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DOE OSTI2022

Monitoring SARS-CoV-2 in wastewater [Slides]

The monitoring of SARS-CoV-2 through individual testing is subject to inaccuracies. Wastewater biosurveillance has been used around the world to detect the presence of drugs, viruses, and other chemicals present in a population. Fecal shedding of SARS-CoV-2 implies that wastewater can be analyzed in order to detect varying levels of the virus within a given community. Pepper Mild Mottle Virus is present consistently in human fecal matter, and can be used to normalize the amount of SARS-CoV-2 detected. In this experiment, the amount of SARS-CoV-2 in the wastewater sample was compared to the amount of PMMoV present. Wastewater samples were separated into three fractions: direct wastewater, a solid pellet, and filter paper extract. An RT-qPCR test was used on the extracted RNA from each fraction to detect the relative amount of SARS-CoV-2 and PMMoV copies in each sample. The amount of SARS-CoV-2 was successfully normalized to the amount of PMMoV.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Safety Considerations for Advanced Material Irradiation at the Advanced Test Reactor

The Advanced Test Reactor (ATR) is a light water reactor with aluminum-clad driver fuel. A primary mission of the ATR is to support the next generation of nuclear reactors. This support necessarily requires irradiation of advanced materials such as sodium, fuel salts, and metal eutectics. Irradiation of advanced materials in the ATR environment presents a challenge when completing accident analyses and demonstrating compliance to the Safety Analysis Report (SAR). Many advanced materials have the possibility to react with the ATR protective barriers such as the cladding or primary coolant system (PCS) boundary during postulated accident scenarios. Further, molten fuel experiments fall outside of the standard regulatory framework for dose consequence analyses. ATR is currently developing new safety analysis methods to support irradiation of advanced materials. The primary considerations for this development are 1) experiment containment design requirements, 2) primary coolant system response to an experiment containment failure, and 3) dose analyses for molten fuels.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Safety Considerations for Advanced Material Irradiation at the ATR

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Super-Resolution Ptychography with Small Segmented Detectors

To overcome the spatial resolution limit set by aperture-limited diffraction in traditional scanning transmission electron microscopy, microscopists have developed ptychography enabled by iterative phase retrieval algorithms and high-dynamic-range pixel array detectors. Current detector designs are limited by the data rate off chip, so a high-pixel-count detector has a proportionally lower frame rate than the few-segment detectors used for differential phase contrast (DPC) imaging. This slower acquisition speed leads to heightened vulnerability to scan noise, drift, and potential sample damage. This creates opportunities for repurposing fast segmented detectors for ptychography by trading a reduction in reciprocal space pixels for an increase in real space pixels. Here, we explore a strategy of oversampling in real space and instead apply detector pixel upsampling during the reconstruction process. Further, we demonstrate the viability of achieving super-resolution ptychography on thin objects using only 2 × 2 detector pixels, surpassing the resolution of integrated DPC (iDPC) imaging. With optimization using simulated datasets and experiments on MoTe 2 /WSe 2 bilayer moiré superlattices, we achieved super-resolution ptychography reconstructions under rapid acquisition conditions (37.5 pA, 1 μs dwell time), yielding over 50% improvements in contrast and information limit compared to annular dark field and iDPC imaging on the same detectors.

2D materials↗

DOE OSTI2021

Comment on “Increased growing-season productivity drives earlier autumn leaf senescence in temperate trees”

Zani et al. propose that enhancement of deciduous tree photosynthesis in a CO 2 -enriched atmosphere will advance autumn leaf senescence. Here, this premise is not supported by consistent observations from free-air CO 2 enrichment (FACE) experiments. In most FACE experiments, leaf senescence or abscission was not altered or was delayed in trees exposed to elevated CO 2 .

