1
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Pandolfi S, Carver T, Hodge D, Leong AFT, Kurzer-Ogul K, Hart P, Galtier E, Khaghani D, Cunningham E, Nagler B, Lee HJ, Bolme C, Ramos K, Li K, Liu Y, Sakdinawat A, Marchesini S, Kozlowski PM, Curry CB, Decker FJ, Vetter S, Shang J, Aluie H, Dayton M, Montgomery DS, Sandberg RL, Gleason AE. Novel fabrication tools for dynamic compression targets with engineered voids using photolithography methods. Rev Sci Instrum 2022; 93:103502. [PMID: 36319339 DOI: 10.1063/5.0107542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Mesoscale imperfections, such as pores and voids, can strongly modify the properties and the mechanical response of materials under extreme conditions. Tracking the material response and microstructure evolution during void collapse is crucial for understanding its performance. In particular, imperfections in the ablator materials, such as voids, can limit the efficiency of the fusion reaction and ultimately hinder ignition. To characterize how voids influence the response of materials during dynamic loading and seed hydrodynamic instabilities, we have developed a tailored fabrication procedure for designer targets with voids at specific locations. Our procedure uses SU-8 as a proxy for the ablator materials and hollow silica microspheres as a proxy for voids and pores. By using photolithography to design the targets' geometry, we demonstrate precise and highly reproducible placement of a single void within the sample, which is key for a detailed understanding of its behavior under shock compression. This fabrication technique will benefit high-repetition rate experiments at x-ray and laser facilities. Insight from shock compression experiments will provide benchmarks for the next generation of microphysics modeling.
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Affiliation(s)
- Silvia Pandolfi
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Thomas Carver
- Stanford Nano Shared Facilities, Stanford University, Palo Alto, California 94305, USA
| | - Daniel Hodge
- Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, USA
| | - Andrew F T Leong
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Kelin Kurzer-Ogul
- Department of Mechanical Engineering, University of Rochester, Rochester, New York 14623, USA
| | - Philip Hart
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Eric Galtier
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Dimitri Khaghani
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Eric Cunningham
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Bob Nagler
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Hae Ja Lee
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Cindy Bolme
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Kyle Ramos
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Kenan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Yanwei Liu
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Anne Sakdinawat
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Stefano Marchesini
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | | | - Chandra B Curry
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Franz-Joseph Decker
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Sharon Vetter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
| | - Jessica Shang
- Department of Mechanical Engineering, University of Rochester, Rochester, New York 14623, USA
| | - Hussein Aluie
- Department of Mechanical Engineering, University of Rochester, Rochester, New York 14623, USA
| | - Matthew Dayton
- Advanced hCMOS Systems, 6300 Riverside Plaza Ln. Suite 100, Albuquerque, New Mexico 87107, USA
| | | | - Richard L Sandberg
- Department of Physics and Astronomy, Brigham Young University, Provo, Utah 84602, USA
| | - Arianna E Gleason
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd., Menlo Park, California 94025, USA
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2
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Mäkinen Y, Marchesini S, Foi A. Ring artifact and Poisson noise attenuation via volumetric multiscale nonlocal collaborative filtering of spatially correlated noise. J Synchrotron Radiat 2022; 29:829-842. [PMID: 35511015 PMCID: PMC9070695 DOI: 10.1107/s1600577522002739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
X-ray micro-tomography systems often suffer from high levels of noise. In particular, severe ring artifacts are common in reconstructed images, caused by defects in the detector, calibration errors, and fluctuations producing streak noise in the raw sinogram data. Furthermore, the projections commonly contain high levels of Poissonian noise arising from the photon-counting detector. This work presents a 3-D multiscale framework for streak attenuation through a purposely designed collaborative filtering of correlated noise in volumetric data. A distinct multiscale denoising step for attenuation of the Poissonian noise is further proposed. By utilizing the volumetric structure of the projection data, the proposed fully automatic procedure offers improved feature preservation compared with 2-D denoising and avoids artifacts which arise from individual filtering of sinograms.
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Affiliation(s)
| | - Stefano Marchesini
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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3
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Tanyag RMP, Bacellar C, Pang W, Bernando C, Gomez LF, Jones CF, Ferguson KR, Kwok J, Anielski D, Belkacem A, Boll R, Bozek J, Carron S, Chen G, Delmas T, Englert L, Epp SW, Erk B, Foucar L, Hartmann R, Hexemer A, Huth M, Leone SR, Ma JH, Marchesini S, Neumark DM, Poon BK, Prell J, Rolles D, Rudek B, Rudenko A, Seifrid M, Swiggers M, Ullrich J, Weise F, Zwart P, Bostedt C, Gessner O, Vilesov AF. Sizes of pure and doped helium droplets from single shot x-ray imaging. J Chem Phys 2022; 156:041102. [PMID: 35105059 DOI: 10.1063/5.0080342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Advancements in x-ray free-electron lasers on producing ultrashort, ultrabright, and coherent x-ray pulses enable single-shot imaging of fragile nanostructures, such as superfluid helium droplets. This imaging technique gives unique access to the sizes and shapes of individual droplets. In the past, such droplet characteristics have only been indirectly inferred by ensemble averaging techniques. Here, we report on the size distributions of both pure and doped droplets collected from single-shot x-ray imaging and produced from the free-jet expansion of helium through a 5 μm diameter nozzle at 20 bars and nozzle temperatures ranging from 4.2 to 9 K. This work extends the measurement of large helium nanodroplets containing 109-1011 atoms, which are shown to follow an exponential size distribution. Additionally, we demonstrate that the size distributions of the doped droplets follow those of the pure droplets at the same stagnation condition but with smaller average sizes.
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Affiliation(s)
- Rico Mayro P Tanyag
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Camila Bacellar
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Weiwu Pang
- Department of Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Charles Bernando
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Luis F Gomez
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Curtis F Jones
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ken R Ferguson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Justin Kwok
- Department of Chemical Engineering and Material Science, University of Southern California, Los Angeles, California 90089, USA
| | - Denis Anielski
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Ali Belkacem
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Rebecca Boll
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - John Bozek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sebastian Carron
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Gang Chen
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tjark Delmas
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Lars Englert
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstraße, 85741 Garching, Germany
| | - Sascha W Epp
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benjamin Erk
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | | | - Alexander Hexemer
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Huth
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Stephen R Leone
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jonathan H Ma
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Stefano Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Daniel M Neumark
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Billy K Poon
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - James Prell
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Daniel Rolles
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benedikt Rudek
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Artem Rudenko
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Martin Seifrid
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Michele Swiggers
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Joachim Ullrich
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Fabian Weise
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Petrus Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christoph Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Oliver Gessner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Andrey F Vilesov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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4
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Mäkinen Y, Marchesini S, Foi A. Ring artifact reduction via multiscale nonlocal collaborative filtering of spatially correlated noise. J Synchrotron Radiat 2021; 28:876-888. [PMID: 33949995 PMCID: PMC8127377 DOI: 10.1107/s1600577521001910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
X-ray micro-tomography systems often suffer severe ring artifacts in reconstructed images. These artifacts are caused by defects in the detector, calibration errors, and fluctuations producing streak noise in the raw sinogram data. In this work, these streaks are modeled in the sinogram domain as additive stationary correlated noise upon logarithmic transformation. Based on this model, a streak removal procedure is proposed where the Block-Matching and 3-D (BM3D) filtering algorithm is applied across multiple scales, achieving state-of-the-art performance in both real and simulated data. Specifically, the proposed fully automatic procedure allows for attenuation of streak noise and the corresponding ring artifacts without creating major distortions common to other streak removal algorithms.
