Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “SITE CHARACTERIZATION”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Characterization of Soil Thermal and Electrical Properties along Multiple Hillslope Transects at Teller Road Site, Seward Peninsula, Alaska, 2017

This dataset has been acquired along five-119 m long transects located on the bottom part of the watershed hillslope at the NGEE Arctic Teller Road site at mile marker 27 (TL_MM27) on the Seward Peninsula, Alaska in July and September 2017. The Distributed Temperature Profiling (DTP) system dataset consist in vertically-resolved profile of soil temperature covering the top 0.8 m of soil with 8 cm interval. In addition to DPT data, electrical resistivity tomography (ERT) data, soil moisture, depth to rock or thaw layer thickness (no differentiation) and ground elevations data have been acquired along each of the transects. A UAV-based geotiff mosaic of the investigated site is also provided. The four data types provided with this dataset of 37 files (*.csv, *.tif, *.DATA): (1) soil temperature profiles, (2) ERT data, (3) the physical measurements of the thaw layer, and (4) an orthomosaic GeoTIFF of the transect study area.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Elucidation of Ce/Zr ratio effects on the physical properties and catalytic performance of CuO x /Ce y Zr 1− y O 2 catalysts

Although cerium oxide (CeO 2 ) is widely used as a catalyst support, its limited defect sites and surface oxygen vacancy/mobility should be improved. The incorporation of zirconium (Zr) in the cerium (Ce) lattice is shown to increase the number of oxygen vacancies and improve catalytic activity. Using a fixed surface density (SD) of copper (∼2.3 Cu atoms per nm 2 ) as a surface species, the role of the support (Ce y Zr 1−y O 2 (y = 1.0, 0.9, 0.6, 0.5, and 0.0)) and defect site effects in the CO oxidation reaction was investigated. Spectroscopic (e.g., Raman, XRD, XPS) and microscopic (e.g., SEM-EDX, HR-TEM) characterization techniques were applied to evaluate the defect sites, crystallite size, lattice parameters, chemical composition, oxidation states of elements and microstructure of the catalysts. Here, the CO oxidation reaction with varied CO : O 2 ratios (1 : 5, 1 : 1, and 1 : 0.5 (stoichiometric)) was used as a model reaction to describe the relationship between the structure and the catalytic performance of each catalyst. Based on the characterization results of Ce y Zr 1−y O 2 materials, the addition of Zr causes physical and chemical changes to the overall material. The inclusion of Zr into the structure of CeO 2 decreased the overall lattice parameter of the catalyst and increased the number of defect sites. The prepared catalysts were able to reach complete CO conversion (∼100%) at low temperature conditions (<200 °C), each showing varied reaction activity. The difference in CO oxidation activity was then analyzed and related to the structure, wherein Cu loading, surface oxygen vacancies, reduction–oxidation ability, CuO x –support interaction and oxygen mobility in the catalyst were the crucial descriptors.

36 MATERIALS SCIENCE↗
DOE OSTI2020

IDENTIFICATION OF ADSORBA TION OF ADSORBATE FT-IR BANDS USING IN-SI -IR BANDS USING IN-SITU TECHNIQUES: Pd SPECIATION AND ADSORPTION CHEMISTRY OF Pd-ZEOLITES FOR PASSIVE NOx ADSORPTION

