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At least 73 records · Page 4

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗

Overview of Solar Panel Recycling for Indigenous Communities

In recent years, Native tribes across the country have embraced solar energy to power their communities. However, in approximately 25-30 years after installation, the solar panels will enter end-of-life (EOL) status, meaning that they will begin to operate less efficiently than upon initial implementation. At this point, tribes can determine the outcome: they can continue to operate the array, or they can dispose of the panels. Recycling is an option that promotes the use of high-value recyclable materials in solar panels in the circular economy. There are several companies across the US that offer recycling of solar panels, but at various costs. It is important that a hazardous waste expert makes an initial assessment of the solar array to identify any solar panels that cannot be recycled. Currently, recycling solar panels is not cost-effective or environmentally sustainable, but significant research into improving the cost and carbon footprint is ongoing.

14 SOLAR ENERGY↗

Reducing Dark Conductivity of Cesium Tin Halide Perovskites with Donor Doping

The inorganic tin halide perovskites (such as Cs Sn Br 3 and Cs Sn I 3 ) exhibit high hole concentrations, which have been attributed to the presence of intrinsic defects such as cation vacancies. Despite their promise as photovoltaic materials, this high intrinsic conductivity limits deployment. Using hybrid density functional theory, we examine the impact of these intrinsic defects on the electronic properties of Cs Sn Br 3 and Cs Sn I 3 . We find that tin and cesium vacancies have low formation energies, especially under Sn -poor conditions, in agreement with prior work, and that the presence of these native acceptor defects can lead to high hole concentrations. However, effective donor doping of these systems can be obtained via Sc or Y incorporation. These impurities substitute on the Sn site, where they act as single donors. By examining the formation energy of these dopants versus the native defects, we show that Sc or Y doping should lead to a strong compensation, reducing hole concentrations under Sn -rich conditions. Published by the American Physical Society 2025

Lyons, John L. (ORCID:0000000180233055)↗

Contrasting Carbon–Water–Energy Dynamics in Perennial and Annual Bioenergy Agroecosystems Using Eddy Covariance and Interpretable Machine Learning

Understanding how agroecosystems respond to environmental variability is fundamental to predicting productivity and sustainability under a changing climate. We analyzed 55 site-years of high-frequency eddy covariance observations from five agroecosystems—two perennial grasses (miscanthus and switchgrass), two annual rotation systems (maize–soybean and sorghum–soybean), and a restored native prairie—to examine ecosystem-scale carbon, water, and energy fluxes. Using an interpretable machine-learning framework with regression tree ensembles, Shapley Additive Explanations, and Accumulated Local Effects, we quantified how environmental and temporal factors regulate gross primary productivity (GPP), evapotranspiration (ET), water-use efficiency, and the Bowen ratio. Perennials exhibited stronger physiological buffering and maintained fluxes across a broader range of temperature and moisture conditions, reflecting deeper rooting and persistent canopy cover. Annuals, in contrast, showed greater short-term variability and stronger coupling to atmospheric demand, with GPP and ET declining rapidly under low humidity or soil moisture. Differences in temperature sensitivity of Bowen ratio further revealed that perennials sustained proportionally greater sensible heat flux under cool conditions, whereas annuals exhibited constrained energy exchange when evaporative demand was low. Together, these results demonstrate that crop life cycle and canopy structure are fundamental determinants of ecosystem-scale carbon–water–energy coupling. By integrating long-term flux observations with interpretable machine learning, this study identifies the environmental drivers that shape agroecosystem function and highlights how conversion from annual to perennial feedstocks can enhance climatic resilience and alter land–atmosphere energy feedbacks. These findings provide a data-driven basis for improving crop and Earth-system models and for guiding bioenergy landscape design under future climate scenarios.

Accumulated Local Effects↗

Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes

Protein–protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishing a natively bound complex from non-native forms. Current protein docking approaches address this problem by sampling multiple binding modes in proteins and scoring each mode, with the lowest-energy (or highest scoring) binding mode being regarded as a near-native complex. However, high-scoring modes often match poorly with the true bound form, suggesting a need for improvement of the scoring function. Here in this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein–protein interfaces. We tested KFC-E on four benchmark sets of unbound examples and two benchmark sets of bound examples, with the results demonstrating a clear improvement over scores that examine conservation and coevolution across the entire interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Strategies for Superconducting Transmon Qubits with Millisecond T$_1$ Relaxation Time

