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DOE OSTI2021

Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining

The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified some time ago by their relative lengths and predicted centromeres, but they have never been associated completely with the mitotic karyotype, linkage maps or genome assembly. We identified 9 of the axolotl LBCs using RNAseq to identify actively transcribed genes and 13 BAC (bacterial artificial clone) probes containing pieces of active genes. Using read coverage analysis to find candidate centromere sequences, we developed a centromere probe that localizes to all 14 centromeres. Measurements of relative LBC arm lengths and polymerase III localization patterns enabled us to identify all LBCs. This study presents a relatively simple and reliable way to identify each axolotl LBC cytologically and to anchor chromosome-length sequences (from the axolotl genome assembly) to the physical LBCs by immunostaining and fluorescence in situ hybridization. Our data will facilitate a more detailed transcription analysis of individual LBC loops.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Complete polarization of electronic spins in OLEDs

At low temperatures and high magnetic fields, electron and hole spins in an organic light-emitting diode become polarized so that recombination preferentially forms molecular triplet excited-state species. For low device currents, magnetoelectroluminescence perfectly follows Boltzmann activation, implying a virtually complete polarization outcome. As the current increases, the magnetoelectroluminescence effect is reduced because spin polarization is suppressed by the reduction in carrier residence time within the device. Under these conditions, an additional field-dependent process affecting the spin-dependent recombination emerges, possibly related to the build-up of triplet excitons and their interaction with free charge carriers. Suppression of the EL alone does not prove electronic spin polarization. We therefore probe changes in the spin statistics of recombination directly in a dual singlet-triplet emitting material, which shows a concomitant rise in phosphorescence intensity as fluorescence is suppressed. Finite spin-orbit coupling in these materials gives rise to a microscopic distribution in effective g-factors of electrons and holes, Δg, i.e., a distribution in Larmor frequencies. This Δg effect in the pair, which mixes singlet and triplet, further suppresses singlet-exciton formation at high fields in addition to thermal spin polarization of the individual carriers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Spatially resolved measurements of plasma ion velocity distributions in a dipole magnetic field

The equilibrium flows of a plasma discharge in a dipole magnetic field are a topic of interest in low temperature plasma physics. Experimentalists typically rely on probe-based and line-integrated diagnostic techniques in these environments to describe plasma behavior. Presented here are measurements of argon ion dynamics with laser induced fluorescence techniques to provide insight into plasma dynamics in dipole magnetic fields with nonperturbative, spatially localized measurements. Simulation results from a Lagrangian approach to track particle orbits are compared to measured density profiles and provide evidence to support the mechanism distinguishing experimental configurations is the initial approach of particles. Applying a negative DC bias to the magnet induces strong E×B flows around the magnet, even exceeding the ion acoustic speed as measured far from the magnet. A strong enough bias also produces two distinct ion populations and provides a method for controlling the density gradient on the equator.

McLaughlin, Jacob W. (ORCID:0000000152661888)↗

DOE OSTI2023

High-fidelity imaging of a band insulator in a three-dimensional optical lattice clock

Here, we report on the observation of a high-density, band insulating state in a three-dimensional optical lattice clock. Filled with a nuclear-spin-polarized degenerate Fermi gas of 87 Sr, the three-dimensional (3D) lattice has one atom per site in the ground motional state, thus guarding against frequency shifts due to contact interactions. At this high density where the average distance between atoms is comparable to the probe wavelength, conventional imaging techniques at saturation intensity suffer from large systematic errors. To spatially probe frequency shifts in the clock and measure thermodynamic properties of this system, accurate imaging techniques at high optical depths are required. Using a combination of highly saturated fluorescence and absorption imaging, we confirm the density distribution in our 3D optical lattice in agreement with a single spin band insulating state. Combining our clock platform with this high filling fraction opens the door to studying new classes of long-lived, many-body states arising from dipolar interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Measurement of engine-oil fuel dilution using laser induced florescence spectroscopy

An optical diagnostic, based on laser-induced fluorescence (LIF), has been developed for on-engine measurements of real-time fuel dilution of engine oil, or fuel in oil (FiO). Fuel dilution of oil is believed to be one of the underlying mechanisms that promotes low speed pre-ignition (LSPI) during high-load engine operations. While standard (e.g., ASTM D3524-90) methods are not capable of transient measurements, the LIF technique resolves transient dilution on the minutes time scale, making it possible to study the relation between FiO and LSPI. The measurement is based on adding a dye (ca. 500 ppm) to the fuel and monitoring for its presence in the oil via LIF. The instrument contains a 532-nm laser diode, and a spectrometer to resolve the LIF spectra. A fiber-optic assembly links the instrument to the engine measurement location; the probe is in a Y-configuration with the six fibers around one on a common probe end that connects to the engine; the Y-assembly legs are connected to the instrument; the two legs are the six fibers for transporting the laser light, and the single fiber for the fluorescence. We have expanded on our previous work (Parks et al, SAE paper 2007-01-4108, 2007), by demonstrating the diagnostic technique with to measure transient oil dilution on a 2.0-liter GM ECOTEC LNF single cylinder SI engine. The proposed LIF diagnostic will be critical in studying oil-dilution correlation with LSPI events.