To meet increasingly stringent automotive emissions standards, further improvements in catalytic converter design are necessary. Current automotive catalyst systems are effective at eliminating emission of nitrogen oxides (NOx) once the catalyst reaches operational temperature (~200 °C). NOx emitted at lower catalyst temperatures now comprises most of the NOx released during a typical test cycle. Referred to as “the cold start problem” this issue has come to the forefront of automotive catalyst development, as mitigating these emissions is necessary to further reduce automotive emissions. Passive NOx adsorbers present an appealing solution to the cold start problem, these being a class of materials that chemisorb exhaust components such as NOx, carbon monoxide (CO) and hydrocarbons at near-ambient temperatures, and then desorb these compounds once the downstream catalyst has reached operational temperature. An effective passive NOx adsorber must have several properties: high NOx adsorption at near-ambient temperatures, near-complete NOx desorption at temperatures within the operational range, high thermal stability, and resistance to automotive exhaust components at high temperatures. The potential environmental impact of such a system is substantial, as NOx emissions currently result in the formation of millions of tons of smog and acid rain each year. Pd-exchanged zeolites have shown promise for deployment as Passive NOx adsorbers, though much remains to be understood about their adsorption chemistry and deactivation. In-situ Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) provides a convenient probe of adsorbed species, most automotive exhaust components possessing IR-active chemical bonds. By examining the evolution of IR bands under various pretreatments and adsorbates, the overall Pd-speciation and adsorptive zeolite sites of each material can be characterized, and the identities of IR bands can be deduced. In this work, microreactor-MS analysis of the adsorption and desorption behavior of these materials was also examined, these results being coupled with in-situ DRIFTS temperature programmed desorption (TPD) to correlate desorption events with specific adsorbed species. A pair of zeolite frameworks of similar Si/Al ratio but differing pore size were examined, Beta zeolite (BEA) and Chabazite (CHA) representing a medium- and small-pore framework, respectively. The effect of Pd-loading on BEA was examined, as well as the various deactivation pathways and active sites of each material.

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

Advanced Laboratory and Field Arrays: Evaluating Sampling Techniques for MHK Biological Monitoring (Task 6)

The overall goal of the task was to identify cost effective biological sampling techniques for MHK environmental monitoring. Protected, demersal, and pelagic fish and selected nektonic invertebrates were surveyed using capture and remote sensing techniques at the PacWave sites. The performance of capture and remote sensing monitoring techniques were evaluated and generic nekton monitoring indices were developed for MHK technologies and sites. In parallel to data collections at the PacWave site, the ability of regression models to characterize, detect, and predict change in acoustic data was evaluated using acoustic data collected in Admiralty Inlet, WA, during a biological monitoring study of the proposed SnoPud tidal turbine project site. Expected outcomes of these efforts included an evaluation of instrumentation and techniques used to monitor biological variability; identification of data streams that can be used to detect and quantify change; and sampling requirements to ensure detection of change in monitored variables.

13 HYDRO ENERGY↗
DOE OSTI2022

Using aircraft measurements to characterize subgrid-scale variability of aerosol properties near the Atmospheric Radiation Measurement Southern Great Plains site

Abstract. Complex distributions of aerosol properties evolve in space and time as a function of emissions, new particle formation, coagulation, condensational growth, chemical transformation, phase changes, turbulent mixing and transport, removal processes, and ambient meteorological conditions. The ability of chemical transport models to represent the multi-scale processes affecting the life cycle of aerosols depends on their spatial resolution since aerosol properties are assumed to be constant within a grid cell. Subgrid-scale-dependent processes that affect aerosol populations could have a significant impact on the formation of particles, their growth to cloud condensation nuclei (CCN) sizes, aerosol–cloud interactions, dry deposition and rainout and hence their burdens, lifetimes, and radiative forcing. To address this issue, we characterize subgrid-scale variability in terms of measured aerosol number, size, composition, hygroscopicity, and CCN concentrations made by repeated aircraft flight paths over the Atmospheric Radiation Measurement (ARM) program's Southern Great Plains (SGP) site during the Holistic Interactions of Shallow Clouds, Aerosols and Land Ecosystem (HI-SCALE) campaign. Subgrid variability is quantified in terms of both normalized frequency distributions and percentage difference percentiles using grid spacings of 3, 9, 27, and 81 km that represent those typically used by cloud-system-resolving models as well as the current and next-generation climate models. Even though the SGP site is a rural location, surprisingly large horizontal gradients in aerosol properties were frequently observed. For example, 90 % of the 3, 9, and 27 km cell mean organic matter concentrations differed from the 81 km cell around the SGP site by as much as ∼ 46 %, large spatial variability in aerosol number concentrations and size distributions were found during new particle formation events, and consequently 90 % of the 3, 9, and 27 km cell mean CCN number concentrations differed from the 81 km cell mean by as much as ∼ 38 %. The spatial variability varied seasonally for some aerosol properties, with some having larger spatial variability during the spring and others having larger variability during the late summer. While measurements at a single surface site cannot reflect the surrounding variability of aerosol properties at a given time, aircraft measurements that are averaged within an 81 km cell were found to be similar to many, but not all, aerosol properties measured at the ground SGP site. This analysis suggests that it is reasonable to directly compare most ground SGP site aerosol measurements with coarse global climate model predictions. In addition, the variability quantified by the aircraft can be used as an uncertainty range when comparing the surface point measurements with model predictions that use coarse grid spacings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Accurate and Rapid Forecasts for Geologic Carbon Storage via Learning-Based Inversion-Free Prediction