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Affiliation(s)
| | - Stefano Marchesini
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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5
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Marchesini S, Shapiro D, Maia FRNC. Introduction to the special issue on Ptychography: software and technical developments. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721002983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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6
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Shapiro DA, Babin S, Celestre RS, Chao W, Conley RP, Denes P, Enders B, Enfedaque P, James S, Joseph JM, Krishnan H, Marchesini S, Muriki K, Nowrouzi K, Oh SR, Padmore H, Warwick T, Yang L, Yashchuk VV, Yu YS, Zhao J. An ultrahigh-resolution soft x-ray microscope for quantitative analysis of chemically heterogeneous nanomaterials. Sci Adv 2020; 6:6/51/eabc4904. [PMID: 33328228 PMCID: PMC7744074 DOI: 10.1126/sciadv.abc4904] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/02/2020] [Indexed: 05/30/2023]
Abstract
The analysis of chemical states and morphology in nanomaterials is central to many areas of science. We address this need with an ultrahigh-resolution scanning transmission soft x-ray microscope. Our instrument provides multiple analysis tools in a compact assembly and can achieve few-nanometer spatial resolution and high chemical sensitivity via x-ray ptychography and conventional scanning microscopy. A novel scanning mechanism, coupled to advanced x-ray detectors, a high-brightness x-ray source, and high-performance computing for analysis provide a revolutionary step forward in terms of imaging speed and resolution. We present x-ray microscopy with 8-nm full-period spatial resolution and use this capability in conjunction with operando sample environments and cryogenic imaging, which are now routinely available. Our multimodal approach will find wide use across many fields of science and facilitate correlative analysis of materials with other types of probes.
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Affiliation(s)
- David A Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | | | - Richard S Celestre
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Weilun Chao
- Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Raymond P Conley
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Peter Denes
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bjoern Enders
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
- National Energy Research Scientific Computing Center, Berkeley, CA 94720, USA
| | - Pablo Enfedaque
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Susan James
- Information Technology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John M Joseph
- Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Harinarayan Krishnan
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stefano Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Krishna Muriki
- Information Technology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kasra Nowrouzi
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Advanced Quantum Testbed, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sharon R Oh
- Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Howard Padmore
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tony Warwick
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lee Yang
- Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Valeriy V Yashchuk
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Young-Sang Yu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jiangtao Zhao
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- University of Science and Technology of China, Hefei, Anhui 230026, China
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7
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Abstract
Linear dichroism is an important tool to characterize the transmission matrix and determine the crystal or orbital orientation in a material. In order to achieve high-resolution mapping of transmission properties, the linear-dichroism scattering model in ptychographic imaging is introduced, and an efficient two-stage reconstruction algorithm is developed. Using the proposed algorithm on a uniaxial material, the dichroic transmission matrix can be recovered without an analyzer by using ptychography measurements with as few as three different polarization angles, with the help of an empty region to remove phase ambiguities.
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8
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Abstract
Spectroscopic ptychography is a powerful technique to determine the chemical composition of a sample with high spatial resolution. This paper presents a novel algorithm to iteratively solve the spectroscopic blind ptychography problem. Spectroscopic ptychography is a powerful technique to determine the chemical composition of a sample with high spatial resolution. In spectro-ptychography, a sample is rastered through a focused X-ray beam with varying photon energy so that a series of phaseless diffraction data are recorded. Each chemical component in the material under investigation has a characteristic absorption and phase contrast as a function of photon energy. Using a dictionary formed by the set of contrast functions of each energy for each chemical component, it is possible to obtain the chemical composition of the material from high-resolution multi-spectral images. This paper presents SPA (spectroscopic ptychography with alternating direction method of multipliers), a novel algorithm to iteratively solve the spectroscopic blind ptychography problem. First, a nonlinear spectro-ptychography model based on Poisson maximum likelihood is designed, and then the proposed method is constructed on the basis of fast iterative splitting operators. SPA can be used to retrieve spectral contrast when considering either a known or an incomplete (partially known) dictionary of reference spectra. By coupling the redundancy across different spectral measurements, the proposed algorithm can achieve higher reconstruction quality when compared with standard state-of-the-art two-step methods. It is demonstrated how SPA can recover accurate chemical maps from Poisson-noised measurements, and its enhanced robustness when reconstructing reduced-redundancy ptychography data using large scanning step sizes is shown.
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Affiliation(s)
- Huibin Chang
- School of Mathematical Sciences, Tianjin Normal University, Tianjin, People's Republic of China
| | - Ziqin Rong
- School of Mathematical Sciences, Tianjin Normal University, Tianjin, People's Republic of China
| | - Pablo Enfedaque
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stefano Marchesini
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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9
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Chang H, Enfedaque P, Zhang J, Reinhardt J, Enders B, Yu YS, Shapiro D, Schroer CG, Zeng T, Marchesini S. Advanced denoising for X-ray ptychography. Opt Express 2019; 27:10395-10418. [PMID: 31052900 DOI: 10.1364/oe.27.010395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
The success of ptychographic imaging experiments strongly depends on achieving high signal-to-noise ratio. This is particularly important in nanoscale imaging experiments when diffraction signals are very weak and the experiments are accompanied by significant parasitic scattering (background), outliers or correlated noise sources. It is also critical when rare events, such as cosmic rays, or bad frames caused by electronic glitches or shutter timing malfunction take place. In this paper, we propose a novel iterative algorithm with rigorous analysis that exploits the direct forward model for parasitic noise and sample smoothness to achieve a thorough characterization and removal of structured and random noise. We present a formal description of the proposed algorithm and prove its convergence under mild conditions. Numerical experiments from simulations and real data (both soft and hard X-ray beamlines) demonstrate that the proposed algorithms produce better results when compared to state-of-the-art methods.
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10
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Marchesini S, Sakdinawat A. Shaping coherent x-rays with binary optics. Opt Express 2019; 27:907-917. [PMID: 30696169 DOI: 10.1364/oe.27.000907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
Diffractive lenses fabricated by lithographic methods are one of the most popular image forming optics in the x-ray regime. Most commonly, binary diffractive optics, such as Fresnel zone plates, are used due to their ability to focus at high resolution and to manipulate the x-ray wavefront. We report here a binary zone plate design strategy to form arbitrary illuminations for coherent multiplexing, structured illumination, and wavefront shaping experiments. Given a desired illumination, we adjust the duty cycle, harmonic order, and zone placement to vary both the amplitude and phase of the wavefront at the lens. This enables the binary lithographic pattern to generate arbitrary structured illumination optimized for a variety of applications such as holography, interferometry, ptychography, imaging, and others.
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11
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Abstract
Phaseless diffraction measurements recorded by CCD detectors are often affected by Poisson noise. In this paper, we propose a dictionary learning model by employing patches based sparsity in order to denoise such Poisson phaseless measurements. The model consists of three terms: (i) A representation term by an orthogonal dictionary, (ii) an L0 pseudo norm of the coefficient matrix, and (iii) a Kullback-Leibler divergence term to fit phaseless Poisson data. Fast alternating minimization method (AMM) and proximal alternating linearized minimization (PALM) are adopted to solve the proposed model, and especially the theoretical guarantee of the convergence of PALM is provided. The subproblems for these two algorithms both have fast solvers, and indeed, the solutions for the sparse coding and dictionary updating both have closed forms due to the orthogonality of learned dictionaries. Numerical experiments for phase retrieval using coded diffraction and ptychographic patterns are conducted to show the efficiency and robustness of proposed methods, which, by preserving texture features, produce visually and quantitatively improved restored images compared with other phase retrieval algorithms without regularization and local sparsity promoting algorithms.
