Meneau
- Brazilian Synchrotron Light Laboratory - LNLS, CNPEM, CP 6192, 13083-970 Campinas, SP, Brazil
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16
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Actin bundles cross-linked with α-actinin studied by nanobeam X-ray diffraction. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 45:383-92. [PMID: 26715112 DOI: 10.1007/s00249-015-1107-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/24/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
We have performed scanning nano-beam small-angle X-ray scattering (nano-SAXS) experiments on in vitro-formed actin filaments cross-linked with [Formula: see text]-actinin. The experimental method combines a high resolution in reciprocal space with a real space resolution as given by the spot-size of the nano-focused X-ray beam, and opens up new opportunities to study local super-molecular structures of actin filaments. In this first proof-of-concept, we show that the local orientation of actin bundles formed by the cross-linking can be visualized by the X-ray darkfield maps. The filament bundles give rise to highly anisotropic diffraction patterns showing distinct streaks perpendicular to the bundle axes. Interestingly, some diffraction patterns exhibit a fine structure in the form of intensity modulations allowing for a more detailed analysis of the order within the bundles. A first empirical quantification of these modulations is included in the present work.
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17
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Salditt T, Osterhoff M, Krenkel M, Wilke RN, Priebe M, Bartels M, Kalbfleisch S, Sprung M. Compound focusing mirror and X-ray waveguide optics for coherent imaging and nano-diffraction. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:867-78. [PMID: 26134789 DOI: 10.1107/s1600577515007742] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/20/2015] [Indexed: 05/23/2023]
Abstract
A compound optical system for coherent focusing and imaging at the nanoscale is reported, realised by high-gain fixed-curvature elliptical mirrors in combination with X-ray waveguide optics or different cleaning apertures. The key optical concepts are illustrated, as implemented at the Göttingen Instrument for Nano-Imaging with X-rays (GINIX), installed at the P10 coherence beamline of the PETRA III storage ring at DESY, Hamburg, and examples for typical applications in biological imaging are given. Characteristic beam configurations with the recently achieved values are also described, meeting the different requirements of the applications, such as spot size, coherence or bandwidth. The emphasis of this work is on the different beam shaping, filtering and characterization methods.
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Affiliation(s)
- Tim Salditt
- Institut für Röntgenphysik, Universität Göttingen, 37077 Göttingen, Germany
| | - Markus Osterhoff
- Institut für Röntgenphysik, Universität Göttingen, 37077 Göttingen, Germany
| | - Martin Krenkel
- Institut für Röntgenphysik, Universität Göttingen, 37077 Göttingen, Germany
| | - Robin N Wilke
- Institut für Röntgenphysik, Universität Göttingen, 37077 Göttingen, Germany
| | - Marius Priebe
- Institut für Röntgenphysik, Universität Göttingen, 37077 Göttingen, Germany
| | - Matthias Bartels
- Institut für Röntgenphysik, Universität Göttingen, 37077 Göttingen, Germany
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18
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Burdet N, Shi X, Parks D, Clark JN, Huang X, Kevan SD, Robinson IK. Evaluation of partial coherence correction in X-ray ptychography. OPTICS EXPRESS 2015; 23:5452-5467. [PMID: 25836778 DOI: 10.1364/oe.23.005452] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Coherent X-ray Diffraction Imaging (CDI) and X-ray ptychography both heavily rely on the high degree of spatial coherence of the X-ray illumination for sufficient experimental data quality for reconstruction convergence. Nevertheless, the majority of the available synchrotron undulator sources have a limited degree of partial coherence, leading to reduced data quality and a lower speckle contrast in the coherent diffraction patterns. It is still an open question whether experimentalists should compromise the coherence properties of an X-ray source in exchange for a higher flux density at a sample, especially when some materials of scientific interest are relatively weak scatterers. A previous study has suggested that in CDI, the best strategy for the study of strong phase objects is to maintain a high degree of coherence of the illuminating X-rays because of the broadening of solution space resulting from the strong phase structures. In this article, we demonstrate the first systematic analysis of the effectiveness of partial coherence correction in ptychography as a function of the coherence properties, degree of complexity of illumination (degree of phase diversity of the probe) and sample phase complexity. We have also performed analysis of how well ptychographic algorithms refine X-ray probe and complex coherence functions when those variables are unknown at the start of reconstructions, for noise-free simulated data, in the case of both real-valued and highly-complex objects.
