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DOE OSTI2026

Importance of Spatially Continuous Urban Surface Properties in Urban‐Resolving Earth System Modeling

Accurate representation of urban properties and processes at higher resolutions in global modeling systems is essential for advancing our ability to capture the complexities of urban systems and informing effective resilience strategies. However, the prescription of coarse global-scale urban properties in most state-of-the-art Earth system models (ESMs) is limiting their potential for capturing urban signals as they advance toward kilometer-scale simulation capabilities. To bridge this gap in inadequate urban property representation and to advance urban-resolving Earth system modeling, this work integrates the newly-developed global 1 km-resolution facet-level urban surface property data set, U-Surf, into the land component of Community Earth System Model (CESM)—Community Terrestrial System Model (CTSM). The land-only CTSM simulations are validated against satellite measurements, ground-based urban weather stations, flux tower observations, and reanalysis data. Results demonstrate that the enhanced urban properties allow improved simulations of urban meteorology and surface energy fluxes compared to the default coarse-resolution categorical urban canopy parameters. Spatial scaling analysis reveals regime-dependent information loss during resolution aggregation, as well as substantial scale-dependent variations in urban surface energy flux representation. Furthermore, these findings have critical implications for coupled Earth system modeling when including the effect of land-atmosphere interaction. This work establishes a foundation for future urban-resolving kilometer-scale ESM development, which will enable systematic intra- and inter-city comparisons that inform urban adaptation strategies across diverse global urban environments.

Cheng, Yifan [University of Illinois Urbana-Champa↗

DOE OSTI2020

Resolving individual atoms of protein complex by cryo-electron microscopy

Breakthroughs in single-particle cryo-electron microscopy (cryo-EM) technology have made near-atomic resolution structure determination possible. Cryo-EM has resolved over four thousand structures at near-atomic resolutions (2–4 Å). It is rapidly becoming the method of choice for structure determination of membrane proteins, large assemblies, and multi-protein complexes partly because it does not require a crystal and partly because it can accommodate specimens with heterogeneous composition and/or conformation. This powerful technique is now capable of resolving protein complexes to better than 2 Å resolution3 and has been used to solve 3.7 Å resolution structure of RNA as small as ~40 kilodaltons.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Resolving the structure of phage–bacteria interactions in the context of natural diversity

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse—with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus , as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood–Ljungdahl pathway.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Resolving electron and hole transport properties in semiconductor materials by constant light-induced magneto transport

The knowledge of minority and majority charge carrier properties enables controlling the performance of solar cells, transistors, detectors, sensors, and LEDs. Here, we developed the constant light induced magneto transport method which resolves electron and hole mobility, lifetime, diffusion coefficient and length, and quasi-Fermi level splitting. We demonstrate the implication of the constant light induced magneto transport for silicon and metal halide perovskite films. We resolve the transport properties of electrons and holes predicting the material’s effectiveness for solar cell application without making the full device. The accessibility of fourteen material parameters paves the way for in-depth exploration of causal mechanisms limiting the efficiency and functionality of material structures. To demonstrate broad applicability, we further characterized twelve materials with drift mobilities spanning from 10 –3 to 10 3 cm 2 V –1 s –1 and lifetimes varying between 10 –9 and 10 –3 seconds. The universality of our method its potential to advance optoelectronic devices in various technological fields.

14 SOLAR ENERGY↗

DOE OSTI2024

Spin-resolved topology and partial axion angles in three-dimensional insulators

Abstract Symmetry-protected topological crystalline insulators (TCIs) have primarily been characterized by their gapless boundary states. However, in time-reversal- ( $${{{{{{{\mathcal{T}}}}}}}}$$ T -) invariant (helical) 3D TCIs—termed higher-order TCIs (HOTIs)—the boundary signatures can manifest as a sample-dependent network of 1D hinge states. We here introduce nested spin-resolved Wilson loops and layer constructions as tools to characterize the intrinsic bulk topological properties of spinful 3D insulators. We discover that helical HOTIs realize one of three spin-resolved phases with distinct responses that are quantitatively robust to large deformations of the bulk spin-orbital texture: 3D quantum spin Hall insulators (QSHIs), “spin-Weyl” semimetals, and $${{{{{{{\mathcal{T}}}}}}}}$$ T -doubled axion insulator (T-DAXI) states with nontrivial partial axion angles indicative of a 3D spin-magnetoelectric bulk response and half-quantized 2D TI surface states originating from a partial parity anomaly. Using ab-initio calculations, we demonstrate that β -MoTe 2 realizes a spin-Weyl state and that α -BiBr hosts both 3D QSHI and T-DAXI regimes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Time-resolved Brownian tomography of single nanocrystals in liquid during oxidative etching

