X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites e
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Lee, Jaeyong↗
SEARCH · Engineering Papers
Results for “SITE CHARACTERIZATION”
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SAVANNAH RIVER SITE LIQUID WASTE TANK STORAGE: TANK 48H HISTORY AND RECENT WASTE CHARACTERIZATION
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ANGEL, FRED A.↗
Elucidating Electric Field-Induced Rate Promotion of Brønsted Acid-Catalyzed Alcohol Dehydration
Applied potentials have been demonstrated as a powerful tool to promote heterogeneous Brønsted acid catalysis by orders of magnitude, leveraging interfacial electric fields to stabilize protonated intermediates. However, the use of flat two-dimensional electrodes with inherently low active site densities limits the application of conventional thermochemical characterization techniques that can probe the nature of catalytic active sites. Here, we use kinetic analyses with an electrostatics-based model to elucidate the intricacies of potential-induced rate promotion, employing liquid-phase dehydration of 1-methylcyclopentanol catalyzed by carboxylic acid groups on carbon nanotubes as a probe system. By using a basket electrode to directly polarize catalyst powder, we demonstrate that thermocatalytic reaction rates can be promoted by 100,000-fold, exhibiting a log–linear dependence on applied potential with rate-potential scalings as high as 125 ± 4 mV per 10-fold rate increase. In agreement with model predictions, we show that lower ionic strengths attenuate potential sensitivity, resulting from a weakening of the interfacial electric field that interacts with the acidic proton. Furthermore, we experimentally confirm the model-predicted “isokinetic potential” (at ∼0.6 V vs Ag/AgCl)─the potential at which all rate scaling lines at various ionic strengths intersect, making the rate independent of ionic strength. Base titrations reveal that only ∼8% of the carboxylic acid sites are catalytically active, yet these same active sites are operational at the highest and lowest potentials. Collectively, our results provide a key methodology for modeling catalytic effects of electric fields, quantifying active sites under applied potential, and demonstrating fundamental principles of electric field-induced rate promotion.
Catalysts↗
Detection of variations in aspen forest habitat from LANDSAT digital data: Bear River Range, Utah
The aspen forests of the Bear River Range were analyzed and mapped using data recorded on July 2, 1979 by the LANDSAT III satellite; study efforts yielded sixty-seven light signatures for the study area, of which three groups were identified as aspen and mapped at a scale of 1:24,000. Analysis and verification of the three groups were accomplished by random location of twenty-six field study plots within the LANDSAT-defined aspen areas. All study plots are included within the Cache portion of the Wasatch-Cache National Forest. The following selected site characteristics were recorded for each study plot: a list of understory species present; average percent cover density for understory species; aspen canopy cover estimates and stem measurements; and general site topographic characteristics. The study plot data were then analyzed with respect to corresponding Landsat spectral signatures. Field studies show that all twenty-six study plots are associated with one of the three aspen groups. Further study efforts concentration on characterizing the differences between the site characteristics of plots falling into each of the three aspen groups.
Merola, J. A.↗
Exploring the role of biotic factors in regulating the spatial variability in land surface phenology across four temperate forest sites
Here, land surface phenology (LSP), the characterization of plant phenology with satellite data, is essential for understanding the effects of climate change on ecosystem functions. Considerable LSP variation is observed within local landscapes, and the role of biotic factors in regulating such variation remains underexplored. In this study, we selected four National Ecological Observatory Network terrestrial sites with minor topographic relief to investigate how biotic factors regulate intra-site LSP variability. We utilized plant functional type (PFT) maps, functional traits, and LSP data to assess the explanatory power of biotic factors for the start and end of season (SOS and EOS) variability. Our results indicate that PFTs alone explain only 0.8–23.4% of intra-site SOS and EOS variation, whereas including functional traits significantly improves explanatory power, with cross-validation correlations ranging from 0.50 to 0.85. While functional traits exhibited diverse effects on SOS and EOS across different sites, traits related to competitive ability and productivity were important for explaining both SOS and EOS variation at these sites. These findings reveal that plants exhibit diverse phenological responses to comparable environmental conditions, and functional traits significantly contribute to intra-site LSP variability, highlighting the importance of intrinsic biotic properties in regulating plant phenology.
