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315 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6, 7, 8 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I12-JEEP: Joint Engineering, Environmental and Processing	Loading of a porous rock with constant micro-seismic event rate suppresses seismicity and promotes subcritical failure Maria-Daphne Mangriotis , Alexis Cartwright-Taylor , Ian G. Main , Andrew Curtis , Andrew F. Bell , Ian B. Butler , Florian Fusseis Scientific Reports 15 DOI: 10.1038/s41598-025-03105-5 Diamond Proposal Number(s): [22517] Open Access Show Abstract ▼ Abstract: Catastrophic failure is the end result of progressive localisation of damage creating brittle failure on a variety of system scales in the Earth. However, the factors controlling this evolution, and the relationship between deformation and the resulting earthquake hazard, are not well constrained. Here we address the question of how to adapt operational controls in a strain-inducing laboratory experiment so as to minimize associated microseismicity. We simultaneously image the induced damage using x-rays at a synchrotron, and detect acoustic emissions which can be fed back to change operational controls on the experiment. We confirm that using continuous servo-control based on acoustic emission event rate not only slows down deformation compared to standard constant strain rate loading, but also suppresses events of all sizes, including extreme events. We develop a new model that explains this observation, based on the observed evolution of microstructural damage and the fracture mechanics of subcritical crack growth. The model is independently consistent with the observed stress history and acoustic emission statistics. Our results imply that including seismic event rate control may improve risk management of induced seismicity over a range of event magnitudes, if similar processes are relevant at larger scales.	Jun 2025
I03-Macromolecular Crystallography	Divergent dimerization mechanisms and conserved DNA-binding function in PFam12 proteins of Borrelia burgdorferi Kalvis Brangulis , Dagnija Tupina , Everita Elina Sinicina , Diana Zelencova-Gopejenko , Inara Akopjana , Janis Bogans , Kaspars Tars Scientific Reports 15 DOI: 10.1038/s41598-025-93944-z Diamond Proposal Number(s): [35587] Open Access Show Abstract ▼ Abstract: Lyme disease, caused by the spirochete Borrelia burgdorferi, is transmitted to mammalian hosts during the feeding process of infected Ixodes ticks. Our previous studies demonstrated that the paralogous gene family 12 (PFam12) consisting of five members (BBK01, BBG01, BBH37, BBJ08, and BB0844) are non-specific DNA-binding proteins. PFam12 proteins share 31–69% sequence identity, are located either on the surface or within the periplasm and are upregulated as the tick starts its blood meal. The crystal structure of BBK01 revealed that the protein forms a homodimer, which is potentially critical for DNA binding. In this study, we determined the crystal structure of another PFam12 member, BBH37, to gain a better insight into this unique paralogous family. Although BBK01 dimerization is mediated by its C-terminal region and is thought to be critical for DNA binding, BBH37 forms dimers through an alternative mechanism where a unique disulfide bond is involved. We found that BBH37 is still able to interact with DNA with micromolar affinity. Molecular dynamics simulations and site-directed mutagenesis was conducted to characterize these unique DNA binding proteins. This study highlights the structural diversity within the PFam12, demonstrating that despite significant differences in dimerization mechanisms, these proteins retain their DNA-binding capability.	Apr 2025