Carbon capture and storage (CCS) is one approach being studied by the U.S. Department of Energy to help mitigate global warming. The process involves capturing CO 2 emissions from industrial sources and permanently storing them in deep geologic formations (storage reservoirs). However, CCS projects generally target “green field sites,” where there is often little characterization data and therefore large uncertainty about the petrophysical properties and other geologic attributes of the storage reservoir. Consequently, ensemble-based approaches are often used to forecast multiple realizations prior to CO 2 injection to visualize a range of potential outcomes. In addition, monitoring data during injection operations are used to update the pre-injection forecasts and thereby improve agreement between forecasted and observed behavior. Thus, a system for generating accurate, timely forecasts of pressure buildup and CO 2 movement and distribution within the storage reservoir and for updating those forecasts via monitoring measurements becomes crucial. This study proposes a learning-based prediction method that can accurately and rapidly forecast spatial distribution of CO 2 concentration and pressure with uncertainty quantification without relying on traditional inverse modeling. The machine learning techniques include dimension reduction, multivariate data analysis, and Bayesian learning. The outcome is expected to provide CO 2 storage site operators with an effective tool for timely and informative decision making based on limited simulation and monitoring data.

58 GEOSCIENCES↗
DOE OSTI2023

Turbulence modeling to aid tidal energy resource characterization in the Western Passage, Maine, USA

Numerical models combined with field measurements are regularly used to characterize tidal energy resources at potential energetic sites. However, most existing works only focus on the tidal hydrodynamic characteristics, and turbulence parameters are often not reported because of the lack of high-quality turbulence measurements and the limitations of numerical models in resolving turbulent eddies. In this study, we used FVCOM - a hydrostatic primitive equation (HPE) model - to characterize the tidal energy resource in the Western Passage, Maine, USA, by taking care of the essential macro-scale turbulence properties. We observed an excellent model performance using the Mellor-Yamada Level 2.5 Turbulence Model; estimating the spatial and vertical distribution of the turbulent kinetic energy and intensity added a new perspective to the site ranking for tidal energy converter (TEC) deployments. In addition, we also examined the role of channel geometry and bathymetry, such as headlands and underwater sills, in enhancing turbulent eddies around potential TEC siting locations. Ultimately, the detailed analysis of the turbulent flow characteristics has changed the site-ranking results and demonstrated that the regional-scale HPE models could be used for the relative understanding of more or less turbulent sites for a refined resource assessment.

16 TIDAL AND WAVE POWER↗
DOE OSTI2023

Recent Developments in Revealing the Impact of Complex Metal Oxide Reconstruction on Catalysis

