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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

MHD Analysis of Dual-Coolant Lead-Lithium Blanket for Spherical Tokamak Advanced Reactor

The tritium breeding blanket is vital for future fusion power plants, with the Spherical Tokamak Advanced Reactor (STAR) project highlighting the dual-coolant lead-lithium (DCLL) design. The DCLL blanket performs shielding, energy exhaust, and tritium breeding using a lead-lithium alloy , with lithium as the breeder and lead as the neutron multiplier. It also serves as the primary coolant, with helium providing supplemental cooling. Reduced-activation ferritic/martensitic steel is used for the blanket structure. Magnetohydrodynamic (MHD) phenomena influence the liquid metal flow in a magnetic field, affecting heat transfer in the breeder affected by energetic neutrons. Understanding key flow parameters in such conditions is critical for efficient DCLL design. This study uses three-dimensional thermofluid MHD analysis with ANSYS CFX software, modified at Princeton Plasma Physics Laboratory, to simulate high Hartmann flows. The neutronics code MCNP, coupled with plasma equilibrium, provides heat source distribution. In conclusion, we examine electromagnetic interactions in adjacent fluid domains and analyze the magnetic field’s impact on flow distribution in the inboard and outboard blanket layout, using detailed mesh generation for accurate results.

DCLL↗
DOE OSTI2022

Toward full simulations for a liquid metal blanket: part 2. Computations of MHD flows with volumetric heating for a PbLi blanket prototype at Ha ~10 4 and Gr ~10 12

On the pathway toward full simulations for a liquid metal (LM) blanket, this part 2 extends a previous study of purely magnetohydrodynamic (MHD) flows in a DCLL blanket in reference Chen et al (2020 Nucl. Fusion 60 076003) to more general conditions when the MHD flow is coupled with heat transfer. The simulated prototypic blanket module includes all components of a real LM blanket system, such as supply ducts, inlet and outlet manifolds, multiple poloidal ducts and a U-turn zone. Volumetric heating generated by fusion neutrons is added to simulate thermal effects in the flowing lead–lithium (PbLi) breeder. The MHD flow equations and the energy equation are solved with a DNS-type finite-volume code ‘MHD-UCAS’ on a very fine mesh of 470 × 10 6 cells. The applied magnetic field is 5 T (Hartmann number Ha ~ 10 4 ), the PbLi velocity in the poloidal ducts is 10 cm s –1 (Reynolds number Re ~10 5 ), whereas the maximum volumetric heating is 30 MW m –3 (Grashof number Gr ~ 10 12 ). Four cases have been simulated, including forced- and mixed-convection flows, and either an electrically conducting or insulating blanket structure. Various comparisons are made between the four computed cases and also against the purely MHD flows computed earlier in reference Chen et al (2020 Nucl. Fusion 60 076003) with regards to the (1) MHD pressure drop, (2) flow balancing, (3) temperature field, (4) flows in particular blanket components, and (5) 3D and turbulent flow effects. The strongest buoyancy effects were found in the poloidal ducts. In the electrically non-conducting blanket, the buoyancy forces lead to significant modifications of the flow structure, such as formation of reverse flows, whereas their effect on the MHD pressure drop is relatively small. In the electrically conducting blanket case, the buoyancy effects on the flow and MHD pressure drop are almost negligible.

Physics↗
DOE OSTI2022

Characterisations of the HinOTORI telescope with a three-color imager at Ali Observatory in Western Tibet