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Inelastic Neutron Scattering Observation of Plasma-Promoted Nitrogen Reduction Intermediates on Ni/γ-Al 2 O 3

Plasma-assisted catalysis is an emerging technology for the atmospheric pressure and low bulk gas temperature synthesis of ammonia from molecular nitrogen and hydrogen. Direct evidence for plasma-induced surface reaction intermediates relevant to ammonia production, including surface hydrides and NH x (x = 1, 2, 3) species, has remained elusive. In this work, we report inelastic neutron scattering (INS) observations of alumina-supported Ni particles after treatment with N 2 and H 2 plasmas. INS experiments reveal the presence of NH x species and hydrides on Ni sites after exposure to sequential N 2 and H 2 plasma treatments. By separating exposure, we exclude the presence of plasma-phase reactions and demonstrate that these species are generated through plasma-facilitated surface reactions. Computed synthetic INS spectra of NH 3 , NH 2 and NH adsorbates on Ni support the experimental assignments of surface intermediates. The results directly implicate plasma stimulation of dinitrogen in generation of surface-bound nitrogen that participates in further hydrogenation reactions driven either thermally or with H 2 plasma.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Facilitating Hydrogen Dissociation over Dilute Nanoporous Ti–Cu Catalysts

The dissociation of H 2 is an essential elementary step in many industrial chemical transformations, typically requiring precious metals. Here, we report a hierarchical nanoporous Cu catalyst doped with small amounts of Ti (npTiCu) that increases the rate of H 2 –D 2 exchange by approximately one order of magnitude compared to the undoped nanoporous Cu (npCu) catalyst. The promotional effect of Ti was measured via steady-state H 2 –D 2 exchange reaction experiments under atmospheric pressure flow conditions in the temperature range of 300–573 K. Pretreatment with flowing H 2 is required for stable catalytic performance, and two temperatures, 523 and 673 K, were investigated. The experimentally determined H 2 –D 2 exchange rate is 5–7 times greater for npTiCu vs the undoped Cu material under optimized pretreatment and reaction temperatures. The H 2 pretreatment leads to full reduction of Cu oxide and partial reduction of surface Ti oxide species present in the as-prepared catalyst as demonstrated using in situ ambient pressure X-ray photoelectron spectroscopy and X-ray absorption spectroscopy. The apparent activation energies and pre-exponential factors measured for H 2 –D 2 exchange are substantially different for Ti-doped vs undoped npCu catalysts. Density functional theory calculations suggest that isolated, metallic Ti atoms on the surface of the Cu host can act as the active surface sites for hydrogen recombination. Furthermore, the increase in the rate of exchange above that of pure Cu is caused primarily by a shift in the rate-determining step from dissociative adsorption on Cu to H/D atom recombination on Ti-doped Cu, with the corresponding decrease in activation entropy that it produces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Assessing the accuracy of compound formation energies with quantum Monte Carlo

Accurately predicting the formation energy of a compound, which describes its thermodynamic stability, is a key challenge in materials physics. Here, we employ a many-body quantum Monte Carlo (QMC) with single-reference trial functions to compute the formation energy of two electronically disparate compounds, the intermetallic VPt2 and the semiconductor CuI, for which standard density functional theory (DFT) predictions using both the Perdew-Burke-Ernzerhof (PBE) and the strongly constrained and appropriately normed (SCAN) density functional approximations deviate markedly from available experimental values. For VPt2, we find an agreement between QMC, SCAN, and PBE0 estimates, which therefore remain in disagreement with the much less exothermic experimental value. For CuI, the QMC result agrees with neither SCAN nor PBE pointing towards DFT exchange-correlation biases, likely related to the localized Cu 3d electrons. Compared to the behavior of some density functional approximations within DFT, spin-averaged QMC exhibits a smaller but still appreciable deviation when compared to experiment. The QMC result is slightly improved by incorporating spin-orbit corrections for CuI and solid I 2 , so that experiment and theory are brought into imperfect but reasonable agreement within about 120 meV/atom.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Excited electronic states of Na 2 and K 2 : The potential for long-lived “reservoir” states leading to collision induced population inversions

