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At least 397 records · Page 22

Pacific Northwest National Laboratory Annual Site Environmental Report for Calendar Year 2021 (Final Report)

The U.S. Department of Energy requires that all its site facilities develop an annual site environmental report to comply with DOE Order 231.1B Chg 1 and DOE Order 458.1 Admin Chg 4. This report provides a synopsis of calendar year 2021 information related to environmental management performance and compliance efforts at the Pacific Northwest National Laboratory. It summarizes site compliance with federal, state, and local environmental laws, regulations, policies, directives, permits, and Orders, and provides environmental management performance benchmarks and their status to the public, regulatory agencies, community officials, Native American tribes, and public interest groups.

54 ENVIRONMENTAL SCIENCES↗

4-Clique network minor embedding for quantum annealers

Quantum annealing is a quantum algorithm for computing solutions to combinatorial optimization problems. This study proposes a method for minor embedding optimization problems onto sparse quantum annealing hardware graphs called 4-clique network minor embedding. This method is in contrast to the standard minor embedding technique of using a path of linearly connected qubits in order to represent a logical variable state. The 4-clique minor embedding is possible on Pegasus graph connectivity, which is the native hardware graph for some of the current D-Wave quantum annealers. The Pegasus hardware graph contains many cliques of size 4, making it possible to form a graph composed entirely of paths of connected 4-cliques on which a problem can be minor-embedded. The 4-clique chains come at the cost of additional qubit usage on the hardware graph, but they allow for stronger coupling within each chain, thereby increasing chain integrity, reducing chain breaks, and allow for greater usage of the available energy scale for programming logical problem coefficients on current quantum annealers. The 4-clique minor embedding technique is compared with the standard linear path minor embedding with experiments on two D-Wave quantum annealing processors with Pegasus hardware graphs. We show proof-of-concept experiments where the 4-clique minor embeddings can use weak chain strengths while successfully carrying out the computation of minimizing random all-to-all spin glass problem instances. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Bacterial α-diglucoside metabolism: perspectives and potential for biotechnology and biomedicine

In a competitive microbial environment nutrient acquisition is a major contributor to the survival of any individual bacterial species, and the ability to access uncommon energy sources can provide a fitness advantage. One set of soluble carbohydrates that have attracted increased attention for use in biotechnology and biomedicine are the α-diglucosides. Maltose is the most well studied member of this class, however the remaining four less common α-diglucosides (trehalose, kojibiose, nigerose, and isomaltose) are increasingly used in processed food and fermented beverages. The consumption of trehalose has recently been shown to be a contributing factor in gut microbiome disease as certain pathogens are using α-diglucosides to outcompete native gut flora. Kojibiose and nigerose have also been examined potential prebiotics and alternative sweeteners for a variety of foods. Compared to the study of maltose metabolism our understanding of the synthesis and degradation of uncommon α-diglucosides is lacking and several fundamental questions that remain unanswered, particularly in regards to the regulation of bacterial metabolism for α-diglucosides. Therefore this minireview attempts to provide a focused analysis of uncommon α-diglucoside metabolism in bacteria, and suggests some future directions for this research area that could potentially accelerate biotechnology and biomedicine developments.

59 BASIC BIOLOGICAL SCIENCES↗

Unveiling the nanoscale architectures and dynamics of protein assembly with in situ atomic force microscopy

Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter- and intra-molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter- and intra-molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high-speed AFM in near-native environments and recent AFM developments in the multimodal high-resolution imaging, bimodal imaging, live cell imaging, and machine-learning-enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.

36 MATERIALS SCIENCE↗

Pb dimerization greatly accelerates charge losses in MAPbI 3 : Time-domain ab initio analysis

Metal halide perovskites constitute a new type of semiconducting materials with long charge carrier lifetimes and efficient light-harvesting. The performance of perovskite solar cells and related devices is limited by nonradiative charge and energy losses, facilitated by defects. Combining nonadiabatic molecular dynamics and time-domain density functional theory, we demonstrate that charge losses depend strongly on the defect chemical state. By considering an extra Pb atom in CH 3 NH 3 PbI 3 , which is a common defect in lead halide perovskites, we investigate its influence on charge trapping and recombination. In a chemically inert form as a Pb interstitial, the extra Pb atom has only a mild influence on charge recombination. However, if the extra Pb atom binds to a native Pb atom to form a dimer, the charge trapping and recombination are greatly accelerated because the Pb-dimer creates a localized midgap trap state that couples strongly to the perovskite valence band edge. Holes disappear from the valence band two orders of magnitude faster than in the pristine perovskite and recombine with conduction band electrons one order of magnitude faster. The simulations identify the phonon modes involved in the nonradiative charge trapping and recombination and highlight the importance of rapid decoherence within the electronic subsystem for long carrier lifetimes. The detailed atomistic analysis of the charge trapping and recombination mechanisms enriches the understanding of defect properties and provides theoretical guidance for improving perovskite performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

