Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “SUSAN”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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

At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

NUB1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome

The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor NUB1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system with human components and revealed that NUB1 uses the intrinsic instability of FAT10 to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin-independent and p97-independent manner. Using hydrogen–deuterium exchange, structural modeling and site-directed mutagenesis, we identified the formation of an intricate complex with FAT10 that activates NUB1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic NUB1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These findings identified a previously unknown mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.

Arkinson, Connor↗
DOE OSTI2022

Enabling FAIR data in Earth and environmental science with community-centric (meta)data reporting formats

Abstract Research can be more transparent and collaborative by using Findable, Accessible, Interoperable, and Reusable (FAIR) principles to publish Earth and environmental science data. Reporting formats—instructions, templates, and tools for consistently formatting data within a discipline—can help make data more accessible and reusable. However, the immense diversity of data types across Earth science disciplines makes development and adoption challenging. Here, we describe 11 community reporting formats for a diverse set of Earth science (meta)data including cross-domain metadata (dataset metadata, location metadata, sample metadata), file-formatting guidelines (file-level metadata, CSV files, terrestrial model data archiving), and domain-specific reporting formats for some biological, geochemical, and hydrological data (amplicon abundance tables, leaf-level gas exchange, soil respiration, water and sediment chemistry, sensor-based hydrologic measurements). More broadly, we provide guidelines that communities can use to create new (meta)data formats that integrate with their scientific workflows. Such reporting formats have the potential to accelerate scientific discovery and predictions by making it easier for data contributors to provide (meta)data that are more interoperable and reusable.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The Arctic Plant Aboveground Biomass Synthesis Dataset

Plant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m -2 ) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Reduction of the molecular hamiltonian matrix using quantum community detection

Abstract Quantum chemistry is interested in calculating ground and excited states of molecular systems by solving the electronic Schrödinger equation. The exact numerical solution of this equation, frequently represented as an eigenvalue problem, remains unfeasible for most molecules and requires approximate methods. In this paper we introduce the use of Quantum Community Detection performed using the D-Wave quantum annealer to reduce the molecular Hamiltonian matrix in Slater determinant basis without chemical knowledge. Given a molecule represented by a matrix of Slater determinants, the connectivity between Slater determinants (as off-diagonal elements) is viewed as a graph adjacency matrix for determining multiple communities based on modularity maximization. A gauge metric based on perturbation theory is used to determine the lowest energy cluster. This cluster or sub-matrix of Slater determinants is used to calculate approximate ground state and excited state energies within chemical accuracy. The details of this method are described along with demonstrating its performance across multiple molecules of interest and bond dissociation cases. These examples provide proof-of-principle results for approximate solution of the electronic structure problem using quantum computing. This approach is general and shows potential to reduce the computational complexity of post-Hartree–Fock methods as future advances in quantum hardware become available.

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

Influence of soil heterogeneity on soybean plant development and crop yield evaluated using time-series of UAV and ground-based geophysical imagery

Understanding the interactions among agricultural processes, soil, and plants is necessary for optimizing crop yield and productivity. This study focuses on developing effective monitoring and analysis methodologies that estimate key soil and plant properties. These methodologies include data acquisition and processing approaches that use unmanned aerial vehicles (UAVs) and surface geophysical techniques. In particular, we applied these approaches to a soybean farm in Arkansas to characterize the soil–plant coupled spatial and temporal heterogeneity, as well as to identify key environmental factors that influence plant growth and yield. UAV-based multitemporal acquisition of high-resolution RGB (red–green–blue) imagery and direct measurements were used to monitor plant height and photosynthetic activity. We present an algorithm that efficiently exploits the high-resolution UAV images to estimate plant spatial abundance and plant vigor throughout the growing season. Such plant characterization is extremely important for the identification of anomalous areas, providing easily interpretable information that can be used to guide near-real-time farming decisions. Additionally, high-resolution multitemporal surface geophysical measurements of apparent soil electrical conductivity were used to estimate the spatial heterogeneity of soil texture. By integrating the multiscale multitype soil and plant datasets, we identified the spatiotemporal co-variance between soil properties and plant development and yield. Our novel approach for early season monitoring of plant spatial abundance identified areas of low productivity controlled by soil clay content, while temporal analysis of geophysical data showed the impact of soil moisture and irrigation practice (controlled by topography) on plant dynamics. Our study demonstrates the effective coupling of UAV data products with geophysical data to extract critical information for farm management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Computing molecular excited states on a D-Wave quantum annealer

