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DOE OSTI2024

Lattice light-sheet microscopy allows for super-resolution imaging of receptors in leaf tissue

Plant leaf tissues are difficult to image via fluorescent microscopy, largely due to the presence of chlorophyll and other pigments that provide large background fluorescence. An advantage of Lattice Light-Sheet microscopy is its use of Bessel beams that illuminate a thin focal region of interest for microscopy, allowing for the excitation of fluorescent molecules within this region without surrounding chlorophyll-like objects outside of the region of interest. Here, we apply STORM Super-resolution techniques to observe Receptor-Like Kinases in Arabidopsis thaliana leaf cells. By applying this technique with the Lattice Light-Sheet, we can localize immune response proteins in sub-100 nm length scales and reconstruct three-dimensional locations of proteins within individual leaf cells. Using this technique, we observed the effect of the elicitors ATP and flg22, where we observed a significant degree of internalization of cognate receptors P2K1 and FLS2. We were also able to similarly observe differences in colocalization due to stimulation with these elicitors, where we observe proteins on the membrane becoming less colocalized as a result of stimulation, suggesting an immune response mechanism involving receptors internalizing via pathways distinct to the receptor. Further, these data show the Lattice Light-Sheet’s capabilities for imaging tissue with problematic background fluorescence that otherwise makes super-resolution fluorescence microscopy difficult.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Self‐Assembly Methods Induce Different Individual‐Polymer‐Block Solvation Responses

An understanding of block-specific responses to stimuli in self-assembled copolymers is essential for the effective design of responsive materials. Here, materials formed from different post-reaction processing methods of the same ROMP block copolymer exhibit different block-specific solvent responses, as characterized in situ by fluorescence lifetime imaging microscopy (FLIM). FLIM data were acquired by tagging the polar or nonpolar block separately with a covalently incorporated viscosity-sensitive fluorescent molecular rotor to measure the changing tightness or looseness of assembly upon changes in solvent composition. Rapid precipitation from an insoluble solvent to form a film results in tighter assembly and less difference in tightness/looseness between the two blocks. Further, it interrupts individual block-solvent response behavior. Both results indicate an apparent disruption of the core–shell assembly. This model from FLIM is further supported by differential scanning calorimetry (DSC) and small-angle X-ray scattering (SAXS) data from isolated solids, which show tighter long-range interactions and more long-range order in these kinetically trapped states. Here, the experiments develop FLIM as a method for pinpointing stimuli-responsive behaviors from different processing methods to individual blocks. Together these outcomes provide a future handle for tailoring solvent-triggered assembly/disassembly behavior.

López, Pía A. [University of California, Irvine, C↗

DOE OSTI2025

Super-resolution imaging reveals resistance to mass transfer in functionalized stationary phases

Chemical separations are costly in terms of energy, time, and money. Separation methods are optimized with inefficient trial-and-error approaches that lack insight into the molecular dynamics that lead to the success or failure of a separation and, hence, ways to improve the process. We perform super-resolution imaging of fluorescent analytes in five different commercial liquid chromatography materials. Unexpectedly, we observe that chemical functionalization can block more than 50% of the material’s porous interior, rendering it inaccessible to small-molecule analytes. Only in situ imaging unveils the inaccessibility when compared to the industry-accepted ex situ characterization methods. Selectively removing some of the functionalization with solvent restores pore access without substantially altering the single-molecule kinetics that underlie the separation and agree with bulk chromatography measurements. Our molecular results determine that commercial “fully porous” stationary phases are over-functionalized and provide an alternative avenue to characterize and direct separation material design from the bottom-up.