HinOTORI is a new telescope supported by an international collaboration project between China and Japan. It is a 50 centimeter telescope equipped with simultaneous three-color imagers (u',R C , and I C bands). It is located at Ali Observatory at an altitude of 5100m. Thanks to the high altitude and extreme dryness, Ali site is one of the most suitable sites for optical astrometry. HinOTORI telescope aims at detecting optical transients such as the counterparts of gravitational wave (GW) sources, supernovae, gamma-ray bursts (GRB) and so on. This paper describes the site information, design of simultaneous three-color optical layout, system instruments and whole control system. We also report some telescope characterisations for three bands (u'/R C /I C ) respectively, such as Hartmann constant (0.49"/0.56"/0.60"), best focus position (3.922/3.920/3.903 mm), PSF FWHM size (3.755/3.328/3.167pixels), total transmittance and limiting magnitude (15.69/17.57/17.05mag, 10 σ 30 seconds exposure time). With different airmass observation data, the atmospheric extinction coefficients of three bands (0.366/0.061/0.026) were also derived.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

X-ray wavefront sensor development at the Advanced Light Source

At Lawrence Berkeley National Laboratory's Advanced Light Source, we are developing x-ray wavefront sensors to support the creation and operation of beamlines with diffraction-limited quality. Our new approach to rapid, intermittent wavefront sensing operates in reflection at glancing incidence angles and is compatible with the high-power densities of modern beamlines. For soft x-ray applications especially, the wavefront sensor can operate upstream of the exit slit in a vertically dispersed beam. This single-shot technique supports lateral shearing interferometry and Hartmann wavefront sensing; it can be adapted to speckle-based techniques as well. The reflected beam is directed to an off-axis YAG crystal that produces scintillated visible light. A small mirror reflects the light to a microscope and camera, and the measured wavefront shape information can be used as feedback to adaptive x-ray mirror elements. A compact array of gratings enables measurement across a broad range of photon energies or wavefront curvatures. We describe recent demonstrations at soft x-ray and hard x-ray wavelengths measuring an adaptive x-ray mirror, and a toroidal focusing mirror.

Goldberg, Kenneth A↗
DOE OSTI2026

FastrSHWFS Analysis

This code analyzes the reflection geometry of modified Shack-Hartmann Wavefront Sensor (SHWFS) masks, with a focus on the fastrSHWFS designs. It takes a height map of a reflective mask, divides it into sub apertures, removes the global focus term by referencing a central block, and fits local surface planes to each sub aperture. From these fits it computes reflection angles and propagates the corresponding rays downstream to determine spot positions and the overall reflected beam footprint as a function of distance. The implementation is parameterized in sub aperture size, number of sub apertures, focal length, and mask dimensions, so it can be adapted to different mask designs beyond the two current fastrSHWFS masks. The code: Converts mask bitmaps into physical height in microns and reconstructs a focus subtracted mask, divides the mask into a grid of sub apertures and assigns pixel and micron coordinates to each block, excludes user specified unused sub apertures from the analysis, fits a plane to each sub aperture to obtain local surface normals, propagates reflected rays to a range of z positions to compute ray spots and the full reflected beam width, computes the effective mask tilt angle with respect to the incoming beam as a function of propagation distance, and provides helper routines for plotting the grid over the mask and for visualizing the beam geometry. These tools are intended for iterating on fastrSHWFS mask designs and for planning downstream optical layouts, for example choosing lens positions and apertures that capture the reflected beam given known focal plane distances and beam widths.

Gerard, BenjaminL [Lawrence Livermore National Lab↗
DOE OSTI2021

Two-dimensional phase cartography for high-harmonic spectroscopy

Extremely nonlinear spectroscopy based on high-order-harmonic generation has become a powerful investigation method for attosecond dynamics in gas and solid targets. In particular, the phase of harmonic emission was shown to carry profound insight into atomic and molecular structure and dynamics. However, current techniques offer phase measurements only along specific directions, thus providing partial characterization. Here we report on a new approach combining optical and quantum interferometers measuring along two dimensions the intensity and phase of harmonic emission from aligned molecules in the exact same experimental conditions. This two-dimensional cartography technique measures the phase with no arbitrary offset and no uncertainty on its sign. Measurements along different dimensions can be combined in two ways: either a single mapping or a redundant mapping allowing high-precision phase recovery using a Shack–Hartmann-like algorithm. We demonstrate both methods in a nitrogen test case, which allows disentangling structural and dynamical effects. Two-dimensional phase cartography paves the way to high-resolution high-harmonic spectroscopy for applications such as quantum orbital tomography and attosecond charge migration in molecules.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Experiment of Sea Breeze Convection, Aerosols, Precipitation, and Environment (ESCAPE) C-band Radar Deployment Field Campaign Report