Colloidal nanocrystals inherently undergo structural changes during chemical reactions. The robust structure-property relationships, originating from their nanoscale dimensions, underscore the significance of comprehending the dynamic structural behavior of nanocrystals in reactive chemical media. Moreover, the complexity and heterogeneity inherent in their atomic structures require tracking of structural transitions in individual nanocrystals at three-dimensional (3D) atomic resolution. In this study, we introduce the method of time-resolved Brownian tomography to investigate the temporal evolution of the 3D atomic structures of individual nanocrystals in solution. The methodology is applied to examine the atomic-level structural transformations of Pt nanocrystals during oxidative etching. The time-resolved 3D atomic maps reveal the structural evolution of dissolving Pt nanocrystals, transitioning from a crystalline to a disordered structure. Our study demonstrates the emergence of a phase at the nanometer length scale that has received less attention in bulk thermodynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Thermodynamics of order and randomness in dopant distributions inferred from atomically resolved imaging

Abstract Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with strong correlations, either in electronic behavior or chemical segregation. In these cases, the details of atomic arrangements are generally not explored and analyzed. The knowledge of the generative physics and chemistry of the material can obviate this problem, since defect configuration libraries as stochastic representation of atomic level structures can be generated, or parameters of mesoscopic thermodynamic models can be derived. To obtain such information for improved predictions, we use data from atomically resolved microscopic images that visualize complex structural correlations within the system and translate them into statistical mechanical models of structure formation. Given the significant uncertainties about the microscopic aspects of the material’s processing history along with the limited number of available images, we combine model optimization techniques with the principles of statistical hypothesis testing. We demonstrate the approach on data from a series of atomically-resolved scanning transmission electron microscopy images of Mo x Re 1- x S 2 at varying ratios of Mo/Re stoichiometries, for which we propose an effective interaction model that is then used to generate atomic configurations and make testable predictions at a range of concentrations and formation temperatures.

25 ENERGY STORAGE↗

DOE OSTI2021

Free energy difference to create the M-OH* intermediate of the oxygen evolution reaction by time-resolved optical spectroscopy

Theoretical descriptors differentiate the catalytic activity of materials for the oxygen evolution reaction by the strength of oxygen binding in the reactive intermediate created upon electron transfer. Recently, time-resolved spectroscopy of a photo-electrochemically driven oxygen evolution reaction followed the vibrational and optical spectra of this intermediate, denoted M-OH*. However, these inherently kinetic experiments have not been connected to the relevant thermodynamic quantities. Here we discover that picosecond optical spectra of the Ti-OH* population on lightly doped SrTiO 3 are ordered by the surface hydroxylation. A Langmuir isotherm as a function of pH extracts an effective equilibrium constant relatable to the free energy difference of the first oxygen evolution reaction step. Thus, time-resolved spectroscopy of the catalytic surface reveals both kinetic and energetic information of elementary reaction steps, which provides a critical new connection between theory and experiment by which to tailor the pathway of water oxidation and other surface reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Resolving complex intralayer transition motifs in high-Ni-content layered cathode materials for lithium-ion batteries

High-Ni-content layered materials are promising cathodes for next-generation lithium-ion batteries. However, investigating the atomic configurations of the delithiation-induced complex phase boundaries and their transitions remains challenging. Here, in this study, by using deep-learning-aided super-resolution electron microscopy, we resolve the intralayer transition motifs at complex phase boundaries in high-Ni cathodes. We reveal that an O3 → O1 transformation driven by delithiation leads to the formation of two types of O1–O3 interface, the continuous- and abrupt-transition interfaces. The interfacial misfit is accommodated by a continuous shear-transition zone and an abrupt structural unit, respectively. Atomic-scale simulations show that uneven in-plane Li+ distribution contributes to the formation of both types of interface, and the abrupt transition is energetically more favourable in a delithiated state where O1 is dominant, or when there is an uneven in-plane Li + distribution in a delithiated O3 lattice. Moreover, a twin-like motif that introduces structural units analogous to the abrupt-type O1–O3 interface is also uncovered. The structural transition motifs resolved in this study provide further understanding of shear-induced phase transformations and phase boundaries in high-Ni layered cathodes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Imaging and spatially resolved mass spectrometry applications in nephrology

