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DOE OSTI2025

Niobium coaxial cavities with internal quality factors exceeding 1.4 × 10 9 for circuit quantum electrodynamics

Group-V materials such as niobium and tantalum have become popular choices for extending the performance of circuit quantum electrodynamics (cQED) platforms, allowing for quantum processors and memories with reduced error rates and more modes. The complex surface chemistry of niobium, however, makes identifying the main modes of decoherence difficult at millikelvin temperatures and single-photon powers. We use niobium coaxial quarter-wave cavities to study the impact of etch chemistry, prolonged atmospheric exposure, and the significance of cavity conditions prior to and during cooldown—in particular, niobium hydride evolution—on single-photon coherence. We demonstrate cavities with quality factors Q int ≳ 1.4 × 10 9 in the single-photon regime, a 15-fold improvement over aluminum cavities of the same geometry. We rigorously quantify the sensitivity of our fabrication process to various loss mechanisms and demonstrate a two- to fourfold reduction in the two-level system loss tangent and a three- to fivefold improvement in the residual resistance over traditional buffered chemical polishing etching techniques. Finally, we demonstrate transmon integration and coherent cavity control while maintaining a cavity coherence of 11.3 ms. The accessibility of our method, which can be easily replicated in academic laboratory settings, together with the demonstration of its performance, mark an advancement in three-dimensional cQED.

Oriani, Andrew E. [Chicago U., EFI; Chicago U.] (O↗

DOE OSTI2025

Inertial Confinement Fusion Design Search Using Bayesian Optimization

Inertial confinement fusion (ICF) experiments rely on complex multi-physics simulation codes such as the Lawrence Livermore National Laboratory-developed HYDRA to guide design work. However, these simulations have several dozen tunable parameters and can be computationally expensive. This makes searching the parameter space challenging and time-consuming. Recently developed automated tools utilize Bayesian optimization to search these high-dimensional parameter spaces for optimal designs. The optimization tools run 2D integrated simulations in HYDRA to converge on a design that produces specified scalar or vector outputs. In this paper, we apply the Bayesian optimization tools to two common tuning scenarios. First, we tune simulation inputs to match measurements of a well-characterized experiment at the National Ignition Facility. This type of tuning is commonly performed to compensate for the use of simplified simulation settings (e.g. reduced resolution) or to account for missing physics in the simulations. Second, we search for an ICF simulation design that has a particular radiation drive profile. These optimizations replicate the kinds of tuning researchers routinely perform, but do so with significantly reduced manual effort. This approach demonstrates a powerful and efficient pathway toward autonomous, high-fidelity design optimization for future ICF experiments.

Bayesian optimization↗

DOE OSTI2025

The Importance of Solution Studies for the Structural Characterization of the Enterovirus 5’ Cloverleaf

Enteroviruses initiate genomic replication via a highly conserved mechanism that is controlled by an RNA platform, also known as the 5’ cloverleaf (5’CL). Here, we present a biophysical analysis of the 5’CL conformation of three enterovirus serotypes under various ionic conditions, utilizing CD spectroscopy, size-exclusion chromatography, and small-angle X-ray scattering. In general, a tendency toward a smaller monomeric hydrodynamic radius in the presence of salts was observed, but the exact structural signature of each 5’CL varied depending upon the serotype. Rhinovirus B14 (RVB14) exhibited at least two monomeric conformations and a low propensity for dimerization, while poliovirus 1 (PV1) showed a high propensity for dimerization, which was enhanced by the presence of salts. Enterovirus D70 was observed to be somewhat intermediate, with primarily a monomeric structure, but possessing some potential for dimerization. The equilibrium between the two monomeric and the dimeric conformations is also discussed. These results indicate that the 5’CL conformation may be more complex than the current literature suggests, thus underscoring the need for a combined crystal and solution approach for the accurate representation of the 5’CL conformation, and the conformation of other RNA structural elements, under native conditions.

