Journal of Synchrotron Radiation最新文献

{"title":"Shedding light on biochemical changes in single neuron-like pheochromocytoma cells following exposure to synchrotron sourced terahertz radiation using synchrotron source Fourier transform infrared microspectroscopy.","authors":"Palalle G Tharushi Perera, Jitraporn Vongsvivut, Denver Linklater, Zoltan Vilagosh, Dominique Appadoo, The Hong Phong Nguyen, Mark J Tobin, Rodney Croft, Elena P Ivanova","doi":"10.1107/S1600577524010944","DOIUrl":"10.1107/S1600577524010944","url":null,"abstract":"<p><p>Synchrotron sourced Fourier transform infrared (SS FTIR) microspectroscopy was employed to investigate the biological effects on the neuron-like pheochromocytoma (PC 12) cells after exposure to synchrotron sourced terahertz (SS THz) radiation. Over 10 min of exposure, the PC 12 cells received a total energy of 600 J m², with a total incident power density of ∼1.0 W m^-2 (0.10 mW cm^-2) at the beam extraction port (BEP) of the THz beamline at the Australian Synchrotron. To investigate the metabolic response of PC 12 cells after synchrotron THz radiation exposure, we utilized the FTIR microscope at the Infrared Microspectroscopy IRM beamline, which offers high photon flux and diffraction-limited spatial resolution enabling the detection of functional group variations in biological molecules at a single-cell level. Principal component analysis (PCA) based on the SS FTIR spectral data revealed a distinct separation of SS THz-exposed and control (non-exposed) cells. According to the PCA loadings, the key changes in the exposed cells involved lipid and protein compositions as indicated by the stretching vibrations of CH₂/CH₃ groups and amide I/II bands, respectively. An increase in lipids, such as cholesterol, or notable changes in their compositions and in some protein secondary structures were observed in the SS THz-exposed cells. The PCA analysis further suggests that PC 12 cells might maintain cell membrane stability after SS THz irradiation through higher volumes of cholesterol and cell morphology via regulation of the synthesis of cytoskeleton proteins such as actin-related proteins. The outcome of this study re-emphasized the exceptional SS FTIR capability to perform single-cell analysis directly, providing (i) unique biological information on cell variability within the population as well as between different groups, and (ii) evidence of molecular changes in the exposed cells that could lead to a deeper understanding of the effect of THz exposure at a single-cell level.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"155-161"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Visualization of four-dimensional X-ray absorption fine structure data using a virtual reality system.","authors":"Haruo Igarashi, Daiki Kido, Yutaka Ishii, Yasuhiro Niwa, Atsushi Okamoto, Masao Kimura","doi":"10.1107/S1600577524011226","DOIUrl":"10.1107/S1600577524011226","url":null,"abstract":"<p><p>X-ray spectromicroscopy is extensively utilized for nondestructive mapping of chemical states in materials. However, understanding and analyzing the geometric and topological aspects of such data pose challenges due to their representation in 4D space, encompassing (x, y, z) coordinates along with the energy (E) axis and often extending to 5D space with the inclusion of time (t) or reaction degree. In this study, we addressed this challenge by developing a new approach and introducing a device named `4D-XASView', specifically designed for visualizing X-ray absorption fine structures (XAFS) data in 4D (comprising 3D space and energy), through a multi-projection system, within the virtual reality (VR) environment. As a test case for the new system, X-ray spectromicroscopy measurements were conducted on a specimen prepared from serpentinized harzburgite sourced from the upper mantle section of the Oman ophiolite. Our 4D-XASView facilitates the visualization and analysis of the geometric and topological aspects of the data using VR goggles, enabling detailed exploration of microstructures via rotation and zooming functionalities. This capability allows us to extract XAFS spectral data by selecting specific positions and regions, thereby aiding in the identification of `trigger sites' (magnetite in serpentine), which are characteristic locations within materials that substantially influence the macroscopic propagation of reactions. Our methodology establishes a new platform for analyzing 4D or 5D XAFS data that has applicability potential in various other multidimensional datasets, including microstructures coupled with spectroscopy and diffraction data.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"162-170"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142869567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-resolution imaging of organic and inorganic nanoparticles at nanometre-scale resolution by X-ray ensemble diffraction microscopy.","authors":"Ning Jung Chen, Chia Hui Yeh, Huai Yu Cao, Nai Chi Chen, Chun Jung Chen, Chun Yu Chen, Yi Wei Tsai, Jhih Min Lin, Yu Shan Huang, Chien Nan Hsiao, Chien Chun Chen","doi":"10.1107/S1600577524010567","DOIUrl":"10.1107/S1600577524010567","url":null,"abstract":"<p><p>Coherent diffraction microscopy (CDM) is a robust direct imaging method due to its unique 2D/3D phase retrieval capacity. Nonetheless, its resolution faces limitations due to a diminished signal-to-noise ratio (SNR) in high-frequency regions. Addressing this challenge, X-ray ensemble diffraction microscopy (XEDM) emerges as a viable solution, ensuring an adequate SNR in high-frequency regions and effectively surmounting resolution constraints. In this article, two experiments were conducted to underscore XEDM's superior spatial resolution capabilities. These experiments employed 55 nm-sized silicon-gold nanoparticles (NPs) and 19 nm-sized nodavirus-like particles (NV-LPs) on the coherent X-ray scattering beamline of the Taiwan Photon Source. The core-shell density distribution of the silicon-gold NPs was successfully obtained with a radial resolution of 3.4 nm per pixel, while NV-LPs in solution were reconstructed at a radial resolution of 1.3 nm per pixel. The structural information was directly retrieved from the diffraction intensities without prior knowledge and was subsequently confirmed through transmission electron microscopy.