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Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB
Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure-function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduces new data archival challenges in terms of data size and complexity in the years to come.
Ultrafast electron diffraction: Visualizing dynamic states of matter
Since the discovery of electron-wave duality, electron scattering instrumentation has developed into a powerful array of techniques for revealing the atomic structure of matter. Beyond detecting local lattice variations in equilibrium structures with the highest possible spatial resolution, recent research efforts have been directed toward the long-sought-after dream of visualizing the dynamic evolution of matter in real time. The atomic behavior at ultrafast timescales carries critical information on phase transition and chemical reaction dynamics, the coupling of electronic and nuclear degrees of freedom in materials and molecules, and the correlation among structure, function, and previously hidden metastable or nonequilibrium states of matter. Ultrafast electron pulses play an essential role in this scientific endeavor, and their generation has been facilitated by rapid technical advances in both ultrafast laser and particle accelerator technologies. Here this review presents a summary of the noteworthy developments in this field in the last few decades. The physics and technology of ultrafast electron beams is presented with an emphasis on the figures of merit most relevant for ultrafast electron diffraction experiments. Recent developments in the generation, manipulation, and characterization of ultrashort electron beams aimed at improving the combined spatiotemporal resolution of these measurements are discussed. The fundamentals of electron scattering from atomic matter and the theoretical frameworks for retrieving dynamic structural information from solid-state and gas-phase samples is described. Essential experimental techniques and several landmark works that have applied these approaches are also highlighted to demonstrate the widening applicability of these methods. Ultrafast electron probes with ever-improving capabilities, combined with other complementary photon-based or spectroscopic approaches, hold tremendous potential for revolutionizing our ability to observe and understand energy and matter at atomic scales.
A novel active veto prototype detector with an inner target for improved rare event searches
Here, we report the fabrication and performance of an annular, cryogenic, phonon-mediated veto detector that can host an inner target detector, allowing substantial reduction in radiogenic backgrounds for rare event search experiments. A germanium veto detector of mass ~500g with an outer diameter of 76 mm and an inner diameter of 28 mm was produced inside of which was mounted a 25 mm diameter germanium inner target detector of mass ~10g. The detector was designed using inputs from a GEANT4 based simulation, where it was modeled to be sandwiched between two germanium detectors. The simulation showed that the background rates (dominated by gamma interactions) could be reduced by >90%, and that such an arrangement is sufficient for aggressive background reduction needed for neutrino and dark matter search experiments. Operating at mK temperatures at the experimental site, the veto detector prototype achieved a baseline resolution of 1.24±0.02 keV while hosting a functional inner target detector. The baseline resolution of the inner target detector was 147±2 eV. The experimental results of an identical detector arrangement are in excellent agreement with the simulation.
Enhanced spatial resolution of Eljen-204 plastic scintillators for use in rep-rated proton diagnostics
A pixelated scintillator has been designed, fabricated, and tested using a laser-accelerated proton source for use in proton diagnostics at rep-rated laser facilities. The work presented here demonstrates the enhanced spatial resolution of thin, organic scintillators through a novel pixelation technique. Furthermore, experimental measurements using laser-generated protons incident onto 130 μm-thick scintillators indicate a >20% reduction in the scintillator point spread function (PSF) for the detectors tested. The best performing pixelated detector reduced the ~200 μm PSF of the stock material to ~150 μm. The fabrication technique may be tailored to reduce the pixel size and achieve higher spatial resolutions.
Development of an operando characterization stage for multi-modal synchrotron x-ray experiments
It is widely accepted that micro- and nanoscale inhomogeneities govern the performance of many thin-film solar cell absorbers. These inhomogeneities yield material properties (e.g., composition, structure, and charge collection) that are challenging to correlate across length scales and measurement modalities. The challenge is compounded if a correlation is sought during device operation or in conditions that mimic aging under particular stressors (e.g., heat and electrical bias). Correlative approaches, particularly those based on synchrotron x-ray sources, are powerful since they can access several material properties in different modes (e.g., fluorescence, diffraction, and absorption) with minimal sample preparation. Small-scale laboratory x-ray instruments have begun to offer multi-modality but are typically limited by low x-ray photon flux, low spatial resolution, or specific sample sizes. To overcome these limitations, a characterization stage was developed to enable multi-scale, multi-modal operando measurements of industrially relevant photovoltaic devices. The stage offers compatibility across synchrotron x-ray facilities, enabling correlation between nanoscale x-ray fluorescence microscopy, microscale x-ray diffraction microscopy, and x-ray beam induced current microscopy, among others. Furthermore, the stage can accommodate device sizes up to 25 × 25 mm 2 , offering access to multiple regions of interest and increasing the statistical significance of correlated properties. The stage materials can sustain humid and non-oxidizing atmospheres, and temperature ranges encountered by photovoltaic devices in operational environments (e.g., from 25 to 100 °C). As a case study, we discuss the functionality of the stage by studying Se-alloyed CdTe photovoltaic devices aged in the stage between 25 and 100 °C.