Science & Technology - Other Topics↗

DOE OSTI2025

Root size and soil physicochemical properties drive microscale spatial patterns of Fe and As retention in the rice rhizosphere

Background and Aims: Radial oxygen loss from rice roots in flooded soils oxidizes and precipitates dissolved Fe(II), Mn(II), and As(III) into mixed Fe(III), Mn(III/IV), and As(V) as root plaque and in the rhizosphere soil. It is unknown how different soils and root sizes impact the spatial extent of Fe and As retention outside the root. Methods: We imaged cross-sections of 90 roots from 6 different soils using synchrotron μXRF imaging followed by k-means clustering and elliptical averaging to distinguish bulk soil, rhizosphere, plaque, and roots based on As and Fe patterns. Results: We found preferential As retention in the plaque and rhizospheres of most roots except small (< 0.45 mm) roots in silty soils with low P or high As. In contrast, clayey soils had similar As-Fe correlations across plaque, rhizosphere, and bulk soil. Large (> 0.45 mm) roots often had no oxidized rhizosphere region. We obtained an extensive dataset of 256 As and 155 Mn synchrotron μXANES measurements, which revealed that rhizosphere and plaque As was mainly inorganic As(V) and As(III), and Mn oxidation state varied between soils but not between belowground locations. Conclusion: Small roots in coarse-textured soils were less likely to have As retention in the plaque or rhizosphere compared to large roots and fine-textured soils. Furthermore, the unique and extensive data in this study provides new insight into soil and root size impacts on As retention in the rhizosphere. It is essential to investigate a representative number of samples to draw conclusions from XRF imaging.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Precision Labeling of Native Antibodies with Lock Coupling

The formation of stable protein complexes enables much of biotechnology, but even high-affinity complexes can dissociate, limiting potential applications in biomaterials, bioimaging, nanomedicine, and other protein-based technologies. Here, in this study, we describe lock coupling, a simple and selective one-step reaction between interfacial lysine and glutamate or aspartate side chains to form stable isopeptide bonds and be used for the precise labeling of native antibodies. We identify conditions in which short-lived activated esters formed by the aqueous carbodiimide EDC promote isopeptide bond formation specifically at preassociated amine-acid pairs. Indiscriminate cross-linking is minimized by formation of protein complexes before addition of catalyst, use of acidic pH to suppress exposed Lys reactivity, and limiting the aqueous stability of activated esters. For native antibody (Ab) labeling, we show that the small IgG-binding protein GB1 can be covalently attached to the Ab Fc domain and that introduction of Cys into GB1 loops allows for facile conjugation of fluorophores, micelles, or inorganic nanocrystals for imaging in live cells and animals. By varying Cys substituents and protein stoichiometry, a defined number of probes can be uniformly attached without the need for extensive purification. In live-cell confocal microscopy, labeled GB1 serves as a stable replacement for secondary Abs, enabling simple multicolor immunostaining and imaging. Lock coupling requires just a single reagent in aqueous buffer and leverages both the innate ability of proteins to form high-affinity complexes and the widespread presence of Lys-Glu/Asp pairs at their interfaces, with the potential for precision synthesis of protein-based probes for imaging, biomaterials, biophysics, and medicine.

antibody↗

DOE OSTI2026

Effects of Polymer Morphology on Solvent and Catalyst Accessibility during Polyethylene and Polystyrene Autoxidation

Efficient catalytic deconstruction of plastics requires facile solvent and catalyst access to polymer substrates to minimize mass transfer effects. Autoxidation using Co(II) acetate, Mn(II) acetate, and a radical carrier in acetic acid is a promising strategy to deconstruct mixed plastic waste, yet the role of polymer morphology in governing solvent and catalyst accessibility remains poorly understood. Here, in situ simultaneous small- and wide-angle X-ray scattering (SAXS/WAXS), complemented by X-ray fluorescence (XRF) imaging and high-pressure differential scanning calorimetry (DSC), were used to elucidate interactions between acetic acid, a Co/Mn catalyst solution, and semicrystalline polyethylene (PE) and amorphous polystyrene (PS) from room temperature to 160 °C. In PE, acetic acid and catalyst access were confined to amorphous regions and cryomilled particle interfaces at room temperature, while crystalline lamellae remained intact after soaking for up to 34 h. Increasing temperature enabled solvent uptake into PE, followed by solvent-assisted softening above 100 °C, and a modest melting-point depression that removed lamellar transport barriers upon melting. Conversely for PS, acetic acid penetrated the glassy polymer without inducing chain mobility until the glass transition was reached, above which the observed structural changes were consistent with enhanced segmental mobility which enabled bulk penetration. These results suggest that polymer morphology and thermally activated physical transitions arising from diffusion and polymer–solvent interactions can influence whether autoxidation of plastics is transport-limited or kinetically controlled, providing a framework for aligning reaction conditions with reaction outcomes.