The application of spatially resolved mass spectrometry (MS) and MS imaging approaches for studying biomolecular processes in the kidney is rapidly growing. These powerful methods, which enable label-free and multiplexed detection of many molecular classes across omics domains (including metabolites, drugs, proteins and protein post-translational modifications), are beginning to reveal new molecular insights related to kidney health and disease. Further, the complexity of the kidney often necessitates multiple scales of analysis for interrogating biofluids, whole organs, functional tissue units, single cells and subcellular compartments. Various MS methods can generate omics data across these spatial domains and facilitate both basic science and pathological assessment of the kidney. Optimal processes related to sample preparation and handling for different MS applications are rapidly evolving. Emerging technology and methods, improvement of spatial resolution, broader molecular characterization, multimodal and multiomics approaches and the use of machine learning and artificial intelligence approaches promise to make these applications even more valuable in the field of nephology. Overall, spatially resolved MS and MS imaging methods have the potential to fill much of the omics gap in systems biology analysis of the kidney and provide functional outputs that cannot be obtained using genomics and transcriptomic methods.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Chemical screening by time-resolved X-ray scattering to discover allosteric probes

Abstract Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis ( k VR ), capture structure–activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF–aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF–aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Time-resolved RIXS experiment with pulse-by-pulse parallel readout data collection using X-ray free electron laser

Abstract Time-resolved resonant inelastic X-ray scattering (RIXS) is one of the developing techniques enabled by the advent of X-ray free electron laser (FEL). It is important to evaluate how the FEL jitter, which is inherent in the self-amplified spontaneous emission process, influences the RIXS measurement. Here, we use a microchannel plate (MCP) based Timepix soft X-ray detector to conduct a time-resolved RIXS measurement at the Ti L 3 -edge on a charge-density-wave material TiSe 2 . The fast parallel Timepix readout and single photon sensitivity enable pulse-by-pulse data acquisition and analysis. Due to the FEL jitter, low detection efficiency of spectrometer, and low quantum yield of RIXS process, we find that less than 2% of the X-ray FEL pulses produce signals, preventing acquiring sufficient data statistics while maintaining temporal and energy resolution in this measurement. These limitations can be mitigated by using future X-ray FELs with high repetition rates, approaching MHz such as the European XFEL in Germany and LCLS-II in the USA, as well as by utilizing advanced detectors, such as the prototype used in this study.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Characterization of a mock up nuclear waste package using energy resolved MeV neutron analysis

Reliable radiographic methods for characterizing nuclear waste packages non-destructively (without the need to open containers) have the potential to significantly contribute to safe handling and future disposal options, particularly for legacy waste of unknown content. Due to required shielding of waste containers and the need to characterize materials consisting of light elements, X-ray methods are not suitable. Here, energy-resolved MeV neutron radiography is demonstrated as a first-of-its-kind application for non-destructive and remote examination of mock up nuclear waste packages from a safe position using time-of-flight techniques enabled by a novel event-mode imaging detector system. Energy-resolved neutron transmission spectra were measured spatially, permitting the detection of analogue materials to actual nuclear waste such as water, melamine, and ion exchange resin within a 2.54 cm wall thickness steel pipe. The results demonstrate the capability to locate the materials through this wall thickness by radiography and tomographic reconstruction, revealing detailed 3D distributions and structural anomalies. The method effectively detects residual water in ion exchange resin, highlighting its sensitivity to moisture content, a crucial parameter for nuclear waste characterization. Monte Carlo simulations are in agreement with the experimental findings, providing a pathway to simulate waste forms more difficult to tackle experimentally. This work paves the way to apply sub-nanosecond intense MeV neutron sources, such as laser-driven neutron sources under development, to nuclear waste characterization.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Determination of excited state molecular structures from time-resolved gas-phase X-ray scattering

We present a comprehensive investigation of a recently introduced method to determine transient structures of molecules in excited electronic states with sub-ångstrom resolution from time-resolved gas-phase scattering signals. The method, which is examined using time-resolved X-ray scattering data measured on the molecule N-methylmorpholine (NMM) at the Linac Coherent Light Source (LCLS), compares the experimentally measured scattering patterns against the simulated patterns corresponding to a large pool of molecular structures to determine the full set of structural parameters. In addition, we examine the influence of vibrational state distributions and find the effect negligible within the current experimental detection limits, despite that the molecules have a comparatively high internal vibrational energy. Here, the excited state structures determined using three structure pools generated using three different computational methods are in good agreement, demonstrating that the procedure is largely independent of the computational chemistry method employed as long as the pool is sufficiently expansive in the vicinity of the sought structure and dense enough to yield good matches to the experimental patterns.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Combined, time-resolved, in situ neutron reflectometry and X-ray diffraction analysis of dynamic SEI formation during electrochemical N 2 reduction