Exploring physics of ferroelectric domain walls via Bayesian analysis of atomically resolved STEM data
The physics of ferroelectric domain walls is explored using the Bayesian inference analysis of atomically resolved STEM data. We demonstrate that domain wall profile shapes are ultimately sensitive to the nature of the order parameter in the material, including the functional form of Ginzburg-Landau-Devonshire expansion, and numerical value of the corresponding parameters. The preexisting materials knowledge naturally folds in the Bayesian framework in the form of prior distributions, with the different order parameters forming competing (or hierarchical) models. Here, we explore the physics of the ferroelectric domain walls in BiFeO 3 using this method, and derive the posterior estimates of relevant parameters. More generally, this inference approach both allows learning materials physics from experimental data with associated uncertainty quantification, and establishing guidelines for instrumental development answering questions on what resolution and information limits are necessary for reliable observation of specific physical mechanisms of interest.
Characterization of a SiPM-based monolithic neutron scatter camera using dark counts
The Single Volume Scatter Camera (SVSC) Collaboration aims to develop portable neutron imaging systems for a variety of applications in nuclear non-proliferation. Conventional double-scatter neutron imagers are composed of several separate detector volumes organized in at least two planes. A neutron must scatter in two of these detector volumes for its initial trajectory to be reconstructed. As such, these systems typically have a large footprint and poor geometric efficiency. We report on the design and characterization of a prototype monolithic neutron scatter camera that is intended to significantly improve upon the geometrical shortcomings of conventional neutron cameras. The detector consists of a 50 mm×56 mm× 60 mm monolithic block of EJ-204 plastic scintillator instrumented on two faces with arrays of 64 Hamamatsu S13360-6075PE silicon photomultipliers (SiPMs). The electronic crosstalk is limited to < 5% between adjacent channels and < 0.1% between all other channel pairs. SiPMs introduce a significantly elevated dark count rate over PMTs, as well as correlated noise from after-pulsing and optical crosstalk. In this article, we characterize the dark count rate and optical crosstalk and present a modified event reconstruction likelihood function that accounts for them. We find that the average dark count rate per SiPM is 4.3 MHz with a standard deviation of 1.5 MHz among devices. The analysis method we employ to measure internal optical crosstalk also naturally yields the mean and width of the single-electron pulse height. Here, we calculate separate contributions to the width of the single-electron pulse-height from electronic noise and avalanche fluctuations. We demonstrate a timing resolution for a single-photon pulse to be (128 ± 4) ps. Finally, coincidence analysis is employed to measure external (pixel-to-pixel) optical crosstalk. We present a map of the average external crosstalk probability between 2×4 groups of SiPMs, as well as the in-situ timing characteristics extracted from the coincidence analysis. Further work is needed to characterize the performance of the camera at reconstructing single- and double-site interactions, as well as image reconstruction.
JWST lensed quasar dark matter survey – I. Description and first results
ABSTRACT The flux ratios of gravitationally lensed quasars provide a powerful probe of the nature of dark matter. Importantly, these ratios are sensitive to small-scale structure, irrespective of the presence of baryons. This sensitivity may allow us to study the halo mass function even below the scales where galaxies form observable stars. For accurate measurements, it is essential that the quasar’s light is emitted from a physical region of the quasar with an angular scale of milliarcseconds or larger; this minimizes microlensing effects by stars within the deflector. The warm dust region of quasars fits this criterion, as it has parsec-size physical scales and dominates the spectral energy distribution of quasars at wavelengths greater than 10 μm. The JWST Mid-Infrared Instrument is adept at detecting redshifted light in this wavelength range, offering both the spatial resolution and sensitivity required for accurate gravitational lensing flux ratio measurements. Here, we introduce our survey designed to measure the warm dust flux ratios of 31 lensed quasars. We discuss the flux-ratio measurement technique and present results for the first target, DES J0405-3308. We find that we can measure the quasar warm dust flux ratios with 3 per cent precision. Our simulations suggest that this precision makes it feasible to detect the presence of 107 M⊙ dark matter haloes at cosmological distances. Such haloes are expected to be completely dark in cold dark matter models.
