Epitaxial YBa $\bf {_{2}}$ Cu$\bf {_{3}}$O$\bf {_{7-\delta }}$/MgO thin films fabricated with pulsed laser deposition are grown as idealised epitaxial systems with a minimal number of different elements for X-ray absorption spectroscopy studies of irradiation damage. These films are characterised in terms of their superconducting performance, crystallinity, surface morphology, and Cu local environment. This reveals a structural heterogeneity of $\bf {[100]}$ oriented material, referred to as “a-axis grains”, decorating the desired $\bf {[001]}$ oriented phase of the thin film, coinciding with suppressed superconducting performance.

Understanding how irradiation degrades superconductivity in REBCO coated conductor is a pressing field of research for the development of compact fusion devices. Here, defect formation in GdBa2Cu3O7-delta coated conductor is studied using a high dose of 2 MeV He+ ion irradiation. While laboratory based X-ray diffraction and magnetometry measurements show that the crystal structure becomes less well ordered with the loss of superconductivity in the material, transmission electron microscopy reveals a complex landscape of structural defects within the as-manufactured tape which complicate the identification and characterisation of irradiation induced structural changes. To resolve this, three sets of polarisation dependent extended X-ray absorption fine structure (EXAFS) spectroscopy experiments were carried out to map the local structure of the Gd, Ba, and Cu atomic sites within the material, providing three independent probes for studying irradiation defects within the structurally anisotropic REBCO unit cell. Here the Ba and Cu environments were the more sensitive to the irradiation treatment, with only small changes to the Gd local structure observed. Both the Ba and Cu local structures retained much of the pristine structure in the a/b-plane following irradiation, with greater shifts evident in the c-axis aligned measurements. In the irradiated Cu K edge EXAFS analysis, a shifted peak in the c-axis aligned measurements is observed that is not compatible with the REBCO local structure. This is attributed to an O site irradiation defect motif consistent with a Frenkel defect.

We present the first experimental observation of long-unresolved many-body satellite features within the Kα1,2 X-ray emission spectra of zinc (Zn) with statistical significance exceeding 50 σse per data point. These novel structures, "Hidden Satellites", were discovered using an extended-range high-energy-resolution fluorescence detection (XR-HERFD) technique at the I20-Scanning beamline of the Diamond Light Source in UK. The measurements employed a 14-crystal analyzer array specifically designed to enhance both energy resolution and statistical accuracy. The Hidden Satellites are revealed within the main Kα1,2 emission peak and exhibit a systematic evolution with increasing incident photon energy. Principal component analysis (PCA) was employed to independently isolate these novel features and trace the evolution of these structures. Remarkably, these hidden features contribute 15% to 20% of the total emission intensity, directly challenging the long-standing assumption that the many-body reduction factor (S02) is constant. We observe that S02 exhibits a clear energy dependence, changing by over 20% over the observed energy range, with broad implications for the analysis and interpretation of X-ray absorption and emission spectra in transition metals and their compounds. Overall, it provides a new foundation for interpreting X-ray spectroscopy, influencing thousands of studies across chemistry, physics, and biology. Despite zinc metal being considered a "simple" d10 metal, the complexity of structure, asymmetry and evolution of these new processes is dramatic and points to a rich new area of inquiry.

Metals play an essential role in cellular homeostasis and are key components of several formulations currently used in the clinic. Synchrotron-based X-ray microscopy at submicron resolution is a powerful approach to map intracellular elemental distributions and to monitor how these patterns change upon genetic or pharmacological perturbations. However, existing sample-preparation protocols often rely on costly and highly specialized equipment for vitrification and dehydration, limiting their widespread adoption. Here, we present an adapted plunge-freezing and freeze-drying workflow that enables the preparation of mammalian cell samples for X-ray fluorescence (XRF) and X-ray absorption spectroscopy (XAS) studies with submicron resolution in a cost-effective and versatile manner. Furthermore, we define acquisition parameters optimized for the reliable detection of low-abundance metals, such as endogenous iron. We anticipate that this accessible protocol will facilitate the broader implementation of synchrotron-based inner-shell spectromicroscopy in cell biology.