Virology↗

DOE OSTI2026

Ensemble Effects on Hydroxide Bond Dissociation Free Energies in Polyoxovanadate Clusters

Understanding structure-property relationships is foundational to numerous modern chemistries, such as proton-coupled electron transfer (PCET). However, an experimentally measured property is the result of the behavior from an ensemble of molecules. Neglecting ensemble effects, especially under complex chemical environments, may obfuscate these relationships and lead to discrepancies between theory and experiment. In this work, we demonstrate the impact of configurational entropy and local chemical environments on hydroxide bond dissociation free energies [BDFE- (O−H)] for a set of polyoxovanadate nanoclusters, at ambient conditions. The O−H bond strengths are investigated via density functional theory (DFT) coupled with statistical thermodynamic analysis and bilinear modeling, and compared with previous experimental results on the same systems, namely electrochemical solutions of: [V 6 O 13−x (OH) x (TRIOL R ) 2 ] −2 (x = 2, 4, 6; R = NO 2 , Me) and [V 6 O 11−x (OMe) 2 (OH) x (TRIOL NO 2 ) 2 ] −2 (x = 2, 4). Interestingly, we find that ensemble effects, even at room temperature, can account for a significant portion of the BDFE(O−H) trend with the degree of reduction via H atom binding, which cannot be fully captured by single-structure, static DFT calculations. Moreover, we find that the ensemble effects may be replicated statistically, requiring only enumeration of energetically accessible H-binding sites. With the ensemble effects resolved, we present a simple bilinear model to reconcile remaining biases between experiment and ensemble-informed theory, which corelate with clusterspecific electronic environment differences. The bilinear model achieves outstanding accuracy vs experiments with a root-mean squared error of 0.4 kcal/mol. Finally, based on the physicochemical characteristics of hydrogen interaction with polyoxometalates, we present a simple methodology that captures the BDFE(O−H) trend while dramatically reducing required DFT calculations by 98% and achieving accuracy within 1 kcal/mol. Overall, this work elucidates the roles and structural origins of configurational entropy and chemical effects on polyoxometalate hydroxide bond energies, with potential applicability to various atomically precise metal oxide systems. Importantly, it introduces models for rapid and highly accurate property calculations in connection with experiments.

Cluster chemistry↗

DOE OSTI2026

Mechanism of Tyrosine-Driven Deprotonation in Photosystem II Revealed by Multiscale Simulations

Photosystem II (PSII) drives light-induced water oxidation via stepwise redox transitions of its oxygen-evolving complex (OEC), a Mn 4 Ca cluster advancing through five intermediate S-states (S 0 –S 4 ). The S 2 → S 3 transition involves a redox event in which a Mn ion donates an electron to the redox-active tyrosine YZ, coupled to deprotonation of an OEC-bound water ligand─yet the underlying coupling mechanism remains unresolved. Time-resolved serial femtosecond crystallography (TR-SFX) has revealed transient electron density shifts near the redox-active tyrosine Y Z , interpreted as sequential oxidation and reduction, with reduction initiating ∼1 μs after excitation and substantially progressed by 30 μs. However, this interpretation conflicts with kinetics from photothermal beam deflection (PBD), time-resolved X-ray absorption spectroscopy (TR-XAS), and electron paramagnetic resonance (EPR), which place electron transfer at 190–400 μs and proton transfer around 30 μs. Here, we reconcile these discrepancies using quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations. We show that oxidation of P680 and Y Z breaks the symmetry of the nearby hydrogen bonds involving water molecule W4, displacing Y Z and replicating the TR-SFX features of Y Z and Q165 observed at 1 μs. This local perturbation propagates through a hydrogen-bond network, transmitting the electrostatic signal from Y Z to the E65-E312 dyad and triggering redox-coupled deprotonation via the Cl1 channel. By 30 μs, the hydrogen-bond symmetry is restored through deprotonation of W2 (or alternatively W1), reproducing the disappearance of TR-SFX density differences around Y Z and Q165 without requiring Y Z reduction. Our proposed mechanism also gives molecular insights into the O6* density, assigning it to water reorganization rather than a discrete Ca-bound hydroxide species. Here, our results reveal a detailed atomistic mechanism linking Y Z oxidation to long-range proton release and suggest a functional role for the nearby Cl – ion in proton transfer. More broadly, this study underscores the importance of hydrogen-bond dynamics in mediating redox-driven proton transport and demonstrates how integrative simulations can resolve mechanistic ambiguities.