Potential energy curves (PECs) for the spin-free (ΛS) and spin–orbit (Ω) states associated with the four lowest-lying dissociation channels of Na 2 and K 2 were calculated at the SA-CASSCF/SO-CASPT2/aug-cc-pwCVQZ-DK level. The PECs of Na 2 were consistent with the experimental data and with the FS-CCSD (2,0) calculations, reproducing the double-well and the “shelf” character for some of the potentials of the excited states. For K 2 , the PECs behaved in a similar way and the spectroscopic parameters for the ground and the excited states are in good agreement with the available experimental values. The dissociation energy of K 2 was predicted to be D e = 4454 cm −1 , within an agreement of 5 cm −1 with the experiments. For Na 2 , D e = 5789 cm −1 compared to the experimental value of 6022 cm −1 . The inclusion of spin–orbit coupling effects resulted in avoided crossings, which affect the PECs. Spin–orbit changes the predicted curves for some excited Ω states arising from ΛS states that overlap each other, affecting their associated vibrational frequencies and bond distances. Here, the current studies of the low-lying states in K 2 reveal a similar structure to those of Na 2 , which suggests the accessibility of long-lived energy storing reservoir states and possible population inversions in K 2 following prior experimental work on the reaction of halogen atoms with Na 3 to produce excited states of Na 2 .

Ab-initio methods↗

DOE OSTI2024

Isovector Axial Charge and Form Factors of Nucleons from Lattice QCD

A survey of the calculations of the isovector axial vector form factor of the nucleon using lattice QCD is presented. Attention is paid to statistical and systematic uncertainties, in particular those due to excited state contributions. Based on a comparison of results from various collaborations, a case is made that lattice results are consistent within 10%. A similar level of uncertainty is in the axial charge gAu−d, the mean squared axial charge radius ⟨rA2⟩, the induced pseudoscalar charge gP∗, and the pion–nucleon coupling gπNN. Even with the current methodology, a significant reduction in errors is expected over the next few years with higher statistics data on more ensembles closer to the physical point. Lattice QCD results for the form factor GA(Q2) are compatible with those obtained from the recent MINERνA experiment but lie 2–3σ higher than the phenomenological extraction from the old ν–deuterium bubble chamber scattering data for Q2>0.3 GeV2. Current data show that the dipole ansatz does not have enough parameters to fit the form factor over the range 0≤Q2≤1 GeV2, whereas even a z2 truncation of the z expansion or a low order Padé are sufficient. Looking ahead, lattice QCD calculations will provide increasingly precise results over the range 0≤Q2≤1 GeV2, and MINERνA-like experiments will extend the range to Q2∼2 GeV2 or higher. Nevertheless, improvements in lattice methods to (i) further control excited state contributions and (ii) extend the range of Q2 are needed.

Astronomy & Astrophysics↗

DOE OSTI2022

Spectroscopic evidence of highly correlated electrons in $\mathrm{VSe_2}$

We present detailed high-resolution angle-resolved photoemission experiments on $\mathrm{VSe_2}$ grown under various conditions. The surface electronic structure optimally grown samples can host high-temperature spectral kink, quasiparticle peak, and the Fermi gap. Collective observation of these electronic features refers to the strong electronic correlation and is usually attributed to the characteristics of superconductors. Temperature evolution of the quasiparticle peak and the Fermi gap also follow the trend observed in high-$T_c$ superconductors as progressive quenching of the quasiparticle peak at a lower temperature than the complete Fermi gap closing. As a result, the quasiparticle peak can be observed up to 100 ± 5 K while the Fermi gap persists up to ~ 150 K. Importantly, these realizations can guide future studies to induce high-temperature superconductivity in transition metal dichalcogenides as well as understand the physics behind high-$T_c$ superconductors.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Paragenetic controls on CO 2 -fluid-rock interaction and weakening in a macroporous-dominated sandstone