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"217-224"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-segment cooling design of a reflection mirror based on the finite-element method.","authors":"Zhen Wang, Yajun Tong, Fang Liu, Chaofan Xue, Limin Jin, Zhi Liu","doi":"10.1107/S1600577524009664","DOIUrl":"10.1107/S1600577524009664","url":null,"abstract":"<p><p>High-repetition-rate free-electron lasers impose stringent requirements on thermal deformations of optics in the beamline. The Shanghai HIgh-repetition-rate XFEL aNd Extreme light facility (SHINE) experiences high average thermal power and demands wavefront preservation. To effectively manage thermal deformation in the first reflection mirrors M1, we optimized the cooling length and position of the cooling groove with numerical calculations. For example, the root mean square of the height error of the thermal deformation of the mirror at a photon energy of 900 eV was optimized, resulting in a 12.7× reduction, from 13.76 nm to 1.08 nm. This optimized design also eliminated stray light in the focus spot at the sample and resulted in a 177% increase in the peak intensity of the beam's focus spot at the sample, from 3.08 × 10⁵ to 8.53 × 10⁵. The multi-segment cooling design of the mirror advanced the quality of the beam's focus spot at the sample and ensured the stable operation of SHINE under high repetition rates.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"10-16"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708864/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142669537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diffractometer for element-specific analysis on local structures using a combination of X-ray fluorescence holography and anomalous X-ray scattering.","authors":"Hiroo Tajiri, Shinji Kohara, Koji Kimura, Sekhar Halubai, Haruto Morimoto, Naohisa Happo, Jens R Stellhorn, Yohei Onodera, Xvsheng Qiao, Daisuke Urushihara, Peidong Hu, Toru Wakihara, Toyohiko Kinoshita, Koichi Hayashi","doi":"10.1107/S1600577524011366","DOIUrl":"10.1107/S1600577524011366","url":null,"abstract":"<p><p>To tackle disorder in crystals and short- and intermediate-range order in amorphous materials, such as glass, we developed a carry-in diffractometer to utilise X-ray fluorescence holography (XFH) and anomalous X-ray scattering (AXS), facilitating element-specific analyses with atomic resolution using the wavelength tunability of a synchrotron X-ray source. Our diffractometer unifies XFH and AXS configurations to determine the crystal orientation via diffractometry. In particular, XFH was realised even for a crystal with blurred emission lines by a standing wave in a hologram, and high-throughput AXS with sufficient count statistics and energy resolution was achieved using three multi-array detectors with crystal analysers. These features increase tractable targets by XFH and AXS, which have novel functionalities.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"125-132"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142869768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"3DCryoHolder: a new open access 3D printable system to store and transport silicon nitride membranes under cryogenic conditions for spectromicroscopy at low temperature.","authors":"Antonio Dominguez-Alfaro, Carlos Sanchez-Cano","doi":"10.1107/S1600577524010919","DOIUrl":"10.1107/S1600577524010919","url":null,"abstract":"<p><p>Data acquisition under cryogenic conditions allows one to avoid unwanted damage caused by beam irradiation. This is particularly important for the study of biological samples at hard X-ray, micro- or nano-probe beamlines, which focus synchrotron radiation to small beam sizes with extremely high flux densities. Sample preparation methods for cryopreserved specimens have been adapted from electron microscopy, and include the use of silicon nitride membranes as they are easy to handle and possess low X-ray absorption. Yet, currently there are no commercially available methods for the storage and transport of silicon nitride membranes under cryogenic conditions. Here, we introduce and provide the design files of 3DCryoHolder, a system that can be 3D printed in-house for the correct storage and transport of multiple silicon nitride membranes under cryogenic conditions, and is compatible with all commercial plunge-freezing instruments.