Neupane, Sneha↗

DOE OSTI2021

Unraveling Cu Chemical Signature in CdTe by Spectral Fluorescence Mapping

X-ray absorption spectroscopy (XAS) has been shown to be a powerful tool to unravel the chemical environment of a given atom within a matrix. When used in correlative X-ray microscopy approaches, XAS allows one to probe with nanoscale precision regions of particular interest in an absorber. Herein, we use X-ray absorption near edge structure (XANES) to evaluate the chemical environment of Cu atoms within a CdTe solar cell. The reconstruction of XANES spectra from XRF maps have unfolded 2D maps of Cu chemical structures. In this work, we found that most Cu atoms exist in Cu 2 Te and Cu 1.4 Te phase. Moreover, we found traces of CuTe, Cu 2 O, CuO, Cu 2 S, CuS, and metallic Cu phase. Investigating Cu chemical structures at different performing areas, we found no observable correlation between Cu chemical structures and electrical performance. This approach allows tracking of Cu chemical structures along with electrical performance and elemental distribution simultaneously, with high spatial resolution in a statistically practical way.

CdTe↗

DOE OSTI2025

A Solvatochromic Near Infrared Fluorophore Sensitive to the Full Amyloid Beta Aggregation Pathway

Alzheimer's disease has long been associated with the aggregation of amyloid beta peptides (Aβ42) into macroscale plaques, although specific neurodegenerative agents have not been definitively identified. Much evidence has pointed to the soluble nanoscale oligomers that form early in the Aβ42 aggregation pathway, but there is little understanding of these structures, their mechanisms of formation, or how they grow into plaques. Here, we show that a solvatochromic fluorophore with near-infrared (NIR) emission can track synthetic Aβ42 aggregation through environment-sensitive spectral shifts from the earliest time points through plaque formation. This azide-functionalized phosphine oxide azetidine rhodol (Phazr-N3) shows large polarity-dependent changes in fluorescence emission, with maxima shifting from 630 nm in toluene to 703 nm in aqueous buffer, and a maximum quantum yield of 62%. Upon induction of Aβ42 aggregation, we observe immediate solvatochromic changes in Phazr-N3 fluorescence, with multiple apparent phases over 12 h, and which culminate before the onset of any major fluorescence changes of conformation-specific aggregation fluorophore thioflavin T. Solution anisotropy measurements show a low micromolar affinity of Phazr-N3 for disordered, free Aβ42 in solution, and real-time measurements are consistent with rapid liquid-liquid phase separation and slow dehydration of the growing aggregate. Spectral imaging of synthetic plaques stained in the presence of live cells and lipid-binding protein albumin shows over 4000-fold Phazr-N3 fluorescence intensity above background under no-wash conditions, and over 100-fold intensity above coplated microglial cells or a large excess of albumin. This use of a solvatochromic probe with structure-independent binding to free Aβ42 offers real-time, minimally invasive insight into the full Aβ42 aggregation pathway.

Wang, Zeming↗

DOE OSTI2021

Directing Energy Transfer in Halide Perovskite–Chromophore Hybrid Assemblies

Directing the flow of energy and the nature of the excited states that are produced in nanocrystal–chromophore hybrid assemblies is crucial for realizing their photocatalytic and optoelectronic applications. Using a combination of steady-state and time-resolved absorption and photoluminescence (PL) experiments, we have probed the excited-state interactions in the CsPbBr 3 –Rhodamine B (RhB) hybrid assembly. PL studies reveal quenching of the CsPbBr 3 emission with a concomitant enhancement of the fluorescence of RhB, indicating a singlet-energy-transfer mechanism. Transient absorption spectroscopy shows that this energy transfer occurs on the ~200 ps time scale. To understand whether the energy transfer occurs through a Förster or Dexter mechanism, we leveraged facile halide-exchange reactions to tune the optical properties of the donor CsPbBr 3 by alloying with chloride. This allowed us to tune the spectral overlap between the donor CsPb(Br 1–x Cl x ) 3 emission and acceptor RhB absorption. For CsPbBr 3 -RhB, the rate constant for energy transfer (k ET ) agrees well with Förster theory, whereas alloying with chloride to produce chloride-rich CsPb(Br 1–x Cl x ) 3 favors a Dexter mechanism. These results highlight the importance of optimizing both the donor and acceptor properties to design light-harvesting assemblies that employ energy transfer. Furthermore, the ease of tuning optical properties through halide exchange of the nanocrystal donor provides a unique platform for studying and tailoring excited-state interactions in perovskite–chromophore assemblies.