Convective clouds play a critical role in the Earth’s climate system, acting as sinks of total water in the atmospheric column through precipitation, thereby contributing to the atmospheric energy balance. They serve as a primary mechanism for the transfer of heat, moisture, and momentum through the troposphere, significantly impacting the large-scale atmospheric circulation and local environment, and affecting the probability of subsequent cloud formation (e.g., Hartmann et al. 1984, Su et al. 2014, Sherwood et al. 2014). Convective characteristics including convective core size (reflectivity and updraft), cloud lifetime, precipitation intensity, total precipitation amount, precipitation efficiency, and lightning flash rates can be strongly related to environmental factors (e.g., wind shear, humidity). Since cumulus clouds evolve rapidly, their microphysical and dynamical properties and life cycles are challenging to resolve in models, and even in observations (e.g., Fridlind et al. 2017, Ladino et al. 2017).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Tracking Aerosol Convection Interactions Experiment (TRACER) Field Campaign Report

Convective clouds serve a critical role in the Earth’s energy and water cycles through their transport of heat, moisture, momentum, and chemical species through the troposphere driving the global circulation (e.g., Hartmann et al. 1984, Del Genio et al. 2012, Su et al. 2014). On more local scales, convective clouds impact the atmospheric heating profile through diabatic heating effects, removal of water from the atmospheric column through precipitation, and conditioning of the local environment impacting further development of clouds (e.g., Sullivan and Voigt 2021). These critical roles underscore the importance of realistic representation of convective processes across scales of models from large-eddy simulation (LES), to convection-permitting models (CPM; e.g., Kendon et al. 2020, Marinescu et al. 2021), to numerical weather prediction (NWP) models used for operational weather forecasting, to Earth system models used to predict climate sensitivity (Sanderson et al. 2011, Sherwood et al. 2014, Tomassini et al. 2014, Zhao et al. 2016, Cronin et al. 2017). A key component of improving model representation of convective clouds is better quantification and parameterization of updraft microphysics and dynamics, including their interactions with the surrounding environment and storm organization (Bony et al. 2015, Hagos and Houze 2016, Donner et al. 2016, Morrison et al. 2020). Aerosol is an important environmental factor that could affect convective clouds and precipitation since cloud droplet and ice formation processes are initiated by it. Andrae et al. (2004) hypothesized that aerosols associated with increased biomass burning particles acting as cloud condensation nuclei (CCN) result in smaller and more monodisperse cloud droplets leading to suppression of warm rain formation, ultimately leading to more cloud water being lofted above the freezing level based on observations in the Amazon region. The subsequent increase in latent heat release increases the buoyancy of rising convective parcels invigorating the deep convection. This work was followed by a description of the theoretical basis for this “cold-phase invigoration” by Rosenfeld et al. (2008), who argued that it could have a significant effect for deep convective clouds with warm cloud-bases. Several modeling studies (e.g., Khain et al. 2005, 2009, van den Heever et al. 2006, Fan et al. 2007, 2009, 2012, Lee et al. 2008, Storer et al. 2010, Lebo et al. 2012, Storer and van den Heever 2013, Chen et al. 2020, Dagan et al. 2022) have investigated these aerosol-convection interactions and the environmental factors that influence their relative importance and magnitude. More recently, several studies have indicated that “warm-phase invigoration”, the enhancement of convection through condensational heating, also appears to play a role in enhancing both shallow cumuli (Seiki and Nakajima 2014, Saleeby et al 2015) and deeper tropical convection (Lebo and Seinfeld 2011, Khain et al. 2012, Sheffield et al 2015, Fan et al. 2018, Igel and van den Heever 2021), as well as Houston thunderstorms (Fan et al. 2007, 2020). However, still other studies have provided additional evidence of systematic biases in simulated convective outflow ice size distribution properties, which are consistent with a lack of poorly understood secondary ice production within convective updrafts (e.g., Fridlind et al. 2017). To help address these critical gaps in our understanding of cloud processes, aerosol processes and aerosol-cloud interactions, the Tracking Aerosol Convection Interactions Experiment was designed building upon efforts by the Aerosol, Cloud, Precipitation and Climate (ACPC) Initiative (http://acpcintiative.org/), a joint effort of the International Geosphere-Biosphere Programme (IGBP) and the World Climate Research Program (WCRP) that focused on resolving uncertainties in the interactions between aerosol and clouds towards better understanding the role that these interactions play in the climate system. The TRACER campaign was motivated by recommendations from a number of pilot studies undertaken by ACPC (van den Heever et al. 2017, Fridlind et al. 2019, Hu et al. 2019, Fan et al. 2020, Marinescu et al. 2021, Hernandez-Deckers et al. 2022) that pointed towards the southeastern Texas region as a locale where aerosol-convection interactions could be studied owing to the copious occurrence of isolated convection during the summer months accompanied by diverse and significant sources of aerosols from both anthropogenic and natural sources. The TRACER campaign began on 01 October 2021 and extended through 30 September 2022 with an intensive operational period (IOP) during June-September 2022. Three main sites (Table 1) were managed by the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