Surface reconstruction of complex metal oxides refers to the alterations of the topmost catalyst surface, relative to the bulk structure, following exposure to pretreatment or reaction conditions during heterogeneous catalysis. (1) This structural and electronic transformation may involve (1) changes of the exposed crystallographic facets, (2) changes in chemical composition, such as the enrichment of specific elements, and, (3) morphological variations, including surface roughness and defects (Scheme 1). Beyond relaxation, surface reconstruction here also encompasses disruptions to the periodicity of the sublayers and changes to its stoichiometry. This change significantly influences the chemical properties of the catalyst surface, such as redox sites, (2) acid/base pairs, hydroxyl groups, (3) and surface defects. Surface reconstruction occurs due to the thermodynamic drive to lower the surface energy of the catalyst under the surrounding environment (e.g., temperature, chemical potential of species present). In addition to the treatment or reaction conditions, the extent of reconstruction also depends on the elements in the metal oxide structure. For instance, annealing ABO 3 perovskites (SrTiO 3 , BaTiO 3 , and BaZrO 3 ) at high temperatures (500 °C) in O 2 has a very different impact on the A/B ratio at the surface (ranging from 0.9 to 2.5), depending on the identity of A and B. (4) Metal oxide surface reconstruction under an electric field and exposure to acidic and alkaline media has recently gained increased attention in electrocatalysis, such as in the oxygen evolution reaction (OER); (5,6) however, in this Viewpoint we focus on the impact of surface reconstruction on thermal catalysis, a critical enduring research theme with ongoing challenges. Here, we start showcasing approaches to characterize surface reconstruction at the topmost surface layer, such as low-energy ion scattering (LEIS), discussing advantages and limitations. Next, we connect characterization of surface reconstruction to site-specific kinetic analysis, enabled via steady-state isotopic transient kinetic analysis (SSITKA), and we express our viewpoint on building structure–performance relationships by deeply understanding reconstructed surfaces. Later, we comment on the potential of tuning surface reconstruction to enhance catalytic performance. Finally, we explore the interplay between surface reconstruction and the “intelligent behavior”.

alcohol conversion↗
DOE OSTI2020

Utah FORGE: Phase 3 Magnetotelluric (MT) Data

New high-quality tensor MT data at 122 sites, including the vertical magnetic field and utilizing ultra-remote referencing, have been acquired over the Utah FORGE project area. The results will be used to delineate the densities of faults and fractures in crystalline basement rocks, to define the heat sources, and to derive baseline 3D resistivity structure for later MT monitoring of temporal changes in resistivity structure following well stimulation in the EGS reservoir. There are three files here related to Utah FORGE magnetotelluric (MT) data acquisition and processing. The FORGE MT EDIs zip file contains the observed MT responses in industry-standard EDI format. For each site, there is an EDI response file that utilized a local independent reference for noise cancellation, and a file that utilized a distant reference cancelling noise associated with the DC transmission line of the Delta IPP passing down the west side of Milford Valley. These two site files could be merged as appropriate. The FORGE Model Cell Center file contains the model volume of the 3D Forge MT inversion for characterizing the resistivity structure in the project area. It was derived using finite element inversion methodology described in Wannamaker et al, in the attached FORGE Phase3 Geophysics paper, from the MT observation EDI files. It is ASCII format (.dat) and entries are defined at top of the file in a simple x-y-z-Rho listing in UTM coordinates. The element layers drape the topography so the Rho value layers are not purely horizontal slices. This greatly simplifies the listing.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