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12
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Pandolfi RJ, Allan DB, Arenholz E, Barroso-Luque L, Campbell SI, Caswell TA, Blair A, De Carlo F, Fackler S, Fournier AP, Freychet G, Fukuto M, Gürsoy D, Jiang Z, Krishnan H, Kumar D, Kline RJ, Li R, Liman C, Marchesini S, Mehta A, N’Diaye AT, Parkinson DY, Parks H, Pellouchoud LA, Perciano T, Ren F, Sahoo S, Strzalka J, Sunday D, Tassone CJ, Ushizima D, Venkatakrishnan S, Yager KG, Zwart P, Sethian JA, Hexemer A. Xi-cam: a versatile interface for data visualization and analysis. J Synchrotron Radiat 2018; 25:1261-1270. [PMID: 29979189 PMCID: PMC6691515 DOI: 10.1107/s1600577518005787] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 05/22/2023]
Abstract
Xi-cam is an extensible platform for data management, analysis and visualization. Xi-cam aims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core of Xi-cam is an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. With Xi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data. Xi-cam's plugin-based architecture targets cross-facility and cross-technique collaborative development, in support of multi-modal analysis. Xi-cam is open-source and cross-platform, and available for download on GitHub.
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Affiliation(s)
- Ronald J. Pandolfi
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Daniel B. Allan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Elke Arenholz
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Luis Barroso-Luque
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Stuart I. Campbell
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Thomas A. Caswell
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Austin Blair
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Francesco De Carlo
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, USA
| | - Sean Fackler
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Amanda P. Fournier
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, USA
| | - Guillaume Freychet
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Masafumi Fukuto
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Doǧa Gürsoy
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, USA
- Department of Electrical Engineering and Computer Science, Northwestern University, 2145 Sheridan Road, Evanston, IL, USA
| | - Zhang Jiang
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, USA
| | | | - Dinesh Kumar
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - R. Joseph Kline
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, USA
| | - Ruipeng Li
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Christopher Liman
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, USA
| | - Stefano Marchesini
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Apurva Mehta
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, USA
| | - Alpha T. N’Diaye
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | | | - Holden Parks
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | | | - Talita Perciano
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Fang Ren
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, USA
| | - Shreya Sahoo
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Joseph Strzalka
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL, USA
| | - Daniel Sunday
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, USA
| | | | - Daniela Ushizima
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | | | - Kevin G. Yager
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Peter Zwart
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - James A. Sethian
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
| | - Alexander Hexemer
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
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13
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Chang H, Enfedaque P, Lou Y, Marchesini S. Partially coherent ptychography by gradient decomposition of the probe. Acta Crystallogr A Found Adv 2018; 74:157-169. [PMID: 29724963 DOI: 10.1107/s2053273318001924] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/01/2018] [Indexed: 11/11/2022]
Abstract
Coherent ptychographic imaging experiments often discard the majority of the flux from a light source to define the coherence of the illumination. Even when the coherent flux is sufficient, the stability required during an exposure is another important limiting factor. Partial coherence analysis can considerably reduce these limitations. A partially coherent illumination can often be written as the superposition of a single coherent illumination convolved with a separable translational kernel. This article proposes the gradient decomposition of the probe (GDP), a model that exploits translational kernel separability, coupling the variances of the kernel with the transverse coherence. An efficient first-order splitting algorithm (GDP-ADMM) for solving the proposed nonlinear optimization problem is described. Numerical experiments demonstrate the effectiveness of the proposed method with Gaussian and binary kernel functions in fly-scan measurements. Remarkably, GDP-ADMM using nanoprobes produces satisfactory results even when the ratio between the kernel width and the beam size is more than one, or when the distance between successive acquisitions is twice as large as the beam width.
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14
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Yu YS, Farmand M, Kim C, Liu Y, Grey CP, Strobridge FC, Tyliszczak T, Celestre R, Denes P, Joseph J, Krishnan H, Maia FRNC, Kilcoyne ALD, Marchesini S, Leite TPC, Warwick T, Padmore H, Cabana J, Shapiro DA. Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography. Nat Commun 2018; 9:921. [PMID: 29500344 PMCID: PMC5834601 DOI: 10.1038/s41467-018-03401-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 02/11/2018] [Indexed: 12/02/2022] Open
Abstract
Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices. Here the authors show the development of soft X-ray ptychographic tomography to quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nano-particles from a composite battery electrode.
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Affiliation(s)
- Young-Sang Yu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Maryam Farmand
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chunjoong Kim
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.,Department of Materials Science and Engineering, Chungnam National University, Daejeon, Chungnam, 305-764, South Korea
| | - Yijin Liu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Clare P Grey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Fiona C Strobridge
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tolek Tyliszczak
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Rich Celestre
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter Denes
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John Joseph
- Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Harinarayan Krishnan
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Filipe R N C Maia
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, 75124, Uppsala, Sweden
| | - A L David Kilcoyne
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Stefano Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Tony Warwick
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Howard Padmore
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jordi Cabana
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - David A Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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15
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Shapiro DA, Celestre R, Denes P, Farmand M, Joseph J, Kilcoyne A, Marchesini S, Padmore H, Venkatakrishnan SV, Warwick T, Yu YS. Ptychographic Imaging of Nano-Materials at the Advanced Light Source with the Nanosurveyor Instrument. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1742-6596/849/1/012028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Daurer BJ, Krishnan H, Perciano T, Maia FRNC, Shapiro DA, Sethian JA, Marchesini S. Nanosurveyor: a framework for real-time data processing. ACTA ACUST UNITED AC 2017; 3:7. [PMID: 28261545 PMCID: PMC5313566 DOI: 10.1186/s40679-017-0039-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/18/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND The ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality. RESULTS Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis. CONCLUSIONS The pipeline provides throughput, compression, and resolution as well as rapid feedback to the microscope operators.
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Affiliation(s)
- Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Hari Krishnan
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Talita Perciano
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - David A Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - James A Sethian
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Mathematics, University of California, Berkeley, Berkeley, CA USA
| | - Stefano Marchesini
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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17
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Marchesini S, Krishnan H, Daurer BJ, Shapiro DA, Perciano T, Sethian JA, Maia FRNC. SHARP: a distributed GPU-based ptychographic solver. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716008074] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Ever brighter light sources, fast parallel detectors and advances in phase retrieval methods have made ptychography a practical and popular imaging technique. Compared to previous techniques, ptychography provides superior robustness and resolution at the expense of more advanced and time-consuming data analysis. By taking advantage of massively parallel architectures, high-throughput processing can expedite this analysis and provide microscopists with immediate feedback. These advances allow real-time imaging at wavelength-limited resolution, coupled with a large field of view. This article describes a set of algorithmic and computational methodologies used at the Advanced Light Source and US Department of Energy light sources. These are packaged as a CUDA-based software environment namedSHARP(http://camera.lbl.gov/sharp), aimed at providing state-of-the-art high-throughput ptychography reconstructions for the coming era of diffraction-limited light sources.
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18
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Venkatakrishnan SV, Mohan KA, Beattie K, Correa J, Dart E, Deslippe JR, Hexemer A, Krishnan H, MacDowell AA, Marchesini S, Patton SJ, Perciano T, Sethian JA, Stromsness R, Tierney BL, Tull CE, Ushizima D, Parkinson DY. Making Advanced Scientific Algorithms and Big Scientific Data Management More Accessible. ACTA ACUST UNITED AC 2016. [DOI: 10.2352/issn.2470-1173.2016.19.coimg-155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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19
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Li Y, Meyer S, Lim J, Lee SC, Gent WE, Marchesini S, Krishnan H, Tyliszczak T, Shapiro D, Kilcoyne ALD, Chueh WC. Effects of Particle Size, Electronic Connectivity, and Incoherent Nanoscale Domains on the Sequence of Lithiation in LiFePO₄ Porous Electrodes. Adv Mater 2015; 27:6591-6597. [PMID: 26423560 DOI: 10.1002/adma.201502276] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/12/2015] [Indexed: 06/05/2023]
Abstract
High-resolution X-ray microscopy is used to investigate the sequence of lithiation in LiFePO4 porous electrodes. For electrodes with homogeneous interparticle electronic connectivity via the carbon black network, the smaller particles lithiate first. For electrodes with heterogeneous connectivity, the better-connected particles preferentially lithiate. Correlative electron and X-ray microscopy also reveal the presence of incoherent nanodomains that lithiate as if they are separate particles.