The FastrSHWFS Project Development Motivation, Analysis, & Test Results

The recent 2020 Decadal Survey of Astronomy and Astrophysics listed habitable exoplanet imaging with future extreme adaptive optics (AO) on 30m-class telescopes as a key priority in the coming decade. However, there is a current 100x contrast gap between the best systems today and what is needed to enable this goal. Astronomical AO is a required approach to enable ground-based diffraction-limited imaging of exoplanets on future extremely large telescopes. Time lag between the end of an exposure and the application of deformable mirror commands is a major contributor to the error budget in many AO systems, and detector read time is often a large component of this lag. We present two designs for a modified Shack Hartmann wavefront sensor (SHWFS), named Focal plane Actualized Shifted Technique Realized for a SHWFS (fastrSHWFS), to reduce the time lag component. This design steers the spot pattern at the focal plane into a rectangular or linear array with a custom aspect ratio, reducing readout time. The mask with focus yields aberrated results while the mask with tip/tilt only yields some defined spots. This essay outlines the current SHWFS concept, our fastrSHWFS theoretical solution to addressing time lag, reflection and quality analysis of printed mask designs, and results from testing both masks on the High Contrast Testbed at Lawrence Livermore National Lab. This work follows the test of a previous fastrSHWFS design.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Global Geo-processed Data of Aquifer Properties by 0.5° Grid, Country and Water Basins