The injection and storage of anthropogenic CO 2 in the subsurface is being deployed as a climate change mitigation tool; however, diagenetic-paragenetic heterogeneity in sandstone reservoirs often contributes to interval specific chemomechanical changes that affect injection and can increase leakage risk.In this paper we address reservoir heterogeneities’ impact on chemomechanical changes in a macroporous-dominated lithofacies of Morrow B sandstone, a formation containing several diagenetically-distinct hydraulic facies while undergoing enhanced oil recovery (EOR) and carbon dioxide (CO 2 ) sequestration. We performed three flow-through experiments using a CO 2 -charged or uncharged formation water combined with four indirect tensile strength tests per post-test sample. We then used the microstructure and paragenetic sequence to understand chemomechanical weakening with key observations as follows: dissolution of carbonates and feldspars changed porosity; increased permeability led to reclassifying each sample in a different hydraulic flow unit; decreased ultrasonic velocity; and did not lead to a loss of tensile strength. Tensile strength maintenance occurred due to the low abundance and minor dissolution of siderite, the stability of quartz, and the relative position of diagenetic ankerite within feldspar. This macroporous-dominated lithofacies is the primary reservoir for the Morrow B Sandstone, and is analogous to other porous sandstone reservoirs. It represents an end-member of a chemomechanically low-risk siliceous CO 2 sequestration and CO 2 -EOR reservoir.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Three rate-determining protein roles in photosynthetic O 2 -evolution addressed by time-resolved experiments on genetically modified photosystems

Light-driven water splitting by plants, algae and cyanobacteria is pivotal for global bioenergetics and biomass formation. A manganese cluster bound to the photosystem II proteins catalyzes the complex reaction at high rate, but the rate-determining factors are insufficiently understood. Here we trace the oxygen-evolution transition by time-resolved polarography and infrared spectroscopy for cyanobacterial photosystems genetically modified at two strategic sites, complemented by computational chemistry. Our results highlight three rate-determining roles of the protein environment of the metal cluster: acceleration of proton-coupled electron transfer, acceleration of substrate-water insertion after O 2 -formation, and balancing of rate-determining enthalpic and entropic contributions. Whereas in general the substrate-water insertion step may be unresolvable in time-resolved experiments, here it likely becomes traceable because of deceleration by genetic modification. Our results may stimulate new time-resolved experiments on substrate-water insertion in photosynthesis, clarification of enthalpy-entropy compensation in enzyme catalysis, and knowledge-guided development of inorganic catalyst materials.

Bioenergetics↗

DOE OSTI2023

Building a DFT+U machine learning interatomic potential for uranium dioxide

Despite uranium dioxide (UO 2 ) being a widely used nuclear fuel, fuel performance models rely extensively on empirical correlations of material behavior, leveraging the historical operating experience of UO 2 . Mechanistic models that consider an atomistic understanding of the processes governing fuel performance (such as fission gas release and creep) will enable a better description of fuel behavior under non-prototypical conditions such as in new reactor concepts or for modified UO 2 fuel compositions. To this end, molecular dynamics simulation is a powerful tool for rapidly predicting physical properties of proposed fuel candidates. However, the reliability of these simulations depends largely on the accuracy of the atomic forces. Traditionally, these forces are computed using either a classical force field (FF) or density functional theory (DFT). While DFT is relatively accurate, the computational cost is burdensome, especially for f-electron elements, such as actinides. By contrast, classical FFs are computationally efficient but are less accurate. For these reasons, we report a new accurate machine learning interatomic potential (MLIP) for UO 2 that provides high-fidelity reproduction of DFT forces at a similar low cost to classical FFs. We employ an active learning approach that autonomously augments the DFT training data set to iteratively refine the MLIP. To further improve the quality of our predictions, we utilize transfer learning to retrain our MLIP to higher-accuracy DFT+U data. We validate our MLIPs by comparing predicted physical properties (e.g., thermal expansion and elastic properties) with those from existing classical FFs and DFT/DFT+U calculations, as well as with experimental data when available.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

