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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Understanding Dynamics and Thermodynamics of ENSO and Its Complexity Simulated by E3SM and Other Climate Models

Despite the seeming success of most state-of-the-art climate models in simulating the El Niño-Southern Oscillation (ENSO), there is strong evidence that models achieve realistic levels of ENSO activity do so often for wrong reasons. This is owing to an often occurred near cancelation of large errors in terms of contributions to ENSO growth rate from coupled dynamic and thermodynamic feedback processes. Climate models remain deficient in simulating the observed ENSO’s spatial and temporal complexity that involves interplays of coupled dynamic and thermodynamic feedbacks, interactions across multiple scales, nonlinear processes in the tropical atmosphere and ocean system, biases in mean sate and physical processes, and influences external to equatorial Pacific coupled ENSO dynamics. Our proposed research aims at advancing predictive and process-level understandings of ENSO simulated in E3SM and other climate models under current and future climate conditions with two main objectives: (i) better understanding the aforementioned broad range interactive processes and sources that control fundamental properties of ENSO in E3SM and CIMP6 outputs as well as in observational (reanalysis) data sets, using a hierarchical of coupled dynamical frameworks consisting of theoretical analysis, intermediate complexity modeling, and coupled dynamic diagnostics; (ii) to use this understanding to explore pathways towards improving E3SM’s capability of simulating ENSO and its complexity. More specifically, we will focus on four main thrusts of research: (1) ENSO’s dynamic and thermodynamic feedbacks; (2) the across-scale interactions of ENSO with annual cycle and MJO/WWB/TIW (Madden Julian Oscillation/Westerly Wind Burst/Tropical Instability Wave) activity; (3) key nonlinear processes of ENSO involving atmospheric convective thresholds, nonlinear ocean dynamic heating, and thermocline outcropping; and (4) the impacts of climate mean-state biases/changes and perturbed physical processes on simulated ENSO and its complexity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

EVALUATION OF OPERATION TEMPERATURES UNDER NATURAL CONVECTION HELIUM FLOW IN A CONFINED CAVITY

The Spallation Neutron Source (SNS) is a high-power accelerator-based pulsed neutron source led by Oak Ridge National Laboratory (ORNL) to achieve high fluxes of neutrons for scientific experiments. Active and passive cooling of the systems and parts forming the SNS have been considered to warrant the safe operation of the facility. The diverse cooling systems make use of conjugated heat transfer mechanisms to provide a stable operation temperature for all components in the machine. Thermal power deposited into stainless-steel piping lines due to particle radiation may reach values of up to 1.2 W/cc in the regions located closer to the center of the lower IRP. These energy deposition levels, in not actively cooled components, such as the transfer-line-outer-vacuum-layer may increase the temperature of the component beyond design requirement limitations. The evaluation of the operation temperatures for the former components relies in the assumption that a low-pressure helium atmosphere provides enough heat removal capacity based on natural convection phenomena. In this work, the evaluation of steady state temperatures in components such as the CMS transfer lines has been evaluated using computational fluid dynamics (CFD), analytical correlations and experimental measurements. The companion experiments were conducted in a closed helium system at pressures varying from 1.1 to 1.5 bar. A copper rod was affixed horizontally between viewing windows and heated at constant power, and measurements were made of both the rod temperature and ambient temperature via a system fiberoptic distributed temperature sensors and RTDs. It was found that the measured heat transfer coefficients agree well with the predictions of Churchill and Chu correlations across the range of cases considered. Additionally, the ambient helium volume above the rod was imaged via background oriented schlieren (BOS), and these data was used to determine the line-averaged density gradients in this region. These gradients were compared to simulation data to validate the predictions of natural convection simulations.

Dominguez-Ontiveros, Elvis [ORNL] (ORCID:000000018↗
DOE OSTI2021

Electron–Nucleus Hyperfine Coupling Calculated from Restricted Active Space Wavefunctions and an Exact Two-Component Hamiltonian

Exact two-component (X2C) relativistic nuclear hyperfine magnetic field operators were incorporated in X2C ab-initio wavefunction calculations at the multi-reference restricted active space (RAS) level for calculations of nuclear hyperfine magnetic properties. Spin-orbit coupling was treated via RAS state interaction (SO-RASSI). The method was tested by calculations of electron – nucleus hyperfine coupling constants. The approach, implemented in the OpenMolcas program, overcomes a major limitation of a previous SO-RASSI implementation for hyperfine coupling that relied on non-relativistic hyperfine operators [J. Chem. Theor. Comput. 2015, 11, 538–549] and therefore had only limited applicability. Furthermore, results from calculations on systems with light and heavy main group elements, transition metals, lanthanides, and one actinide complex, demonstrate reasonably good agreement with experimental data, where available, as long as the active space can generate sufficient spin polarization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Quantitative Proteome Profiling Reveals Cellobiose-Dependent Protein Processing and Export Pathways for the Lignocellulolytic Response in Neurospora crassa