Significant strides have been made in extending qubit lifetimes by mitigating lossy materials at various surfaces and interfaces of superconducting transmon qubits. We have recently demonstrated a five-fold improvement of T$_1$ energy relaxation time by encapsulating the Nb surface to prevent native oxide formation. To further extend qubit coherence to millisecond timescales and beyond, we are actively exploring novel strategies. Such strategies include substrate preparation, alternative materials as low loss platforms, novel non-oxide forming low loss capping layers, optimized qubit designs & qubit packaging, and optimized Josephson junction materials, processing, and design. Qubit relaxation time T$_1$ measurements will be reported with best T$_1$’s in excess of a millisecond. This material is based upon work supported by the U.S. Department of Energy, Office of Science, National Quantum Information Science Research Centers, Superconducting Quantum Materials and Systems Center (SQMS) under contract number DE-AC02-07CH11359.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Tailoring the Physicochemical Properties of Nb Thin Films via Surface Engineering Methods

The modification of surface oxide layers formed on niobium (Nb) thin films via chemical mechanical planarization (CMP) and accelerated neutral atom beam (ANAB) processing provides a promising route toward tailoring their emergent properties and performance when used as superconducting qubits. Here, in this study, we show that CMP- and ANAB-formed Nb oxides are significantly thinner and smoother than the native oxide, as revealed by transmission electron microscopy (TEM) and atomic force microscopy. Scanning TEM and energy-dispersive X-ray spectroscopy along with X-ray photoelectron spectroscopy identified an oxidation gradient within the native and surface-engineered oxides. The topside layer is dominated by Nb 5+ (Nb 2 O 5 ), with various Nb suboxides present closer to the oxide/metal interface. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling confirmed the presence of an oxygen content gradient and demonstrated the enhanced resistance of the CMP- and ANAB-formed oxides to oxygen surface exchange and subsequent diffusion via 18 O 2 isotopic labeling experiments. ToF-SIMS also identified an interfacial layer containing trapped hydrogen (H)-containing species at the Nb oxide/metal interface. In situ ToF-SIMS and TEM revealed migration of the H/OH interfacial layer coinciding with decomposition of the surface oxide. Furthermore, our density functional theory calculations indicated that both H from moisture present in ambient air and bulk H in Nb films tend to segregate at the interface. These findings underscore the importance of understanding surface oxidation mechanisms, hydrogen incorporation, and their impact on the designed functionalities of Nb-based devices.

36 MATERIALS SCIENCE↗

Two- and three-body fragmentation of multiply charged tribromomethane by ultrafast laser pulses

We investigate the two- and three-body fragmentation of tribromomethane (bromoform, CHBr 3 ) resulting from multiple ionization by 28-femtosecond near-infrared laser pulses with a peak intensity of 6 × 10 14 W cm -2 . The analysis focuses on channels consisting exclusively of ionic fragments, which are measured by coincidence momentum imaging. The dominant two-body fragmentation channel is found to be Br + + CHBr 2 +. Weaker HBr + + CBr 2 +, CHBr + + Br 2 +, CHBr 2+ + Br 2 +, and Br + + CHBr 2 2+ channels, some of which require bond rearrangement prior to or during the fragmentation, are also observed. The dominant three-body fragmentation channel is found to be Br + + Br + + CHBr + . This channel includes both concerted and sequential fragmentation pathways, which we identify using the native frames analysis method. We compare the measured kinetic energy release and momentum correlations with the results of classical Coulomb explosion simulations and discuss the possible isomerization of CHBr 3 to BrCHBr–Br (iso-CHBr 3 ) prior to the fragmentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Overcoming the doping limit in GaAs by ion implantation and pulsed laser melting