Nucleophosmin (NPM1) is a nucleolar protein commonly mutated in ~30% of newly diagnosed acute myeloid leukemia (AML) cases. These mutations occur in the terminal exon of the NPM1 gene, affecting the C-terminal DNA-binding domain of the protein and causing its delocalization to the cytoplasm-a hallmark of NPM1-mutated AML. NPM1 shuttling to the nucleoplasm is tightly regulated by posttranslational modifications, such as phosphorylation of Ser254, Ser260, and Tyr271 of the DNA-binding domain. However, the structural mechanisms underlying this process remain unclear. In this work, we show that Ser-to-Asp (S254D-S260D) and Tyr-to-pCMF (para-carboxymethyl phenylalanine) (Y271pCMF) phosphomimetic mutations induce significant structural and dynamical rearrangements, as well as drastic modifications in electrostatic surface potential. These changes compromise recognition of a G-quadruplex sequence from the c-MYC promoter by reducing DNA-binding affinity, reshape histone capturing dynamics, and fade charge segregation in the histone-binding domain. Combination of such substitutions in a triple phosphomimetic variant (S254D-S260D-Y271pCMF) further destabilizes the domain's structure and triggers protein aggregation. Altogether, these findings suggest that phosphorylation of Ser254, Ser260, and Tyr271 of the C-end DNA-binding domain weakens both DNA affinity and charge block-driven liquid-liquid phase separation, offering a molecular explanation for the delocalization of NPM1 outside of the nucleolus.

Epitaxial YBa2Cu3O7-delta/MgO thin films fabricated with pulsed laser deposition are grown as idealised epitaxial systems with a minimal number of different elements for X-ray absorption spectroscopy studies of irradiation damage. These films are characterised in terms of their superconducting performance, crystallinity, surface morphology, and Cu local environment. This reveals a structural heterogeneity of [100] oriented material, referred to as "a-axis grains", decorating the desired [001] oriented phase of the thin film, coinciding with suppressed superconducting performance

We report the technical design, implementation and operation of a newly developed X-ray emission spectrometer on the I20 beamline at Diamond Light Source. The spectrometer consists of 14 crystal analysers arranged in an up-down configuration, allowing for operation in one- or two-colour acquisition modes. Since beginning operations in 2023, the spectrometer has substantially enhanced the capability of the beamline to perform X-ray emission spectroscopy (XES) and has demonstrated high reliability with minimal operational issues during user experiments. The latter achievement is particularly significant given the complexity of the instrument, and the difficulty of maintaining the Rowland condition when scanning the energy. We show that the spectrometer can effectively measure spectra in two-colour mode and is capable of detecting weak valence-to-core emission features with a significantly improved signal-to-background ratio. We also present data taken using a newly developed quick-scanning XES acquisition mode, which enables data collection in seconds rather than minutes. This mode opens up possibilities for time-resolved studies and investigating radiation-sensitive materials.

We discover satellites in Zn at emission energies of 8670-8675 eV. The satellite is detected with a significance exceeding 51.6 [Formula: see text] per pixel, enabled by the exceptional signal-to-noise ratio of the new dataset and novel technique. We have created the eXtended-range high-energy-resolution fluorescence detection (XR-HERFD) technique and applied it to Zn (Z = 30) using a novel 14-crystal analyser spectrometer. For this current work, data collection developed the first DOSE-S collection macros for Discovery-Onset-Spectrometry-Evolution of new Satellite processes. The energy dependence of the discovered satellite is tracked from the onset of the process at approximately 10791.7 eV through its evolution to higher energies. The satellite exhibits a clear manifold structure, consistent with multiple shake-off processes. We develop and apply Principal Component Analysis (PCA) and independently isolate the manifold of the satellite and prove the incident-energy evolution. We also fit the evolution to theoretical quantum mechanical models of such processes to provide strong confirmation of the physical origin. These findings demonstrate XR-HERFD's capability to resolve weak many-body features and suggest new opportunities for studying shake processes and the many-body reduction factor [Formula: see text]. By resolving these satellites in what many people believed was a nominally simple [Formula: see text] metal and revealing rich many-body behaviour, this work opens a pathway to a physically grounded understanding of many-body effects in X-ray spectroscopy.

The discovery of the novel n = 2 satellite transition in the Kβ emission spectrum of manganese and its evolution with incident photon energy are presented. Using the XR-HERFD (extended-range high-energy-resolution fluorescence detection) technique, we conclusively demonstrate the existence of this phenomenon with a statistical significance corresponding to 652 σse across the measured spectrum, far above the discovery threshold of 3–6 σse. We apply principal component analysis (PCA) to the XR-HERFD data to extract advanced structural insights. The evolution of this novel spectral feature and physical process are quantified by incorporating regression, revealing the increase in intensity over a wide range of incident photon energies. We validate these findings through independent test data. These results directly challenge the conventional treatment of the many-body reduction factor S02 as a constant independent of incident photon energy in the standard XAFS (X-ray absorption fine structure) equation. Thereby, these results present compelling evidence that S02 should be modelled as a varying function of incident photon energy, marking the first observation of this behaviour in Kβ spectra. This facilitates a greater quantitative understanding of HERFD spectra and a comprehensive representation of many-body effects in condensed matter systems.