14 SOLAR ENERGY↗

DOE OSTI2025

Interface instabilities in hafnium hydride entrained iron metal matrix composites

The chemical interactions in Fe–HfH 2 metal matrix composites (MMCs) are studied across multiple length scales to elucidate the decomposition of the parent phases and corresponding reaction zone physics during direct current sintering. Fe–HfH 2 composites were synthesized with increasing as-mixed hydride contents of Fe–25% HfH 2 , Fe–40% HfH 2 , Fe–55% HfH 2 , and Fe–70% HfH 2 (all in vol. %) to demonstrate the ability to achieve sintered MMCs with target hydride contents. Samples were probed across multiple length scales through a multi-modal workflow employing x-ray diffraction, scanning electron microscopy and segmentation analysis, and synchrotron techniques including hard x-ray fluorescence mapping and nanoprobe x-ray absorption near-edge structure measurements. Under the selected sintering temperature and pressure conditions, hydrogen evolution is seen to evolve through parallel paths: thermal decomposition from during the transformation of HfH 2 to HfH x<2 and through subsequent reaction with the Fe matrix leading to intermetallic phase formation. Specifically, HfFe and HfFe 2 intermetallic formation accelerates the release of hydrogen with a subsequent HfO 2 phase forming at grain boundaries. For this MMC, the consumption or loss of hydrogen can be considerable in compacts with initial hydride loading of 25%–40% HfH 2 approaching 83% hydrogen loss for the lower volume fraction composites. Increasing the volume fraction of HfH 2 to 70% enhanced the retained hydrogen content to 53% and attributed to the reduced interfacial area intrinsic to the increased HfH 2 loading in this MMC.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

Abstract The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption—impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01–4.7 fmol SO42− cell−1 h−1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23–40 nmol h−1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Lindsay, Melody R.↗

DOE OSTI2023

Propidium Monoazide (PMAxx)-Recombinase Polymerase Amplification Exo (RPA Exo) Assay for Rapid Detection of Burkholderia cepacia Complex in Chlorhexidine Gluconate (CHX) and Benzalkonium Chloride (BZK) Solutions

Both sterile and non-sterile pharmaceutical products, which include antiseptics, have been recalled due to Burkholderia cepacia complex (BCC) contamination. Therefore, minimizing the frequency of outbreaks may be conducive to the development of a quick and sensitive approach that can distinguish between live and dead loads of BCC. We have assessed an exo probe-based recombinase polymerase amplification (RPA) with 10 µM propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in various concentrations of antiseptics (i.e., chlorhexidine gluconate (CHX) and benzalkonium chloride (BZK) solutions) after 24 h. The optimized assay conducted using a set of primer–probes targeting gbpT was performed at 40 °C for 20 min and shows a detection limit of 10 pg/µL of genomic DNA from B. cenocepacia J2315, equivalent to 10 4 colony-forming units (CFU/mL). The specificity of a newly designed primer and probe was 80% (20 negatives out of 25). The readings for total cells (i.e., without PMAxx) from 200 µg/mL CHX using PMAxx-RPA exo assay was 310 relative fluorescence units (RFU), compared to 129 RFU with PMAxx (i.e., live cells). Furthermore, in 50–500 µg/mL BZK-treated cells, a difference in the detection rate was observed between the PMAxx-RPA exo assay in live cells (130.4–459.3 RFU) and total cells (207.82–684.5 RFU). This study shows that the PMAxx-RPA exo assay appears to be a valid tool for the simple, rapid and presumptive detection of live BCC cells in antiseptics, thereby ensuring the quality and safety of pharmaceutical products.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Imaging from Macro to Nanoscale: Multimodal Advances in Chemical and Biomedical Imaging