This repository of global hydrogeologic datasets contains aquifer properties on 0.5° scale, including depth to groundwater (Fan et al., 2013), aquifer thickness (de Graaf et al., 2015), WHYMap aquifer classes (Richts et al., 2011), porosity and permeability (Gleeson et al., 2014), digitized and geo-processed from their respective sources. Globally gridded aquifer properties could be used independently to estimate global groundwater availability or used as critical inputs to the superwell model to simulate groundwater extraction and provide estimates of pumped volumes and unit costs under user-specific scenarios. Key resources related to this data are: Niazi, H., Ferencz, S., Graham, N., Yoon, J., Wild, T., Hejazi, M., Watson, D., & Vernon, C. (2024; In-prep). Long-term Hydro-economic Assessment Tool for Evaluating Global Groundwater Cost and Supply: Superwell v1. Geoscientific Model Development. superwell model repository which uses this data to simulate groundwater extraction and provides estimates of the global extractable volumes and unit-costs ($/km3) of accessible groundwater production under user-specified extraction scenarios. Repository Overview Main output: aquifer_properties.csv contains all processed outputs, including aquifer properties like porosity, permeability, aquifer thickness, and depth to groundwater. shapefiles.zip: contains all digitized GIS databases and shapefile for all aquifer properties prep_inputs.R: R script that processes the shapefiles to produce the aquifer_properties file plot_inputs.R: R script for plotting the maps and conducting preliminary analysis on the available groundwater volume basin_to_country_mapping.csv, basin_country_region_mapping.csv and continent_county_mapping.csv provide the mapping between continents, 32 energy-economic macro regions, countries, and water basins for post-processing aquifer_properties.csv Maps: Each map visualizes the spatial distribution of one of the aquifer properties across the globe map_in_Porosity.png map_in_Permeability.png map_in_Aquifer_thickness.png map_in_Depth_to_water.png map_in_Grid_area_km.png map_in_WHYClass.png Sample inputs sample_inputs.py: this script samples inputs from the aquifer_properties dataset, ensuring the sampled and original inputs maintain the same distributions sampled_data_100.csv contains 100 sampled data points and sampled_data_100.png compares their distributions Dataset Overview The main outputs are consolidated in a comprehensive aquifer_properties.csv file and include the following fields: GridCellID: Unique identifier for each (roughly 0.5°) grid cell Continent: Continent name Country: Country name GCAM_basin_ID: Identifier for GCAM hydrologic basin Basin_long_name: Full name of the basin WHYClass: Hydrogeologic classification based on WHYMap aquifer classes (Richts et al., 2011) Porosity: Soil porosity (%) (Gleeson et al., 2014) Permeability: Soil permeability (in square meters; Gleeson et al., 2014) Aquifer_thickness: Thickness of the aquifer (in meters; de Graaf et al., 2015) Depth_to_water: Depth to groundwater (in meters; Fan et al., 2013) Grid_area: Area of the grid cell (in square meters) Key References The datasets are digitized versions of global hydrogeologic properties from the following key literature sources: Depth to Groundwater: Fan, Y., Li, H., & Miguez-Macho, G. (2013). Global Patterns of Groundwater Table Depth. Science, 339(6122), 940-943. https://doi.org/10.1126/science.1229881 Aquifer Thickness: de Graaf, I. E. M., Sutanudjaja, E. H., van Beek, L. P. H., & Bierkens, M. F. P. (2015). A high-resolution global-scale groundwater model. Hydrol. Earth Syst. Sci., 19(2), 823-837. https://doi.org/10.5194/hess-19-823-2015 Porosity and Permeability: Gleeson, T., Moosdorf, N., Hartmann, J., & van Beek, L. P. H. (2014). A glimpse beneath earth's surface: GLobal HYdrogeology MaPS (GLHYMPS) of permeability and porosity. Geophysical Research Letters, 41(11), 3891-3898. https://doi.org/10.1002/2014GL059856 Aquifer classes: Richts, A., Struckmeier, W. F., & Zaepke, M. (2011). WHYMAP and the Groundwater Resources Map of the World 1:25,000,000. In J. A. A. Jones (Ed.), Sustaining Groundwater Resources: A Critical Element in the Global Water Crisis (pp. 159-173). Springer Netherlands. https://doi.org/10.1007/978-90-481-3426-7_10 Cite as Niazi, H., Watson, D., Hejazi, M., Yonkofski, C., Ferencz, S., Vernon, C., Graham, N., Wild, T., & Yoon, J. (2024). Global Geo-processed Data of Aquifer Properties by 0.5° Grid, Country and Water Basins. MSD-LIVE Data Repository. https://doi.org/10.57931/2307831 Contact Reach out to Hassan Niazi or open an issue in superwell repository for questions or suggestions.

aquifer thickness↗
DOE OSTI2024

Global Geo-processed Data of Aquifer Properties by 0.5° Grid, Country and Water Basins