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Affiliation(s)
- Yiyang Li
- Department of Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, CA, 94305, USA
| | - Sophie Meyer
- Department of Physics, Stanford University, 382 Via Pueblo Mall, Stanford, CA, 94305, USA
| | - Jongwoo Lim
- Department of Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, CA, 94305, USA
| | - Sang Chul Lee
- Department of Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, CA, 94305, USA
| | - William E Gent
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Stefano Marchesini
- Advanced Light Source One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Harinarayan Krishnan
- Advanced Light Source One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tolek Tyliszczak
- Advanced Light Source One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David Shapiro
- Advanced Light Source One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Arthur L David Kilcoyne
- Advanced Light Source One Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - William C Chueh
- Department of Materials Science and Engineering, Stanford University, 496 Lomita Mall, Stanford, CA, 94305, USA
- Stanford Institute of Materials and Energy Sciences, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
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20
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Yu YS, Kim C, Shapiro DA, Farmand M, Qian D, Tyliszczak T, Kilcoyne ALD, Celestre R, Marchesini S, Joseph J, Denes P, Warwick T, Strobridge FC, Grey CP, Padmore H, Meng YS, Kostecki R, Cabana J. Dependence on Crystal Size of the Nanoscale Chemical Phase Distribution and Fracture in LixFePO₄. Nano Lett 2015; 15:4282-8. [PMID: 26061698 DOI: 10.1021/acs.nanolett.5b01314] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The performance of battery electrode materials is strongly affected by inefficiencies in utilization kinetics and cycle life as well as size effects. Observations of phase transformations in these materials with high chemical and spatial resolution can elucidate the relationship between chemical processes and mechanical degradation. Soft X-ray ptychographic microscopy combined with X-ray absorption spectroscopy and electron microscopy creates a powerful suite of tools that we use to assess the chemical and morphological changes in lithium iron phosphate (LiFePO4) micro- and nanocrystals that occur upon delithiation. All sizes of partly delithiated crystals were found to contain two phases with a complex correlation between crystallographic orientation and phase distribution. However, the lattice mismatch between LiFePO4 and FePO4 led to severe fracturing on microcrystals, whereas no mechanical damage was observed in nanoplates, indicating that mechanics are a principal driver in the outstanding electrode performance of LiFePO4 nanoparticles. These results demonstrate the importance of engineering the active electrode material in next generation electrical energy storage systems, which will achieve theoretical limits of energy density and extended stability. This work establishes soft X-ray ptychographic chemical imaging as an essential tool to build comprehensive relationships between mechanics and chemistry that guide this engineering design.
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Affiliation(s)
- Young-Sang Yu
- †Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- §Department of NanoEngineering, University of California, San Diego, La Jolla, California 92121, United States
- ∥Energy Storage and Distributed Resources Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Chunjoong Kim
- †Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - David A Shapiro
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Maryam Farmand
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Danna Qian
- §Department of NanoEngineering, University of California, San Diego, La Jolla, California 92121, United States
| | - Tolek Tyliszczak
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - A L David Kilcoyne
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rich Celestre
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stefano Marchesini
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John Joseph
- ⊥Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Peter Denes
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tony Warwick
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Fiona C Strobridge
- #Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Clare P Grey
- #Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- ∇Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Howard Padmore
- ‡Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ying Shirley Meng
- §Department of NanoEngineering, University of California, San Diego, La Jolla, California 92121, United States
| | - Robert Kostecki
- ∥Energy Storage and Distributed Resources Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jordi Cabana
- †Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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21
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Aquila A, Barty A, Bostedt C, Boutet S, Carini G, dePonte D, Drell P, Doniach S, Downing KH, Earnest T, Elmlund H, Elser V, Gühr M, Hajdu J, Hastings J, Hau-Riege SP, Huang Z, Lattman EE, Maia FRNC, Marchesini S, Ourmazd A, Pellegrini C, Santra R, Schlichting I, Schroer C, Spence JCH, Vartanyants IA, Wakatsuki S, Weis WI, Williams GJ. The linac coherent light source single particle imaging road map. Struct Dyn 2015; 2:041701. [PMID: 26798801 PMCID: PMC4711616 DOI: 10.1063/1.4918726] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/06/2015] [Indexed: 05/19/2023]
Abstract
Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources.
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Affiliation(s)
| | - A Barty
- Center for Free-Electron Laser Science, DESY , Notkestr. 85, 22607 Hamburg, Germany
| | - C Bostedt
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S Boutet
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - G Carini
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - D dePonte
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - K H Downing
- Lawrence Berkeley National Laboratory , 1 Cyclotron Rd., Berkeley, California 94720, USA
| | | | | | | | - M Gühr
- PULSE Institute , SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | - J Hastings
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - S P Hau-Riege
- Lawrence Livermore National Laboratory , Livermore, California 94550, USA
| | - Z Huang
- SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - S Marchesini
- Lawrence Berkeley National Laboratory , 1 Cyclotron Rd., Berkeley, California 94720, USA
| | - A Ourmazd
- Department of Physics, University of Wisconsin Milwaukee , 1900 E. Kenwood Blvd, Milwaukee, Wisconsin 53211, USA
| | | | | | - I Schlichting
- Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - C Schroer
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85, 22607 Hamburg, Germany
| | - J C H Spence
- Department of Physics, Arizona State University , Rural Rd, Tempe, Arizona 85287, USA
| | | | | | - W I Weis
- School of Medicine, Stanford University , 299 Campus Drive, Stanford, California 94305, USA
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22
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Donatelli J, Haranczyk M, Hexemer A, Krishnan H, Li X, Lin L, Maia F, Marchesini S, Parkinson D, Perciano T, Shapiro D, Ushizima D, Yang C, Sethian J. CAMERA: The Center for Advanced Mathematics for Energy Research Applications. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/08940886.2015.1013413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Gomez LF, Ferguson KR, Cryan JP, Bacellar C, Tanyag RMP, Jones C, Schorb S, Anielski D, Belkacem A, Bernando C, Boll R, Bozek J, Carron S, Chen G, Delmas T, Englert L, Epp SW, Erk B, Foucar L, Hartmann R, Hexemer A, Huth M, Kwok J, Leone SR, Ma JHS, Maia FRNC, Malmerberg E, Marchesini S, Neumark DM, Poon B, Prell J, Rolles D, Rudek B, Rudenko A, Seifrid M, Siefermann KR, Sturm FP, Swiggers M, Ullrich J, Weise F, Zwart P, Bostedt C, Gessner O, Vilesov AF. Shapes and vorticities of superfluid helium nanodroplets. Science 2014; 345:906-9. [DOI: 10.1126/science.1252395] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Luis F. Gomez
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Ken R. Ferguson
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - James P. Cryan
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Camila Bacellar
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Rico Mayro P. Tanyag
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Curtis Jones
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Sebastian Schorb
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Denis Anielski
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
| | - Ali Belkacem
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Charles Bernando
- Department of Physics and Astronomy, USC, Los Angeles, CA 90089, USA
| | - Rebecca Boll
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - John Bozek
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sebastian Carron
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gang Chen
- Advanced Light Source, LBNL, Berkeley, CA 94720, USA
| | - Tjark Delmas
- CFEL, DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Lars Englert
- Max-Planck-Institut für Extraterrestrische Physik, Giessenbachstraße, 85741 Garching, Germany
| | - Sascha W. Epp
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
| | - Benjamin Erk
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Lutz Foucar
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | | | | | - Martin Huth
- PNSensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Justin Kwok
- Mork Family Department of Chemical Engineering and Materials Science, USC, Los Angeles, CA 90089, USA
| | - Stephen R. Leone
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathan H. S. Ma
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