Most semiconductors exhibit a saturation of free carriers when heavily doped with extrinsic dopants. This carrier saturation or “doping limit” is known to be related to the formation of native compensating defects, which, in turn, depends on the energy positions of their conduction band minimum and valence band maximum. Here, we carried out a systematic study on the n-type doping limit of GaAs via ion implantation and showed that this doping limitation can be alleviated by the transient process of pulsed laser melting (PLM). For n-type doping, both group VI (S) and amphoteric group IV (Si and Ge) dopants were implanted in GaAs. For comparison, p-type doping was also studied using Zn as the acceptor. Implanted dopants were activated by the PLM method, and the results are compared to rapid thermal annealing (RTA). Our results reveal that for all n-type dopants, while implantation followed by the RTA results in a similar saturation electron concentration of 2–3 × 10 18 cm –3 , the transient PLM process is capable of trapping high concentration of dopants in the substitutional site, giving rise to a carrier concentration of >10 19 cm –3 , exceeding the doping limit of GaAs. However, due to scatterings from point defects generated during PLM, the mobility of n-type GaAs after PLM is low (~80–260 cm 2 /V s). Subsequent RTA after PLM (PLM + RTA) is able to remove these point defects and recover the mobility to ~1000–2000 cm2/V s. The carrier concentrations of these PLM + RTA samples are reduced but are still a factor of 3 higher than RTA only GaAs. This can be understood as the dopants are already incorporated in the substitutional site after PLM; they are less likely to be “deactivated” by subsequent RTA. This work is significant to the understanding of doping mechanisms in semiconductors and provides a means for device applications, which require materials with ultra-high doping.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Milestone 1.2.14: Surface Characterization of Irradiated Surrogate Non-Native Corrosion Plumes on Aluminum 6061-T6 Specimens

The United States Department of Energy is seeking to evaluate the feasibility of extended dry storage of aluminum-clad spent nuclear fuel (ASNF) in helium-backfilled cannisters. A significant research effort has been devoted to determining the amount of radiation-induced molecular hydrogen generation from corrosion layers that would be present on the fuel assembly surfaces. However, to date, no evidence of radiation-induced changes in the microstructure of the corroded aluminum surfaces have been reported. This report provides surface characterization, in terms of corrosion layer composition and morphology, for aluminum alloy 6061-T6 “plume” samples subjected to one of three potential ASNF drying techniques—“vacuum only”, “vacuum + 4 hours at 100 oC”, and “vacuum + 4 hours at 220 oC”—and gamma irradiated (= 53 MGy) in the presence of helium gas with ~0% added relative humidity. At these high absorbed gamma doses, for the first time ever, radiation-induced circular defects were found on the sample surface, regardless of the drying regime employed. Additionally, large cracks that penetrated through the corrosion layer to expose bare aluminum metal were observed in irradiated “plume” specimens subjected to drying conditions of “vacuum + 4 hours at 220 oC”. The nature and implications of these defects on the extended dry storage of ASNF is unclear, requiring further study.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Climate cooling benefits of cellulosic bioenergy crops from elevated albedo

Abstract Changes in land surface albedo can alter ecosystem energy balance and potentially influence climate. We examined the albedo of six bioenergy cropping systems in southwest Michigan USA: monocultures of energy sorghum ( Sorghum bicolor ), switchgrass ( Panicum virgatum L.), and giant miscanthus ( Miscanthus × giganteus) , and polycultures of native grasses, early successional vegetation, and restored prairie. Direct field measurements of surface albedo ( α s ) from May 2018 through December 2020 at half‐hourly intervals in each system quantified the magnitudes and seasonal differences in albedo (∆ α ) and albedo‐induced radiative forcing (RF ∆ α ). We used a nearby forest as a historical native cover type to estimate reference albedo and RF ∆ α change upon original land use conversion, and a continuous no‐till maize ( Zea mays L .) system as a contemporary reference to estimate change upon conversion from annual row crops. Annually, α s differed significantly ( p < 0.05) among crops in the order: early successional (0.288 ± 0.012SE) >> miscanthus (0.271 ± 0.009) ≈ energy sorghum (0.270 ± 0.010) ≥ switchgrass (0.265 ± 0.009) ≈ restored prairie (0.264 ± 0.012) > native grasses (0.259 ± 0.010) > maize (0.247 ± 0.010). Reference forest had the lowest annual α s (0.134 ± 0.003). Albedo differences among crops during the growing season were also statistically significant, with growing season α s in perennial crops and energy sorghum on average ~20% higher (0.206 ± 0.003) than in no‐till maize (0.184 ± 0.002). Average non‐growing season (NGS) α s (0.370 ± 0.020) was much higher than growing season α s (0.203 ± 0.003) but these NGS differences were not significant. Overall, the original conversion of reference forest and maize landscapes to perennials provided a cooling effect on the local climate (RF αMAIZE : −3.83 ± 1.00 W m −2 ; RF αFOREST : −16.75 ± 3.01 W m −2 ). Significant differences among cropping systems suggest an additional management intervention for maximizing the positive climate benefit of bioenergy crops, with cellulosic crops on average ~9.1% more reflective than no‐till maize, which itself was about twice as reflective as the reference forest.