Filamentous fungi are intensively used for producing industrial enzymes, including lignocellulases. Employing insoluble cellulose to induce the production of lignocellulases causes some drawbacks, e.g., a complex fermentation operation, which can be overcome by using soluble inducers such as cellobiose. Here, a triple β-glucosidase mutant of Neurospora crassa, which prevents rapid turnover of cellobiose and thus allows the disaccharide to induce lignocellulases, was applied to profile the proteome responses to cellobiose and cellulose (Avicel). Our results revealed a shared proteomic response to cellobiose and Avicel, whose elements included lignocellulases and cellulolytic product transporters. While the cellulolytic proteins showed a correlated increase in protein and mRNA levels, only a moderate correlation was observed on a proteomic scale between protein and mRNA levels (R 2 = 0.31). Ribosome biogenesis and rRNA processing were significantly overrepresented in the protein set with increased protein but unchanged mRNA abundances in response to Avicel. Ribosome biogenesis, as well as protein processing and protein export, was also enriched in the protein set that showed increased abundance in response to cellobiose. NCU05895, a homolog of yeast CWH43, is potentially involved in transferring a glycosylphosphatidylinositol (GPI) anchor to nascent proteins. This protein showed increased abundance but no significant change in mRNA levels. Disruption of CWH43 resulted in a significant decrease in cellulase activities and secreted protein levels in cultures grown on Avicel, suggesting a positive regulatory role for CWH43 in cellulase production. The findings should have an impact on a systems engineering approach for strain improvement for the production of lignocellulases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Star-spots and magnetism: testing the activity paradigm in the Pleiades and M67

We measure star-spot filling fractions for 240 stars in the Pleiades and M67 open star clusters using APOGEE high-resolution H-band spectra. For this work, we developed a modified spectroscopic pipeline which solves for star-spot filling fraction and star-spot temperature contrast. We exclude binary stars, finding that the large majority of binaries in these clusters (80 per cent) can be identified from Gaia DR3 and APOGEE criteria – important for field star applications. Our data agree well with independent activity proxies, indicating that this technique recovers real star-spot signals. In the Pleiades, filling fractions saturate at a mean level of 0.248 ± 0.005 for active stars with a decline at slower rotation; we present fitting functions as a function of Rossby number. In M67, we recover low mean filling fractions of 0.030 ± 0.008 and 0.003 ± 0.002 for main sequence GK stars and evolved red giants, respectively, confirming that the technique does not produce spurious spot signals in inactive stars. Star-spots also modify the derived spectroscopic effective temperatures and convective overturn time-scales. Effective temperatures for active stars are offset from inactive ones by −109 ± 11 K, in agreement with the Pecaut & Mamajek empirical scale. Star-spot filling fractions at the level measured in active stars changes their inferred overturn time-scale, which biases the derived threshold for saturation. Finally, we identify a population of stars statistically discrepant from mean activity–Rossby relations and present evidence that these are genuine departures from a Rossby scaling. Our technique is applicable to the full APOGEE catalogue, with broad applications to stellar, galactic, and exoplanetary astrophysics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Elucidating facet dependent electronic and electrochemical properties of Cu 2 O nanocrystals using AFM/SCEM and DFT

Cuprous oxide (Cu 2 O) has extensively been studied owing to its excellent optical, magnetic, and catalytic properties. Many of these properties are facet-dependent and have not been well elucidated. This work synthesized cubic, cuboctahedral, octahedral, and rhombic dodecahedral shaped Cu 2 O nanocrystals of ~300 nm in size to evaluate the facet-dependent electrochemical activities. Here, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were firstly used to reveal the average electrochemical activities at the ensemble level. Atomic force microscopy-scanning electrochemical microscopy (AFM-SECM) was further used to assess the electrochemical activities of different Cu 2 O nanocrystals at the facet level. Hexaammineruthenium (III) chloride ({Ru(NH 3 ) 6 }Cl 3 ) was employed as the probe molecules that reacted with four different Cu 2 O nanocrystals under —400mV and yielded ~300 pA current between the probing tip and the nanocrystal surface. The tip-current mapping results indicate that rhombic dodecahedral Cu 2 O exhibits higher electrocatalytic activity than other shaped Cu 2 O, due to the presence of dominant exposed facet of {110} as indicated by the relatively high tip current. Density-functional theory (DFT) calculations confirmed the facet dependence of local surface energy and electronic structure of Cu 2 O nanocrystals. Besides electrochemical activity, the surface work function and adsorptive properties were both observed to vary with the shape and dominant exposed facets of Cu 2 O. This study presented a unique experimental and computational chemistry approach to analyze surface electrochemical properties of Cu 2 O crystals at a crystalline facet level.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Performance Assessment of the Active Trenches in 200 East and 200 West Low-Level Burial Grounds at the Hanford Site