Abstract The possibility of using quantum computers for electronic structure calculations has opened up a promising avenue for computational chemistry. Towards this direction, numerous algorithmic advances have been made in the last five years. The potential of quantum annealers, which are the prototypes of adiabatic quantum computers, is yet to be fully explored. In this work, we demonstrate the use of a D-Wave quantum annealer for the calculation of excited electronic states of molecular systems. These simulations play an important role in a number of areas, such as photovoltaics, semiconductor technology and nanoscience. The excited states are treated using two methods, time-dependent Hartree–Fock (TDHF) and time-dependent density-functional theory (TDDFT), both within a commonly used Tamm–Dancoff approximation (TDA). The resulting TDA eigenvalue equations are solved on a D-Wave quantum annealer using the Quantum Annealer Eigensolver (QAE), developed previously. The method is shown to reproduce a typical basis set convergence on the example $$\hbox {H}_2$$ H 2 molecule and is also applied to several other molecular species. Characteristic properties such as transition dipole moments and oscillator strengths are computed as well. Three potential energy profiles for excited states are computed for $$\hbox {NH}_3$$ NH 3 as a function of the molecular geometry. Similar to previous studies, the accuracy of the method is dependent on the accuracy of the intermediate meta-heuristic software called qbsolv.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

A new platform for ultra-high dose rate radiobiological research using the BELLA PW laser proton beamline

Abstract Radiotherapy is the current standard of care for more than 50% of all cancer patients. Improvements in radiotherapy (RT) technology have increased tumor targeting and normal tissue sparing. Radiations at ultra-high dose rates required for FLASH-RT effects have sparked interest in potentially providing additional differential therapeutic benefits. We present a new experimental platform that is the first one to deliver petawatt laser-driven proton pulses of 2 MeV energy at 0.2 Hz repetition rate by means of a compact, tunable active plasma lens beamline to biological samples. Cell monolayers grown over a 10 mm diameter field were exposed to clinically relevant proton doses ranging from 7 to 35 Gy at ultra-high instantaneous dose rates of 10 7 Gy/s. Dose-dependent cell survival measurements of human normal and tumor cells exposed to LD protons showed significantly higher cell survival of normal-cells compared to tumor-cells for total doses of 7 Gy and higher, which was not observed to the same extent for X-ray reference irradiations at clinical dose rates. These findings provide preliminary evidence that compact LD proton sources enable a new and promising platform for investigating the physical, chemical and biological mechanisms underlying the FLASH effect.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Molecular dynamics on quantum annealers

Abstract In this work we demonstrate a practical prospect of using quantum annealers for simulation of molecular dynamics. A methodology developed for this goal, dubbed Quantum Differential Equations (QDE), is applied to propagate classical trajectories for the vibration of the hydrogen molecule in several regimes: nearly harmonic, highly anharmonic, and dissociative motion. The results obtained using the D-Wave 2000Q quantum annealer are all consistent and quickly converge to the analytical reference solution. Several alternative strategies for such calculations are explored and it was found that the most accurate results and the best efficiency are obtained by combining the quantum annealer with classical post-processing (greedy algorithm). Importantly, the QDE framework developed here is entirely general and can be applied to solve any system of first-order ordinary nonlinear differential equations using a quantum annealer.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Assessing the potential of composite confining systems for secure and long-term CO 2 retention in geosequestration