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Weckert E. The potential of future light sources to explore the structure and function of matter. IUCRJ 2015; 2:230-45. [PMID: 25866660 PMCID: PMC4392416 DOI: 10.1107/s2052252514024269] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/03/2014] [Indexed: 05/15/2023]
Abstract
Structural studies in general, and crystallography in particular, have benefited and still do benefit dramatically from the use of synchrotron radiation. Low-emittance storage rings of the third generation provide focused beams down to the micrometre range that are sufficiently intense for the investigation of weakly scattering crystals down to the size of several micrometres. Even though the coherent fraction of these sources is below 1%, a number of new imaging techniques have been developed to exploit the partially coherent radiation. However, many techniques in nanoscience are limited by this rather small coherent fraction. On the one hand, this restriction limits the ability to study the structure and dynamics of non-crystalline materials by methods that depend on the coherence properties of the beam, like coherent diffractive imaging and X-ray correlation spectroscopy. On the other hand, the flux in an ultra-small diffraction-limited focus is limited as well for the same reason. Meanwhile, new storage rings with more advanced lattice designs are under construction or under consideration, which will have significantly smaller emittances. These sources are targeted towards the diffraction limit in the X-ray regime and will provide roughly one to two orders of magnitude higher spectral brightness and coherence. They will be especially suited to experiments exploiting the coherence properties of the beams and to ultra-small focal spot sizes in the regime of several nanometres. Although the length of individual X-ray pulses at a storage-ring source is of the order of 100 ps, which is sufficiently short to track structural changes of larger groups, faster processes as they occur during vision or photosynthesis, for example, are not accessible in all details under these conditions. Linear accelerator (linac) driven free-electron laser (FEL) sources with extremely short and intense pulses of very high coherence circumvent some of the limitations of present-day storage-ring sources. It has been demonstrated that their individual pulses are short enough to outrun radiation damage for single-pulse exposures. These ultra-short pulses also enable time-resolved studies 1000 times faster than at standard storage-ring sources. Developments are ongoing at various places for a totally new type of X-ray source combining a linac with a storage ring. These energy-recovery linacs promise to provide pulses almost as short as a FEL, with brilliances and multi-user capabilities comparable with a diffraction-limited storage ring. Altogether, these new X-ray source developments will provide smaller and more intense X-ray beams with a considerably higher coherent fraction, enabling a broad spectrum of new techniques for studying the structure of crystalline and non-crystalline states of matter at atomic length scales. In addition, the short X-ray pulses of FELs will enable the study of fast atomic dynamics and non-equilibrium states of matter.
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Eriksson M, van der Veen JF, Quitmann C. Diffraction-limited storage rings - a window to the science of tomorrow. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:837-42. [PMID: 25177975 DOI: 10.1107/s1600577514019286] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 05/20/2023]
Abstract
This article summarizes the contributions in this special issue on Diffraction-Limited Storage Rings. It analyses the progress in accelerator technology enabling a significant increase in brightness and coherent fraction of the X-ray light provided by storage rings. With MAX IV and Sirius there are two facilities under construction that already exploit these advantages. Several other projects are in the design stage and these will probably enhance the performance further. To translate the progress in light source quality into new science requires similar progress in aspects such as optics, beamline technology, detectors and data analysis. The quality of new science will be limited by the weakest component in this value chain. Breakthroughs can be expected in high-resolution imaging, microscopy and spectroscopy. These techniques are relevant for many fields of science; for example, for the fundamental understanding of the properties of correlated electron materials, the development and characterization of materials for data and energy storage, environmental applications and bio-medicine.
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Affiliation(s)
- Mikael Eriksson
- MAX IV Laboratory, Lund University, POB 118, Lund 22100, Sweden
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Hitchcock AP, Toney MF. Spectromicroscopy and coherent diffraction imaging: focus on energy materials applications. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1019-1030. [PMID: 25177991 DOI: 10.1107/s1600577514013046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/04/2014] [Indexed: 06/03/2023]
Abstract
Current and future capabilities of X-ray spectromicroscopy are discussed based on coherence-limited imaging methods which will benefit from the dramatic increase in brightness expected from a diffraction-limited storage ring (DLSR). The methods discussed include advanced coherent diffraction techniques and nanoprobe-based real-space imaging using Fresnel zone plates or other diffractive optics whose performance is affected by the degree of coherence. The capabilities of current systems, improvements which can be expected, and some of the important scientific themes which will be impacted are described, with focus on energy materials applications. Potential performance improvements of these techniques based on anticipated DLSR performance are estimated. Several examples of energy sciences research problems which are out of reach of current instrumentation, but which might be solved with the enhanced DLSR performance, are discussed.
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Affiliation(s)
- Adam P Hitchcock
- Brockhouse Institute for Materials Research, McMaster University, Hamilton, Ontario, Canada L8S 4M1
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