The purpose of this document is to provide the assessment of the long-term human health and environmental risk associated with the continued disposal of radioactive wastes in the active trenches of the 200 East and 200 West Area Low-Level Burial Grounds (LLBGs) at the Hanford Site (Figure ES-1), as required by DOE O 435.1, Radioactive Waste Management1. Since July 1, 2004, the only active trenches in the 200 West Area LLBGs are the lined Trenches 31 and 34 used for the disposal of containerized low-level waste and mixed low-level waste (Figure ES-2). The only active trench in the 200 East Area LLBGs is the unlined Trench 94 that was used for the disposal of naval reactor compartments (Figure ES-3). Trenches 31 and 34 are intended to be used until they reach their disposal capacity while Trench 94 will be used and expanded as necessary to meet the needs of the U.S. Navy.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Data and scripts associated with a manuscript investigating dissolved organic matter and microbial community linkages across seven globally distributed rivers

This data package is associated with the publication “Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers” submitted to Science of the Total Environment. This data package includes the data necessary to replicate the analyses presented within the manuscript to investigate dissolved organic matter (DOM) development across broad spatial distances and within divergent biomes. Specifically, we included the Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data, geochemistry data, annotated metagenomic data, and results from ecological null modeling analyses in this data package. Additionally, we included the scripts necessary to generate the figures from the manuscript. Complete metagenomic data associated with this data package can be found at the National Center for Biotechnology (NCBI) under Bioproject PRJNA946291. This dataset consists of (1) four folders; (2) a file-level metadata (flmd) file; (3) a data dictionary (dd) file; (4) a factor sheet describing samples; and (5) a readme. The FTICR Data folder contains (1) the processed Fourier transform ion cyclotron mass spectrometry (FTICR-MS) data; (2) a transformation-weighted characteristics dendrogram generated from the FTICR-MS data; and (3) the script used to generate all FTICR-MS related figures. The Geochemical Data folder contains (1) the single geochemistry data file and (2) the R script responsible for generating associated figures. The Metagenomic Data folder contains (1) annotation information across different levels; (2) carbohydrate active enzyme (CAZyme) information from the dbCAN database (Yin et al., 2012); (3) phylogenetic tree data (FASTAs, alignments, and tree file); and (4) the scripts necessary to analyze all of these data and generate figures. The Null Modeling Data folder contains (1) data generated during null modeling for each river and all rivers combined and (2) the R scripts necessary to process the data. All files are .csv, .pdf, .tsv, .tre, .faa, .afa, .tree, or .R.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Corrosion Testing of Refractory inContact with Molten Glasses Designed for Waste Vitrification - VSL Touchpoint Matrix Glasses