Quantifying the impact of climate change on erosion - 20397

The New York State Energy Research and Development Authority (NYSERDA) is the owner of the Western New York Nuclear Service Center (WNYNSC), a 1,351-ha (3,338-ac) site located approximately 48 km (30 mi) south of Buffalo, New York. In 1962, Nuclear Fuel Services, Inc. (NFS) entered into Agreements with the Atomic Energy Commission and New York State to construct the first commercial reprocessing plant of nuclear fuel in the United States. NFS, a private company, built and operated the spent fuel reprocessing plant and waste disposal facilities, processing 640 Mg (metric tons, or 705 short tons) of spent nuclear fuel from 1966 to 1972 under an Atomic Energy Commission license. Nuclear fuel reprocessing operations ended in 1972 and never reopened, leaving behind radioactive and chemical wastes. Erosion can play an important role in the fate and transport of waste at sites where disposal of long-lived waste is anticipated. The statistical characterization of key processes related to erosion is essential to the understanding of site stability through time. One of the key processes governing erosion is extreme precipitation and it is critical that trends in the distribution of extreme precipitation events through time be represented. The evidence of climate change is increasingly well documented and projected impacts on extreme precipitation events should be incorporated in performance assessment studies when relevant. Not evaluating future climate states in a performance assessment is contradictory to good modeling practice. Specifically, excluding climate change limits development of modeling information that could aid in effective decision making. The current climate literature provides both observational evidence and climate model projections of climate trends and/or climate change in the late 20. and early 21. centuries for North America and the northeast United States. In this work, this information was used to assess the impacts of potential changes in climate on erosion processes. The goal was to understand how projections of future climate relate to the performance of the WNYNSC through time. In the first stage of this work multi-temporal historical aerial images were analyzed in conjunction with orthophotography and Lidar data to develop probability distributions for variables representing important erosion processes. The information from these analyses was then used in conjunction with simulated data from the West Valley Erosion Working Group (EWG). Analysis of EWG simulations provides estimates for the change in erosion rates through time that is driven by changes in climate. The time-varying rates of erosion change were applied to the historical aerial imagery data in order to inform time-varying rates of erosion that are driven by changes in climate. Ultimately, this process resulted in the identification of locations for features like gully heads using both the Lidar dataset and projection of the estimated location from the historical aerial photo under consideration back to the Lidar dataset. The distance between the estimate of the location from the historical image and that of the Lidar dataset was the estimated distance the feature has moved. This distance was then divided by the number of years between the Lidar dataset and the year of the historical aerial image of interest to get a rate of movement through time. This was done for several dozen points on each historical aerial image. The analyses from the EWG were used to characterize the relative impact of climate change on the erosion rates. This relative impact was quantified by comparing the LEM based estimates of erosion that were derived using historical climate data with LEM based estimates of erosion that were derived using projections of future climate. The relative increase in the erosion rates was then applied to the historical estimates of erosion derived from the analysis of the historical aerial imagery. This approach was used since the LEM-based estimated of the historical erosion rates from the past century have a bias towards underestimating erosion. This underestimation is hypothesized to be a consequence of an inability of the LEMs to account for the impacts of land-use change (i.e. deforestation) which had been shown to significantly increase erosion in similar Northern hardwood forest ecosystems. In summary, gully head retreat rate and gully widening rate were characterized using statistical probability distributions from the historical aerial image analysis. Simulated data from the EWG was used to estimate the climatically-driven changes in erosion rates through time. The changes through time from the EWG were applied to the gully head retreat rate and gully widening rate characterized using the historical aerial image analysis. This information can be used to inform PPA models to project future risks from a given site. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Fine Root and Soil Organic Carbon Depth Distributions are Inversely Related Across Fertility and Rainfall Gradients in Lowland Tropical Forests

Humid tropical forests contain some of the largest soil organic carbon (SOC) stocks on Earth. Much of this SOC is in subsoil, yet variation in the distribution of SOC through the soil profile remains poorly characterized across tropical forests. We used a correlative approach to quantify relationships among depth distributions of SOC, fine root biomass, nutrients and texture to 1 m depths across 43 lowland tropical forests in Panama. The sites span rainfall and soil fertility gradients, and these are largely uncorrelated for these sites. We used fitted b parameters to characterize depth distributions, where b is a numerical index based on an asymptotic relationship, such that larger b values indicate greater concentrations of root biomass or SOC at depth in the profile. Root b values ranged from 0.82 to 0.95 and were best predicted by soil pH and extractable potassium (K) stocks. For example, the three most acidic (pH < 4) and Kpoor (< 20 g K m -2 ) soils contained 76 ± 5% of fine root biomass from 0 to 10 cm depth, while the three least acidic (pH > 6.0) and most K-rich (> 50 g K m -2 ) soils contained only 41 ± 9% of fine root biomass at this depth. Root b and SOC b values were inversely related, such that a large fine root biomass in surface soils corresponded to large SOC stocks in subsoils (50–100 cm). SOC b values were best predicted by soil pH and base cation stocks, with the three most base-poor soils containing 34 ± 8% of SOC from 50 to 100 cm depth, and the three most base-rich soils containing just 9 ± 2% of SOC at this depth. Nutrient depth distributions were not related to Root b or SOC b values. Here, these data show that large surface root biomass stocks are associated with large subsoil C stocks in strongly weathered tropical soils. Further studies are required to evaluate why this occurs, and whether changes in surface root biomass, as may occur with global change, could in turn influence SOC storage in tropical forest subsoils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Detecting multi‐scale riverine topographic variability and its influence on Chinook salmon habitat selection