This repository of global hydrogeologic datasets contains aquifer properties on 0.5° scale, including depth to groundwater (Fan et al., 2013), aquifer thickness (de Graaf et al., 2015), WHYMap aquifer classes (Richts et al., 2011), recharge (Döll and Fiedler, 2008; Gleeson et al., 2016), lakes (Messager et al., 2016), porosity and permeability (Gleeson et al., 2014), digitized and geo-processed from their respective sources. Globally gridded aquifer properties could be used independently to estimate global groundwater availability or used as critical inputs to the superwell model to simulate groundwater extraction and provide estimates of pumped volumes and unit costs under user-specific scenarios. Key resources related to this data are: Niazi, H., Ferencz, S. B., Graham, N. T., Yoon, J., Wild, T. B., Hejazi, M., Watson, D. J., & Vernon, C. R. (2025). Long-term hydro-economic analysis tool for evaluating global groundwater cost and supply: Superwell v1.1. Geoscientific Model Development, 18(5), 1737-1767. https://doi.org/10.5194/gmd-18-1737-2025 superwell model repository which uses this data to simulate groundwater extraction and provides estimates of the global extractable volumes and unit-costs ($/km3) of accessible groundwater production under user-specified extraction scenarios. Repository Overview Main output: aquifer_properties_rec.csv contains all processed outputs, including aquifer properties like porosity, permeability, recharge, lake areas, aquifer thickness, and depth to groundwater. shapefiles.zip: contains all digitized GIS databases and shapefile for all aquifer properties prep_inputs.R and prep_inputs_recharge_lakes.R: R scripts that process the shapefiles to produce the aquifer_properties_rec.csv file plot_inputs.R: R script for plotting the maps and conducting preliminary analysis on the available groundwater volume basin_to_country_mapping.csv, basin_country_region_mapping.csv and continent_county_mapping.csv provide the mapping between continents, 32 energy-economic macro regions, countries, and water basins for post-processing aquifer_properties_rec.csv Maps: Each map visualizes the spatial distribution of one of the aquifer properties across the globe map_in_Porosity.png map_in_Permeability.png map_in_Aquifer_thickness.png map_in_Depth_to_water.png map_in_Recharge.png map_in_Grid_area_km.png map_in_Lake_area_km.png map_in_WHYClass.png Sample inputs sample_inputs.py: this script samples inputs from the aquifer_properties_rec dataset, ensuring the sampled and original inputs maintain the same distributions sampled_data_100.csv contains 100 sampled data points and sampled_data_100.png compares their distributions Dataset Overview The main outputs are consolidated in a comprehensive aquifer_properties_rec.csv file and include the following fields: GridCellID: Unique identifier for each (roughly 0.5°) grid cell Continent: Continent name Country: Country name GCAM_basin_ID: Identifier for GCAM hydrologic basin Basin_long_name: Full name of the basin WHYClass: Hydrogeologic classification based on WHYMap aquifer classes (Richts et al., 2011) Porosity: Soil porosity (%) (Gleeson et al., 2014) Permeability: Soil permeability (in square meters; Gleeson et al., 2014) Aquifer_thickness: Thickness of the aquifer (in meters; de Graaf et al., 2015) Depth_to_water: Depth to groundwater (in meters; Fan et al., 2013) Recharge: long-term annual averaged recharge rates (in m/yr; Döll and Fiedler, 2008; Gleeson et al., 2016) Grid_area: Area of the grid cell (in square meters) Lakes_area: Area of inland lakes (in square meters; Messager et al., 2016) Key References The datasets are digitized versions of global hydrogeologic properties from the following key literature sources: Depth to Groundwater: Fan, Y., Li, H., & Miguez-Macho, G. (2013). Global Patterns of Groundwater Table Depth. Science, 339(6122), 940-943. https://doi.org/10.1126/science.1229881 Aquifer Thickness: de Graaf, I. E. M., Sutanudjaja, E. H., van Beek, L. P. H., & Bierkens, M. F. P. (2015). A high-resolution global-scale groundwater model. Hydrol. Earth Syst. Sci., 19(2), 823-837. https://doi.org/10.5194/hess-19-823-2015 Porosity and Permeability: Gleeson, T., Moosdorf, N., Hartmann, J., & van Beek, L. P. H. (2014). A glimpse beneath earth's surface: GLobal HYdrogeology MaPS (GLHYMPS) of permeability and porosity. Geophysical Research Letters, 41(11), 3891-3898. https://doi.org/10.1002/2014GL059856 Aquifer classes: Richts, A., Struckmeier, W. F., & Zaepke, M. (2011). WHYMAP and the Groundwater Resources Map of the World 1:25,000,000. In J. A. A. Jones (Ed.), Sustaining Groundwater Resources: A Critical Element in the Global Water Crisis (pp. 159-173). Springer Netherlands. https://doi.org/10.1007/978-90-481-3426-7_10 Recharge: Döll, P., & Fiedler, K. (2008). Global-scale modeling of groundwater recharge. Hydrol. Earth Syst. Sci., 12(3), 863-885. https://doi.org/10.5194/hess-12-863-2008; Gleeson, T., Befus, K. M., Jasechko, S., Luijendijk, E., & Cardenas, M. B. (2016). The global volume and distribution of modern groundwater. Nature Geoscience, 9(2), 161-167. https://doi.org/10.1038/ngeo2590 Inland Lakes: Messager, M. L., Lehner, B., Grill, G., Nedeva, I., & Schmitt, O. (2016). Estimating the volume and age of water stored in global lakes using a geo-statistical approach. Nature Communications, 7(1), 13603. https://doi.org/10.1038/ncomms13603 Cite as Niazi, H., Watson, D., Hejazi, M., Yonkofski, C., Ferencz, S., Vernon, C., Graham, N., Wild, T., & Yoon, J. (2024). Global Geo-processed Data of Aquifer Properties by 0.5° Grid, Country and Water Basins. MultiSector Dynamics-Living, Intuitive, Value-adding, Environment. https://doi.org/10.57931/2484226 Contact Reach out to Hassan Niazi or open an issue in the superwell repository for questions or suggestions.