It is known that the predictive life of the refractory ceramic liner of nuclear waste glass melters is conservative, as demonstrated by performance of these materials such as in the Defense Waste Processing Facility (DWPF). The motivation for this task is to maximize the useful life of the melters that will be operated at the Waste Treatment and Immobilization Plant (WTP), which will in turn minimize procurement and disposal costs and melter outage times, as well as to identify maximum loadings in the waste glass of those species that corrode melter components. This task was initiated jointly with Pacific Northwest National Laboratory (PNNL) with the objective to develop a methodology and model to enable more accurate prediction of refractory service life under prototypic conditions from laboratory-scale material corrosion tests. Refractory corrosion is generally reported as physical material loss, measured in units of distance (e.g., inch) or as physical material loss rate, measured in units of distance per time (e.g., inch/day). In post-operational melters, the refractory corrosion is measured directly, sometimes reported as corrosion depth. Crucible tests are used in the laboratory to accelerate the refractory corrosion to facilitate a meaningful measurement in a commensurate amount of time. Crucible tests are particularly useful in understanding refractory corrosion across a large glass composition space, where operational testing would be prohibitive. Some of the critical parameters that are known to influence refractory corrosion by molten glass in a crucible test are temperature, system redox, molten salt phases, glass chemistry, and test duration. The majority of data collected for Monofrax® K-3 (hereafter referred to as K-3) corrosion is from crucible tests, but a small amount comes directly from scaled and production melters. Crucible test data has been collected under varying conditions, whereas data collected from operational melters is relatively fewer and represents conditions specific to the melter campaign. The result is that the published data can be grouped and analyzed in multiple ways, not all of which are readily comparable. The Standard Test Method for Isothermal Corrosion Resistance of Refractories to Molten Glass (ASTM C621) outlines the general guidelines used across industry. That method describes a sealed, static test in which the surface area of the refractory coupon and the volume of glass are fixed. A significant portion of the crucible data pertaining to nuclear waste glasses has been collected in a modified configuration; the most notable differences being the surface area of the refractory coupon to volume of the glass and use of a method for bubbling the melt. To our knowledge, the influence of those parameters on the refractory corrosion has not been quantified. In this work, it was determined that static tests and bubbled tests would be performed. Savannah River National Laboratory (SRNL) was tasked with setting up and performing static testing while PNNL was tasked with setting up and performing bubbled testing. Initial activities were performed to establish laboratory methods that reproduce data comparable to existing data sets of K-3 refractory corrosion by low activity waste (LAW) and high-level waste (HLW) glass compositions. Later activities were focused on refining the test parameters to establish a standard test practice to be used between Laboratories and collecting additional data to be used in the enhanced waste glass model development. This document serves primarily to convey the refractory loss measurement results from corrosion testing of K-3 refractory with waste glass compositions developed for use in the WTP melters. The data will be used in the enhanced property/composition models being developed for waste glass vitrification and melter operations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale

The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Incorporating civilian radioxenon background estimates in anomaly detection

A nuclear explosion screening exercise in 2023 (Maurer et al., 2023) found challenges with discerning anomalous radioxenon activity concentrations relative to elevated background concentrations. Research has continued into methods to detect anomalous radioxenon concentrations by comparing samples to estimates of atmospheric radioxenon background concentrations caused by releases at nuclear reactors or medical isotope production facilities. A new approach estimates the sample concentrations using time-varying radioxenon release rates obtained using optimization techniques that constrain the facility release rates to plausible amounts based on historical data or facility knowledge. The purpose of the optimization is to determine whether any combination of plausible release rates from emitting facilities can explain a series of radioxenon measurements at one or more sampling stations. A case study uses radioxenon data collected at three locations in western Europe for a month in 2021 and considers releases from 77 locations. Fewer samples are identified as being anomalous using a simplistic flagging rule than from an application of the current International Monitoring System (IMS) activity concentration-level rule.

Environmental sciences↗
DOE OSTI2022

Mass transport in a highly immiscible alloy on extended shear deformation

Forced mixing to a single phase or supersaturated solid solution (SSS) and its prerequisite microstructure evolution in immiscible systems has been a focus of research for both fundamental science and a variety of applications. Controlling the formation of SSS by shear deformation assisted processing could enable a material design beyond conventional equilibrium microstructure in immiscible systems. Here, a highly immiscible (mixing enthalpy of ~ 20 kJ·mol -1 ) Cu-50 at. % Cr binary alloy was employed to investigate the microstructure evolution and localized tendencies of SSS during severe shear deformation. The present results demonstrate distinctive microstructure refinement process in each phase and how they lead to localized SSS as a function of shear strain. Preferential dynamic recrystallization occurs in the softer Cu phase due to strain localization, leading to substantial grain refinement. The refinement of Cr phase in the top-most layer, however, is enabled by the progressive evolution of grain lamination, splitting, and fragmentation as a function of shear strain. The eventual SSS is found to be strongly dependent on the local environments that affect the dislocation activity, including the level of microstructure refinement, the interfacial orientation relationship, hardness difference, and supposed stability of oxidation. Ab initio simulations comfirm that it is more favorable to oxidize Cr than Cu at incoherent Cu/Cr interfaces which then limits the mass transport on an incoherent boundary. Our results shed light on the underpinning mechanism for non-equilibrium mass transport in immiscible systems upon severe deformation that can be applicable to a variety of processing techniques aimed at producing immiscible alloys with superior mechanical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Real-time monitoring of the orthohydrogen fraction in a liquid hydrogen moderator