- Department of Physics, The Chinese University of Hong Kong, Hong Kong, China
| | - Filipe R. N. C. Maia
- National Energy Research Scientific Computing Center, LBNL, Berkeley, CA 94720, USA
| | - Erik Malmerberg
- Physical Biosciences Division, LBNL, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of Calfornia Berkeley, Berkeley, CA 94720, USA
| | - Stefano Marchesini
- Advanced Light Source, LBNL, Berkeley, CA 94720, USA
- Department of Physics, University of California Davis, Davis, CA 95616, USA
| | - Daniel M. Neumark
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
- Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Billy Poon
- Physical Biosciences Division, LBNL, Berkeley, CA 94720, USA
| | - James Prell
- Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Daniel Rolles
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Benedikt Rudek
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
| | - Artem Rudenko
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
- James R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Martin Seifrid
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
| | - Katrin R. Siefermann
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Felix P. Sturm
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Michele Swiggers
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Joachim Ullrich
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Max Planck Advanced Study Group at the Center for Free-Electron Laser Science (CFEL), Notkestraße 85, 22607 Hamburg, Germany
| | - Fabian Weise
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Petrus Zwart
- Physical Biosciences Division, LBNL, Berkeley, CA 94720, USA
| | - Christoph Bostedt
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- PULSE Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Oliver Gessner
- Ultrafast X-ray Science Laboratory, Chemical Sciences Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - Andrey F. Vilesov
- Department of Chemistry, University of Southern California (USC), Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, USC, Los Angeles, CA 90089, USA
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24
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Liu C, Marchesini S, Kim MK. Quantitative phase-contrast confocal microscope. Opt Express 2014; 22:17830-17839. [PMID: 25089404 PMCID: PMC4162347 DOI: 10.1364/oe.22.017830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 05/30/2023]
Abstract
We present a quantitative phase-contrast confocal microscope (QPCCM) by combining a line-scanning confocal system with digital holography (DH). This combination can merge the merits of these two different imaging modalities. High-contrast intensity images with low coherent noise, and the optical sectioning capability are made available due to the confocality. Phase profiles of the samples become accessible thanks to DH. QPCCM is able to quantitatively measure the phase variations of optical sections of the opaque samples and has the potential to take high-quality intensity and phase images of non-opaque samples such as many biological samples. Because each line scan is recorded by a hologram that may contain the optical aberrations of the system, it opens avenues for a variety of numerical aberration compensation methods and development of full digital adaptive optics confocal system to emulate current hardware-based adaptive optics system for biomedical imaging, especially ophthalmic imaging. Preliminary experiments with a microscope objective of NA 0.65 and 40 × on opaque samples are presented to demonstrate this idea. The measured lateral and axial resolutions of the intensity images from the current system are ~0.64μm and ~2.70μm respectively. The noise level of the phase profile by QPCCM is ~2.4nm which is better than the result by DH.
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Affiliation(s)
- Changgeng Liu
- Digital Holography and Microscopy Laboratory, Department of Physics, University of South Florida, Tampa, FL 33620,
USA
| | - Stefano Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720,
USA
| | - Myung K. Kim
- Digital Holography and Microscopy Laboratory, Department of Physics, University of South Florida, Tampa, FL 33620,
USA
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25
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Abstract
We employ a coded aperture pattern in front of a pixilated charge couple device detector to image fluorescent x-rays (6-25 KeV) from samples irradiated with synchrotron radiation. Coded apertures encode the angular direction of x-rays, and given a known source plane, allow for a large numerical aperture x-ray imaging system. The algorithm to develop and fabricate the free standing No-Two-Holes-Touching aperture pattern was developed. The algorithms to reconstruct the x-ray image from the recorded encoded pattern were developed by means of a ray tracing technique and confirmed by experiments on standard samples.
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Affiliation(s)
- A Haboub
- Lawrence Berkeley National Laboratories, Berkeley, California 94720, USA
| | - A A MacDowell
- Lawrence Berkeley National Laboratories, Berkeley, California 94720, USA
| | - S Marchesini
- Lawrence Berkeley National Laboratories, Berkeley, California 94720, USA
| | - D Y Parkinson
- Lawrence Berkeley National Laboratories, Berkeley, California 94720, USA
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26
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Park HJ, Loh ND, Sierra RG, Hampton CY, Starodub D, Martin AV, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Lomb L, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ, Elser V. Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers. Opt Express 2013; 21:28729-42. [PMID: 24514385 DOI: 10.1364/oe.21.028729] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.
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27
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Loh ND, Starodub D, Lomb L, Hampton CY, Martin AV, Sierra RG, Barty A, Aquila A, Schulz J, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege S, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Strueder L, Ullrich J, Bucksbaum P, Frank M, Schlichting I, Chapman HN, Bogan MJ. Sensing the wavefront of x-ray free-electron lasers using aerosol spheres. Opt Express 2013; 21:12385-12394. [PMID: 23736456 DOI: 10.1364/oe.21.012385] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.
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Affiliation(s)
- N Duane Loh
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
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28
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Shapiro D, Roy S, Celestre R, Chao W, Doering D, Howells M, Kevan S, Kilcoyne D, Kirz J, Marchesini S, Seu KA, Schirotzek A, Spence J, Tyliszczak T, Warwick T, Voronov D, Padmore HA. Development of coherent scattering and diffractive imaging and the COSMIC facility at the Advanced Light Source. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/425/19/192011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Chen G, Modestino MA, Poon BK, Schirotzek A, Marchesini S, Segalman RA, Hexemer A, Zwart PH. Structure determination of Pt-coated Au dumbbells via fluctuation X-ray scattering. J Synchrotron Radiat 2012; 19:695-700. [PMID: 22898947 DOI: 10.1107/s0909049512023801] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Accepted: 05/24/2012] [Indexed: 06/01/2023]
Abstract
A fluctuation X-ray scattering experiment has been carried out on platinum-coated gold nanoparticles randomly oriented on a substrate. A complete algorithm for determining the electron density of an individual particle from diffraction patterns of many particles randomly oriented about a single axis is demonstrated. This algorithm operates on angular correlations among the measured intensity distributions and recovers the angular correlation functions of a single particle from measured diffraction patterns. Taking advantage of the cylindrical symmetry of the nanoparticles, a cylindrical slice model is proposed to reconstruct the structure of the nanoparticles by fitting the experimental ring angular auto-correlation and small-angle scattering data obtained from many scattering patterns. The physical meaning of the refined structure is discussed in terms of their statistical distributions of the shape and electron density profile.
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Affiliation(s)
- Gang Chen
- Physical Bioscience Division, Lawrence Berkeley National Laboratories, Berkeley, CA, USA
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30
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Loh ND, Hampton CY, Martin AV, Starodub D, Sierra RG, Barty A, Aquila A, Schulz J, Lomb L, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege SP, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Bucksbaum P, Hodgson KO, Strüder L, Ullrich J, Frank M, Schlichting I, Chapman HN, Bogan MJ. Erratum: Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight. Nature 2012. [DOI: 10.1038/nature11426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Loh ND, Hampton CY, Martin AV, Starodub D, Sierra RG, Barty A, Aquila A, Schulz J, Lomb L, Steinbrener J, Shoeman RL, Kassemeyer S, Bostedt C, Bozek J, Epp SW, Erk B, Hartmann R, Rolles D, Rudenko A, Rudek B, Foucar L, Kimmel N, Weidenspointner G, Hauser G, Holl P, Pedersoli E, Liang M, Hunter MS, Hunter MM, Gumprecht L, Coppola N, Wunderer C, Graafsma H, Maia FRNC, Ekeberg T, Hantke M, Fleckenstein H, Hirsemann H, Nass K, White TA, Tobias HJ, Farquar GR, Benner WH, Hau-Riege SP, Reich C, Hartmann A, Soltau H, Marchesini S, Bajt S, Barthelmess M, Bucksbaum P, Hodgson KO, Strüder L, Ullrich J, Frank M, Schlichting I, Chapman HN, Bogan MJ. Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight. Nature 2012; 486:513-7. [PMID: 22739316 DOI: 10.1038/nature11222] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 05/09/2012] [Indexed: 11/09/2022]
Abstract
The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.