09 BIOMASS FUELS↗

DOE OSTI2024

In situ detection of ferric reductase activity in the intestinal lumen of an insect

The rise of atmospheric oxygen as a result of photosynthesis in cyanobacteria and chloroplasts has transformed most environmental iron into the ferric state. In contrast, cells within organisms maintain a reducing internal milieu and utilize predominantly ferrous iron. Ferric reductases are enzymes that transfer electrons to ferric ions, either extracellularly or within endocytic vesicles, enabling cellular ferrous iron uptake through Divalent Metal Transporter 1. In mammals, duodenal cytochrome b is a ferric reductase of the intestinal epithelium, but how insects reduce and absorb dietary iron remains unknown. Here we provide indirect evidence of extracellular ferric reductase activity in a small subset of Drosophila melanogaster intestinal epithelial cells, positioned at the neck of the midgut’s anterior region. Dietary-supplemented bathophenanthroline sulphate (BPS) captures locally generated ferrous iron and precipitates into pink granules, whose chemical identity was probed combining in situ X-ray absorption near edge structure and electron paramagnetic resonance spectroscopies. An increased presence of manganese ions upon BPS feeding was also found. Control animals were fed with ferric ammonium citrate, which is accumulated into ferritin iron in distinct intestinal subregions suggesting iron trafficking between different cells inside the animal. Spectroscopic signals from the biological samples were compared to purified Drosophila and horse spleen ferritin and to chemically synthesized BPS-iron and BPS-manganese complexes. The results corroborated the presence of BPS-iron in a newly identified ferric iron reductase region of the intestine, which we propose constitutes the major site of iron absorption in this organism.

EPR↗

DOE OSTI2025

Plant genotype and rhizobia strain combinations strongly influence the transcriptome under heavy metal stress conditions in Medicago truncatula

Heavy metals such as cadmium (Cd) and mercury (Hg) pose significant threats to plant health and food safety as they are absorbed from the environment. Legumes are generally considered sensitive to heavy metals but possess standing genetic variation for accumulation and tolerance to toxic ions. We conducted a transcriptomic analysis on hydroponically and soil grown Medicago truncatula plants to investigate gene expression responses to Cd and Hg exposure in roots, leaves, and nodules. By using plant genotypes with varying metal tolerance or accumulation levels, we observed distinct clustering of gene ontologies, indicating tissue-specific, genotype-specific, and metal-specific gene expression patterns. Considering the symbiotic relationship between legumes and nitrogen-fixing bacteria, we further examined plant phenotypes and transcriptomes of plant genotypes with contrasting Hg accumulation levels and inoculated them with high or low Hg-tolerant Sinorhizobium medicae strains that have presence-absence variation for a mercury reductase (Mer) operon. Host plants inoculated with the Hg-tolerant rhizobia strain possessing a Mer operon exhibited less reduction in nodule number and plant biomass. A smaller reduction in iron (Fe) distribution in nodules after Hg stress was measured using X-ray Fluorescence (XRF) imaging. Dual transcriptome (host plant and bacteria) analysis of nodules revealed a remarkable decrease in the number of differentially expressed genes (DEGs) and clustering of gene ontologies in plants inoculated with the Hg-tolerant rhizobia strain, including symbiosis related genes. This finding suggests that the Hg-tolerant rhizobia strain has the potential to mitigate Hg stress in host plants. Furthermore, we observed genotype by-genotype interactions between the high Hg accumulating plant genotype and the Hg-tolerant rhizobia strain. These findings provide insights into enhancing plant resilience in contaminated environments through optimizing legume-rhizobia interactions for heavy metal tolerance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Strain-Modulated Exciton Localization and Enhanced Emission in Multilayer GaSe