P-type conductivity in Sn-doped Sb 2 Se 3

Abstract Antimony selenide (Sb 2 Se 3 ) is a promising absorber material for thin-film photovoltaics. However, certain areas of fundamental understanding of this material remain incomplete and this presents a barrier to further efficiency gains. In particular, recent studies have highlighted the role of majority carrier type and extrinsic doping in drastically changing the performance of high efficiency devices (Hobson et al 2020 Chem. Mater. 32 2621–30). Herein, Sn-doped Sb 2 Se 3 bulk crystals are shown to exhibit p-type conductivity using Hall effect and hot-probe measurements. The measured conductivities are higher than those achieved through native defects alone, but with a carrier density (up to 7.4 × 10 14 cm −3 ) several orders of magnitude smaller than the quantity of Sn included in the source material. Additionally, a combination of ultraviolet, x-ray and hard x-ray photoemission spectroscopies are employed to obtain a non-destructive depth profile of the valence band maximum, confirming p-type conductivity and indicating a majority carrier type inversion layer at the surface. Finally, these results are supported by density functional theory calculations of the defect formation energies in Sn-doped Sb 2 Se 3 , showing a possible limit on the carrier concentration achievable with Sn as a dopant. This study sheds light on the effectiveness of Sn as a p-type dopant in Sb 2 Se 3 and highlights avenues for further optimisation of doped Sb 2 Se 3 for solar energy devices.

36 MATERIALS SCIENCE↗

Integrating New Arctic Plant Functional Types in a Land Surface Model Using Above- and Belowground Field Observations: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic publication "Integrating New Arctic Plant Functional Types in a Land Surface Model Using Above- and Belowground Field Observations". We used field observations of biomass and leaf traits (Salmon et al., 2019b) across a gradient of plant communities on the Seward Peninsula in northwest Alaska (Breen et al., 2020; Iversen et al., 2017) to replace the original ELM configuration with nine, arctic-specific PFTs. Original arctic PFTs in the model were (1) broadleaf deciduous boreal shrub and (2) C3 arctic grass. New PFTs were (1) lichen, (2) bryophyte, (3) evergreen dwarf shrub, (4) deciduous dwarf shrub, (5) deciduous low shrub, (6) deciduous low to tall shrub, (7) alder shrub, (8) forb, and (9) graminoid. New PFTs were parameterized and evaluated using site-level trait and biomass measurements (Salmon et al., 2019b), root C:N ratios and rooting depth patterns (Salmon et al., 2019c), and root biomass (Salmon et al., 2020). This archive contains forcing data and model output from ELM simulations conducted at the Kougarok Hillslope site (Kougarok Road Mile Marker 64). Simulations were conducted for the Kougarok Hillslope site using meteorological driving data from the Scenarios Network for Alaska and Arctic Planning (SNAP) downscaled climate projection dataset using NCAR-CCSM forcing (Bieniek et al., 2020 dataset; Walsh et al., 2018). The archive includes three versions of model simulations representing a progression from the original model configuration to an Arctic-specific configuration (see Output section below). Simulation 1 used grid cell data from a global E3SM configuration, including the fractional area of E3SM PFTs assigned to the grid cell containing the Kougarok Hillslope site in global simulations. This simulation did not distinguish between different plant communities on the Kougarok Hillslope, but instead used a single point simulation to represent the entire area. Simulation 2 used default E3SM PFT definitions combined with adjusted depth to bedrock for plant communities with shallow rocky layers to represent the role of abiotic soil factors in driving site differences (based on depth measurements of Iversen et al., 2019a), and adjusted the relative areas of the broadleaf deciduous boreal shrub and C3 arctic grass PFTs to reflect the observed spatial coverage of shrub and non-shrub PFTs across Kougarok Hillslope plant communities. Simulation 3 used the new arctic PFT definitions and parameterizations based on the vegetation types present at the site, along with the adjusted soil depths used in Simulation 2. Included are *.pdf, *.nc (NetCDF), *tar.gz, *.py, and *.bash files. We would like to thank Mary's Igloo Native Corporation for allowing us to perform this research on their land and giving us the opportunity to share this research with their community. Thanks to Shawn Serbin and Alistair Rogers for helpful discussions. Holly Vander Stel, Joanne Childs, and Stan Wullschleger helped with collection of field data. 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↗