We report the first experimental discovery of Hidden Satellites within the K α _1,2 emission lines of manganese metal (Mn, Z = 25 ) with a total integrated statistical significance exceeding 270 σ _s.e. (standard error), far beyond the discovery threshold. Experimental data were collected at the I20-Scanning beamline at the Diamond Light Source using our new eXtended-Range High-Energy-Resolution Fluorescence Detection (XR-HERFD) technique. The Hidden Satellites, embedded in the core emission structure, represent novel quantum many-body processes that evolve systematically as the incident photon energy increases. Principal Component Analysis (PCA) was applied to extract the major separable physical processes and validate the significance of the observed Hidden Satellites. The application of physical insight to the PCA method allowed us to isolate the satellites, and measure the evolutionary profile. Our paper reveals that the total intensity of shake-off satellites can reach as high as 20–25

Understanding irradiation damage of REBCO is increasingly of interest for compact tokamak fusion reactor designs, as these materials are critical for the proposed magnetic plasma confinement systems. Here commercially sourced samples of REBCO coated conductor are irradiated with 300 keV He+ ions to a damage level of 169 x 10-3 displacements-per-atom, to the point where superconductivity is no longer detectable, meaning these samples correspond to a non-functional end-of-life component in a fusion reactor context. Subsequent analysis of the crystal structure through a combination of x-ray diffraction and x-ray absorption spectroscopy measurements reveals a complex variation away from the as-grown structure. The local structure probed by the spectroscopy measurements is further observed to change as a function of the relative polarisation of the incident x-ray beam, indicating that within this damage regime the structural anisotropy of the REBCO unit cell plays a determining role in where defects accumulate within the material. Here the local structure measurements probing the a-b plane of the system vary significantly less than those probing the c-axis direction following irradiation, mirroring the observed trend in the x-ray diffraction data that the a:b ratio is preserved upon irradiation whilst the absolute values increase, whereas the c-axis parameter expands. These observations highlight the role of oxygen defect formation in driving the degradation of superconductivity within irradiated REBCO. These changes are observed to preferentially accumulate along the c-axis of the material, indicating a possible mechanistic signature of the degradation of the superconducting properties within these systems that are evident using a local structure probe such as extended x-ray absorption fine structure.

A free-standing and compact reaction cell for combined in situ/operando x-ray spectroscopy, scattering, and imaging measurements at high pressures and high temperatures is described. The cell permits measurements under realistic operating conditions (up to 50 bar and 1000 degrees C), under static and flow conditions (up to 100 ml/min), over a wide range of hard x-ray energies, variable detection modes (transmission, fluorescence, and scattering), and at all angles of rotation. An operando XAS, x-ray fluorescence, x-ray computed tomography, and x-ray diffraction computed tomography case study on the reduction of a heterogeneous catalyst is presented to illustrate the performance of the reaction cell.

Accurate analysis of the rich information contained within X-ray spectra usually calls for detailed electronic structure theory simulations. However, density functional theory (DFT), time-dependent DFT and many-body perturbation theory calculations increasingly require the use of advanced codes running on high-performance computing (HPC) facilities. Consequently, many researchers who would like to augment their experimental work with such simulations are hampered by the compounding of nontrivial knowledge requirements, specialist training and significant time investment. To this end, we present Web-CONEXS, an intuitive graphical web application for democratizing electronic structure theory simulations. Web-CONEXS generates and submits simulation workflows for theoretical X-ray absorption and X-ray emission spectroscopy to a remote computing cluster. In the present form, Web-CONEXS interfaces with three software packages: ORCA, FDMNES and Quantum ESPRESSO, and an extensive materials database courtesy of the Materials Project API. These software packages have been selected to model diverse materials and properties. Web-CONEXS has been conceived with the novice user in mind; job submission is limited to a subset of simulation parameters. This ensures that much of the simulation complexity is lifted and preliminary theoretical results are generated faster. Web-CONEXS can be leveraged to support beam time proposals and serve as a platform for preliminary analysis of experimental data.

X-ray absorption spectroscopy (XAS) is an established experimental technique for studying the electronic and local geometric structures of materials. As a short-range order structural probe, it can be applied to all states of matter: crystalline or amorphous solids, liquids and gases. The method is element selective and highly sensitive, with little compromise required to integrate complex sample environment set-ups. These characteristics make the technique suitable for applications in a range of scientific disciplines, from chemistry and catalysis to environmental science, materials science, physics, biology, medicine and cultural heritage. An XAS spectrum is obtained by measuring the modulation of the sample absorption coefficient as a function of the incident X-ray beam energy. Data are usually collected in transmission detection mode, although fluorescence and electron yield detection modes are often used. The XAS spectrum is divided into two regimes: X-ray absorption near-edge structure and extended X-ray absorption fine structure. In this Primer, an overview of XAS fundamentals is given, together with a description of the experimental set-ups, sample requirements, data analysis and possible applications. X-ray absorption spectroscopy is an element-specific and orbital-specific technique that can probe local atomic and electronic structures, without the need for long-range order. This Primer discusses the background principles, experimental methods and data analysis processes used in X-ray absorption spectroscopy to derive oxidation states, coordination and bond lengths of solids, liquids and gases.