60 APPLIED LIFE SCIENCES↗
Integrating Electrical Resistivity Tomography with Vadose Zone Characterization - 20246
The environmental management mission at the U.S. Department of Energy Hanford Site includes addressing subsurface contaminants that are present in the vadose zone because of historical waste discharges. Characterization is needed to support evaluation of whether contaminants at specific disposal sites will migrate to and contaminate the groundwater in the future. Drilling of boreholes and analysis of retrieved sediment samples is a standard approach to evaluating contaminant distribution in the vadose zone for the types of inorganic and radionuclide contaminants at the Hanford Site. However, borehole sampling has limitations for understanding the volumetric distribution of contaminants. The Hanford Site is now applying electrical resistivity tomography to characterize the path and volumetric extent of contaminant migration in the vadose zone. This information aids selection of appropriate locations for obtaining borehole samples and provides three-dimensional contaminant distribution information for incorporation into conceptual site models and to help configure fate and transport models. (authors)
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Tuning the Molecular Structure and Reaction Mechanism of Olefin Metathesis by Model Bilayered Supported MoO x /AlO x /SiO 2 Catalysts
The molecular structure and activity of supported MoO x olefin metathesis catalysts are heavily impacted by the choice of catalyst support. In this study, surface modification of the SiO 2 support with AlO x and selective anchoring of the MoO x on the surface AlO x sites were used to tune the structure, activation, and reactivity of the resulting surface MoO x sites. Extensive in situ molecular characterization, chemical probe studies, and density functional theory (DFT) calculations reveal that the enhanced activity of the supported MoO x /AlO x /SiO 2 catalyst over the MoO x / SiO 2 catalyst is associated with more favorable activation and kinetics of surface MoO x anchored at AlO x sites.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sampling in Long-Screened Wells: Issues, Misconceptions, and Solutions
The issues associated with long-screened wells (LSWs) (and open boreholes) at contaminated sites are well documented in the groundwater literature but are still not fully appreciated in practice. As established in seminal and review papers going back over three decades, the interpretation of sampling results from LSWs is challenging in the presence of vertical hydraulic gradients and borehole flow; furthermore, LSWs allow for vertical redistribution of contamination between aquifer layers. Acknowledgment of these issues has led to the development of new technologies and well designs to enable discrete-zone monitoring (DZM), yet LSWs remain common for many reasons, for example, as multipurpose wells, for geophysical logging, and (or) as legacy installations. Despite the literature on LSWs and despite the adoption of DZM at many sites, the use of LSWs persists and the challenges of interpreting sampling results from LSWs remain. In this issue paper, we provide a conceptual overview of the problems posed by LSWs and review existing literature and past work to improve the interpretation of sampling in LSWs. We draw on experience from previous studies at the Hanford Site in eastern WA, USA, and use synthetic examples to illustrate key concepts and challenges for interpretation. A recently published analytical modeling framework is used to develop illustrative synthetic examples and demonstrate a workflow for building scientific intuition to understand issues around interpreting samples from LSWs, which is critical to effective characterization and groundwater remediation at sites with LSWs.
54 ENVIRONMENTAL SCIENCES↗
Integrating the Fields of Catalysis: Active Site Engineering in Metal Cluster, Metal Organic Framework and Metal Single Site
Research evolved using nanoparticles synthesized and characterized under reaction conditions opened the door to study all three fields of catalysis: heterogeneous, homogenous, and enzyme. Fundamental studies of catalytic reactions ranging from hydrogenation to understand Fischer-Tropsch synthesis and isomerization ultimately led to the integration of three fields of catalysis. Our recent work on bridging heterogeneous, homogenous, and enzymatic catalysis was present including functionalization of dendrimer encapsulated metal clusters surface for lactonization, active site engineering in metal organic framework catalysts for methanol production and oligomerization, and single site catalyst for hydrogen production. We envision that the combination of active site engineering and unifying fields of catalysis could be applied to solve practical issues of science-based technology and develop new fields useful in energy research.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Southwest Regional Partnership on Carbon Sequestration: Phase III (Final Scientific/Technical Report)