Probing elemental speciation in hydrochar produced from hydrothermal liquefaction of anaerobic digestates using quantitative X-ray diffraction

Valorization of hydrochar, a solid byproduct from hydrothermal liquefaction (HTL) of anaerobically-digested agriculture wastes (digestates), requires fundamental knowledge of elemental speciation. This study investigated the effects of reaction temperatures (320–360 °C), digestate pH (3.5–8), and digestate cellulose-to-lignin ratios (0.2–1.8) on the speciation (chemical form) and composition of organics and inorganics in hydrochars produced during hydrothermal treatment. Quantitative X-ray diffraction (XRD) method was the primary technique used to characterize hydrochars. The comprehensive XRD pattern processing including the Rietveld refinement protocols demonstrated that the organic phase was comprised of mostly crystalline monocyclic, heterocyclic, and polycyclic aromatics with diverse aliphatic and aromatic substituents, while the inorganic mineral phase consisted of calcium-phosphates, magnesium-phosphates, calcium-carbonates, and magnesium-carbonates. Further, XRD results were validated by the elemental yields of products and the distribution of chemical functionalities measured using solid-state nuclear magnetic resonance (NMR) spectroscopy. The characterization data were used to evaluate proposed mechanistic pathways using compositional analysis of biocrude and aqueous-phase coproducts. Mechanistic pathways developed in the study suggested that benzoic acids, phenols, benzaldehydes, phenolic aldehydes, α-dicarbonyls, and α-hydroxycarbonyls were responsible for the precipitation of organics through various reactions depending on operating conditions. Meanwhile, the formation of inorganic compounds appeared to be consistently represented by reactions including dehydration, hydrolysis, endergonic reduction, and structure rearrangement of native minerals in the digestates. This study provides basic knowledge needed to create and assess potential elemental speciation pathways. In addition, the results of the study facilitate the specification of process conditions to optimize targeted utilization routes of hydrochar for more economically-feasible and sustainable HTL processing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Decorated networks of native proteins: nanomaterials with tunable mesoscopic domain size

Natural and artificial proteins with designer properties and functionalities offer unparalleled opportunity for functional nanoarchitectures formed through self-assembly. However, to exploit this potential we need to design the system such that assembly results in desired architecture forms while avoiding denaturation and therefore retaining protein functionality. Here we address this challenge with a model system of fluorescent proteins. By manipulating self-assembly using techniques inspired by soft matter where interactions between the components are controlled to yield the desired structure, we have developed a methodology to assemble networks of proteins of one species which we can decorate with another, whose coverage we can tune. Consequently, the interfaces between domains of each component can also be tuned, with potential applications for example in energy – or electron – transfer. Our model system of eGFP and mCherry with tuneable interactions reveals control over domain sizes in the resulting networks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Soft Lattice and Defect Covalency Rationalize Tolerance of β‐CsPbI 3 Perovskite Solar Cells to Native Defects

Abstract Although all‐inorganic metal halide perovskites (MHPs) have shown tremendous improvement, they are still inferior to the hybrid organic–inorganic MHPs in efficiency. Recently, a conceptually new β‐CsPbI 3 perovskite reached 18.4 % efficiency combined with good thermodynamic stability at ambient conditions. We use ab initio non‐adiabatic molecular dynamics to show that native point defects in β‐CsPbI 3 are generally benign for nonradiative charge recombination, regardless of whether they introduce shallow or deep trap states. These results indicate that MHPs do not follow the simple models used to explain defect‐mediated charge recombination in the conventional semiconductors. The strong tolerance is due to the softness of the perovskite lattice, which permits separation of electrons and holes upon defect formation, and only allows carriers to couple to the low‐frequency vibrations. Both factors decrease notably the non‐adiabatic coupling and slow down the dissipation of energy to heat.