Lei, Cheyenne↗

Low-energy electron driven reactions in 2-bromo-5-nitrothiazole

Thiazole derivatives are biologically relevant molecules, used also in pharmaceutical applications. Herein, we report results for electron attachment to 2-bromo-5-nitrothiazole (BNT) in the gas phase. Employing two crossed electron–molecule beam experiments, we determined the efficiency curves of various fragment anions as a function of the initial electron energy between about 0 and 10 eV as well as the emission angle and kinetic energy distributions of Br− and NO2− ions formed from a resonance near 4 eV. The experiments were supported by quantum chemical calculations, exploring possible dissociation pathways along with their reaction energies. We also compared the electron attachment characteristics of BNT with those of the native thiazole molecule by performing electron attachment experiments and calculations for this molecule as well. Compared to thiazole, which is primarily degraded only by electrons with kinetic energies between about 5 and 10 eV, BNT is susceptible to low-energy electrons near 0 eV with enhanced cross section for (dissociative) electron attachment. However, although BNT offers two localization sites with high electron affinity (Br and NO2 moieties), we do not find the corresponding anions as the dominant negatively charged species formed upon electron attachment. Instead, the reaction channels with an abstraction of Br and NO2 as neutral radicals prevail, accompanied by the opening of the thiazole ring due to the relatively weak C–S bond.

Chen, Jiakuan (ORCID:0009000729608641)↗

Native Top-Down Mass Spectrometry Characterization of Model Integral Membrane Protein Bacteriorhodopsin

Bacteriorhodopsin (bR) from Halobacterium salinarum has been a model system for structural biology and is a structural template for the characterization of membrane G-protein couple receptors (GPCRs) in particular. Here, in this study, wild-type bacteriorhodopsin and two single-residue mutants were characterized by native top-down mass spectrometry (nTD-MS) with Orbitrap-based high-energy collision dissociation (HCD) and electron capture dissociation (ECD). After in-source dissociation ejected the membrane protein from detergent micelles, high-resolution native MS measurement allowed for identification of multiple proteoforms as well as lipid-bound forms. Further top-down MS measurements by HCD produced a large number of product ions for in-depth sequencing and unambiguous localization of post-translational modifications. For the first time, native TD-MS with ECD was used to characterize an integral membrane protein. ECD yielded fragments originating from all helices and loop regions, even accessing a sequence stretch that HCD could not. Combining HCD and ECD fragmentation patterns significantly enhanced the sequence coverage of bR. We propose bR to be a model analyte for testing nTD-MS performance for membrane proteins.

crystal cleavage↗

Identifying native point defect configurations in α-alumina

Intimately intertwined atomic and electronic structures of point defects govern diffusion-limited corrosion and underpin the operation of optoelectronic devices. For some materials, complex energy landscapes containing metastable defect configurations challenge first-principles modeling efforts. Here, we thoroughly reevaluate native point defect geometries for the illustrative case of α-Al 2 O 3 by comparing three methods for sampling candidate geometries in density functional theory calculations: displacing atoms near a naively placed defect, initializing interstitials at high-symmetry points of a Voronoi decomposition, and Bayesian optimization. We find symmetry-breaking distortions for oxygen vacancies in some charge states, and we identify several distinct oxygen split-interstitial geometries that help explain literature discrepancies involving this defect. We also report a surprising and, to our knowledge, previously unknown trigonal geometry favored by aluminum interstitials in some charge states. Importantly, these new configurations may have transformative impacts on our understanding of defect migration pathways in aluminum-oxide scales protecting metal alloys from corrosion. Overall, the Voronoi scheme appears most effective for sampling candidate interstitial sites because it always succeeded in finding the lowest-energy geometry identified in this study, although no approach found every metastable configuration. Finally, we show that the position of defect levels within the band gap can depend strongly on the defect geometry, underscoring the need to conduct careful searches for ground-state geometries in defect calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Introduction to this special section: Geothermal energy

Geothermal energy is a global renewable resource that has the potential to provide a significant portion of baseload energy in many regions. In the United States, it has the potential to provide 8.5% of the electric generation capacity by the middle of the century. In general, geothermal systems require heat, permeability, and water to be viable for energy generation. However, with current technologies, only heat is strictly necessary in a native system. Engineered geothermal systems (EGS) introduce water into the subsurface at elevated pressures and reduced temperatures and enhance permeability through hydraulic and/or shear fracturing. Additionally, although moderate- to high-temperature resources currently dominate geothermal energy production, low-temperature resources have been utilized for direct-use cases. When well balanced and maintained, geothermal resources can produce significant amounts of heat and achieve long-term sustainability on the order of an estimated tens to hundreds of years.