KGML-ag: a modeling framework of knowledge-guided machine learning to simulate agroecosystems: a case study of estimating N<sub>2</sub>O emission using data from mesocosm experiments

Abstract. Agricultural nitrous oxide (N2O) emission accounts for a non-trivial fraction of global greenhouse gas (GHG) budget. To date, estimating N2O fluxes from cropland remains a challenging task because the related microbial processes (e.g., nitrification and denitrification) are controlled by complex interactions among climate, soil, plant and human activities. Existing approaches such as process-based (PB) models have well-known limitations due to insufficient representations of the processes or uncertainties of model parameters, and due to leverage recent advances in machine learning (ML) a new method is needed to unlock the “black box” to overcome its limitations such as low interpretability, out-of-sample failure and massive data demand. In this study, we developed a first-of-its-kind knowledge-guided machine learning model for agroecosystems (KGML-ag) by incorporating biogeophysical and chemical domain knowledge from an advanced PB model, ecosys, and tested it by comparing simulating daily N2O fluxes with real observed data from mesocosm experiments. The gated recurrent unit (GRU) was used as the basis to build the model structure. To optimize the model performance, we have investigated a range of ideas, including (1) using initial values of intermediate variables (IMVs) instead of time series as model input to reduce data demand; (2) building hierarchical structures to explicitly estimate IMVs for further N2O prediction; (3) using multi-task learning to balance the simultaneous training on multiple variables; and (4) pre-training with millions of synthetic data generated from ecosys and fine-tuning with mesocosm observations. Six other pure ML models were developed using the same mesocosm data to serve as the benchmark for the KGML-ag model. Results show that KGML-ag did an excellent job in reproducing the mesocosm N2O fluxes (overall r2=0.81, and RMSE=3.6 mgNm-2d-1 from cross validation). Importantly, KGML-ag always outperforms the PB model and ML models in predicting N2O fluxes, especially for complex temporal dynamics and emission peaks. Besides, KGML-ag goes beyond the pure ML models by providing more interpretable predictions as well as pinpointing desired new knowledge and data to further empower the current KGML-ag. We believe the KGML-ag development in this study will stimulate a new body of research on interpretable ML for biogeochemistry and other related geoscience processes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Field-scale fault reactivation experiments by fluid injection highlight aseismic leakage in caprock analogs: Implications for CO 2 sequestration

Observations on tens-of-meter scale experiments of fault activation by fluid injection conducted in shales allow exploring how aseismic and seismic events may jeopardize the integrity of a sealing caprock overlying a CO 2 sequestration reservoir. We contrast the behavior of shale faults with another set of experiments conducted in carbonates. Significant fluid leakage occurs along the initially low-permeability shale faults when rupture is activated. Most of the leakage pathway closes when fluid injection ceases and fluid pressure drops. Dilatant slip on the fault plane alone does not explain the observed leakage behavior, which is also caused by fault opening favored by the softness of the shale, and by the structure of the fault zone that prevents fluids from diffusing into the adjacent damage zone. Experiments show a large amount of aseismic deformation. Small-magnitude seismicity (M w < -2.5) is observed outside the pressurized leakage patch. Stress transferred from this aseismic deformation patch can build up to stress-criticality and favor seismicity. Thus, in terms of fault activation in caprocks, aseismic fault slip leading to increased permeability and a loss of seal integrity is of great concern.