Strain engineering is one of the most effective routes for tuning the electrical and optical properties of two-dimensional layered materials. Besides reproducing the results of other groups on the tunability and photoluminescence (PL) enhancement of free and bound excitons under mechanical deformation or thermal effects, we systematically studied the mechanical strain (wrinkle) and local thermal strain (laser heating) effects on the PL lifetime and polarization in GaSe multilayers and their interplay, revealing their coupled impact on excitonic dynamics. Here, the PL intensity of localized excitons in the wrinkle region of GaSe increases superlinearly with the excitation laser power. The polarization effect has been observed for the bound exciton in GaSe under mechanical strain, but not in GaSe under thermal strain. Fluorescence lifetime imaging (FLIM) measurements reveal strain-tunable lifetimes for both free and bound excitons, and the lifetime of the bound exciton is longer than the free exciton in the mechanical strain region, correlating with the enhanced emission of the bound exciton. These results highlight previously uncharacterized optoelectronic tunability in GaSe and broaden the design space for strain (or thermally)-controlled 2D layered devices.

, GaSe, Exciton localization↗

DOE OSTI2025

Quantum Emitters Induced by High Pressure and UV Laser Irradiation in Multilayer GaSe

In this work, we report on defect generation in multilayer GaSe through hydrostatic pressure quenching and UV laser irradiation. The Raman line width from the UV 266 nm irradiated sample is much wider than that in pressure-quenched GaSe, corresponding to a wider defect energy distribution range in the former sample than the latter. After quenching from 11.2 GPa, three photoluminescence (PL) peaks from defect states are observed at 657, 681, and 695 nm at a low temperature of 93 K. Defect-related peaks at 649, 694, 750, and 774 nm also appear in low-temperature PL spectra after UV laser irradiation, with a nonmonotonous intensity dependence on irradiation duration. There are common features in defects produced by these two methods: the PL peaks with the lowest energy are sharp, and their PL intensities increase linearly with the excitation laser power and saturate above a certain excitation laser power. These two features are similar to those in defects for single-photon emission (SPE) in other 2D materials at even lower temperatures. Fluorescence lifetime imaging shows distinguished short (2.3 ns) and long (75.6 nm) lifetimes of the 695 nm PL line in pressure-quenched GaSe. The density functional theory predicts defect energy levels related to Se vacancy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

100 kHz OH PLIF of High-Pressure H2/NH3 and H2/CH4 Flames

The reaction zones in a multi-element, multi-stage, micromix injector are investigated using planar laser-induced fluorescence (PLIF) imaging of the hydroxyl (OH) radical at a 100 kHz repetition rate. The combustor is operated at a pressure of ∼10 bar. Multiple fuel blends of hydrogen, methane, and ammonia are considered to study the effect of changing fuel composition on the flame structure. Compact regions of high OH signal are observed in each flame for fuel mixtures with high hydrogen content, indicating rapid reactant consumption in the shear layers. Instantaneous images exhibit wrinkled flame fronts and the formation of unreacted pockets due to highly turbulent burning. The addition of methane is observed to reduce the reactivity and flame speed, resulting in more diffuse regions of OH between each flame. The shape of the reactant core is altered, and the length scale of the flame surface wrinkling is increased. Ammonia addition has a more severe effect on the distribution of OH and the local flame structure than methane addition. A time series of images shows the presence of OH vortical structures and significant turbulent fluctuations in the flames near the wall, suggesting the presence of a recirculation zone that could drive the observed disparity in flame lengths.

Hodge, Alexander J. [Purdue University]↗

DOE OSTI2025

Post-Wildfire Mobilization of Organic Carbon

Wildfires significantly alter watershed functions, particularly the mobilization of organic carbon (OC). This study investigated OC mobility and the physicochemical characteristics of wildfire-impacted soils and ashes from the northern California and Nevada fires (Dixie, Beckworth, Caldor). Organic carbon in wildfire-derived ashes (9.2–57.3 mg/g) generally exceeded levels in the background soils (4.3–24.4 mg/g), except at the Dixie fire sites. The mobile OC fraction varied from 0.0093 to 0.029 in ashes and 0.010 to 0.065 in soils, though no consistent trend was observed between the ashes and soils. Notably, the ash samples displayed lower OC mobility compared with the soils beneath them. A negative correlation was found between the mobile OC fraction and bulk OC content. Wildfire increased the total amount of mobile OC substantially by 5.2–574% compared to the background soils. Electron paramagnetic resonance (EPR) spectra confirmed the presence of environmentally persistent free radicals (EPFRs), which correlated with observed redox reactivity. Additionally, X-ray absorption near edge structure (XANES) and X-ray fluorescence (XRF) imaging revealed that Fe(II) oxidation in soils beneath the ashes may have enhanced the OC mobility, likely driven by pyrogenic carbon and free radicals. These findings enhance our understanding of post-wildfire OC mobilization and the impact of ash–soil physicochemical properties on watershed health.