Abstract Quantifying geomorphic conditions that impact riverine ecosystems is critical in river management due to degraded riverine habitat, changing flow and thermal conditions, and increasing anthropogenic pressure. Geomorphic complexity at different scales directly impacts habitat heterogeneity and affects aquatic biodiversity resilience. Here we showed that the combination of continuous spatial survey at high resolution, topobathymetric light detection and ranging (LiDAR), and continuous wavelet analysis can help identify and characterize that complexity. We used a continuous wavelet analysis on 1‐m resolution topobathymetry in three rivers in the Salmon River Basin, Idaho (USA), to identify different scales of topographic variability and the potential effects of this variability on salmonid redd site selection. On each river, wavelet scales characterized the topographic variability by portraying repeating patterns in the longitudinal profile. We found three major representative spatial wavelet scales of topographic variability in each river: a small wavelet scale associated with local morphology such as pools and riffles, a mid‐wavelet scale that identified larger channel unit features, and a large wavelet scale related to valley‐scale controls. The small wavelet scale was used to identify pools and riffles along the entire lengths of each river as well as areas with differing riffle‐pool development. Areas along the rivers with high local topographic variability (high wavelet power) at all wavelet scales contained the largest features (i.e., deepest or longest pools) in the systems. By comparing the wavelet power for each wavelet scale to Chinook salmon redd locations, we found that higher small‐scale wavelet power, which is related to pool‐riffle topography, is important for redd site selection. The continuous wavelet methodology objectively identified scales of topographic variability present in these rivers, performed efficient channel‐unit identification, and provided geomorphic assessment without laborious field surveys.

Duffin, Jenna↗
DOE OSTI2022

Mechanical Activation and Cation Site Disorder in MgAl 2 O 4

The synthesis and crystallographic site occupancy were investigated for MgAl 2 O 4 with and without mechanical activation of the precursor powders. Heating to 1200 °C or higher resulted in the formation of a single spinel phase regardless of whether the powders were mechanically activated or not. Neutron diffraction analysis was used to determine cation site occupancy and revealed that mechanical activation resulted in a lower degree of cation site inversion compared to the nonactivated materials, which indicated that the powders were closer to thermodynamic equilibrium. This is the first study to characterize the effects of mechanical activation on crystallographic site occupancy in magnesium aluminate spinel using neutron diffraction.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Organo-mineral interactions in active layer and permafrost soils along aging Arctic landscapes

Rising temperatures are accelerating permafrost thaw, exposing large soil organic carbon (SOC) stocks to microbial decomposition with implications for global climate. Understanding how permafrost carbon is stored and protected through associations with minerals is critical for predicting its vulnerability to decomposition upon thaw. However, how landscape age, substrate chemistry, and soil depth influence mineral associations remain relatively unexplored. We investigated organo-mineral associations in active layer and permafrost soils across a landscape age and geochemical gradient on Alaska’s North Slope, spanning three glaciated (~11,500–125,000 years) and one unglaciated site. Using selective dissolution extractions, X-ray diffraction, and Mössbauer spectroscopy, we characterized minerals and their relationship with SOC. The three recently deglaciated sites had low soil pH that decreased with age and greater abundances of pyrophosphate- and oxalate-extractable Al and Fe, whereas the oldest unglaciated site exhibited near-neutral pH, greater pyrophosphate-extractable Ca, and distinct mineralogy. Across sites, SOC was positively associated with Al and Fe mineral phases, with stronger relationships in acidic soils. Pyrophosphate-extractable Ca also showed strong relationships with SOC at the acidic sites (up to ~10x greater), suggesting that Ca-mediated protection may operate beyond traditionally recognized high-pH soils. Permafrost soils showed depth-related changes in pH, SOC, and Fe mineralogy, suggesting chemically active, heterogeneous layers may shape mineral dynamics and associated carbon. Our results highlight how landscape age, parent material, and depth create distinct geochemical environments that govern mineral-organic associations. As thaw exposes soil to new conditions, these mineral-mediated protection mechanisms may be altered, potentially affecting the permafrost carbon-climate feedback.