Deprotonation↗

DOE OSTI2024

Microbial Community Changes across Time and Space in a Constructed Wetland

Constructed wetlands are artificial ecosystems designed to replicate natural wetland processes. Microbial communities play a pivotal role in cycling essential elements, particularly sulfur, which is crucial for trace metal fixation and remobilization in these ecosystems. By their response to their environment, microbial communities act as biological indicators of the wetland performance. To address knowledge gaps pertinent to the changes in trace metal bioavailability in relation to microbial activities in the H-02 constructed wetland, we performed this study to investigate temporal and spatial variations in microbial communities by using molecular biology tools. Quantitative polymerase chain reaction and next generation sequencing techniques were employed to analyze archaeal and bacterial groups associated with sulfur and methane cycling. Alpha diversity indices were used to assess species richness, evenness, and dominance. Results indicated high gene abundance of Desulfuromonas (5.37 × 10 6 g.cell –1 ), methane oxidizing bacteria (6.92 × 10 6 g.cell –1 ), and methanogenic microorganisms (3.02 × 10 5 g.cell –1 ) during cool months. Warm months were marked by sulfate reducing bacteria dominance (3.31 × 10 6 g.cell –1 ), potentially due to competitive interactions and environmental conditions, higher temperatures, and lower redox potential. Spatial variability among microbial groups was insignificant, but trends in gene abundance indicated complex factors influencing these groups. Next generation sequencing data demonstrated Firmicutes as the most abundant phylum with over 50% regardless of the season or sampling location. Cool months exhibited higher alpha diversity than warm months. Overall, this study showed that seasonal changes significantly impacted the microbial communities in the H-02 constructed wetland that are associated with the sulfur cycle and eventually trace metal biogeochemistry, revealing two distinct mechanisms of the sulfur cycle between the two main seasons, whereas spatial variability effects were not conclusive.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

3D nanolithography with metalens arrays and spatially adaptive illumination

The growing demand for advanced materials, miniaturized devices and integrated microsystems calls for the reliable fabrication of complex, multiscale, three-dimensional (3D) architectures, a need increasingly addressed through light-based and laser-based processes. However, owing to the field-of-view (FOV) limitations of conventional imaging optics, existing 3D laser nanofabrication techniques face fundamental challenges in throughput, proximity error and stitching defects on the path to scaling. Here, in this study, we present a scalable 3D nanofabrication platform that uses a metalens-generated focal spot array to parallelize two-photon lithography (TPL) beyond centimetre-scale write field areas. Metalenses are ideally suited for producing submicron-scale focal spots for high-throughput nanolithography, as they uniquely feature large numerical apertures (NAs), immersion media compatibility and large-scale manufacturability. We experimentally demonstrate a printing system that uses a 12-cm 2 metalens array to produce more than 120,000 cooperative focal spots, corresponding to a throughput exceeding 10 8 voxels s −1 . By programmatically patterning the focal spot array using a spatial light modulator (SLM), an adaptive parallel printing strategy is developed for precise greyscale linewidth modulation and choreographed printing of semiperiodic and fully aperiodic 3D geometries. We demonstrate parallel printing of replicated microstructures (>50 M microparticles per day), centimetre-scale 3D architectures with feature sizes down to 113 nm, and photonic and mechanical metamaterials. This work demonstrates the potential of 3D nanolithography towards wafer-scale production, showing how TPL could be used at scale for applications in microelectronics, biomedicine, quantum technology and high-energy laser targets.