58 GEOSCIENCES↗

DOE OSTI2021

Experimental and modeling studies of PR and ND oxalate solubility to high ionic strengths: Insight into actinide(III) oxalates

Actinide oxalates are chemical compounds important to nuclear industry, ranging from actinide separation in waste reprocessing, to production of specialty actinides, and to disposal of high level nuclear waste (HLW) and spent nuclear fuel (SNF). In this study, the solubility constants for Pr 2 (C 2 O 4 ) 3 •10H 2 O and Nd 2 (C 2 O 4 ) 3 •10H 2 O by performing solubility experiments in HNO 3 and mixtures of HNO 3 and H 2 C 2 O 4 at 23.0 ± 0.2 °C have been determined. The targeted starting materials, Pr 2 (C 2 O 4 ) 3 •10H 2 O and Nd 2 (C 2 O 4 ) 3 •10H 2 O, were successfully synthesized at room temperature using PrCl 3 , NdCl 3 and oxalic acid as the source metrials. Then, we utilized the targeted solubility-controlling phases to conduct solubility measurements. There was no phase change over the entire periods of experiments, demonstrating that Pr 2 (C 2 O 4 ) 3 •10H 2 O and Nd 2 (C 2 O 4 ) 3 •10H 2 O were the solubility-controlling phases in our respective experiments. Based on our experimental data, we have developed a thermodynamic model for Pr 2 (C 2 O 4 ) 3 •10H 2 O and Nd 2 (C 2 O 4 ) 3 •10H 2 O in the mixtures of HNO 3 and H 2 C 2 O 4 to high ionic strengths. The model for Pr 2 (C 2 O 4 ) 3 •10H 2 O reproduces well the reported experimental data for Pu 2 (C 2 O 4 ) 3 •10H 2 O, which are not utilized for the model development, demonstrating that Pr(III) is an excellent analog for Pu(III). Similarly, the model for Nd 2 (C 2 O 4 ) 3 •10H 2 O reproduces the solubility of Am 2 (C 2 O 4 ) 3 •10H 2 O and Cm 2 (C 2 O 4 ) 3 •10H 2 O. The Pitzer model was used for the calculation of activity coefficients. Based on the published, well established model for dissociation constants for oxalic acid and stability constants for actinide-oxalate complexes [i.e., AmC 2 O 4 + , and Am(C 2 O 4 ) 2 - ] to high ionic strengths, we have obtained the solubility constants (log 10 K 0 ) for the following reactions at 25 °C, Pr 2 (C 2 O 4 ) 3 •10H 2 O ⇌ 2Pr 3+ + 3C 2 O 4 2- + 10H 2 O(l). Nd 2 (C 2 O 4 ) 3 •10H 2 O ⇌ 2Nd 3+ + 3C 2 O 4 2- + 10H 2 O(l). to be -30.82 ± 0.30 (2σ), and - 31.14 ± 0.35 (2σ), respectively. These values for can be directly applied to Pu 2 (C 2 O 4 ) 3 •10H 2 O, Am 2 (C 2 O 4 ) 3 •10H 2 O and Cm 2 (C 2 O 4 ) 3 •10H 2 O. The model established for actinide oxalates by this study provides the needed knowledge with regard to solubilities of actinide/REE oxalates at various ionic strengths, and is expected to find applications in many fields, including the geological disposal of nuclear waste and the mobility of REE under the surface conditions, as Pr 2 (C 2 O 4 ) 3 •10H 2 O and Nd 2 (C 2 O 4 ) 3 •10H 2 O can be regarded as the pure Pr and Nd end-members of deveroite, a recently discovered natural REE oxalate with the following stoichiometry, (Ce 1.01 Nd 0.33 La 0.32 Pr 0.11 Y 0.11 Sm 0.01 Pb 0.04 U 0.03 Th 0.01 Ca 0.04 ) 2.01 (C 2 O 4 ) 2.99 •9.99H 2 O. Regarding its importance in the geological disposal of nuclear waste, Am 2 (C 2 O 4 ) 3 •10H 2 O/Pu 2 (C 2 O 4 ) 3 •10H 2 O/Cm 2 (C 2 O 4 ) 3 •10H 2 O can be the source-term phase for actinides, as demonstrated by the instance in the disposal in clay/shale formations. This is exemplified by the stability of Am 2 (C 2 O 4 ) 3 •10H 2 O in comparison with Am(OH) 3 (am), Am(OH) 3 (s) and AmCO 3 (OH)(s) under the relevant geological repository conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