Stomata in-sight: Integrating live confocal microscopy with leaf gas exchange and environmental control
Stomatal anatomy (aperture area, length, and width) influences leaf-level physiology traits including conductance to water vapor. Stomatal anatomy can be visualized in situ by microscopy, but the difficulty of regulating the atmospheric environment of a microscope stage means that the conditions under which imaging is done are rarely physiologically relevant. Alternatively, leaf gas exchange instruments that measure gas fluxes reflect stomatal anatomical characteristics in aggregate, but the relative strengths of anatomical traits to control water use (e.g. size vs density) cannot be firmly established. To reconcile the microscopic stomatal characteristics with leaf-level gas exchange, we describe a tool that combines laser scanning confocal microscopy, gas exchange instruments, and machine-learning image analysis to simultaneously observe anatomical characteristics of many (>40) stomata alongside leaf-level traits like photosynthesis, transpiration, and stomatal conductance. We demonstrate how the tool has the resolution capable of quantifying aperture sizes and variability in maize (Zea mays) leaves under 5 steady-state light/pCO 2 treatments while tightly controlling other environmental variables like relative humidity and temperature. A model used to calculate stomatal conductance from measured apertures and stomatal density accurately matched stomatal conductance measured by gas exchange. This technical advancement will provide insight on how stomatal anatomy and function trade off to influence stomatal conductance and leaf-level water use efficiency.
TeV Emission of Galactic Plane Sources with HAWC and H.E.S.S.
The High Altitude Water Cherenkov (HAWC) observatory and the High Energy Stereoscopic System (H.E.S.S.) are two leading instruments in the ground-based very-high-energy γ-ray domain. HAWC employs the water Cherenkov detection (WCD) technique, while H.E.S.S. is an array of Imaging Atmospheric Cherenkov Telescopes (IACTs). The two facilities therefore differ in multiple aspects, including their observation strategy, the size of their field of view, and their angular resolution, leading to different analysis approaches. Until now, it has been unclear if the results of observations by both types of instruments are consistent: several of the recently discovered HAWC sources have been followed up by IACTs, resulting in a confirmed detection only in a minority of cases. With this paper, we go further and try to resolve the tensions between previous results by performing a new analysis of the H.E.S.S. Galactic plane survey data, applying an analysis technique comparable between H.E.S.S. and HAWC. Events above 1 TeV are selected for both data sets, the point-spread function of H.E.S.S. is broadened to approach that of HAWC, and a similar background estimation method is used. This is the first detailed comparison of the Galactic plane observed by both instruments. H.E.S.S. can confirm the γ-ray emission of four HAWC sources among seven previously undetected by IACTs, while the three others have measured fluxes below the sensitivity of the H.E.S.S. data set. Remaining differences in the overall γ-ray flux can be explained by the systematic uncertainties. Therefore, we confirm a consistent view of the γ-ray sky between WCD and IACT techniques.
Opportunities for gas-phase science at short-wavelength free-electron lasers with undulator-based polarization control
Free-electron lasers (FELs) are the world's most brilliant light sources with rapidly evolving technological capabilities in terms of ultrabright and ultrashort pulses over a large range of photon energies. Their revolutionary and innovative developments have opened new fields of science regarding nonlinear light-matter interaction, the investigation of ultrafast processes from specific observer sites, and approaches to imaging matter with atomic resolution. A core aspect of FEL science is the study of isolated and prototypical systems in the gas phase with the possibility of addressing well-defined electronic transitions or particular atomic sites in molecules. Notably for polarization-controlled short-wavelength FELs, the gas phase offers new avenues for investigations of nonlinear and ultrafast phenomena in spin-orientated systems, for decoding the function of the chiral building blocks of life as well as steering reactions and particle emission dynamics in otherwise inaccessible ways. This roadmap comprises descriptions of technological capabilities of facilities worldwide, innovative diagnostics and instrumentation, as well as recent scientific highlights, novel methodology, and mathematical modeling. The experimental and theoretical landscape of using polarization controllable FELs for dichroic light-matter interaction in the gas phase will be discussed and comprehensively outlined to stimulate and strengthen global collaborative efforts of all disciplines. Published by the American Physical Society 2025
Production of microchannel plates using nano-scale additive manufacturing
Microchannel plate (MCP) detectors have been the workhorse detector for many applications, including space borne ultra-violet imaging and spectrographic instruments. Recent advances in additive manufacturing (AM) have enabled fabrication of complex structures with nano-scale resolution facilitating the production of highly customizable MCPs. Using AM to produce MCPs potentially has many advantages over traditional fused glass substrates, including better material control (e.g., more robust glasses or ceramics), better control of microscopic features (e.g., unique pore geometries to improve performance), and better control of macroscopic features (e.g., printing precision curved surfaces for focal plane matching). Through a collaboration with industry, national laboratory, and university partners, small format microcapillary array substrates were produced using a standard polymer photoresin. In conclusion, these substrates were functionalized using atomic layer deposition and their performance was compared to current state-of-the-art Pb-glass and borosilicate-glass MCPs.