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Affiliation(s)
- N D Loh
- PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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32
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Martin AV, Loh ND, Hampton CY, Sierra RG, Wang F, Aquila A, Bajt S, Barthelmess M, Bostedt C, Bozek JD, Coppola N, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Kassemeyer S, Kimmel N, Liang M, Lomb L, Maia FRNC, Marchesini S, Nass K, Pedersoli E, Reich C, Rolles D, Rudek B, Rudenko A, Schulz J, Shoeman RL, Soltau H, Starodub D, Steinbrener J, Stellato F, Strüder L, Ullrich J, Weidenspointner G, White TA, Wunderer CB, Barty A, Schlichting I, Bogan MJ, Chapman HN. Femtosecond dark-field imaging with an X-ray free electron laser. Opt Express 2012; 20:13501-12. [PMID: 22714377 DOI: 10.1364/oe.20.013501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.
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Affiliation(s)
- A V Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
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33
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Kassemeyer S, Steinbrener J, Lomb L, Hartmann E, Aquila A, Barty A, Martin AV, Hampton CY, Bajt S, Barthelmess M, Barends TRM, Bostedt C, Bott M, Bozek JD, Coppola N, Cryle M, DePonte DP, Doak RB, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Hömke A, Holl P, Jönsson O, Kimmel N, Krasniqi F, Liang M, Maia FRNC, Marchesini S, Nass K, Reich C, Rolles D, Rudek B, Rudenko A, Schmidt C, Schulz J, Shoeman RL, Sierra RG, Soltau H, Spence JCH, Starodub D, Stellato F, Stern S, Stier G, Svenda M, Weidenspointner G, Weierstall U, White TA, Wunderer C, Frank M, Chapman HN, Ullrich J, Strüder L, Bogan MJ, Schlichting I. Femtosecond free-electron laser x-ray diffraction data sets for algorithm development. Opt Express 2012; 20:4149-58. [PMID: 22418172 DOI: 10.1364/oe.20.004149] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.
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Affiliation(s)
- Stephan Kassemeyer
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
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34
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Aquila A, Hunter MS, Doak RB, Kirian RA, Fromme P, White TA, Andreasson J, Arnlund D, Bajt S, Barends TRM, Barthelmess M, Bogan MJ, Bostedt C, Bottin H, Bozek JD, Caleman C, Coppola N, Davidsson J, DePonte DP, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Frank M, Fromme R, Graafsma H, Grotjohann I, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hau-Riege S, Hauser G, Hirsemann H, Holl P, Holton JM, Hömke A, Johansson L, Kimmel N, Kassemeyer S, Krasniqi F, Kühnel KU, Liang M, Lomb L, Malmerberg E, Marchesini S, Martin AV, Maia FRNC, Messerschmidt M, Nass K, Reich C, Neutze R, Rolles D, Rudek B, Rudenko A, Schlichting I, Schmidt C, Schmidt KE, Schulz J, Seibert MM, Shoeman RL, Sierra R, Soltau H, Starodub D, Stellato F, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Williams GJ, Weidenspointner G, Weierstall U, Wunderer C, Barty A, Spence JCH, Chapman HN. Time-resolved protein nanocrystallography using an X-ray free-electron laser. Opt Express 2012; 20:2706-16. [PMID: 22330507 PMCID: PMC3413412 DOI: 10.1364/oe.20.002706] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/16/2011] [Accepted: 12/18/2011] [Indexed: 05/17/2023]
Abstract
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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Affiliation(s)
- Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestraße 85, 22607 Hamburg, Germany.
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35
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Barty A, Caleman C, Aquila A, Timneanu N, Lomb L, White TA, Andreasson J, Arnlund D, Bajt S, Barends TRM, Barthelmess M, Bogan MJ, Bostedt C, Bozek JD, Coffee R, Coppola N, Davidsson J, DePonte DP, Doak RB, Ekeberg T, Elser V, Epp SW, Erk B, Fleckenstein H, Foucar L, Fromme P, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann R, Hartmann A, Hauser G, Hirsemann H, Holl P, Hunter MS, Johansson L, Kassemeyer S, Kimmel N, Kirian RA, Liang M, Maia FRNC, Malmerberg E, Marchesini S, Martin AV, Nass K, Neutze R, Reich C, Rolles D, Rudek B, Rudenko A, Scott H, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Spence JCH, Stellato F, Stern S, Strüder L, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Wunderer CB, Chapman HN. Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nat Photonics 2012; 6:35-40. [PMID: 24078834 PMCID: PMC3783007 DOI: 10.1038/nphoton.2011.297] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1-4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.
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Affiliation(s)
- Anton Barty
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Correspondence and requests for materials should be addressed to A.B. and H.N.C., ;
| | - Carl Caleman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Aquila
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nicusor Timneanu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Lukas Lomb
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jakob Andreasson
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - David Arnlund
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Saša Bajt
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas R. M. Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Michael J. Bogan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Christoph Bostedt
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - John D. Bozek
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Ryan Coffee
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Nicola Coppola
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Davidsson
- Department of Photochemistry and Molecular Science, Uppsala University, Box 523, SE-75120 Uppsala, Sweden
| | - Daniel P. DePonte
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - R. Bruce Doak
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Veit Elser
- Department of Physics, Cornell University, Ithaca, New York 14853, USA
| | - Sascha W. Epp
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Benjamin Erk
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Heinz Graafsma
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Christina Y. Hampton
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | | | | | - Günter Hauser
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | | | - Peter Holl
- PN Sensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Mark S. Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
| | - Linda Johansson
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Stephan Kassemeyer
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nils Kimmel
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Mengning Liang
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Erik Malmerberg
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | - Andrew V. Martin
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Karol Nass
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Richard Neutze
- Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | - Daniel Rolles
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Benedikt Rudek
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Artem Rudenko
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Howard Scott
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joachim Schulz
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - M. Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Robert L. Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstr. 29, 69120 Heidelberg, Germany
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Raymond G. Sierra
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Heike Soltau
- PN Sensor GmbH, Otto-Hahn-Ring 6, 81739 München, Germany
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Francesco Stellato
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stephan Stern
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lothar Strüder
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
| | - Joachim Ullrich
- Max Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - X. Wang
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | - Georg Weidenspointner
- Max-Planck-Institut Halbleiterlabor, Otto-Hahn-Ring 6, 81739 München, Germany
- Max-Planck-Institut für extraterrestrische Physik, Giessenbachstrasse, 85741 Garching, Germany
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
| | | | - Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Correspondence and requests for materials should be addressed to A.B. and H.N.C., ;
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36
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Lomb L, Barends TRM, Kassemeyer S, Aquila A, Epp SW, Erk B, Foucar L, Hartmann R, Rudek B, Rolles D, Rudenko A, Shoeman RL, Andreasson J, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Bozek JD, Caleman C, Coffee R, Coppola N, Deponte DP, Doak RB, Ekeberg T, Fleckenstein H, Fromme P, Gebhardt M, Graafsma H, Gumprecht L, Hampton CY, Hartmann A, Hauser G, Hirsemann H, Holl P, Holton JM, Hunter MS, Kabsch W, Kimmel N, Kirian RA, Liang M, Maia FRNC, Meinhart A, Marchesini S, Martin AV, Nass K, Reich C, Schulz J, Seibert MM, Sierra R, Soltau H, Spence JCH, Steinbrener J, Stellato F, Stern S, Timneanu N, Wang X, Weidenspointner G, Weierstall U, White TA, Wunderer C, Chapman HN, Ullrich J, Strüder L, Schlichting I. Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Phys Rev B Condens Matter Mater Phys 2011; 84:214111. [PMID: 24089594 PMCID: PMC3786679 DOI: 10.1103/physrevb.84.214111] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
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Affiliation(s)
- Lukas Lomb
- Max-Planck Institut für medizinische Forschung, Jahnstrasse 29, DE-69120 Heidelberg, Germany ; Max Planck Advanced Study Group, Center for Free-Electron Laser Science, Notkestrasse 85, DE-22607 Hamburg, Germany
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37
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Gambaro G, Bonfante L, Abaterusso C, Gemelli A, Ferraro PM, Marchesini S, De Conti G, D'Angelo A, Lupo A. High chronic nephropathy detection yield in CKD subjects identified by the combination of albuminuria and estimated GFR. Nephrol Dial Transplant 2011; 27:746-51. [DOI: 10.1093/ndt/gfr360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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38
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Hunter MS, DePonte DP, Shapiro DA, Kirian RA, Wang X, Starodub D, Marchesini S, Weierstall U, Doak RB, Spence JCH, Fromme P. X-ray diffraction from membrane protein nanocrystals. Biophys J 2011; 100:198-206. [PMID: 21190672 DOI: 10.1016/j.bpj.2010.10.049] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/02/2010] [Accepted: 10/13/2010] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins constitute > 30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is < 300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain < 100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain < 200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.