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"225-229"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thermal deformation compensation scheme to the sub-nanometre level of a piezoelectric offset mirror for MHz repetition rate free-electron laser.","authors":"Baoning Sun, Qinming Li, Chuan Yang, Kai Hu, Zhongmin Xu, Xiaohao Dong, Weiqing Zhang, Xueming Yang","doi":"10.1107/S1600577524011469","DOIUrl":"10.1107/S1600577524011469","url":null,"abstract":"<p><p>Free-electron laser (FEL) facilities operating at MHz repetition rates can emit lasers with average powers reaching hundreds of watts. Partial absorption of this power induces thermal deformation of a few micrometres on the mirror surface. Such deformation degrades the characteristics of the reflected photon beam, leading to focal spot aberrations and wavefront distortions that fail to meet experimental requirements. A robust method is necessary to correct the mirror surface shape to meet the Maréchal criterion. This paper proposes a thermal deformation compensation scheme for offset mirrors operating at MHz repetition rates using a piezoelectric deformable mirror. The mirror is side-mounted with slots filled with an indium-gallium alloy, which house copper tubes for water cooling. Eighteen groups of piezo actuators are symmetrically attached to the top and bottom surfaces. The scheme incorporates finite-element analysis for simulation and post-processing verification, utilizing a differential evolution (DE) algorithm for global optimization. The DE algorithm effectively addresses the voltage constraints that the traditional singular value decomposition algorithm cannot handle. Under an X-ray wavelength of 1 nm, the peak-to-valley (PV) height error of the mirror was reduced from 1340.8 nm to 1.1 nm, and the root-mean-square (RMS) height error decreased from 859.1 nm to 0.18 nm. The slope error was corrected to 154 nrad PV and 24 nrad RMS. Significant results were also achieved at an X-ray wavelength of 3 nm. Wave-optics simulations verified the reliability of this approach, and effects on key mirror parameters and conditions were systematically analysed.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"46-56"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"30 years of Journal of Synchrotron Radiation and synchrotron science.","authors":"S Samar Hasnain","doi":"10.1107/S1600577524010798","DOIUrl":"10.1107/S1600577524010798","url":null,"abstract":"<p><p>Journal of Synchrotron Radiation (JSR) came into being with the publication of its inaugural issue in October 1994 that contained 15 full articles comprising 100 pages. Thirty years of JSR has coincided with several Nobel Prizes that have arisen from the work undertaken on synchrotron radiation sources, with the first of these awarded to Sir John Walker in 1997, just three years after the launch of JSR, and celebrated on the front cover of the journal's July 1999 issue. This article provides an insight into the motivation as well as the journey of establishing this important journal for the IUCr and the synchrotron radiation community which has continued to grow. We also highlight some of the well cited papers for each of the five-year-periods during these 30 years and demonstrate how the journal has become the natural home for all aspects of synchrotron radiation science and technology.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"1-9"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142669536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A fully contained sample holder capable of electron-yield detection at soft X-ray energies.","authors":"S Olivia Gunther, Patrick W Smith, Jacob A Branson, Alexander S Ditter, Stefan G Minasian, Alpha T N'Diaye, Bianca Schacherl, David K Shuh","doi":"10.1107/S1600577524011354","DOIUrl":"10.1107/S1600577524011354","url":null,"abstract":"<p><p>A holder has been developed that enables electron yield-detected soft X-ray spectroscopy of fully contained samples at low temperature. Crucially, this design uses elements of the sample containment to collect ejected electrons, removing the need to expose samples directly to the vacuum environment of the spectrometer. The design is modular and should be adaptable to a number of different endstation configurations, enabling spectroscopy of air-sensitive, radioactive and vacuum-sensitive (biological) samples.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"230-233"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142869763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review and experimental comparison of speckle-tracking algorithms for X-ray phase contrast imaging.","authors":"Rafael Celestre, Laurène Quénot, Christopher Ninham, Emmanuel Brun, Luca Fardin","doi":"10.1107/S1600577524010117","DOIUrl":"10.1107/S1600577524010117","url":null,"abstract":"<p><p>X-ray speckles have been used in a wide range of experiments, including imaging (and tomography), wavefront sensing, spatial coherence measurements, X-ray photon correlation spectroscopy and ptychography. In this review and experimental comparison, we focus on using X-ray near-field speckle grains as wavefront markers and numerical methods for retrieving the phase information they contain. We present the most common tracking methods, introducing the existing algorithms with their specifications and comparing their performances under various experimental conditions. This comparison includes applications to different types of samples: phantoms for quantitative analysis and complex samples for assessing image quality. Our goal is to unify concepts from several speckle tracking methods using consistent terminology and equation formalism, while keeping the discussion didactic and accessible to a broad audience.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"180-199"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}