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Nikbakht T, Kakuee O, Solé VA, Vosuoghi Y, Lamehi-Rachti M. An efficient approach to integrated MeV ion imaging. Ultramicroscopy 2018; 186:112-119. [PMID: 29291437 DOI: 10.1016/j.ultramic.2017.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/13/2017] [Accepted: 12/22/2017] [Indexed: 11/25/2022]
Abstract
An ionoluminescence (IL) spectral imaging system, besides the common MeV ion imaging facilities such as µ-PIXE and µ-RBS, is implemented at the Van de Graaff laboratory of Tehran. A versatile processing software is required to handle the large amount of data concurrently collected in µ-IL and common MeV ion imaging measurements through the respective methodologies. The open-source freeware PyMca, with image processing and multivariate analysis capabilities, is employed to simultaneously process common MeV ion imaging and µ-IL data. Herein, the program was adapted to support the OM_DAQ listmode data format. The appropriate performance of the µ-IL data acquisition system is confirmed through a case study. Moreover, the capabilities of the software for simultaneous analysis of µ-PIXE and µ-RBS experimental data are presented.
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Affiliation(s)
- T Nikbakht
- Physics & Accelerators Research School, Nuclear Science and Technology Research Institute (NSTRI), P O Box 14395-836, Tehran, Iran.
| | - O Kakuee
- Physics & Accelerators Research School, Nuclear Science and Technology Research Institute (NSTRI), P O Box 14395-836, Tehran, Iran
| | - V A Solé
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, Grenoble 38000, France
| | - Y Vosuoghi
- Physics & Accelerators Research School, Nuclear Science and Technology Research Institute (NSTRI), P O Box 14395-836, Tehran, Iran
| | - M Lamehi-Rachti
- Physics & Accelerators Research School, Nuclear Science and Technology Research Institute (NSTRI), P O Box 14395-836, Tehran, Iran
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2
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Salomé M, Cotte M, Baker R, Barrett R, Benseny-Cases N, Berruyer G, Bugnazet D, Castillo-Michel H, Cornu C, Fayard B, Gagliardini E, Hino R, Morse J, Papillon E, Pouyet E, Rivard C, Solé VA, Susini J, Veronesi G. The ID21 Scanning X-ray Microscope at ESRF. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/425/18/182004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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3
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Ravel B, Hester JR, Solé VA, Newville M. Towards data format standardization for X-ray absorption spectroscopy. J Synchrotron Radiat 2012; 19:869-874. [PMID: 23093744 DOI: 10.1107/s0909049512036886] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 08/26/2012] [Indexed: 06/01/2023]
Abstract
A working group on data format standardization for X-ray absorption spectroscopy (XAS) has recently formed under the auspices of the International X-ray Absorption Society and the XAFS Commission of the International Union of Crystallography. This group of beamline scientists and XAS practitioners has been tasked to propose data format standards to meet the needs of the world-wide XAS community. In this report, concepts for addressing three XAS data storage needs are presented: a single spectrum interchange format, a hierarchical format for multispectral X-ray experiment, and a relational database format for XAS data libraries.
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Affiliation(s)
- B Ravel
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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4
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Cotte M, Welcomme E, Solé VA, Salomé M, Menu M, Walter P, Susini J. Synchrotron-Based X-ray Spectromicroscopy Used for the Study of an Atypical Micrometric Pigment in 16th Century Paintings. Anal Chem 2007; 79:6988-94. [PMID: 17691752 DOI: 10.1021/ac0708386] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Grünewald is a famous German painter of the 16th century, whose celebrity is associated with his unique skill in handling colors. This article presents the analysis of materials used to render a metallic aspect in the Isenhein Altarpiece and the Basel's Crucifixion. Such samples are challenging objects for microanalysis due to both chemical and physical complexity. Their study by synchrotron-based X-ray microscopy techniques was made possible thanks to recent developments carried out at the ID21 beam line (European Synchrotron Radiation Facility, ESRF). A submicron X-ray fluorescence probe revealed the main presence of lead, sulfur, antimony, and calcium. The fluorescence-line interferences (in particular K-lines of sulfur with M-lines of lead, and K-lines of calcium with L-lines of antimony) were resolved with the fitting program, PyMCA. 2D-mapping highlighted the presence of micrometer grains of sulfur and antimony into a lead matrix. XANES measurements were performed at both the sulfur K-edge and the antimony L-edge to refine information from an atomic to a molecular level. Beam stability was a key point in this study to selectively probe micrometer pigment grains, dispersed in the lead matrix. They confirm that the grains are made of stibnite (antimony sulfide), a very atypical pigment. Chemical mapping of sulfides is perfectly correlated with antimony mapping and provides a clear visualization of the stibnite pigments, in addition to their identification. Besides its artistic relevancy, this work aims at illustrating developments of synchrotron X-ray microprobe methods for the chemical characterization and observation of complex and micrometer-scale materials.