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Affiliation(s)
- M S Hunter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, USA
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39
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Saldin DK, Poon HC, Bogan MJ, Marchesini S, Shapiro DA, Kirian RA, Weierstall U, Spence JCH. New light on disordered ensembles: ab initio structure determination of one particle from scattering fluctuations of many copies. Phys Rev Lett 2011; 106:115501. [PMID: 21469876 DOI: 10.1103/physrevlett.106.115501] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Indexed: 05/25/2023]
Abstract
We report on the first experimental ab initio reconstruction of an image of a single particle from fluctuations in the scattering from an ensemble of copies, randomly oriented about an axis. The method is applicable to identical particles frozen in space or time (as by snapshot diffraction from an x-ray free electron laser). These fluctuations enhance information obtainable from an experiment such as conventional small angle x-ray scattering.
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Affiliation(s)
- D K Saldin
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA
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40
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Spence JCH, Kirian RA, Wang X, Weierstall U, Schmidt KE, White T, Barty A, Chapman HN, Marchesini S, Holton J. Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals. Opt Express 2011; 19:2866-73. [PMID: 21369108 DOI: 10.1364/oe.19.002866] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The scattering between Bragg reflections from nanocrystals is used to aid solution of the phase problem. We describe a method for reconstructing the charge density of a typical molecule within a single unit cell, if sufficiently finely-sampled "snap-shot" diffraction data (as provided a free-electron X-ray laser) are available from many nanocrystals of different sizes lying in random orientations. By using information on the particle-size distribution within the patterns, this digital method succeeds, using all the data, without knowledge of the distribution of particle size or requiring atomic-resolution data.
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Affiliation(s)
- John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
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41
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Sokolowski-Tinten K, Barty A, Boutet S, Shymanovich U, Chapman H, Bogan M, Marchesini S, Hau-Riege S, Stojanovic N, Bonse J, Rosandi Y, Urbassek HM, Tobey R, Ehrke H, Cavalleri A, Düsterer S, Redlin H, Frank M, Bajt S, Schulz J, Seibert M, Hajdu J, Treusch R, Bostedt C, Hoener M, Möeller T. Short-pulse Laser Induced Transient Structure Formation and Ablation Studied with Time-resolved Coherent XUV-scattering. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-1230-mm05-03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe structural dynamics of short-pulse laser irradiated surfaces and nano-structures has been studied with nm spatial and ultrafast temporal resolution by means of single-shot coherent XUV-scattering techniques. The experiments allowed us to time-resolve the formation of laser-induced periodic surface structures, and to follow the expansion and disintegration of nano-objects during laser ablation.
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42
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Maia FRNC, Yang C, Marchesini S. Compressive auto-indexing in femtosecond nanocrystallography. Ultramicroscopy 2010; 111:807-11. [PMID: 21093986 DOI: 10.1016/j.ultramic.2010.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/26/2010] [Accepted: 10/26/2010] [Indexed: 10/18/2022]
Abstract
Ultrafast nanocrystallography has the potential to revolutionize biology by enabling structural elucidation of proteins for which it is possible to grow crystals with 10 or fewer unit cells on the side. The success of nanocrystallography depends on robust orientation-determination procedures that allow us to average diffraction data from multiple nanocrystals to produce a three-dimensional (3D) diffraction data volume with a high signal-to-noise ratio. Such a 3D diffraction volume can then be phased using standard crystallographic techniques. "Indexing" algorithms used in crystallography enable orientation determination of diffraction data from a single crystal when a relatively large number of reflections are recorded. Here we show that it is possible to obtain the exact lattice geometry from a smaller number of measurements than standard approaches using a basis pursuit solver.
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Affiliation(s)
- Filipe R N C Maia
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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43
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Steinbrener J, Nelson J, Huang X, Marchesini S, Shapiro D, Turner JJ, Jacobsen C. Data preparation and evaluation techniques for x-ray diffraction microscopy. Opt Express 2010; 18:18598-614. [PMID: 20940752 PMCID: PMC3076089 DOI: 10.1364/oe.18.018598] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The post-experiment processing of X-ray Diffraction Microscopy data is often time-consuming and difficult. This is mostly due to the fact that even if a preliminary result has been reconstructed, there is no definitive answer as to whether or not a better result with more consistently retrieved phases can still be obtained. We show here that the first step in data analysis, the assembly of two-dimensional diffraction patterns from a large set of raw diffraction data, is crucial to obtaining reconstructions of highest possible consistency. We have developed software that automates this process and results in consistently accurate diffraction patterns. We have furthermore derived some criteria of validity for a tool commonly used to assess the consistency of reconstructions, the phase retrieval transfer function, and suggest a modified version that has improved utility for judging reconstruction quality.
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Affiliation(s)
- Jan Steinbrener
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794, USA.
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44
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Loh ND, Bogan MJ, Elser V, Barty A, Boutet S, Bajt S, Hajdu J, Ekeberg T, Maia FRNC, Schulz J, Seibert MM, Iwan B, Timneanu N, Marchesini S, Schlichting I, Shoeman RL, Lomb L, Frank M, Liang M, Chapman HN. Cryptotomography: reconstructing 3D Fourier intensities from randomly oriented single-shot diffraction patterns. Phys Rev Lett 2010; 104:225501. [PMID: 20867179 DOI: 10.1103/physrevlett.104.225501] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Indexed: 05/09/2023]
Abstract
We reconstructed the 3D Fourier intensity distribution of monodisperse prolate nanoparticles using single-shot 2D coherent diffraction patterns collected at DESY's FLASH facility when a bright, coherent, ultrafast x-ray pulse intercepted individual particles of random, unmeasured orientations. This first experimental demonstration of cryptotomography extended the expansion-maximization-compression framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. This work is an important step towards realizing single-shot diffraction imaging of single biomolecules.