aquifer thickness↗
DOE OSTI2021

Site-specific interrogation of an ionic chiral fragment during photolysis using an X-ray free-electron laser

Abstract Short-wavelength free-electron lasers with their ultrashort pulses at high intensities have originated new approaches for tracking molecular dynamics from the vista of specific sites. X-ray pump X-ray probe schemes even allow to address individual atomic constituents with a ‘trigger’-event that preludes the subsequent molecular dynamics while being able to selectively probe the evolving structure with a time-delayed second X-ray pulse. Here, we use a linearly polarized X-ray photon to trigger the photolysis of a prototypical chiral molecule, namely trifluoromethyloxirane (C 3 H 3 F 3 O), at the fluorine K-edge at around 700 eV. The created fluorine-containing fragments are then probed by a second, circularly polarized X-ray pulse of higher photon energy in order to investigate the chemically shifted inner-shell electrons of the ionic mother-fragment for their stereochemical sensitivity. We experimentally demonstrate and theoretically support how two-color X-ray pump X-ray probe experiments with polarization control enable XFELs as tools for chiral recognition.

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

Comprehensive characterization of N- and O- glycosylation of SARS-CoV-2 human receptor angiotensin converting enzyme 2

The emergence of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created the need for development of new therapeutic strategies. Understanding the mode of viral attachment, entry and replication has become a key aspect of such interventions. The coronavirus surface features a trimeric spike (S) protein that is essential for viral attachment, entry and membrane fusion. The S protein of SARS-CoV-2 binds to human angiotensin converting enzyme 2 (hACE2) for entry. Herein, we describe glycomic and glycoproteomic analysis of hACE2 expressed in HEK293 cells. We observed high glycan occupancy (73.2 to 100%) at all seven possible N-glycosylation sites and surprisingly detected one novel O-glycosylation site. To deduce the detailed structure of glycan epitopes on hACE2 that may be involved in viral binding, we have characterized the terminal sialic acid linkages, the presence of bisecting GlcNAc and the pattern of N-glycan fucosylation. We have conducted extensive manual interpretation of each glycopeptide and glycan spectrum, in addition to using bioinformatics tools to validate the hACE2 glycosylation. Our elucidation of the site-specific glycosylation and its terminal orientations on the hACE2 receptor, along with the modeling of hACE2 glycosylation sites can aid in understanding the intriguing virus-receptor interactions and assist in the development of novel therapeutics to prevent viral entry. Here, the relevance of studying the role of ACE2 is further increased due to some recent reports about the varying ACE2 dependent complications with regard to age, sex, race and pre-existing conditions of COVID-19 patients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular Mechanism of Polysaccharide Acetylation by the Arabidopsis Xylan O-acetyltransferase XOAT1

Xylans are a major component of plant cell walls. O-Acetyl moieties are the dominant backbone substituents of glucuronoxylan in dicots and play a major role in the polymer-polymer interactions that are crucial for wall architecture and normal plant development. Here, we describe the biochemical, structural, and mechanistic characterization of Arabidopsis (Arabidopsis thaliana) xylan O-acetyltransferase 1 (XOAT1), a member of the plant-specific Trichome Birefringence Like (TBL) family. Detailed characterization of XOAT1-catalyzed reactions by real-time NMR confirms that it exclusively catalyzes the 2-O-acetylation of xylan, followed by nonenzymatic acetyl migration to the O-3 position, resulting in products that are monoacetylated at both O-2 and O-3 positions. In addition, we report the crystal structure of the catalytic domain of XOAT1, which adopts a unique conformation that bears some similarities to the a/ß/a topology of members of the GDSL-like lipase/acylhydrolase family. Finally, we use a combination of biochemical analyses, mutagenesis, and molecular simulations to show that XOAT1 catalyzes xylan acetylation through formation of an acyl-enzyme intermediate, Ac–Ser-216, by a double displacement bi-bi mechanism involving a Ser-His-Asp catalytic triad and unconventionally uses an Arg residue in the formation of an oxyanion hole.

acetylation↗
DOE OSTI2026

Structural Mechanism of an Efficacy Photoswitch Targeting the β 2 ‐adrenergic Receptor

The field of photopharmacology develops light-responsive drugs that can modulate protein activity, enabling precise and dynamic investigations of their roles in health and disease. Adrenergic receptors are prominent targets for this approach because they are prototypical G protein-coupled receptors with high clinical relevance in bronchial and cardiovascular diseases. Here, we employed the azobenzene-based compound photoazolol-1 in combination with time-resolved serial crystallography at X-ray free-electron lasers to resolve the molecular mechanisms by which photoswitchable β-blockers modulate activity of the β 2 -adrenoceptor (β 2 AR). Time-resolved structures of the receptor bound to trans-photoazolol-1 (pre-photoconversion), a strained intermediate in the nanosecond range, and the fully photoisomerized cis-photoazolol-1 reveal how isomerization of the azobenzene moiety induces distinct conformational changes within the orthosteric ligand binding pocket. Within seconds, light-excited photoazolol-1 adopts a new binding pose, altering interactions with extracellular loop 2 and shifting the positions of transmembrane helices 5, 6, and 7. Functional assays of β 2 AR in cellular membranes show that photoazolol-1 acts as an efficacy photoswitch, changing from an inverse agonist to a neutral antagonist upon isomerization without leaving the binding pocket. In combination, these findings suggest a molecular mechanism for activity modulation via efficacy photoswitches and provide a framework for designing ligands that exploit light-driven transitions within the binding pocket to achieve spatiotemporal control of receptor function.

G protein-coupled receptors↗