organic carbon↗

DOE OSTI2026

Toward Intelligent Multimodal Holography for Real-Time Chemical Imaging of Dynamic Ion Separation

Molecular-level visualization of ion transport and separation dynamics in complex environments is crucial for advancing energy systems, water purification, and critical materials recovery. Achieving this requires imaging platforms that combine structural sensitivity, chemical specificity, and real-time operation. Digital off-axis holography (DOAH) provides high-throughput, label-free quantitative phase imaging but inherently lacks chemical selectivity. Integrating DOAH with complementary spectroscopic channels such as fluorescence or hyperspectral imaging introduces the needed molecular specificity, while also creating challenges in multimodal data fusion, synchronization, and computational throughput. Artificial intelligence offers a powerful route to address these limitations by uniting physics-based reconstruction with data-driven interpretation. In this Perspective, we outline a framework for intelligent multimodal holography and demonstrate its potential using a preliminary AI-driven test case. Raw DOAH holograms of lanthanide solutions subjected to magnetic field gradients were analyzed using multi-agent AI workflows that autonomously selected reconstruction tools, extracted NMF components, and generated scientific claims consistent with true paramagnetic and diamagnetic behavior. This demonstration shows how AI-enabled reasoning can deliver real-time chemical–structural interpretation directly from raw holograms. Together, these advances define a path toward adaptive, intelligent holography platforms capable of supporting in situ chemical separations, dynamic ion transport analysis, and next-generation interfacial science.

Ricchiuti, Giovanna↗

DOE OSTI2025

DNA-PAINT Imaging with Hydrogel Imprinting and Clearing

Hydrogel-embedding is a versatile technique in fluorescence microscopy, offering stabilization, optical clearing, and the physical expansion of biological specimens. DNA-PAINT is a super-resolution microscopy approach based on the diffusion and transient binding of fluorescently labeled oligos, but its feasibility in hydrogels has not yet been explored. In this study, we demonstrate that polyacrylamide hydrogels support sufficient diffusion for effective DNA-PAINT imaging. Using acrydite-anchored oligonucleotides imprinted from patterned DNA origami nanostructures and microtubule filaments in fixed cells, we find that hydrogel embedding preserves docking strand positioning at the nanoscale. Sample clearing via protease treatment had minor structural effects on the microtubule structure and enhanced diffusion and accessibility to hydrogel-imprinted docking strands. Our work demonstrates promising potential for diffusion and binding-based fluorescence imaging applications in hydrogel-embedded samples.

DNA origami↗

DOE OSTI2026

Quantum Light Imaging of the Plant Root─Rhizobacteria─System Using iLOV Fluorescence

It has been demonstrated recently that the use of specific quantum states of light for two-photon microscopy can lead to a substantial reduction of the intensity of light needed for the imaging of biological objects. This opens new ways to better understand the delicate mechanisms of the interactions of living organisms in the rhizosphere on an extended time scale without optical damage or alteration of their native behavior. Herein, we report a successful realization of entangled two-photon excited fluorescence microscopy of wheat plant roots and a set of biological samples, including purified iLOV protein, bacterial cells expressing iLOV, and combination of these under an extremely low excitation intensity. The entangled two-photon coupling strength of iLOV was modeled using electronic structure calculations which demonstrated that the FMN chromophore in the iLOV protein has an entangled two-photon absorption (ETPA) cross section that is large enough for imaging using weak quantum light for fluorescence excitation. Successful imaging of plant-associated Pantoea sp. YR343 cells expressing iLOV validates the feasibility of using iLOV as a molecular label for characterizing plant-microbe interactions based on entangled photon imaging. In conclusion, the results demonstrate the advantageous use of entangled photon imaging under noninvasive and nondestructive conditions.