Imaging increasingly serves as a multiscale framework for linking molecular mechanisms to cellular behavior, tissue architecture, and organ phenotypes in biology and unraveling fundamental processes in chemistry, physics and materials science. This Perspective highlights recent advances in chemical and biomedical imaging across macro-, micro-, and nanoscales, using representative examples published in Chemical and Biomedical Imaging (CBMI). At the macroscale, we discuss chemically selective MRI, including endogenous and exogenous CEST strategies, together with photoacoustic imaging as a hybrid modality with functional and chemical contrast. At the microscale, we consider fluorescence, label-free optical and vibrational imaging, and selected X-ray approaches that expand sensitivity, specificity, and temporal resolution in biological and materials systems. At the nanoscale, we highlight super-resolution fluorescence microscopy, single-molecule methods, tip-enhanced Raman spectroscopy, and correlative imaging strategies that resolve local heterogeneity and molecular organization. Across scales, a common theme emerges that advances in probes, contrast mechanisms, instrumentation, and sample handling are enabling chemically informed imaging that connects molecular specificity with biological context.

multiscale imaging↗

DOE OSTI2025

Generation of a fluorescent short-lifetime oxygen nanosensor by coupling of an exciplex forming dye pair

Typical oxygen-sensitive dyes have lifetimes in the μs-ms regime for sensitive oxygen detection based on molecular quenching. Due to the long triplet-state lifetimes and poor quenching efficiency of these probes, it has been difficult to develop short lifetime probes. We have developed oxygen sensors using a short-lifetime dye (∼30–60 ns) that forms an anthracene-aniline exciplex, which is quenched by molecular oxygen through an excited-state charge transfer mechanism. To achieve measurements in aqueous systems, we have tethered the dyes together via a C3 alkyl linker to facilitate greater exciplex formation at low dye concentration (20 μg mL −1 ) and encapsulated the resulting compound into polymeric nanoparticles to form an aqueous-dispersible short-lifetime oxygen nanosensor. The sensors emit at 420 nm (unfolded dye) and 500 nm (exciplex), and the ratiometric Stern-Volmer Constant is 1.52 ± 0.02 L mol −1 , showing good sensitivity from 0 % to 40 % dissolved oxygen without the tradeoff of a long lifetime needed for direct molecular quenching. In this paper, we characterize this sensor for both lifetime-based measurements using time-correlated single-photon counting and ratiometric intensity-based measurements using the unfolded dye emission as an internal reference peak.

Biological and medical sciences↗

DOE OSTI2026

Probing boron vacancy defects in hBN via single spin relaxometry

Spin defects in solids offer promising platforms for quantum sensing and memory due to their long coherence times and optical addressability. Here, we integrate a single nitrogen-vacancy (NV) center in diamond with scanning probe microscopy to detect, read out, and spatially map spin-based quantum sensors at the nanoscale. Using the boron vacancy ($V$$^{–}_{B}$) center in hexagonal boron nitride—an emerging two-dimensional spin system—as a model, we detect its electron spin resonance indirectly via changes in the spin relaxation time (T 1 ) of a nearby NV center, eliminating the need for optical excitation or fluorescence detection of the $V$$^{–}_{B}$. Cross-relaxation between NV and $V$$^{–}_{B}$ ensembles significantly reduces NV T1, enabling quantitative nanoscale mapping of defect densities beyond the optical diffraction limit and clear resolution of hyperfine splitting in isotopically enriched h 10 B 15 N. Our method demonstrates interactions between spin sensors in 3D and 2D materials, establishing NV centers as versatile probes for characterizing otherwise inaccessible spin defects.

Quantum metrology↗

DOE OSTI2021

Chemical state mapping of simulant Chernobyl lava-like fuel containing material using micro-focused synchrotron X-ray spectroscopy

Uranium speciation and redox behaviour is of critical importance in the nuclear fuel cycle. X-ray absorption near-edge spectroscopy (XANES) is commonly used to probe the oxidation state and speciation of uranium, and other elements, at the macroscopic and microscopic scale, within nuclear materials. Two-dimensional (2D) speciation maps, derived from microfocus X-ray fluorescence and XANES data, provide essential information on the spatial variation and gradients of the oxidation state of redox active elements such as uranium. In the present work, we elaborate and evaluate approaches to the construction of 2D speciation maps, in an effort to maximize sensitivity to the U oxidation state at the U L 3 -edge, applied to a suite of synthetic Chernobyl lava specimens. Our analysis shows that calibration of speciation maps can be improved by determination of the normalized X-ray absorption at excitation energies selected to maximize oxidation state contrast. The maps are calibrated to the normalized absorption of U L 3 XANES spectra of relevant reference compounds, modelled using a combination of arctangent and pseudo-Voigt functions (to represent the photoelectric absorption and multiple-scattering contributions). We validate this approach by microfocus X-ray diffraction and XANES analysis of points of interest, which afford average U oxidation states in excellent agreement with those estimated from the chemical state maps. This simple and easy-to-implement approach is general and transferrable, and will assist in the future analysis of real lava-like fuel-containing materials to understand their environmental degradation, which is a source of radioactive dust production within the Chernobyl shelter.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Subsurface spectroscopy of heterogeneous materials using optical wavefront shaping