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Affiliation(s)
- M Cotte
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex, France.
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5
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Petit PE, Farges F, Wilke M, Solé VA. Determination of the iron oxidation state in earth materials using XANES pre-edge information. J Synchrotron Radiat 2001; 8:952-954. [PMID: 11512990 DOI: 10.1107/s0909049500021063] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2000] [Accepted: 12/21/2000] [Indexed: 05/23/2023]
Abstract
Fe K-edge XANES spectra have been measured in more than 35 Fe(II) and Fe(III)-bearing minerals. The separation between the average pre-edge centroid positions for Fe(II) and Fe(III) is 1.4 +/- 0.1 eV. Examination of calculated pre-edge features of mechanical mixtures of phases containing different proportions of Fe(II) and Fe(III) reveals that different trends of pre-edge position vs. pre-edge intensity can be observed, depending on the coordination environment. Both pre-edge parameters have been used to estimate the ferric/ferrous ratio in 12 natural minerals.
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Affiliation(s)
- P E Petit
- European Synchrotron Radiation Facility, Grenoble, France.
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6
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Meinke C, Solé VA, Pospisil P, Dau H. Does the structure of the water-oxidizing photosystem II-manganese complex at room temperature differ from its low-temperature structure? A comparative X-ray absorption study. Biochemistry 2000; 39:7033-40. [PMID: 10852700 DOI: 10.1021/bi9924258] [Citation(s) in RCA: 30] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed information on room-temperature structure and oxidation state of the Photosystem II (PS II) manganese complex is needed to put mechanistic considerations on solid grounds. Because previously this information had not been available, the tetranuclear manganese complex was investigated by X-ray absorption spectroscopy (XAS) on PS II membrane particles at 290 K. Due to methodical progress (collection of XAS spectra within 10 s or less), significant X-ray radiation damage can be avoided; room-temperature XAS investigations on the PS II in its native membrane environment become feasible. Thus, the ambiguity with respect to the mechanistic relevance of low-temperature XAS results is avoidable. At 290 K as well as at 18 K, the manganese complex in its dark-stable state (S(1)-state) seemingly is a Mn(III)(2)Mn(IV)(2) complex comprising two di-mu(2)-oxo bridged binuclear manganese units characterized by the same Mn-Mn distance of 2.71-2.72 A at both temperatures. Most likely, manganese oxidation states and the protonation state of the bridging oxides are fully temperature independent. Remarkably, at room-temperature manganese-ligand distances of 3.10 and 3.65 A are clearly discernible in the EXAFS spectra. The type of bridging assumed to result in Mn-Mn or Mn-Ca distances around 3.1 A is, possibly, temperature-dependent as suggested by distance lengthening upon cooling by 0.13 A. However, mechanistic proposals on photosynthetic water oxidation, which involve the dimer-of-dimers model [Yachandra, V. K., et al. (1993) Science 260, 675-679] are not invalidated by the presented results.
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Affiliation(s)
- C Meinke
- FB Biologie, Philipps-Universität Marburg, Lahnberge, Germany
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Gauthier C, Solé VA, Signorato R, Goulon J, Moguiline E. The ESRF beamline ID26: X-ray absorption on ultra dilute sample. J Synchrotron Radiat 1999; 6:164-166. [PMID: 15263234 DOI: 10.1107/s0909049598016835] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/1998] [Accepted: 12/07/1998] [Indexed: 05/24/2023]
Affiliation(s)
- C Gauthier
- European Synchrotron Radiation Facility, Grenoble, France.