Synthetic Biology↗
DOE OSTI2023

A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants

Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like protease inhibitors.

3CLpro inhibitor↗
DOE OSTI2020

Caught in the H inact : Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O 2 -stable State of [FeFe] Hydrogenase

[FeFe] hydrogenases are the most active H 2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O 2 -stable state called H inact . To date, the structure and mechanism of formation of H inact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in-depth spectroscopic characterization by X-ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O 2 -stable hydrogenases and molecular catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Operando XAS/SAXS: Guiding Design of Single-Atom and Subnanocluster Catalysts

Single-atom and subnanocluster catalysts (SSCs) represent a highly promising class of low-cost materials with high catalytic activity and high atom-utilization efficiency. However, SSCs are susceptible to undergo restructuring during the reactions. Exploring the active sites of catalysts through in situ characterization techniques plays a critical role in studying reaction mechanism and guiding the design of optimum catalysts. In situ X-ray absorption spectroscopy/small-angle X-ray scattering (XAS/SAXS) is promising and widely used for monitoring electronic structure, atomic configuration, and size changes of SSCs during real-time working conditions. Unfortunately, there is no detailed summary of XAS/SAXS characterization results of SSCs. The recent advances in applying in situ XAS/SAXS to SSCs are thoroughly summarized in this review, including the atomic structure and oxidation state variations under open circuit and realistic reaction conditions. Furthermore, the reversible transformation of single-atom catalysts (SACs) to subnanoclusters/nanoparticles and the application of in situ XAS/SAXS in subnanoclusters are discussed. To conlcude, the outlooks in modulating the SSCs and developing operando XAS/SAXS for SSCs are highlighted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals

Boceprevir is an HCV NSP3 inhibitor that was explored as a repurposed drug for COVID-19. It inhibits the SARS-CoV-2 main protease (M Pro ) and contains an α-ketoamide warhead, a P1 β-cyclobutylalanyl moiety, a P2 dimethylcyclopropylproline, a P3 tert-butylglycine, and a P4 N-terminal tert-butylcarbamide. By introducing modifications at all four positions, we synthesized 20 boceprevir-based M Pro inhibitors including PF-07321332 and characterized their M Pro inhibition potency in test tubes (in vitro) and 293T cells (in cellulo). Crystal structures of M Pro bound with 10 inhibitors and cytotoxicity and antiviral potency of 4 inhibitors were characterized as well. Replacing the P1 site with a β-(S-2-oxopyrrolidin-3-yl)-alanyl (Opal) residue and the warhead with an aldehyde leads to high in vitro potency. The original moieties at P2, P3 and the P4 N-terminal cap positions in boceprevir are better than other tested chemical moieties for high in vitro potency. In crystal structures, all inhibitors form a covalent adduct with the M Pro active site cysteine. Here, the P1 Opal residue, P2 dimethylcyclopropylproline and P4 N-terminal tert-butylcarbamide make strong hydrophobic interactions with M Pro , explaining high in vitro potency of inhibitors that contain these moieties. A unique observation was made with an inhibitor that contains a P4 N-terminal isovaleramide. In its M Pro complex structure, the P4 N-terminal isovaleramide is tucked deep in a small pocket of M Pro that originally recognizes a P4 alanine side chain in a substrate. Although all inhibitors show high in vitro potency, they have drastically different in cellulo potency to inhibit ectopically expressed M Pro in human 293T cells. In general, inhibitors with a P4 N-terminal carbamide or amide have low in cellulo potency. This trend is reversed when the P4 N-terminal cap is changed to a carbamate. The installation of a P3 O-tert-butyl-threonine improves in cellulo potency. Three molecules that contain a P4 N-terminal carbamate were advanced to cytotoxicity tests on 293T cells and antiviral potency tests on three SARS-CoV-2 variants. They all have relatively low cytotoxicity and high antiviral potency with EC 50 values around 1 μM. A control compound with a nitrile warhead and a P4 N-terminal amide has undetectable antiviral potency. Based on all observations, we conclude that a P4 N-terminal carbamate in a boceprevir derivative is key for high antiviral potency against SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