B16-Test Beamline	Electronic structure, reflectivity and X-ray luminescence of MAPbCl3 crystal in orthorhombic phase Volodymyr Kolomiets , Volodymyr Kapustianyk , Mariya Kovalenko , Hans Kraus , Oksana Chukova , Yaroslav Zhydachevskyy , Wagas Zia , Michael Saliba , Vitaliy Mykhaylyk Scientific Reports 15 DOI: 10.1038/s41598-025-96694-0 Diamond Proposal Number(s): [31228] Open Access Show Abstract ▼ Abstract: This study provides a comprehensive analysis of the electronic structure, reflectivity, and luminescent spectra of the organic-inorganic, metal-halide MAPbCl3 perovskite, which has considerable potential for various optoelectronic applications. Using density functional theory (DFT) calculations, we investigated the electronic structure of MAPbCl3 and interpreted the key features of its reflectivity spectra across a wide energy range from 3 to 10 eV. The reflectivity spectra reveal prominent excitonic features at 3.22 eV near the absorption edge and additional optical transitions at higher energies, highlighting the material’s intricate electronic structure. Furthermore, we examined the temperature dependence of radiative decay dynamics under high-energy radiation through X-ray luminescence spectra and decay time measurements. We observe emission from free and bound excitons with an exceptionally short decay time (≤ 1 ns) and significant thermal quenching at low temperatures (100 K) in the 385–430 nm range. These findings underline the importance of continued exploration of optoelectronic properties of the material to enhance its performance in practical applications.	Apr 2025
I18-Microfocus Spectroscopy	Prostate microcalcification crystallography as a marker of pathology Sarah B. Gosling , Emily L. Arnold , Lois Adams , Paul Cool , Kalotina Geraki , Mark O. Kitchen , Iain D. Lyburn , Keith D. Rogers , Tim Snow , Nick Stone , Charlene E. Greenwood Scientific Reports 15 DOI: 10.1038/s41598-025-98692-8 Diamond Proposal Number(s): [31847] Open Access Show Abstract ▼ Abstract: Prostate cancer remains the most common male cancer; however, treatment regimens remain unclear in some cases due to a lack of agreement in current testing methods. Therefore, there is an increasing need to identify novel biomarkers to better counsel patients about their treatment options. Microcalcifications offer one such avenue of exploration. Microfocus spectroscopy at the i18 beamline at Diamond Light Source was utilised to measure X-ray diffraction and fluorescence maps of calcifications in 10 µm thick formalin fixed paraffin embedded prostate sections. Calcifications predominantly consisted of hydroxyapatite (HAP) and whitlockite (WH). Kendall’s Tau statistics showed weak correlations of ‘a’ and ‘c’ lattice parameters in HAP with GG (rτ = − 0.323, p = 3.43 × 10–4 and rτ = 0.227, p = 0.011 respectively), and a negative correlation of relative zinc levels in soft tissue (rτ = − 0.240, p = 0.022) with GG. Negative correlations of the HAP ‘a’ axis (rτ = − 0.284, p = 2.17 × 10–3) and WH ‘c’ axis (rτ = − 0.543, p = 2.83 × 10–4) with pathological stage were also demonstrated. Prostate calcification chemistry has been revealed for the first time to correlate with clinical markers, highlighting the potential of calcifications as biomarkers of prostate cancer.	Apr 2025
	A molecular dynamics study of the sputtering processes of beryllium species by hydrogenic plasma Alexander Liptak , Kerry D. Lawson , Mohammad I. Hasan Scientific Reports 15 DOI: 10.1038/s41598-025-98065-1 Open Access Show Abstract ▼ Abstract: The plasma-facing components of nuclear fusion reactors are continuously subjected to high thermal loads and bombardment by hydrogenic ions, resulting in erosion of the first-wall material and sputtering of atomic and molecular species into the edge plasma. The management of reactor component lifetimes and control of sputtered plasma impurities remain open problems in fusion research, where quantifying the sputtering yields and understanding the sputtering processes of each impurity species is pivotal for planning an effective maintenance schedule and ensuring optimal plasma performance. Although the sputtering of atomic species is historically well-established, the sputtering of molecules from metallic first-wall materials such as beryllium has only recently been confirmed possible and relevant for fusion reactors. In this study, a molecular dynamics model is used to investigate the sputtering of atomic beryllium, Be dimers, Be trimers, beryllium hydrides, and hydrogenic dimers. The sputtering yield of each species is reported, and the observed ion trajectory preferential sputtering behaviour is presented; beryllium lattice thermal effects as well as bombarding ion isotope effects are discussed where relevant. A theoretical description of the universal sputtering yield relation and its various corrections are explored in detail, and the molecular dynamics model is benchmarked against analytical, computational and experimental data.	Apr 2025