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Solé VA, Gauthier C, Goulon J, Natali F. Undulator QEXAFS at the ESRF beamline ID26. J Synchrotron Radiat 1999; 6:174-175. [PMID: 15263238 DOI: 10.1107/s0909049598017531] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/1998] [Accepted: 12/14/1998] [Indexed: 05/24/2023]
Affiliation(s)
- V A Solé
- European Synchrotron Radiation Facility, Grenoble, France.
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9
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Signorato R, Solé VA, Gauthier C. Performance of the ESRF ID26 beamline reflective optics. J Synchrotron Radiat 1999; 6:176-178. [PMID: 15263239 DOI: 10.1107/s0909049598013971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/1998] [Accepted: 10/26/1998] [Indexed: 05/24/2023]
Affiliation(s)
- R Signorato
- European Synchrotron Radiation Facility, Grenoble, France.
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10
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Schiller H, Dittmer J, Iuzzolino L, Dörner W, Meyer-Klaucke W, Solé VA, Nolting H, Dau H. Structure and orientation of the oxygen-evolving manganese complex of green algae and higher plants investigated by X-ray absorption linear dichroism spectroscopy on oriented photosystem II membrane particles. Biochemistry 1998; 37:7340-50. [PMID: 9585548 DOI: 10.1021/bi972329b] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
X-ray absorption spectroscopy at the Mn K-edge has been performed on multilayers of photosystem II-enriched fragments of the native thylakoid membrane prepared from a higher plant (spinach) and a unicellular green alga (Scenedesmus obliquus). Spectra collected for various angles between the prevailing orientation of the thylakoid membrane normal and the X-ray electric field vector contain information on the atomic structure of the tetranuclear manganese complex of photosystem II (PS II) and its orientation with respect to the membrane normal. The previously used approach for evaluation of the dichroism of extended X-ray absorption fine structure (EXAFS) spectra [George, G. N., et al. (1989) Science 243, 789-791] is modified, and the following results are obtained for PS II in its dark-stable state (S1-state): (1) structure and orientation of the PS II manganese complexes of green algae and higher plants are highly similiar or fully identical; (2) two 2.7-A vectors, which, most likely, connect the Mn nuclei of a planar Mn2(mu-O2) structure, are at an average angle of 80 degrees +/- 10 degrees with respect to the thylakoid normal; (3) the plane of the Mn2(mu-O2) structures is rather in parallel with the thylakoid plane than perpendicular. Structural models for the oxygen-evolving manganese complex and its orientation in the thylakoid membrane are discussed within the context of the presented results.
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Affiliation(s)
- H Schiller
- FB Biologie/Botanik and FB Chemie, Philipps-Universität Marburg, Germany
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11
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Abstract
We investigated the geometry of the iron ligand sphere of the native rabbit 15-lipoxygenase (15-LOX) by X-ray absorption spectroscopy using synchrotron radiation. The soybean LOX-1 was used as a reference compound because its iron ligand sphere is well characterized. For structural information the X-ray absorption spectra were evaluated using the Excurve Program (CCLRC Daresbury Laboratory, Warrington, U.K.). From the positions of the absorption edges and from the intensities of the 1s-3d pre-edge transition peaks a six-coordinate ferrous iron was concluded for the rabbit 15-LOX. Evaluation of the extended region of the absorption spectra suggested six nitrogen and/or oxygen atoms as direct iron ligands, and the following binding distances were determined (means+/-S.D.; estimated accuracy is +/-0.001nm for bond distances, on the basis of more than 22 X-ray absorption spectra): 0.213+/-0.001nm, 0.213+/-0. 001 nm, 0.236+/-0.001 nm, 0.293+/-0.001 nm, 0.189+/-0.001 nm and 0. 242+/-0.001. Lyophilization of the LOX altered the binding distances but did not destroy the octahedral iron ligand sphere. For construction of a structural model of the iron ligand sphere the binding distances extracted from the X-ray spectra were assigned to specific amino acids (His-360, -365, -540, -544 and the C-terminal Ile-662) by molecular modelling using the crystal coordinates of the soybean LOX-1 and of a rabbit 15-LOX-inhibitor complex.
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Affiliation(s)
- R J Kuban
- Institute of Biochemistry, University Clinics Charité, Humboldt University, Hessische Str. 3-4, D-10115 Berlin, Germany
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