15 GEOTHERMAL ENERGY↗

Making Northway, Alaska Resilient and Sustainable Through Energy Efficiency and Solar Power

This project implemented energy efficiency measures and installed 6 kW solar arrays on three community buildings in Northway, Alaska, in a collaboration between the Department of Energy - Office of Indian Energy Policy and Programs, the Northway Village Council (NVC), the Tanana Chiefs Conference (TCC), and the Alaska Native Tribal Health Consortium (ANTHC). Northway is a small community in interior Alaska, close to the Canadian border, with high fuel and energy costs: $3.00 per gallon of diesel and $0.56 per kWh, respectively, in 2016, when the project began. The energy efficiency and solar power installation plans aligned with Northway’s long-term energy goals of increasing renewable energy and decreasing reliance on fossil fuels, per the Northway Community Energy Action Plan, the Alaska Interior Regional Energy Plan, and TCC Comprehensive Economic Development Strategy. The project focused on three buildings: (1) the community hall (and later office) building, (2) the washeteria building, and (3) the water/sewer garage. It included multiple directions for energy efficiency measures, such as installing LED lighting upgrades, programmable thermostats, vending machine energy misers, efficient pumps, and adding glycol loops at the water/sewer plant. Since the village has a high potential for solar energy, in order to increase resilience and decrease costs, solar systems were installed on three community buildings. Later, a battery was installed in the community hall to capture solar power produced but not used during the day, and allow the flexibility to use that power during evening and night, further decreasing the reliance on grid power for that building. Electricity savings realized by the village between 2011-2012 and 2018-2019 by improving energy efficiencies in the buildings and adding solar was 23%. This is despite the community hall doubling in size during the same time period. If that is taken into consideration (by adding community hall usage into the 2011-2012 usage one additional time), the energy savings from 2011-2012 to 2018-2019 was 37%.

14 SOLAR ENERGY↗

Combining Spatial and Temporal Resolution in Cryo-TEM of Device Materials: Preprint

Cryogenic transmission electron microscopy (cryo-TEM) has been instrumental to reducing the effects of electron-beam sample interactions and enabling higher spatial resolution studies of beam sensitive materials. However, the process of thinning and freezing samples for cryo-TEM characterization is often complex and frequently involves removing materials from their environment or stimuli of interest for extended times. This can allow for structural relaxation, diffusion, and other dynamic processes to occur prior to characterization; for energy materials like battery electrodes, this makes it difficult to precisely correlate the imaged structure with native structures that evolve in-situ during device processing, operation, or aging. Here, we present methods to prepare cryo-TEM samples from energy materials during these critical processes in the relevant device lifetimes. This offers insights into improving the temporal resolution of cryo-TEM, while still exploiting its ability to achieve high spatial resolutions in characterizing beam sensitive materials.

BASIC BIOLOGICAL SCIENCES,MATERIALS SCIENCE↗

Investigating the Effect of Water on the Mechanical Properties of Cellulose from Multiscale Molecular Dynamics Simulations

Classical molecular dynamics (MD) simulations provide insight into the structure and physicochemical properties of materials with atomic resolution. However, the length and time scales accessible to atomistic MD are orders of magnitude smaller than many relevant processes such as the response of a bulk material to experimentally accessible strain rates, which presents challenges when comparing models to experimental measurements. Bottom-up coarse-graining provides a means for systematically mapping atomistic information to lower resolution models to increase the length and time scales achievable by simulation. Cellulose is an abundant carbohydrate biopolymer with applications to many fields of research, such as materials science and renewable energy, due to its desirable mechanical properties and viability for conversion into biofuel. The effect of moisture content on the Young's modulus of cellulose is of special interest due to its native environment often being in the hydrated secondary plant cell wall and the grinding energy requirements for biomass feedstock preprocessing. The current work investigates the effects of water solvent on the Young's modulus of cellulose calculated from coarse-grained MD mechanical stress simulations. The coarse-grained model was parametrized from atomistic MD calculations of cellulose-cellulose potentials of mean force using umbrella sampling techniques under vacuum and solvated conditions. The Young's moduli of the coarse-grained cellulose assemblies parametrized from cellulose in vacuum or solvated in water were computed via mechanical stress simulations to highlight the importance of capturing solvent interactions for modeling the mechanical behavior of cellulose.

BASIC BIOLOGICAL SCIENCES,RADIATION PROTECTION AND↗