A potential geologic target for CO 2 storage should ensure secure containment of injected CO 2 . Traditionally, this objective has been achieved by targeting reservoirs with overlying seals-regionally extensive, low permeability units that have been proven capable of retaining buoyant fluid accumulations over geologic time. However, considering that the amount of CO 2 is limited by a decadal injection period, vertical migration of CO 2 can be effectively halted by a composite system of discontinuous shale/silt/mudstone barriers in bedded sedimentary rocks. Here, we studied the impact of depositional architectures in a composite confining system on CO 2 migration and confinement at reservoir scale. We stochastically generated lithologically heterogeneous reservoir models containing discontinuous barriers consistent with statistical distributions of net-sand-to-gross-shale ratio (NTG) and horizontal correlation lengths derived from well log data and observations of producing hydrocarbon fields in Southern Louisiana. We then performed an extensive suite of reservoir simulations of CO 2 injection and post-injection to evaluate the sensitivity of CO 2 plume migration and pressure response of the composite system to a series of geologic and fluid parameters including the lateral continuity of barriers, NTG, permeability anisotropy within the sand body, and capillary pressure contrast between the sand and shale facies. The results indicate that lateral continuity of barriers and NTG are the dominant controls on CO 2 plume geometry and pressure build-up in the reservoir, while the impact of NTG is particularly pronounced. The significance of intraformational barriers becomes apparent as they facilitate the local capillary trapping of CO 2 . Those barriers improve the pore space occupancy by promoting a more dispersed shape of the plume and ultimately retard the buoyancy-driven upward migration of the plume post injection.

58 GEOSCIENCES↗
DOE OSTI2024

Long-term, non-invasive FTIR detection of low-dose ionizing radiation exposure

Non-invasive methods of detecting radiation exposure show promise to improve upon current approaches to biological dosimetry in ease, speed, and accuracy. Here we developed a pipeline that employs Fourier transform infrared (FTIR) spectroscopy in the mid-infrared spectrum to identify a signature of low dose ionizing radiation exposure in mouse ear pinnae over time. Mice exposed to 0.1 to 2 Gy total body irradiation were repeatedly measured by FTIR at the stratum corneum of the ear pinnae. We found significant discriminative power for all doses and time-points out to 90 days after exposure. Classification accuracy was maximized when testing 14 days after exposure (specificity > 0.9 with a sensitivity threshold of 0.9) and dropped by roughly 30% sensitivity at 90 days. Infrared frequencies point towards biological changes in DNA conformation, lipid oxidation and accumulation and shifts in protein secondary structure. Since only hundreds of samples were used to learn the highly discriminative signature, developing human-relevant diagnostic capabilities is likely feasible and this non-invasive procedure points toward rapid, non-invasive, and reagent-free biodosimetry applications at population scales.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2024

Identifying Bayesian optimal experiments for uncertain biochemical pathway models

Abstract Pharmacodynamic (PD) models are mathematical models of cellular reaction networks that include drug mechanisms of action. These models are useful for studying predictive therapeutic outcomes of novel drug therapies in silico. However, PD models are known to possess significant uncertainty with respect to constituent parameter data, leading to uncertainty in the model predictions. Furthermore, experimental data to calibrate these models is often limited or unavailable for novel pathways. In this study, we present a Bayesian optimal experimental design approach for improving PD model prediction accuracy. We then apply our method using simulated experimental data to account for uncertainty in hypothetical laboratory measurements. This leads to a probabilistic prediction of drug performance and a quantitative measure of which prospective laboratory experiment will optimally reduce prediction uncertainty in the PD model. The methods proposed here provide a way forward for uncertainty quantification and guided experimental design for models of novel biological pathways.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Tuning transport across MoS2/graphene interfaces via as-grown lateral heterostructures

An unexploited property of graphene-based heterojunctions is the tunable doping of the junction via electrostatic gating. This unique property may be key in advancing electronic transport across interfaces with semiconductors. Here, we engineer transport in semiconducting TMDs by constructing a lateral heterostructure with epitaxial graphene and tuning its intrinsic doping to form a p–n junction between the graphene and the semiconducting TMDs. Graphene grown on SiC (epitaxial graphene) is intrinsically doped via substrate polarization without the introduction of an external dopant, thus enabling a platform for pristine heterostructures with a target band alignment. We demonstrate an electrostatically tunable graphene/MoS 2 p–n junction with >20× reduction and >10× increased tunability in contact resistance (R c ) compared with metal/TMD junctions, attributed to band alignment engineering and the tunable density of states in graphene. This unique concept provides improved control over transport across 2D p–n junctions.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A