The Southwest Regional Partnership on Carbon Sequestration (SWP) is one of 7 regional partnerships formed in 2003 under the U.S. Department of Energy’s (DOE) Regional Carbon Sequestration Partnerships (RCSPs) initiative. The overall purpose of the initiative was to help determine and implement the technology, infrastructure, and regulations most appropriate to promote carbon storage in different regions of the country. Covering Arizona, Colorado, New Mexico, Oklahoma, Utah, and parts of Texas, Wyoming, and Kansas, the SWP evaluated regional carbon storage and utilization potential and focused on technologies and sites that could complement the region’s strong position in energy production. The project progressed through three phases: • Phase I (2003–2005): Characterized regional geologic formations and CO 2 sources, assessed sequestration potential, and identified pilot test sites. • Phase II (2005–2013): Conducted small-scale field tests to validate sequestration methods, including geologic and terrestrial projects. • Phase III (2008–2022): Demonstrated large-scale CO 2 injection at a commercial oil field to test monitoring, verification, and long-term storage strategies. This report covers Phase III. The final project site, the Farnsworth Unit (FWU) in Texas, provided real-world testing of reservoir characterization, monitoring, and risk evaluation tools and processes that could be used in any commercial scale carbon capture, utilization, and storage (CCUS) project. Extensive data collection and analysis helped refine best practices for reservoir characterization, injection monitoring, and storage verification. The SWP contributed to national databases, DOE best practice manuals, and regional geological assessments to support future sequestration efforts. Key lessons learned include the importance of robust data management, strategic site selection, regulatory navigation, and effective industry collaboration. The project’s findings will inform ongoing and future carbon storage initiatives. Task 1 (Regional Characterization) • The SWP continued to participate in national outreach efforts and NATCARB. • The SWP evaluated multiple potential sites before selecting the FWU as the primary field test location. Task 2 (Public Outreach and Education) • The SWP contributed to national databases, DOE best practice manuals, and regional geological assessments to support future sequestration efforts. Task 3 (Permitting and Regulatory Compliance) • The SWP ensured compliance with federal and state regulations, including National Environmental Policy Act (NEPA) requirements. • The SWP obtained all necessary permits for drilling, injection, and monitoring activities. Task 4 (Site Characterization and Planning) • The SWP developed work plans for four key activities: characterization, simulation, monitoring and verification, and risk evaluation. • The SWP collected and synthesized legacy data from multiple sources to build initial static geological models and dynamic reservoir models demonstrating project feasibility. • The SWP conducted an initial risk evaluation and developed mitigation plans. Task 5 (Field Operations and Data Collection) • The SWP drilled, logged, and cored three characterization wells to gather critical subsurface data. • The SWP conducted multiple geophysical surveys, including 3D seismic, crosswell seismic, and vertical seismic profiling, to improve reservoir characterization. Task 6 (Monitoring and Verification) • The SWP performed extensive geological characterization using data from characterization wells and seismic surveys. • The SWP established a surface monitoring network to track CO 2 flux in soil gas, groundwater chemistry, and near-surface atmospheric CO 2 levels. • The SWP built and refined reservoir models to study the effects of relative permeability on simulation behavior and improve calibration with experimental data. Task 7 (Risk Assessment and Model Refinement) • The SWP conducted multiple studies to evaluate reservoir integrity, predict CO 2 plume behavior and improve predictive modeling capabilities. • The SWP refined geological models and used them to enhance the accuracy of simulation models. • The SWP continued quantitative risk assessment of top-ranked risks and strengthened the link between qualitative and quantitative risk methodologies.
02 PETROLEUM↗
Response Versus Scan-Angle Assessment of MODIS Reflective Solar Bands in Collection 6.1 Calibration
The Moderate Resolution Imaging Spectroradiometer (MODIS) instruments onboard the Aqua and Terra satellites have been operated for nearly two decades, producing high-quality earth observation data sets suitable for a broad range of scientific studies regarding the earth’s land, ocean, and atmospheric processes. The high radiometric accuracy of MODIS reflective solar band (RSB) calibration has also served as benchmark measurements for on-orbit cross-calibration studies. As the two MODIS instruments have operated well beyond their design lifespan of six years, the measurements from the onboard calibrators alone become inadequate to characterize the sensor’s response at all scan angles, as evinced by long-term drifts observed at certain scan positions of the Aqua-MODIS 0.64- and 0.86-μm bands in Collection 6 (C6) data set. The latest MODIS Level 1B C6.1 data set incorporates earth-view response trending from invariant desert sites as supplemental inputs to characterize the scan-angle calibration dependencies for all RSB. This article presents a deep convective cloud (DCC)-based calibration approach for an independent evaluation of the MODIS RSB response versus scan-angle (RVS) performance in C6.1. The long-term calibration stability and RVS differences in C6.1 have been significantly improved for Aqua-MODIS RSB. The observed RVS differences of more than 2% in Aqua-MODIS C6 bands 1 and 2 have been reduced to within 1% in C6.1. Some RSBs of Terra-MODIS have suffered temporal drifts up to ~2% and calibration shifts up to 3%, particularly around 2016 when the Terra satellite entered into safe mode. The DCC approach has been found very effective in tracking the on-orbit RVS changes over time.