One means of improving performance for electrochemical ammonia production through the Li-mediated N 2 reduction reaction (Li-NRR) is by cycling the current driving the reaction between open-circuit conditions and periods of applied current density. Herein, we have investigated the dynamics of the electrode–electrolyte interface under Li-NRR conditions during current cycling using in situ time-resolved neutron reflectometry and grazing-incidence synchrotron X-ray diffraction. During cycling, measured neutron reflectivity curves indicated bilayer formation in which Li-containing species such as LiOH, Li 2 O, and small quantities of Li 3 N and metallic Li primarily appeared in a thin layer at the cathode surface, above which formed a much larger, porous, ‘solid–electrolyte interface’ (SEI) layer. Upon return to open-circuit conditions, Li-containing species quickly moved out of the thin layer, leaving a compact, stable layer of decomposition products underneath the SEI layer. This SEI layer concomitantly filled with electrolyte or dissolved, becoming indistinguishable from the electrolyte via contrast in scattering-length density (SLD). During the second current cycle, Li-containing species again preferentially deposited directly atop the cathode, with the thick SEI-like layer again appearing within a minute. This SEI layer exhibited a lower SLD more quickly than in the first cycle, which might suggest that Li-containing species become distributed within the porous SEI layer. Furthermore, these time-resolved observations of SEI and plated layers during current cycling suggest that benefits associated with return to open-circuit conditions between periods of applied current density may be related to the concomitant loss of Li-containing species from a thin layer at the cathode surface into a porous SEI layer that becomes filled with electrolyte or dissolves.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Angle-resolved polarimetry of hybrid perovskite emission for photonic technologies

Coupling between light and matter strongly depends on the polarization of the electromagnetic field and the nature of excitations in a material. As hybrid perovskites emerge as a promising class of materials for light-based technologies such as LEDs, LASERs, and photodetectors, it is critical to understand how their microstructure changes the intrinsic properties of the photon emission process. While the majority of optical studies have focused on the spectral content, quantum efficiency and lifetimes of emission in various hybrid perovskite thin films and nanostructures, few studies have investigated other properties of the emitted photons such as polarization and emission angle. Here, we use angle-resolved cathodoluminescence microscopy to access the full polarization state of photons emitted from large-grain hybrid perovskite films with spatial resolution well below the optical diffraction limit. In this work, mapping these Stokes parameters as a function of the angle at which the photons are emitted from the thin film surface, we reveal the effect of a grain boundary on the degree of polarization and angle at which the photons are emitted. Such studies of angle- and polarization-resolved emission at the single grain level are necessary for future development of perovskite-based flat optics, where effects of grain boundaries and interfaces need to be mitigated.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

Time-resolved quantification of key species and mechanistic insights in low-temperature tetrahydrofuran oxidation

Here, we investigate the kinetics and report the time-resolved concentrations of key chemical species in the oxidation of tetrahydrofuran (THF) at 7500 torr and 450–675 K. Experiments are carried out using high-pressure multiplexed photoionization mass spectrometry (MPIMS) combined with tunable vacuum ultraviolet radiation from the Berkely Lab Advanced Light Source. Intermediates and products are quantified using reference photoionization (PI) cross sections, when available, and constrained by a global carbon balance tracking approach at all experimental temperatures simultaneously for the species without reference cross sections. From carbon balancing, we determine time-resolved concentrations for the ROO˙ and ˙OOQOOH radical intermediates, butanedial, and the combined concentration of ketohydroperoxide (KHP) and unsaturated hydroperoxide (UHP) products stemming from the ˙QOOH + O 2 reaction. Furthermore, we quantify a product that we tentatively assign as fumaraldehyde, which arises from UHP decomposition via H 2 O or ˙OH + H loss. The experimentally derived species concentrations are compared with model predictions using the most recent literature THF oxidation mechanism of Fenard et al., (Combust. Flame, 2018, 191, 252–269). Our results indicate that the literature mechanism significantly overestimates THF consumption and the UHP + KHP concentration at our conditions. The model predictions are sensitive to the rate coefficient for the ROO˙ isomerization to ˙QOOH, which is the gateway for radical chain propagating and branching pathways. Comparisons with our recent results for cyclopentane (Demireva et al., Combust. Flame, 2023, 257, 112506) provide insights into the effect of the ether group on reactivity and highlight the need to determine accurate rate coefficients of ROO˙ isomerization and subsequent reactions.

Demireva, Maria↗