High-Frequency 3D Photoacoustic Computed Tomography Using an Optical Microring Resonator
3D photoacoustic computed tomography (3D-PACT) has made great advances in volumetric imaging of biological tissues, with high spatial-temporal resolutions and large penetration depth. The development of 3D-PACT requires high-performance acoustic sensors with a small size, large detection bandwidth, and high sensitivity. In this work, we present a new high-frequency 3D-PACT system that uses a microring resonator (MRR) as the acoustic sensor. The MRR sensor has a size of 80 μ m in diameter and was fabricated using the nanoimprint lithography technology. Using the MRR sensor, we have developed a transmission-mode 3D-PACT system that has achieved a detection bandwidth of ~23 MHz, an imaging depth of ~8 mm, a lateral resolution of 114 μ m, and an axial resolution of 57 μ m. We have demonstrated the 3D PACT’s performance on in vitro phantoms, ex vivo mouse brain, and in vivo mouse ear and tadpole. The MRR-based 3D-PACT system can be a promising tool for structural, functional, and molecular imaging of biological tissues at depths.
Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme
Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Further, our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.
Single-shot in-line x-ray phase-contrast imaging of void-shockwave interactions in fusion energy materials
Recent breakthroughs in nuclear fusion, specifically the report of reactions exceeding scientific breakeven at the National Ignition Facility (NIF), highlight the potential of inertial fusion energy (IFE) as a sustainable and virtually limitless energy source. However, further progress in IFE requires characterization of defects in ablator materials and how they affect fuel capsule compression. Voids within the ablator can degrade energy yield, but their impact on the density distribution has primarily been studied through simulations, with limited high-resolution experimental validation. To address this, we used the x-ray free-electron laser (XFEL) at the matter in extreme conditions (MECs) instrument at the Linac coherent light source (LCLS) to capture 2D x-ray phase-contrast (XPC) images of a void-bearing sample with a composition similar to inertial confinement fusion (ICF) ablators. By driving a compressive shockwave through the sample using MEC's long-pulse laser system, we analyzed how voids influence shockwave propagation and density distribution during compression. To quantify this impact, we extracted phase information using two phase retrieval algorithms. First, we applied the contrast transfer function (CTF) method, paired with Tikhonov regularization and a fast optimization approach to generate an initial phase estimate. We then refined the result using a projected gradient descent (PGD) method that works directly with the sample's refractive index. Comparing these results with radiation adaptive grid Eulerian (xRAGE) radiation hydrodynamic simulations enables identification of model validation needs or improvements. By calculating phase maps in situ, it becomes possible to reconstruct areal density maps, improving understanding of laser-capsule interactions and advancing IFE research.
Light Element Abundances and Multiple Populations in M53
We present results from a study of 94 red giant stars in the globular cluster M53. We use low-resolution spectra to measure the strength of CN and CH features at ∼3800 and 4300 Å, respectively. The strengths of these features are used to classify stars into a CN-enhanced and CN-normal population and to measure C and N abundances in all 94 stars. We find the red giant branch stars to be evenly split between the two populations identified, and observe the presence of CN-enhanced stars on the asymptotic giant branch. In addition, we identify five CH star candidates based on the strength of their CN and CH band features, and the presence of a P-branch in their CH band. We compare our identification of multiple populations to those based on the Na–O anticorrelation and pseudo-color indices in Hubble Space Telescope UV photometry, and find general agreement between all three methods. Our large sample size also allows us to study the radial distribution of each population, and we find that the CN-enhanced population is more centrally concentrated. We use our C and N measurements to compare the evolutionary changes in these elements as a function of magnitude between the two populations, and show that both populations experience similar evolutionary changes to the surface abundances of C and N. Finally, we calculate C+N+O abundances for each population and compare them to similar measurements made in M10; we find that in both clusters, CN-enhanced stars have a slightly enhanced C+N+O (Δ(C+N+O) ∼ 0.2 dex).
Terahertz 2D coherent spectroscopy for probing and controlling multicorrelations in quantum matter
Terahertz 2D coherent spectroscopy (THz-2DCS) is an emerging technique that brings multidimensional resolution to the ultrafast spectral–temporal dynamics of non-equilibrium quantum phases of matter, enabling new capabilities for precise coherent control in many-body dynamics and multiorder correlations. Here, by mapping and disentangling complex excitation and detection pathways across distinct time and frequency dimensions, THz-2DCS provides a form of coherence tomography of light-induced quantum matter — revealing multiquantum coherences, separating nonlinear response functions and capturing collective modes and quantum kinetics on ultrafast THz timescales. This Perspective discusses the technical capabilities of THz-2DCS, provides a comparison to other multidimensional and coherent transient spectroscopies and looks ahead towards opportunities for advancing THz-2DCS instrumentation and experimental strategies towards new frontier discoveries.