Clouds and the Earth’s Radiant Energy System (CERE↗
Multi-Sensor Characterization of the Boreal Forest: Initial Findings
Results are presented in an initial apriori knowledge approach toward using complementary multi-sensor multi-temporal imagery in characterizing vegetated landscapes over a site in the Boreal Ecosystem-Atmosphere Study (BOREAS). Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and Airborne Synthetic Aperture Radar (AIRSAR) data were segmented using multiple endmember spectral mixture analysis and binary decision tree approaches. Individual date/sensor land cover maps had overall accuracies between 55.0% - 69.8%. The best eight land cover layers from all dates and sensors correctly characterized 79.3% of the cover types. An overlay approach was used to create a final land cover map. An overall accuracy of 71.3% was achieved in this multi-sensor approach, a 1.5% improvement over our most accurate single scene technique, but 8% less than the original input. Black spruce was evaluated to be particularly undermapped in the final map possibly because it was also contained within jack pine and muskeg land coverages.
Reith, Ernest↗
Chemistry and Properties of Imide Oligomers from Phenylethynyl-Containing Diamines
As an extension of work on pendent phenylethynlyl-containing imide oligomer, three new diamines containing pendent phenylethynyl groups were prepared and characterized. These diamines were used to prepare pendent and pendent and terminal phenylethynyl imide oliogomers via the amide acid route in N-methyl-2-pyrrolidinone at a calculated number average molecular weight of 5000 g mol (exp -1). The pendent phenylethynyl groups were randomly distributed along the oliogomer backbone and provided a means of controlling the distance between reactive sites. The imide oligomers were characterized and thermally cured, and the cured polymers evaluated as thin films and compared with materials of similar composition prepared from 3,5-diamino-4'-phenylethynylbenzophenone. This work was performed as part of a continuing research effort to develop structural resins for potential aeronautical applications.
Smith, J. G., Jr.↗
Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs
Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. Here, to understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.
59 BASIC BIOLOGICAL SCIENCES↗
Geology of the One Earth Energy Site
The One Earth Energy site is one of two sites in the Illinois Storage Corridor (ISC) project. The objectives of the ISC project is to accelerate commercial deployment of carbon capture utilization and storage at two individual sites and receive approvals for Underground Injection Control (UIC) Class VI permits for construction at each site. At the One Earth Energy site, an extensive data collection program was undertaken, which included the drilling of a test well (One Earth Energy #1 [OEE #1]), four 2D seismic lines, and a small 3D seismic survey. The OEE #1 well was drilled in 2022 and acquired extensive core, log, and testing data to characterize the subsurface geology of the site. Coring was focused on the storage interval, the Mt. Simon Sandstone, and the confining interval, the Eau Claire Formation. The core and log data were used to evaluate the sedimentology and sequence stratigraphy, as well as to develop the conceptual geologic model. This report includes the geological summaries of the Mt. Simon Sandstone and the Eau Claire Formation. The extensive analysis of the log data is included in the petrophysical section, showing ranges of porosity, estimated pore size, and the mineral content of selected zones in the well. The separate petrographic technical report entitled “Petrographic and Advanced Geologic Characterization Report on One Earth Energy #1 (API# 1211325373)”, report number DOE-UIUC-0031892-04, details thin section point-counting analysis that includes mineralogical and pore space analysis, including grain size analysis, annotated thin section photomicrographs, scanning electron microscopy (SEM) with energy dispersive X-ray spectroscopy (EDS), and statistics of grain size analysis on Mt. Simon thin sections from OEE #1. The final OEE #1 well data to be included in this geology report is the routine core analysis of both whole core plugs and rotary sidewall core plugs. In addition to the OEE #1 well, four 2D seismic lines and a small 3D survey were acquired as part of the overall subsurface geological characterization. This geology report references the seismic interpretation report, entitled “One Earth Energy Site Seismic Interpretation Task 5.0”, report number DOE-UIUC-0031892-07. This report details the stratigraphic and structural interpretation of the 2D and 3D seismic data acquired at the One Earth Energy site. The 2D seismic data was acquired in 2019 and 2021, and the 3D survey was acquired in 2022. The objectives of the seismic programs were to contribute to the subsurface characterization of the Mt. Simon-Eau Claire Storage Complex by evaluating the continuity of potential storage reservoirs and containment intervals across the project area, and to determine if any geologic features are present that would increase containment risk to the proposed carbon storage project.