An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-C DNAJB1 ) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-C DNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera’s allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-C DNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

An integrated host-microbiome response to atrazine exposure mediates toxicity in Drosophila

Abstract The gut microbiome produces vitamins, nutrients, and neurotransmitters, and helps to modulate the host immune system—and also plays a major role in the metabolism of many exogenous compounds, including drugs and chemical toxicants. However, the extent to which specific microbial species or communities modulate hazard upon exposure to chemicals remains largely opaque. Focusing on the effects of collateral dietary exposure to the widely used herbicide atrazine, we applied integrated omics and phenotypic screening to assess the role of the gut microbiome in modulating host resilience in Drosophila melanogaster . Transcriptional and metabolic responses to these compounds are sex-specific and depend strongly on the presence of the commensal microbiome. Sequencing the genomes of all abundant microbes in the fly gut revealed an enzymatic pathway responsible for atrazine detoxification unique to Acetobacter tropicalis . We find that Acetobacter tropicalis alone, in gnotobiotic animals, is sufficient to rescue increased atrazine toxicity to wild-type, conventionally reared levels. This work points toward the derivation of biotic strategies to improve host resilience to environmental chemical exposures, and illustrates the power of integrative omics to identify pathways responsible for adverse health outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1

Huntington’s disease results from expansion of a glutamine-coding CAG tract in the huntingtin (HTT) gene, producing an aberrantly functioning form of HTT. Both wildtype and disease-state HTT form a hetero-dimer with HAP40 of unknown functional relevance. Here, we demonstrate in vivo and in cell models that HTT and HAP40 cellular abundance are coupled. Integrating data from a 2.6 Å cryo-electron microscopy structure, cross-linking mass spectrometry, small-angle X-ray scattering, and modeling, we provide a near-atomic-level view of HTT, its molecular interaction surfaces and compacted domain architecture, orchestrated by HAP40. Native mass spectrometry reveals a remarkably stable hetero-dimer, potentially explaining the cellular inter-dependence of HTT and HAP40. The exon 1 region of HTT is dynamic but shows greater conformational variety in the polyglutamine expanded mutant than wildtype exon 1. Our data provide a foundation for future functional and drug discovery studies targeting Huntington’s disease and illuminate the structural consequences of HTT polyglutamine expansion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins

X-ray radiolytic labeling uses broadband X-rays for in situ hydroxyl radical labeling to map protein interactions and conformation. High flux density beams are essential to overcome radical scavengers. However, conventional sample delivery environments, such as capillary flow, limit the use of a fully unattenuated focused broadband beam. An alternative is to use a liquid jet, and we have previously demonstrated that use of this form of sample delivery can increase labeling by tenfold at an unfocused X-ray source. Here we report the first use of a liquid jet for automated inline quantitative fluorescence dosage characterization and sample exposure at a high flux density microfocused synchrotron beamline. Our approach enables exposure times in single-digit microseconds while retaining a high level of side-chain labeling. This development significantly boosts the method’s overall effectiveness and efficiency, generates high-quality data, and opens up the arena for high throughput and ultrafast time-resolved in situ hydroxyl radical labeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mycorrhizal feedbacks influence global forest structure and diversity

One mechanism proposed to explain high species diversity in tropical systems is strong negative conspecific density dependence (CDD), which reduces recruitment of juveniles in proximity to conspecific adult plants. Although evidence shows that plant-specific soil pathogens can drive negative CDD, trees also form key mutualisms with mycorrhizal fungi, which may counteract these effects. Across 43 large-scale forest plots worldwide, we tested whether ectomycorrhizal tree species exhibit weaker negative CDD than arbuscular mycorrhizal tree species. We further tested for conmycorrhizal density dependence (CMDD) to test for benefit from shared mutualists. We found that the strength of CDD varies systematically with mycorrhizal type, with ectomycorrhizal tree species exhibiting higher sapling densities with increasing adult densities than arbuscular mycorrhizal tree species. Moreover, we found evidence of positive CMDD for tree species of both mycorrhizal types. Collectively, these findings indicate that mycorrhizal interactions likely play a foundational role in global forest diversity patterns and structure.

59 BASIC BIOLOGICAL SCIENCES↗