Here, we present the first direct measurements of the orthohydrogen fraction in an operating liquid hydrogen moderator loop at a high-powered neutron source. We have developed a Raman immersion probe capable of characterizing the orthohydrogen and parahydrogen makeup of a liquid hydrogen loop approximately every ten seconds, which can see orthohydrogen fractions lower than 0.20 without difficulty. At the Spallation Neutron Source, where the time-averaged power deposition in the studied moderator system is around 0.02 W/cm 3 , the orthohydrogen fraction increases with beam power and equilibrates at levels of 0.40 and responds to beam trips in a dynamic fashion. Additionally, we find that without deliberate catalyst systems in place, the relaxation due to the piping in the system has insignificant effect in catalyzing the relaxation of freshly condensed hydrogen toward thermodynamic equilibrium, and that the radiation levels associated with activation in a non-operating spallation neutron source target-moderator-reflector assembly likewise has insignificant effect on the liquid hydrogen kinetics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Late Holocene history of Tokotan Lake (Kuril Archipelago, Russian Far East): The use of lacustrine records for paleoclimatic reconstructions from geologically dynamic settings

A high-resolution, multiproxy analysis of a core from Tokotan Lake, Urup Island, illustrates the complex paleoenvironmental signals that can be preserved in sedimentary deposits from geologically active areas, such as the Kuril Archipelago. Diatom and geochemical analyses of the Tokotan core suggest a shallowing and lessening of the lake area over the last ~3450 cal BP. Without other proxies, the record could be interpreted as showing a general decrease in precipitation over the Late Holocene. However, palynological data indicate no change in vegetation, thereby implying no significant climatic variation. Neither of these paleoclimatic interpretations agrees with Late Holocene reconstructions from the Kuril Archipelago or the Russian mainland. Paleomagnetic data imply variable sediment sources during the lake's history, indicating alterations within the Tokotan catchment (e.g., shifts in gradients or sediment loads in the inflowing streams). Such changes would be particularly important in the Shabalina River, which today has formed a partial dam across the lake's outlet. Here, the results of the Tokotan study indicate that other factors (e.g., volcanism, seismic activity, sea-level changes) rather than climate were more probable determinants of the Late Holocene lake record. Given the geologic dynamism of the region, it is perhaps not surprising that paleo-records from the Kuril Islands display an inconsistency in the numbers and/or duration of proposed Holocene climatic oscillations, underscoring the importance of multiproxy investigations in areas that are or have been geologically dynamic.

58 GEOSCIENCES↗
DOE OSTI2022

The contribution of the neuroendocrine system to adaption after repeated daily ozone exposure in rats

Ozone-induced lung injury/inflammation dissipates despite continued exposure for 3 or more days; however, the mechanisms of adaptation/habituation remain unclear. Since ozone effects are mediated through adrenal-derived stress hormones, which also regulate longevity of centrally-mediated stress response, we hypothesized that ozone-adaptation is linked to diminution of neuroendocrine stress-axes activation and glucocorticoid levels. Male Wistar-Kyoto-rats (12-week-old) were injected with vehicle or a therapeutically-relevant dexamethasone dose (0.01-mg/kg/day; intraperitoneal) for 1-month to determine if suppression of glucocorticoid signaling was linked to adaptation. Vehicle- and dexamethasone-treated rats were exposed to air or 0.8-ppm ozone, 4 h/day × 2 or 4 days to assess the impacts of acute exposure and adaptation, respectively. Dexamethasone reduced thymus and spleen weights, circulating lymphocytes, corticosterone and increased insulin. Ozone increased lavage-fluid protein and neutrophils and decreased circulating lymphocytes at day-2 but not day-4. Ozone-induced hyperglycemia, glucose intolerance and inhibition of beta-cell insulin release occurred at day-1 but not day-3. Ozone depleted circulating prolactin, thyroid-stimulating hormone, and luteinizing-hormone at day-2 but not day-4, suggesting central mediation of adaptation. Adrenal epinephrine biosynthesis gene, Pnmt, was up-regulated after ozone exposure at both timepoints. However, genes involved in glucocorticoid biosynthesis were up-regulated after day-2 but not day-4, suggesting that acute 1- or 2-day ozone-mediated glucocorticoid increase elicits feedback inhibition to dampen hypothalamic stimulation of ACTH release in response to repeated subsequent ozone exposures. Although dexamethasone pretreatment affected circulating insulin, lymphocytes and adrenal genes, it had modest effect on ozone adaptation. In conclusion, ozone adaptation likely involves lack of hypothalamic response due to reduced availability of circulating glucocorticoids.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization

Enhancing the thermostability of enzymes without impacting their catalytic function represents an important yet challenging goal in protein engineering and biocatalysis. We recently introduced a novel method for enzyme thermostabilization that relies on the computationally guided installation of genetically encoded thioether “staples” into a protein via cysteine alkylation with the noncanonical amino acid O-2-bromoethyl tyrosine (O2beY). Here, we demonstrate the functionality of an expanded set of electrophilic amino acids featuring chloroacetamido, acrylamido, and vinylsulfonamido side-chain groups for protein stapling using this strategy. Using a myoglobin-based cyclopropanase as a model enzyme, our studies show that covalent stapling with pchloroacetamido-phenylalanine (pCaaF) provides higher stapling efficiency and enhanced stability (thermodynamic and kinetic) compared to the other stapled variants and the parent protein. Interestingly, molecular simulations of conformational flexibility of the cross-links show that the pCaaF staple allows fewer energetically feasible conformers than the other staples, and this property may be a broader indicator of stability enhancement. Using this strategy, pCaaF-stapled variants with significantly enhanced stability against thermal denaturation (ΔT m ' = +27 °C) and temperature-induced heme loss (ΔT 50 = +30 °C) were obtained while maintaining high levels of catalytic activity and stereoselectivity. Crystallographic analyses of singly and doubly stapled variants provide key insights into the structural basis for stabilization, which includes both direct interactions of the staples with protein residues and indirect interactions through adjacent residues involved in heme binding. This work expands the toolbox of protein stapling strategies available for protein stabilization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Quantitative DNA Stable Isotope Probing Identifies Active Microorganisms Assimilating Volatile Fatty Acids in Full-Scale Enhanced Biological Phosphorus Removal Processes

Enhanced biological phosphorus removal (EBPR) systems often rely on exogenous carbon sources, such as volatile fatty acids (VFAs), to achieve higher P removal. Here, we employed DNA quantitative stable isotope probing (qSIP) using two VFAs, acetate and propionate, in cyclic anaerobic/aerobic incubations to assess their effects on P cycling and microbial activity with biomass from two full-scale EBPR water resource-recovery facilities that utilize VFA addition. We found that anaerobic VFA uptake preferences differed within known groups of PAOs, such as Candidatus Accumulibacter and Tetrasphaera-affiliated members (e.g., Ca. Phosphoribacter), between the two biomasses. The combination of qSIP with metagenomics identified isotopically labeled phages that were linked to active PAOs, highlighting their potential roles in modulating EBPR community composition and activity. The highest levels of anaerobic labeling from acetate were in genomes belonging to Saccharimonadales and Rickettsiales, which are generally host-associated with bacteria and eukaryotes, respectively. Furthermore, this finding highlights the possibility of cross-feeding between PAO hosts and their parasites or predators, as well as the role of so-far uncharacterized organisms participating in carbon cycling under EBPR conditions. Collectively, these results expand our understanding of the ecological interactions involved in communities anaerobically uptaking VFAs and cycling P that are central to EBPR.

Polyphosphate accumulating organisms↗
DOE OSTI2022

Preparation and Characterization of Model Homotopic Catalysts: Rh Adatoms, Nanoparticles, and Mixed Oxide Surfaces on Fe 3 O 4 (001)

The atomic-level characterization of active sites is essential to understanding the mechanisms behind catalytic reactions. In this study, using scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS), we follow the morphological changes of a model Rh catalysts supported on Fe 3 O 4 (001) as a function of temperature and Rh coverage. Here, we identify the preparation conditions leading to model catalysts containing homotopic or nearly homotopic Rh species bound as adatoms, small clusters, substitutional within the Fe 3 O 4 (001), and nanoparticles. Adsorbates such as CO and CO 2 are further subsequently used to characterize the properties of different Rh sites. Using temperature programmed desorption (TPD), we demonstrate that adatoms, clusters, and nanoparticles exhibit high-temperature CO desorption (250-600 K). Strong binding on such sites further allows for CO oxidation to CO 2 via the Mars-van-Krevelen mechanism. In contrast, CO 2 was found to interact weakly with all Rh sites. Differences in desorption temperature enable the use of CO and CO 2 as titration methods for nanoparticles and Fe 3 O 4 (001), respectively. A small quantity of CO 2 was found to be reduced to CO on Rh adatoms and clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