Chu, Weibin↗

Molecular Design Principles for Photosystem I-Based Biohybrid Solar Fuel Catalysts

Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase, can be repurposed for solar-fuel production by coupling its photochemistry to catalytic interfaces. However, the molecular determinants that govern productive electron transfer to abiotic catalysts remain poorly understood. Here, we present molecular structures of active PSI-Pt nanoparticle (PtNP) biohybrids that reveal how protein architecture controls catalyst access, binding geometry, and photocatalytic efficiency. Removal of stromal subunits exposes the electron transfer chain and enables PtNP binding proximal to the F X cluster, demonstrating that steric occlusion limits access to native acceptor regions in PSI. In contrast, in trimeric PSI, PtNPs bind at multiple sites per monomer, but only a subset are positioned within electron transfer distance of terminal cofactors, resulting in a heterogeneous population of productive and nonproductive configurations. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances that govern catalyst binding and electron transfer. These results establish that catalytic inefficiency arises not only from intrinsic electron transfer constraints but also from the distribution of binding geometries imposed by the protein scaffold. Together, these findings provide a molecular framework linking protein structure to biohybrid function and define design principles for engineering PSI-based solar fuel systems and protein-nanomaterial interfaces for light-driven catalysis.

biohybrid↗

Numerical Simulations of Carbon Dioxide Storage Efficiency in Heterogeneous Reservoir Models

The U.S. Department of Energy’s National Energy Technology Laboratory (DOE-NETL) has been developing methods and tools (the online Carbon Dioxide Storage prospeCtive Resource Estimation Excel aNalysis (CO2-SCREEN) tool) to estimate carbon dioxide (CO2) storage potential in subsurface reservoirs. The CO2 storage efficiency terms are input in the tool to calculate storage potential in targeted reservoirs. In this effort, two CO2 storage efficiency terms were evaluated: volumetric displacement ( E V ) and microscopic displacement ( E d ). The first term deals with efficiency of CO2 propagation into an accessible reservoir volume, while the second term evaluates effectiveness of native fluid displacement with CO2. The interpreted well logs and core sample measurements were applied to create the heterogeneous reservoir models including geostatistical realizations of porosity and intrinsic permeability fields. Supercritical CO2 was injected over the course of 30 years into brine-saturated reservoir models for clastics, limestone, and dolomite lithologies and deltaic fluvial, aeolian, shallow marine, and reef depositional environments by means of varying reservoir parameters and injection scenarios. The reservoir models providing vertically heterogeneous petrophysical properties and designated as “layered reservoir models” (with homogeneous parameters along each layer of the model) were not determined to be a transition between the homogeneous and heterogeneous models in respect to storage efficiency. Another finding shows that high-efficiency factors do not necessarily mean increased CO2 storage; they rather indicate that the available volume and pore space are more fully utilized. The CO2 storage efficiency factors were evaluated dynamically at the select time points using P 10 ‐ P 50 ‐ P 90 percentiles. The results of this study show that the P 10 ‐ P 90 distribution for volumetric efficiency is wider when compared to the microscopic efficiency. It was found that where dominant buoyancy forces drive the plume to the top of a target formation, the volumetric efficiency is low. Tighter sandstone and carbonate formations show prevalence of capillary forces and better utilization of reservoir volume.

Myshakin, Evgeniy M.↗

FIFE data analysis: Testing BIOME-BGC predictions for grasslands

The First International Satellite Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE) was conducted in a 15 km by 15 km research area located 8 km south of Manhattan, Kansas. The site consists primarily of native tallgrass prairie mixed with gallery oak forests and croplands. The objectives of FIFE are to better understand the role of biology in controlling the interactions between the land and the atmosphere, and to determine the value of remotely sensed data for estimating climatological parameters. The goals of FIFE are twofold: the upscale integration of models, and algorithm development for satellite remote sensing. The specific objectives of the field campaigns carried out in 1987 and 1989 were the simultaneous acquisition of satellite, atmospheric, and surface data; and the understanding of the processes controlling surface energy and mass exchange. Collected data were used to study the dynamics of various ecosystem processes (photosynthesis, evaporation and transpiration, autotrophic and heterotrophic respiration, etc.). Modelling terrestrial ecosystems at scales larger than that of a homogeneous plot led to the development of simple, generalized models of biogeochemical cycles that can be accurately applied to different biomes through the use of remotely sensed data. A model was developed called BIOME-BGC (for BioGeochemical Cycles) from a coniferous forest ecosystem model, FOREST-BGC, where a biome is considered a combination of a life forms in a specified climate. A predominately C4-photosynthetic grassland is probably the most different from a coniferous forest possible, hence the FIFE site was an excellent study area for testing BIOME-BGC. The transition from an essentially one-dimensional calculation to three-dimensional, landscape scale simulations requires the introduction of such factors as meteorology, climatology, and geomorphology. By using remotely sensed geographic information data for important model inputs, process-based ecosystem simulations at a variety of scales are possible. The second objective of this study is concerned with determining the accuracy of the estimated fluxes from BIOME-BGC, when extrapolated spatially over the entire 15-km by 15-km FIFE site. To accomplish this objective, a topographically distributed map of soil depth at the FIFE site was developed. These spatially-distributed fluxes were then tested with data from aircraft by eddy-flux correlation obtained during the FIFE experiment.