I18-Microfocus Spectroscopy	Anisotropy visualisation from X-ray diffraction of biological apatite in mixed phase calcified tissue samples Robert Scott , Iain D. Lyburn , Eleanor Cornford , Pascaline Bouzy , Nicholas Stone , Charlene Greenwood , Sarah Gosling , Emily L. Arnold , Ihsanne Bouybayoune , Sarah E. Pinder , Keith Rogers Scientific Reports 15 DOI: 10.1038/s41598-025-88940-2 Diamond Proposal Number(s): [30215] Open Access Show Abstract ▼ Abstract: X-ray diffraction is widely used to characterise the mineral component of calcified tissue. Broadening of the diffraction peaks yields valuable information on the size of coherently diffracting domains, sometimes loosely described as crystallite size or crystallinity. These domains are markedly anisotropic, hence a single number describing their size is misleading. We present a novel variation on a method for visualising crystallographic anisotropy in X-ray diffraction data. This provides an intuitively interpretable depiction of crystalline domain size and anisotropy. The new method involves creating a polar plot of calculated domain thickness for peaks in a diffractogram versus crystallographic direction. Points with the least error are emphasised. Anisotropic domain dimensions are calculated by refining an ellipsoidal model in a whole pattern fit. These dimensions are then used to overlay an ellipse on the peak broadening plot. This is illustrated by application of the method to calcifications in breast tissue with suspected cancer, which frequently contain whitlockite as well as nanocrystalline apatite. Like most biogenic apatite, this exhibits markedly anisotropic peak broadening. The nature of this anisotropy offers potentially useful information on normal function and pathology of calcified tissue and is a frequently neglected crystallographic feature of these materials.	Feb 2025
I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Broadening alloselectivity of T cell receptors by structure guided engineering Vijaykumar Karuppiah , Dhaval Sangani , Lorraine Whaley , Robert Pengelly , Pelin Uluocak , Ricardo J. Carreira , Miriam Hock , Pietro Della Cristina , Paulina Bartasun , Paula Dobrinic , Nicola Smith , Keir Barnbrook , Ross A. Robinson , Stephen Harper Scientific Reports 14 DOI: 10.1038/s41598-024-75140-7 Diamond Proposal Number(s): [22870, 28224] Open Access Show Abstract ▼ Abstract: Specificity of a T cell receptor (TCR) is determined by the combination of its interactions to the peptide and human leukocyte antigen (HLA). TCR-based therapeutic molecules have to date targeted a single peptide in the context of a single HLA allele. Some peptides are presented on multiple HLA alleles, and by engineering TCRs for specific recognition of more than one allele, there is potential to expand the targetable patient population. Here, as a proof of concept, we studied two TCRs, S2 and S8, binding to the PRAME peptide antigen (ELFSYLIEK) presented by HLA alleles HLA-A03:01 and HLA-A11:01. By structure-guided affinity maturation targeting a specific residue on the HLA surface, we show that the affinity of the TCR can be modulated for different alleles. Using a combination of affinity maturation and functional T cell assay, we demonstrate that an engineered TCR can target the same peptide on two different HLA alleles with similar affinity and potency. This work highlights the importance of engineering alloselectivity for designing TCR based therapeutics suitable for differing global populations.	Nov 2024