Materials science↗

DOE OSTI2024

Evaluating the Importance of Conformers for Understanding the Vacuum-Ultraviolet Spectra of Oxiranes: Experiment and Theory

Vacuum-ultraviolet (VUV) absorption spectroscopy enables electronic transitions that offer the unambiguous identification of molecules. As target molecules become more complex, multifunctional species present a great challenge to both experimental and computational spectroscopy. This research reports both experimental and theoretical studies of oxiranes. Computationally, the nuclear ensemble approach has been used to accurately predict experimental spectra for a variety of molecules. However, this approach incurs great computational cost, as ensembles generally consist of thousands of geometries. The present study aims to drastically reduce the ensemble by evaluating the significance of the conformers to the predicted spectra. This approach was applied to 11 substituted oxiranes using the Conformer Rotamer Ensemble Sampling Tool (CREST) of Grimme to generate an ensemble of unique conformers determined by their Boltzmann populations. Five TD-DFT functionals (BMK, CAM-B3LYP, M06-2X, MN15, ωB97X-D) and EOM-CCSD were used to simulate the spectrum of each substituted oxirane ensemble. Computed spectra were then compared to the experiment using both qualitative and quantitative metrics. Based on these metrics, it was observed that certain conformers may not be necessary to characterize this set of oxiranes despite the temperature (323 K) of the experiment. A single conformer can then be used with TD-DFT and EOM-CCSD to replicate the experimental spectra of these medium-sized combustion species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

ROOT RNTuple and EOS: The Next Generation of Event Data I/O

For several years, the ROOT team is developing the new RNTuple I/O subsystem in preparation of the next generation of collider experiments. Both HL-LHC and DUNE are expected to start data taking by the end of this decade. They pose unprecedented challenges to event data I/O in terms of data rates, event sizes, and event complexity. At the same time, the I/O landscape is becoming more diverse. HPC cluster file systems and object stores, NVMe disk cache layers in analysis facilities, and S3 storage on cloud resources are mixing with traditional XRootD-managed spinning disk pools.The ROOT team will finalize a first production version of the RNTuple binary format by the end of 2024. After this point, ROOT will provide backward compatibility for RNTuple data. This contribution provides an overview of the RNTuple feature set, the related R&D activities and the long-term vision for RNTuple. We report on performance, interface design, tooling, robustness, integration with experiment frameworks, and validation results, as well as recent R&D on parallel reading and writing and exploitation of modern hardware and storage systems. We will give an outlook on possible future features after a first production release.Collaboratively, the IT and EP departments at CERN have launched a formal project within the Research and Computing sector to evaluate the novel data format for physics analysis data utilized in LHC experiments and other fields. This part of the project focuses on validating the scalability of the EOS storage backend during the transition from the over 25 years old TTree production format to the newly developed RNTuple format, using both replicated and erasure-coded storage profiles.

Blomer, Jakob [CERN]↗

DOE OSTI2026

Novel Cell-Type-Specific Drought-Responsive Proteins in Root Tips of Field-Grown Perennial Switchgrass