Plastic-bonded explosives and propellants consist of energetic molecular crystals embedded in a polymer matrix that also includes additives, such as taggants, plasticizers, grit, antioxidants, etc. Furthermore, this heterogeneous composition renders these materials optically opaque, limiting optical characterization techniques (e.g., Raman spectroscopy) to probing chemical reactions at the sur-face. However, many reactions of interest are believed to occur inside the material where current optical techniques can not probe. To address this challenge, we have developed a new optical technique that utilizes feedback assisted wavefront shaping (using spatial light modulators) to focus probe light inside a heterogeneous material, such that we can perform subsurface spectroscopy. Recently, we demonstrated this technique by monitoring subsurface photodegradation and thermal degradation of Eu-doped molecular crystals using both fluorescence and Raman spectroscopy. Based off these successes we are now looking into improvements to this technique to allow for greater time resolution, including replacing our spatial light modulators with fast digital mirror devices, using ns optical phase conjugation, and self-healing optical beams.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

One-colour (~220 nm) resonance-enhanced (S 1 –S 0 ) multi-photon dissociation of acetylene: probe of the C 2 A 1 Π u – X 1 Σ + g band by frequency-modulation spectroscopy

In a recent paper, we demonstrated that one-colour (~220 nm), resonance-enhanced (S 1 –S 0 ), photodissociation of acetylene generates strong $C_2$ Swan band ($d^3Π_g–a^3Π_u$) and $C_2$ Deslandres-d'Azambuja band ($C^1Π_g–A^1Π_u$) fluorescence, and long-lived (>3 µs) fluorescence from an electronically-excited $C_2$H * species. It was not known whether the $C_2A^1Π_u$ and $X^1Σ^+_g$ states are also directly populated in this process. In this paper, multiple vibration-rotation transitions between the $C_2A$-state v = 2 and the X-state v = 0 level are examined by time-resolved frequency-modulation (FM) spectroscopy. The photolysis laser wavelength is tuned into resonance at the one-photon level with S 1 –S 0 transitions that populate individual rotational levels of the S 1 $_{trans}$-conformer $3^2,3^3,$ and $3^4$ vibrational states. By comparing the phase of the FM signals from the $C_2A–X$ transitions with that from the Rb D 1 -line absorption transition, we determine that, for all of the probed A–X transitions, the X-state level is more populated than the A-state level. We propose that the acetylene S 1 level is excited by the second photon to an acetylene dissociation precursor state, which undergoes sequential C-H bond-breaking to produce the $C_2X$ state. The dissociation precursor is assigned as the $1^1B_g(trans-bent)/1^1B_1(cis-bent)$ valence state, which correlates to a doubly-excited configuration, $(1π_u)^2(1π_g)^2$, at linear geometry. Based on the rotational distributions of the $C_2X$-state fragments, we believe that at least one of the transition states involved in the photolysis via S 1 $3^4$ has a larger CC-H bend-angle for the departing H-atom than that involved in the S 1 $3^2$ and $3^3$ photolysis.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Simultaneous 10 kHz three-dimensional CH 2 O and tomographic PIV measurements in a lifted partially-premixed jet flame

High-speed, three-dimensional (3D) scalar-velocity field measurements are demonstrated in a lifted partially-premixed dimethyl-ether/air jet flame using simultaneous laser-induced fluorescence (LIF) of formaldehyde (CH 2 O) and tomographic particle image velocimetry (TPIV). The 3D LIF measurements are performed by raster scanning the laser beam from a 100 kHz pulse-burst laser across the probe volume using an acousto-optic deflector. The volumetric reconstruction of the LIF signal from ten parallel planes provides quasi-instantaneous 3D LIF measurements that are synchronized with 10 kHz TPIV measurements. Here, the temporally resolved CH 2 O-LIF and velocity field data are used to analyze Lagrangian particle trajectories and displacement speeds at the base of the lifted flame. The particle trajectories reveal flow structures that are difficult to observe in an Eulerian reference frame. Positive and negative displacement speeds are observed at the CH 2 O-LIF surfaces at the inner and outer regions of the jet flame with a maximum displacement speed of approximately eight times the laminar flame speed of a stoichiometric dimethyl-ether/air mixture. The observations in present study support formation of lean premixed flames near the flame base whose role in flame stabilization should be investigated in more detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