Hunt, E. Raymond, Jr.↗

Use of Existing CAD Models for Radiation Shielding Analysis

The utility of a radiation exposure analysis depends not only on the accuracy of the underlying particle transport code, but also on the accuracy of the geometric representations of both the vehicle used as radiation shielding mass and the phantom representation of the human form. The current NASA/Space Radiation Analysis Group (SRAG) process to determine crew radiation exposure in a vehicle design incorporates both output from an analytic High Z and Energy Particle Transport (HZETRN) code and the properties (i.e., material thicknesses) of a previously processed drawing. This geometry pre-process can be time-consuming, and the results are less accurate than those determined using a Monte Carlo-based particle transport code. The current work aims to improve this process. Although several Monte Carlo programs (FLUKA, Geant4) are readily available, most use an internal geometry engine. The lack of an interface with the standard CAD formats used by the vehicle designers limits the ability of the user to communicate complex geometries. Translation of native CAD drawings into a format readable by these transport programs is time consuming and prone to error. The Direct Accelerated Geometry -United (DAGU) project is intended to provide an interface between the native vehicle or phantom CAD geometry and multiple particle transport codes to minimize problem setup, computing time and analysis error.

Lee, K. T.↗

First-principles study of hydrogen- and oxygen-related complexes in ScN

Scandium nitride (ScN) is an attractive material for electronic applications due to its high n-type conductivity. Native defects and unintentional impurities may limit its electron concentration and reduce its mobility; therefore, it is important to control their formation and incorporation. Hydrogen and oxygen are unintentional impurities that are commonly present during growth and processing. They act as shallow donors in ScN and hence may be regarded as harmless or even favorable to achieving n-type conductivity. Here we show, using state-of-the-art first-principles calculations, that these impurities can be detrimental because they readily form complexes with scandium vacancies (V Sc ). Isolated V Sc have relatively high formation energies and thus have low concentrations and little impact on electronic properties. However, complexes between V Sc and either hydrogen or oxygen form more readily than the pristine vacancy and will act as both compensating and scattering centers. Our results point to the importance of controlling the incorporation of hydrogen and oxygen in ScN (and AlScN alloys) to avoid degradation of the electronic properties.

36 MATERIALS SCIENCE↗

Valorization of CO 2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator

Coupling recent advancements in genetic engineering of diverse microbes and gas-driven fermentation provides a path toward sustainable commodity chemical production. Cupriavidus necator H16 is a suitable species for this task because it effectively utilizes H 2 and CO 2 and is genetically tractable. Here, we demonstrate the versatility of C. necator for chemical production by engineering it to produce three products from CO 2 under lithotrophic conditions: sucrose, polyhydroxyalkanoates (PHAs), and lipochitooligosaccharides (LCOs). We engineered sucrose production in a co-culture system with heterotrophic growth 30 times that of WT C. necator. We engineered PHA production (20-60% DCW) and selectively altered product composition by combining different thioesterases and phaCs to produce copolymers directly from CO 2 . And, we engineered C. necator to convert CO 2 into the LCO, a plant growth enhancer, with titers of ~1.4 mg/L—equivalent to yields in its native source, Bradyrhizobium. Here, we applied the LCOs to germinating seeds as well as corn plants and observed increases in a variety of growth parameters. Taken together, these results expand our understanding of how a gas-utilizing bacteria can promote sustainable production.

09 BIOMASS FUELS↗