09 BIOMASS FUELS↗
Nearby Sites Show Similar Upwind Sources and Differing Semivolatile Concentrations in Coastal Aerosol Particles
The Eastern Pacific Cloud Aerosol Precipitation Experiment (EPCAPE) characterized aerosol composition using measurements at two sites within 3 km (Scripps Pier and Mt. Soledad) from 15 February 2023 to 14 February 2024. Comparing the two sites shows the strong influence of upwind sources that results in similar monthly compositions at both sites. The seasonal changes in chemical mass concentrations were largely driven by the upwind source regions, with coastal northwesterly back-trajectories occurring 63−65% of the year and bringing submicrometer mass concentrations that were lower than the EPCAPE average for all trajectories at each site. In contrast, refractory black carbon (rBC) and nonrefractory (NR)-organics and nitrate mass concentrations exceeded EPCAPE average concentrations for back-trajectories from urban areas such as Los Angeles-Long Beach. For hourly measurements, NR-organics and non-sea-salt (NSS)-sulfate mass concentrations at Mt. Soledad were correlated strongly (r = 0.73−0.82) to those measured at Scripps Pier, but NR-nitrate was correlated only moderately (r = 0.63). The explanation for the lower correlation of NR-nitrate is both emissions between the sites and semivolatility, with semivolatility accounting for site-to-site changes in daily averages of +0.01 μg m −3 per percentage site-to-site difference in relative humidity and −0.07 μg m −3 per degree Celsius site-to-site difference in temperature. On average, comparing Scripps Pier to Mt. Soledad, NR-nitrate was higher by 29% because of relative humidity and lower by −26% because of temperature. NR-nitrate and rBC mass concentrations at Scripps Pier for nighttime were 13−15% higher than those for daytime because land breezes brought higher inland concentrations. Concentrations of rBC were 52% higher at Mt. Soledad than those measured at Scripps Pier, accompanied by increases in tracers for brake wear because of traffic on the steep roads within 10 m of that site. The implications are that these nearby sites had comparable monthly concentrations of measured components due to their similar backtrajectories, but hourly and daily concentration differences supported quantification of the meteorological effects from relative humidity and temperature on semivolatile NR-nitrate as well as minor differences from land−sea breezes and local emissions.
Aerosols↗
Reactive membrane networks for CWA protection
A membrane includes a first layer, and a second layer coupled to the first layer. The second layer includes a network of catalytic sites, each catalytic site having a catalytic center characterized by promoting a chemical reaction of a target material. A method of forming a chemically reactive membrane includes applying a first solution to a structure, the first solution includes a macrocyclic ligand having electron-donating ligands and a side functional group for crosslinking, crosslinking a plurality of the macrocyclic ligand to form a first network of crosslinked macrocyclic ligands, and applying a second solution to the structure, the second solution comprising a catalytic center. Each catalytic center complexes with the electron-donating ligands of each macrocyclic ligand to form catalytic sites in the first network of crosslinked macrocyclic ligands.
Fornasiero, Francesco↗
On the spectral reflectance properties of materials exposed at the Viking landing sites
Reflectance data derived from Viking Lander multispectral data were used to characterize the types of soils and blocks exposed at the landing sites and to search for evidence of relatively unaltered igneous rocks. A comprehensive effort was mounted to examine multispectral data that combines testing of camera radiometric calibrations, explicitly removing the effects of atmospheric attenuation and skylight, and quantitatively comparing the corrected data to reflectance data from laboratory materials. Bi-directional reflectances for blue, green and red channels were determined for 31 block and soil exposures at Viking landing sites.
Guinness, E.↗