The root-tip region of plants, including the root cap, forms the most basal terminal of the root and exhibits a high degree of cellular complexity in terms of morphology, cytological function, and interaction with environmental cues in the soil. Cells in this region follow a developmental trajectory, transitioning from stem cells to meristematic cells, and ultimately to fully differentiated cell types. However, our understanding of root-tip cell-type specific proteomic responses to abiotic stresses, such as drought, particularly under field conditions, remains limited. This study aimed to identify spatially resolved, cell type-specific proteomes in switchgrass (Panicum virgatum) root tips under drought stress. Root tips were collected from seven-year-old, field-grown switchgrass ‘Alamo’ plants excavated under both well-watered and long-term drought conditions. Cell type-specific proteins were identified using laser capture microdissection (LCM) coupled with nanoPOTS (Nanodroplet Processing in One Pot for Trace Samples) and nano-LC-MS proteomics analysis. Five distinct cell types were targeted: (1) cells in the quiescent center and stem cell niche (QuC), (2) protodermal epidermal cells (PEC) in the meristematic zone, (3) epidermal cells in the transition and elongation zones above the root cap (Epi), (4) peripheral root cap cells (PRC), forming 2–3 layers below the PEC and 1–2 layers above the root border cells, and (5) columella root cap cells (Col) comprising of the columella initials and a single underlying layer of cells undergoing active growth. Principal component analysis (PCA) revealed clear separation among the five targeted cell types, confirming distinct proteomic profiles. Proteins predominantly enriched in each cell type were linked to distinct cellular functions, with QuC cells showing involvement in chromosomal behavior, DNA replication, and mitosis—key processes for stem cell niche regulation. Drought stress resulted in alterations of proteostasis, as evidenced by significant decreases in ribosomal proteins and increases in protein synthesis inhibitors. Moreover, drought stress induced unique cell-type–specific proteins involved in phytohormone biosynthesis and signaling pathways, including auxin, cytokinin, and jasmonic acid. In particular, QuC cells were more highly enriched in proteins associated with DNA repair and mitotic processes. Metabolic pathways related to amino acids, carbohydrates, and lipids were differentially affected in a cell-type–dependent manner, whereas general stress-responsive proteins exhibited consistent changes across all five cell types. Overall, this study provides unique spatially resolved, cell-type-specific proteomic profiles in root tips, representing a significant advancement in our understanding of the cellular mechanisms underlying plant responses to drought stress in natural field conditions.

perennial grass↗

DOE OSTI2025

BOPTest As a Platform for Building Controls and Grid-Interactive Buildings Workforce Training

Building automation and controls are becoming increasingly complex with the emergence of Grid Integrated Efficient Buildings (GEBs) as well as new highly efficient sequences of operation and data-driven control schemes. However, there remains a significant gap in hands-on training opportunities for building operators and technicians to gain practical experience with advanced control systems in a low-risk environment. This paper presents BOPTEST (Building Optimization Performance Test) as a suitable platform for workforce training in building controls and GEB technologies. BOPTEST provides a suite of standardized building simulation test cases with a REST API, real-time control interfaces through BACnet, semantic models connecting users to building data, and built-in calculation of control metrics and performance indicators. The platform enables trainees to interact with virtual buildings using industry-standard protocols while learning how to implement and innovate control strategies. The training platform is designed to offer a structured and interactive learning experience for building engineers, helping them effectively develop, learn, and retain skills in fault identification, troubleshooting, and correction. The workflow is divided into three main phases: 1) Setup, 2) Exercise, and 3) Review, each comprising specific activities performed by either the instructor or the student. Initial pilot training sessions have yielded positive feedback from instructors and participants and demonstrates that BOPTEST effectively fills an industry need for a low-risk training resource via simulation of real building control systems, allowing trainees to gain practical experience before working in the field. The platform's ability to provide immediate performance feedback while maintaining familiar industry interfaces makes it particularly suitable for workforce development programs. This work provides a replicable model for leveraging building simulation in control education and training.

Paul, Lazlo↗

DOE OSTI2025

BOPTEST as a Platform for Building Controls and Grid-Interactive Buildings Workforce Training