I09-Surface and Interface Structural Analysis	Surface polarization profile of ferroelectric thin films probed by X-ray standing waves and photoelectron spectroscopy Le Phuong Hoang , Irena Spasojevic , Tien-Lin Lee , David Pesquera , Kai Rossnagel , Jorg Zegenhagen , Gustau Catalan , Ivan A. Vartanyants , Andreas Scherz , Giuseppe Mercurio Scientific Reports 14 DOI: 10.1038/s41598-024-72805-1 Diamond Proposal Number(s): [27468] Open Access Show Abstract ▼ Abstract: Understanding the mechanisms underlying a stable polarization at the surface of ferroelectric thin films is of particular importance both from a fundamental point of view and to achieve control of the surface polarization itself. In this study, we demonstrate that the X-ray standing wave technique allows the surface polarization profile of a ferroelectric thin film, as opposed to the average film polarity, to be probed directly. The X-ray standing wave technique provides the average Ti and Ba atomic positions, along the out-of-plane direction, near the surface of three differently strained thin films. This technique gives direct access to the local ferroelectric polarization at and below the surface. By employing X-ray photoelectron spectroscopy, a detailed overview of the oxygen-containing species adsorbed on the surface is obtained. The different amplitude and orientation of the local ferroelectric polarizations are associated with surface charges attributed to different type, amount and spatial distribution of the oxygen-containing adsorbates.	Oct 2024
	Structure of the RNA-dependent RNA polymerase P2 from the cystovirus φ8 Merlyn Latimer-Smith , Paula S. Salgado , Ismay Forsyth , Eugene Makeyev , Minna M. Poranen , Dave I. Stuart , Jonathan M. Grimes , Kamel El Omari Scientific Reports 14 DOI: 10.1038/s41598-024-75213-7 Open Access Show Abstract ▼ Abstract: The replication of RNA viruses relies on the activity of RNA-dependent RNA polymerases (RdRps). Despite large variations in their genomic sequences, viral RdRps share a common architecture generally known as a closed right hand. The P2 polymerase of cystovirus φ6 is currently among the best characterized viral RdRps. This polymerase is responsible for carrying out both replication and transcription of the viral double-stranded RNA genome using de novo initiation. Despite the extensive biochemical and structural studies conducted on φ6 P2, further structural information on other cystoviral RdRps is crucial to elucidate the structural and functional diversity of viral RdRps. Here, we have determined the atomic X-ray structure of the RdRp P2 from the φ6-related cystovirus φ8 at 3Å resolution. This structure completes the existing set of structural information on the φ8 polymerase complex and sheds light on the difference and similarities with related cystoviral RdRps.	Oct 2024
B16-Test Beamline	Development of a nanometre scale X-ray speckle-based CT technique through the 3-D histological assessment of an acute respiratory distress syndrome model Matthew Donoghue , Hongchang Wang , Daniel O'Toole , Charles E. Connelly , Shahd Horie , Peter Woulfe , Cornelio Salinas , Brid King , Brendan Tuohy , Evan Kiely , Kazimir Wanelik , Kawal Sawhney , Christoph Kleefeld Scientific Reports 14 DOI: 10.1038/s41598-024-72660-0 Diamond Proposal Number(s): [24649] Open Access Show Abstract ▼ Abstract: The study of biological soft tissue structures at the micron scale details the function of healthy and pathological tissues, which is vital in the diagnosis and treatment of diseases. Speckle based X-ray phase contrast tomographic scans at a nanometer scale have the potential to thoroughly analyse such tissues in a quantitative and qualitative manner. Diamond light source, the UKs national synchrotron facility developed and refined a 1-D X-ray speckle-based imaging technique, referred to as Fly scan mode. This novel image acquisition technique was used to perform a rapid structural composition scan of rodent lung histology samples. The rodent samples were taken from healthy and Staphylococcus aureus induced acute respiratory distress syndrome models. The analysis and cross comparison of the fly scan method, absorption-based tomography and conventional histopathology H&E staining microscopy are discussed in this paper. This analysis and cross comparison outline the ways the speckle-based technique can be of benefit. These advantages include improved soft tissue contrast, 3-D volumetric rendering, segmentation of specific gross tissue structures, quantitative analysis of gross tissue volume. A further advantage is the analysis of cellular distribution throughout the volumetric rendering of the tissue sample. The study also details the current limitations of this technique and points to ways in which future work on this imaging modality may progress.	Oct 2024

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