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Affiliation(s)
- N D Loh
- Laboratory of Atomic and Solid State Physics, Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York 14853-2501, USA
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45
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Zhao Y, Shapiro D, McGloin D, Chiu DT, Marchesini S. Direct observation of the transfer of orbital angular momentum to metal particles from a focused circularly polarized Gaussian beam. Opt Express 2009; 17:23316-23322. [PMID: 20052258 DOI: 10.1364/oe.17.023316] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
It is well known that a circularly polarized Gaussian beam carries spin angular momentum, but not orbital angular momentum. This paper demonstrates that focusing a beam carrying spin angular momentum can induce an orbital angular momentum which we used to drive the orbital motion of a micron-sized metal particle that is trapped off the beam axis. The direction of the orbital motion is controlled by the handedness of the circular polarization. The orbiting dynamics of the trapped particle, which acted as an optical micro-detector, were quantitatively measured and found to be in excellent agreement with the theoretical predictions.
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Affiliation(s)
- Yiqiong Zhao
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 947202, USA.
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46
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Huang X, Nelson J, Kirz J, Lima E, Marchesini S, Miao H, Neiman AM, Shapiro D, Steinbrener J, Stewart A, Turner JJ, Jacobsen C. Soft X-ray diffraction microscopy of a frozen hydrated yeast cell. Phys Rev Lett 2009; 103:198101. [PMID: 20365955 PMCID: PMC2866741 DOI: 10.1103/physrevlett.103.198101] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 07/29/2009] [Indexed: 05/07/2023]
Abstract
We report the first image of an intact, frozen hydrated eukaryotic cell using x-ray diffraction microscopy, or coherent x-ray diffraction imaging. By plunge freezing the specimen in liquid ethane and maintaining it below -170 degrees C, artifacts due to dehydration, ice crystallization, and radiation damage are greatly reduced. In this example, coherent diffraction data using 520 eV x rays were recorded and reconstructed to reveal a budding yeast cell at a resolution better than 25 nm. This demonstration represents an important step towards high resolution imaging of cells in their natural, hydrated state, without limitations imposed by x-ray optics.
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Affiliation(s)
- Xiaojing Huang
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Johanna Nelson
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Janos Kirz
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Enju Lima
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Stefano Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Huijie Miao
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Aaron M. Neiman
- Department of Biochemistry & Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
| | - David Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Steinbrener
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Andrew Stewart
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Joshua J. Turner
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
| | - Chris Jacobsen
- Department of Physics & Astronomy, Stony Brook University, Stony Brook, New York 11794-3800, USA
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47
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Arbelo Lainez E, Garcia Quintana A, Caballero Dorta E, Diaz Escofet M, Moreno Djadou B, Rios Diaz C, Novoa Medina J, Medina Fernandez-Aceytuno A, Fatemi M, Le Gal G, Castellant P, Fersi I, Etienne Y, Blanc JJ, Zanon F, Aggio S, Baracca E, Pastore F, Vaccari D, Verlato R, Davinelli M, Comisso J, Barsheshet A, Abu Sham'a R, Sandach A, Luria D, Bar Lev D, Gurevitz O, Eldar M, Glikson M, Ramos R, Oliveira M, Nogueira Da Silva M, Toste A, Lousinha A, Branco L, Alves S, Ferreira RC, Baptista R, Saraiva F, Jorge E, Hermida P, Monteiro P, Elvas L, Providencia LA, Delnoy PPHM, Ottervanger JP, Oude Luttikhuis H, Elvan A, Ramdat Misier AR, Beukema WP, Van Hemel NM, Lunati M, Maines M, Landolina M, Santini M, Proclemer A, Sassara M, Marchesini S, Varbaro A, Maines M, Catanzariti D, Cemin C, Vimercati M, Valsecchi S, Vergara G, Bertini M, Ajmone Marsan N, Delgado V, Van Bommel RJ, Nucifora G, Borleffs CJW, Schalij MJ, Bax JJ. Moderated posters: Cardiac resynchronisation therapy. Europace 2009. [DOI: 10.1093/europace/euq242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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48
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Howells MR, Beetz T, Chapman HN, Cui C, Holton JM, Jacobsen CJ, Kirz J, Lima E, Marchesini S, Miao H, Sayre D, Shapiro DA, Spence JCH, Starodub D. An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy. J Electron Spectros Relat Phenomena 2009; 170:4-12. [PMID: 20463854 PMCID: PMC2867487 DOI: 10.1016/j.elspec.2008.10.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
X-ray diffraction microscopy (XDM) is a new form of x-ray imaging that is being practiced at several third-generation synchrotron-radiation x-ray facilities. Nine years have elapsed since the technique was first introduced and it has made rapid progress in demonstrating high-resolution three-dimensional imaging and promises few-nm resolution with much larger samples than can be imaged in the transmission electron microscope. Both life- and materials-science applications of XDM are intended, and it is expected that the principal limitation to resolution will be radiation damage for life science and the coherent power of available x-ray sources for material science. In this paper we address the question of the role of radiation damage. We use a statistical analysis based on the so-called "dose fractionation theorem" of Hegerl and Hoppe to calculate the dose needed to make an image of a single life-science sample by XDM with a given resolution. We find that for simply-shaped objects the needed dose scales with the inverse fourth power of the resolution and present experimental evidence to support this finding. To determine the maximum tolerable dose we have assembled a number of data taken from the literature plus some measurements of our own which cover ranges of resolution that are not well covered otherwise. The conclusion of this study is that, based on the natural contrast between protein and water and "Rose-criterion" image quality, one should be able to image a frozen-hydrated biological sample using XDM at a resolution of about 10 nm.
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Affiliation(s)
- M. R. Howells
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - T. Beetz
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - H. N. Chapman
- Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550, USA
| | - C. Cui
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - J. M. Holton
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA
| | - C. J. Jacobsen
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - J. Kirz
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - E. Lima
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - S. Marchesini
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - H. Miao
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - D. Sayre
- Department of Physics, State University of New York, Stony Brook, NY 11794, USA
| | - D. A. Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
| | - J. C. H. Spence
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720 USA
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA
| | - D. Starodub
- Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA
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Shapiro DA, Chapman HN, Deponte D, Doak RB, Fromme P, Hembree G, Hunter M, Marchesini S, Schmidt K, Spence J, Starodub D, Weierstall U. Powder diffraction from a continuous microjet of submicrometer protein crystals. J Synchrotron Radiat 2008; 15:593-9. [PMID: 18955765 DOI: 10.1107/s0909049508024151] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 07/29/2008] [Indexed: 05/06/2023]
Abstract
Atomic-resolution structures from small proteins have recently been determined from high-quality powder diffraction patterns using a combination of stereochemical restraints and Rietveld refinement [Von Dreele (2007), J. Appl. Cryst. 40, 133-143; Margiolaki et al. (2007), J. Am. Chem. Soc. 129, 11865-11871]. While powder diffraction data have been obtained from batch samples of small crystal-suspensions, which are exposed to X-rays for long periods of time and undergo significant radiation damage, the proof-of-concept that protein powder diffraction data from nanocrystals of a membrane protein can be obtained using a continuous microjet is shown. This flow-focusing aerojet has been developed to deliver a solution of hydrated protein nanocrystals to an X-ray beam for diffraction analysis. This method requires neither the crushing of larger polycrystalline samples nor any techniques to avoid radiation damage such as cryocooling. Apparatus to record protein powder diffraction in this manner has been commissioned, and in this paper the first powder diffraction patterns from a membrane protein, photosystem I, with crystallite sizes of less than 500 nm are presented. These preliminary patterns show the lowest-order reflections, which agree quantitatively with theoretical calculations of the powder profile. The results also serve to test our aerojet injector system, with future application to femtosecond diffraction in free-electron X-ray laser schemes, and for serial crystallography using a single-file beam of aligned hydrated molecules.
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Affiliation(s)
- D A Shapiro
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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50
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Shapiro D, Deponte D, Doak B, Fromme P, Hembree G, Hunter M, Marchesini S, Schmidt K, Spence J. Serial crystallography: use of a micro-jet for diffraction of protein nano-crystals or molecules. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308099170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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