Paul, Lazlo↗

DOE OSTI2024

DECOVALEX-2023: Task C Final Report

The Full-scale Emplacement (FE) heater experiment at the Mont Terri Underground Rock Laboratory (URL) was designed and conducted by Nagra to replicate an emplacement tunnel of Nagra’s reference repository design at 1:1 scale. Alongside testing the technical feasibility of constructing disposal tunnels, emplacing waste containers in the tunnels and then backfilling them, the main goals of the FE experiment are (1) to obtain a better understanding of the coupled effects of induced thermo-hydro-mechanical (THM) processes that may occur and (2) to validate existing coupled THM models (Müller et al., 2017). A key aspect of ensuring safety for repositories located in low-permeability rock involves minimizing any damage to the rock itself, thereby preserving its integrity and promoting a stable environment Amongst a number of processes that could damage the rock is the increase in pore pressure due to thermal loading caused by heat emitted from the waste. To reduce the potential damage of the rock, it is important to analyse the evolution of heat over time due to the heat load of the containers and assess possible consequences by coupled THM models. The aim of Task C of DECOVALEX-2023 was to build 3D numerical models of the FE experiment, focussing in particular on the heating induced pore pressure change in the Opalinus Clay. Data from a large number of sensors were available from the FE experiment for model comparison. These sensors measured temperature and relative humidity in the bentonite around the heaters, and temperature, pressure and displacement/strain in the surrounding Opalinus clay. Data were available from the start of excavation (April 2012) up to August 2020 for most sensors (more than 5 years from the start of heating in December 2014). To fulfil the overall aim of the task, the work was broken down into a number of steps, starting with simpler models to build confidence in each team’s approach and then moving to more complex models that better represent the FE experiment. Step 0 consisted of 2D benchmark models, gradually increasing the number of processes that are represented from thermal (T) only models in Step 0a, to coupled thermal hydraulic (TH) models in Step 0b with a representation of changing porosity, to coupled thermo-hydro-mechanical (THM) models in Step 0c, where porosity changes are calculated by the mechanical model. A detailed specification of processes, parameters, initial and boundary conditions was provided for this step, with the ambition that all teams would work towards close agreement in their model results, thus building confidence in the model implementations. vi It was not straightforward to achieve agreement between the teams, so additional steps (Step 0b2, 0b3, 0c2, 0c3) were added along with derivation of some analytical solutions against which the models could be compared. The reasons for the differences between teams were investigated and found to be caused primarily by different conceptual model assumptions (including temperature dependence of the thermal expansion of water), different model formulations (including porosity evolution) and differences in modelled domain sizes, boundary conditions and grid discretisation. This demonstrates that comparisons between multiple modelling teams and/or comparison with analytical results and experimental data are highly beneficial in providing an indication of uncertainty in model predictions. At the conclusion of Step 0, almost all teams had achieved a close agreement in model results and those that had not achieved an agreement knew the reason for this. Step 1 moved from 2D models to 3D models of the FE experiment without adding technical features like shotcrete or EDZ, and only considering the heating phase. Initially the 3D model was tightly specified to continue to build confidence in the model implementations (Step 1a). The results of Step 1a were compared to the data from the FE-experiment without the teams seeing the data. The teams were then provided with a sub-set of the data from the FE-experiment and invited to consider how best to use the large dataset for model comparison (Step 1b). Teams were then asked to use the data provided to calibrate their models, only changing material property values rather than adding features or processes to their models (Step 1c). In Step 1, teams were asked to only model the heating phase of the experiment, so pressure in the Opalinus Clay was reported as change in pressure since the initial conditions were specified rather than modelled. The change from 2D to 3D models was accompanied by an increase in the dispersion of results between the teams. Some of this was resolved during the task, but some remained and is potentially due to model discretisation. Calibration of parameters was useful in improving the fit of the models to the data but the remaining differences indicated that the models were missing features or processes. In Step 2, the teams were asked to update their models with additional features and processes as well as calibrating parameters to try and improve the fit of the models to the data. Teams were encouraged to represent ventilation of the open FE tunnel prior to backfilling with heaters and bentonite and in Step 2, the absolute pressure in the Opalinus Clay was compared between the teams. Teams took different approaches, but there was consideration of adding shotcrete and an EDZ into the model, representing stress change during excavation and different approaches to modelling ventilation of the FE tunnel. Overall, the documented results showed a very good agreement for temperature. The results for porewater pressure evolution showed a significant improvement for most teams compared to Step 1c with a good agreement to the measurements for several teams whereas some teams overpredicted the pressure increase and others overpredicted the drainage effect especially for the sensors close to the heater. Step 3 was an opportunity for teams to use the models developed in Step 1 and Step 2 to make predictions about the temperature and pressure changes that will be expected at the FE experiment over the next few years in light of the planned changes in thermal output of the heaters.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