Varnavksi, Oleg [Univ. of Michigan, Ann Arbor, MI ↗

DOE OSTI2026

Nuclear recoil detection with color centers in bulk lithium fluoride

We present initial results on the detection of nuclear recoils in lithium fluoride (LiF) through the fluorescence of color centers created by particle interactions in the crystal lattice. Using light-sheet fluorescence microscopy, we image nuclear recoil tracks from both fast and thermal neutron interactions deep within a cubic-centimeter-scale sample. Automated three-dimensional feature extraction based on machine-learning tools enables the identification and classification of individual events. We observe that the fluorescence response of LiF to gamma irradiation is strongly suppressed, by a factor of 30–50 compared to neutron exposure, demonstrating intrinsic insensitivity to electromagnetic backgrounds. The observed and simulated event characteristics are consistent, including their number, size, and topology. These results establish the feasibility of LiF as a scalable detection medium for rare nuclear-recoil events and constitute a first step toward 10–1000 g scale detectors with single-event sensitivity for applications in reactor-neutrino detection, neutron spectroscopy, and dark matter searches.

Aroujo, G R [University of Zurich]↗

DOE OSTI2026

Thermal cycling-driven microstructural changes of eutectic Al–Si phase change materials in SS304 containers revealed by multi-modal imaging

Aluminum-based Al–Si alloys are widely used as phase change materials (PCMs) in thermal energy storage (TES) systems owing to their high volumetric latent heat and superior thermal conductivity. However, their long-term reliability is limited by degradation processes that remain insufficiently understood. In this work, we employ a multimodal, correlative characterization framework to systematically resolve the degradation behavior of eutectic Al–Si PCMs in contact with SS304 containers under repeated thermal cycling. By integrating high-resolution electron microscopy, three-dimensional X-ray fluorescence (3D XRF) imaging, and differential scanning calorimetry (DSC), we directly link spatially resolved compositional and microstructural evolution to changes in thermophysical properties. The correlative analysis reveals that elemental leaching of Fe, Cr, and Ni from the stainless-steel container into the PCM drives the formation of intermetallic compounds (IMCs) both at the interface and within the bulk PCM, leading to pronounced compositional heterogeneity. These interfacial reactions and diffusion-induced transformations progressively destabilize the Al–Si eutectic, reducing the effective phase-transforming fraction. Consistent with these observations, DSC measurements show a decrease in melting temperature and latent heat of fusion with thermal cycling. These results underscore the critical influence of interfacial reactions and material compatibility on the stability, durability, and overall performance of Al–Si-based TES systems.

25 ENERGY STORAGE↗

DOE OSTI2026

Evaluation of an event-driven 3FI ASIC for spectroscopic X-ray detection with synchrotron radiation

The novel design and evaluation on the NSLS-II beamline of the 3FI application-specific integrated circuit (ASIC) bump-bonded to a simple, planar, 2D segmented silicon sensor are presented. The ASIC was developed for full-field fluorescence spectral X-ray imaging (3FI). It is a small-scale prototype that features a square array of 32 × 32 pixels, and the size of the pixels is 100 µm × 100 µm. The ASIC was implemented in a 65 nm CMOS integrated circuit fabrication process. Each pixel incorporates a charge-sensitive amplifier, a shaping filter, a discriminator, a peak detector and a sample-and-hold circuit, allowing detection of events and storage of signal amplitudes. The system operates in a frameless event-driven readout mode, outputting analog values for threshold-triggered events, allowing high-speed multi-element X-ray fluorescence data acquisition. The 3FI ASIC achieves per-channel spectrometric performance at a power consumption of only 200 µW per pixel, with nearly all dissipation confined to the analog front-end. An energy resolution is measured at the level of 308 eV full width at half-maximum (FWHM) at 8.04 keV (Cu Kα), and 138 eV FWHM at 3.69 keV (Ca Kα). This per-pixel capability makes the prototype suitable for in situ trace element microanalysis in biological and environmental studies. Moreover, the frameless architecture of the detector is designed to address limitations of conventional X-ray fluorescence microscopy, which typically requires mechanical scanning, by enabling continuous high-throughput data acquisition in future full-field implementations.

47 OTHER INSTRUMENTATION↗