Here, the novel technique of extended-range high-energy-resolution fluorescence detection (XR-HERFD) has successfully observed the n = 2 satellite in manganese to a high accuracy. The significance of the satellite signature presented is many hundreds of standard errors and well beyond typical discovery levels of three to six standard errors. This satellite is a sensitive indicator for all manganese-containing materials in condensed matter. The uncertainty in the measurements has been defined, which clearly observes multiple peaks and structure indicative of complex physical quantum-mechanical processes. Theoretical calculations of energy eigenvalues, shake-off probability and Auger rates are also presented, which explain the origin of the satellite from physical n = 2 shake-off processes. The evolution in the intensity of this satellite is measured relative to the full Kα spectrum of manganese to investigate satellite structure, and therefore many-body processes, as a function of incident energy. Results demonstrate that the many-body reduction factor S02 should not be modelled with a constant value as is currently done. This work makes a significant contribution to the challenge of understanding many-body processes and interpreting HERFD or resonant inelastic X-ray scattering spectra in a quantitative manner.

Understanding the nature of intermediates/active species in reactions is a major challenge in chemistry. This is because spectator species typically dominate the experimentally derived data and consequently active phase contributions are masked. Transient methods offer a means to bypass this difficulty. In particular, modulation excitation with phase-sensitive detection (ME-PSD) provides a mechanism to distinguish between spectator and reacting species. Herein, modulation excitation (ME) time-resolved (energy dispersive) X-ray absorption spectroscopy, assisted by phase sensitive detection (PSD) analysis, has been applied to the study of a liquid phase process; in this case the classic ferrocyanide/ferricyanide redox couple. Periodic switches of the electrical potential (anodic/cathodic) enabled the use of the ME approach. Structural changes at fractions as low as 2 % of the total number of electroactive species were detected within the X-ray beam probe volume containing ~30 pmol of Fe(II)/Fe(III).

The discovery of a new physical process in manganese metal is reported. This process will also be present for all manganese-containing materials in condensed matter. The process was discovered by applying our new technique of XR-HERFD (extended-range high-energy-resolution fluorescence detection), which was developed from the popular high-resolution RIXS (resonant inelastic X-ray scattering) and HERFD approaches. The acquired data are accurate to many hundreds of standard deviations beyond what is regarded as the criterion for `discovery'. Identification and characterization of many-body processes can shed light on the X-ray absorption fine-structure spectra and inform the scientist on how to interpret them, hence leading to the ability to measure the dynamical nanostructures which are observable using the XR-HERFD method. Although the many-body reduction factor has been used universally in X-ray absorption spectroscopy in analysis over the past 30 years (thousands of papers per year), this experimental result proves that many-body effects are not representable by any constant reduction factor parameter. This paradigm change will provide the foundation for many future studies and X-ray spectroscopy.

Understanding the effects of high energy neutron damage on REBa 2 Cu 3 O 7 − δ (REBCO) coated conductor is of vital importance for the design of the magnetic confinement systems for compact nuclear fusion power plants. However, neutron irradiation campaigns can only be carried out in a few facilities, and the experiments are very slow and expensive partly because the samples become radioactive. Ion irradiation provides an easily accessible alternative route to studying the effects of radiation on high temperature superconductors, which not only increases the volume of technical data that can be obtained but also enables more complex experiments such as in situ cryogenic irradiation. The question is, does ion damage offer a good proxy for neutrons? Here we use high energy resolution fluorescence detected x-ray absorption spectroscopy to probe the effects of fast neutron irradiation on the local environment around the copper ions in the REBCO layer of coated conductor tapes. We find that the spectral changes are similar to those induced by helium ion irradiation, suggesting that both projectiles produce the same types of structural defect in the REBCO lattice, although there is some evidence of an additional type of defect present in the sample heavily damaged by He + ion irradiation. It is also shown that the linear degradation of superconducting transition temperature (T c ) of coated conductors with the calculated number of displacements per atom occurs at the same rate for neutrons and helium ions. Together these results provide new evidence suggesting that helium ions can emulate neutron point defect damage in REBCO high temperature superconductor reasonably well, increasing confidence that helium ions could be used as a useful proxy for neutrons in future experiments.