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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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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Pore architecture and particulate organic matter in soils under monoculture switchgrass and restored prairie in contrasting topography

Bioenergy cropping systems can substantially contribute to climate change mitigation. However, limited information is available on how they affect soil characteristics, including pores and particulate organic matter (POM), both essential components of the soil C cycle. The objective of this study was to determine effects of bioenergy systems and field topography on soil pore characteristics, POM, and POM decomposition under new plant growth. We collected intact soil cores from two systems: monoculture switchgrass (Panicum virgatum L.) and native prairie, at two contrasting topographical positions (depressions and slopes), planting half of the cores with switchgrass. Pore and POM characteristics were obtained using X-ray computed micro-tomography (μCT) (18.2 µm resolution) before and after new switchgrass growth. Diverse prairie vegetation led to higher soil C than switchgrass, with concomitantly higher volumes of 30–90 μm radius pores and greater solid-pore interface. Yet, that effect was present only in the coarse-textured soils on slopes and coincided with higher root biomass of prairie vegetation. Surprisingly, new switchgrass growth did not intensify decomposition of POM, but even somewhat decreased it in monoculture switchgrass as compared to non-planted controls. Our results suggest that topography can play a substantial role in regulating factors driving C sequestration in bioenergy systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Quantized electronic transitions in electrodeposited copper indium selenide nanocrystalline homojunctions

Pairing semiconductors with electrochemical processing offers an untapped opportunity to create novel nanostructures for practical devices. Here we report the results of one such pairing: the in-situ formation of highly-doped, interface-matched, sharp nanocrystalline homojunctions (NHJs) with single step electrodeposition of two copper-indium-selenide (CISe) compounds on flexible foil. It produces a homogenous film, comprising inherently ordered, 3-dimensional interconnected network of pn -CISe NHJs. These CISe NHJs exhibit surprising non-linear emissions, quantized transitions, large carrier mobility, low trap-state-density, long carrier lifetime and possible up-conversion. They facilitate efficient separation of minority carriers, reduce recombination and essentially function like quantum materials. This approach mitigates the material issues and complex fabrication of incumbent nanoscale heterojunctions; it also overcomes the flexibility and scale-up challenges of conventional planar pn junctions. The self-stabilized CISe NHJ film can be roll-to-roll processed in ambient atmosphere, thus providing a promising platform for a range of optoelectronic technologies. This concept exemplified by CISe compounds can be adapted to create nano-scale pn junctions with other inorganic semiconductors.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Chromatin structure predicts survival in glioma patients

The pathological changes in epigenetics and gene regulation that accompany the progression of low-grade to high-grade gliomas are under-studied. The authors use a large set of paired atac-seq and RNA-seq data from surgically resected glioma specimens to infer gene regulatory relationships in glioma. Thirty-eight glioma patient samples underwent atac-seq sequencing and 16 samples underwent additional RNA-seq analysis. Using an atac-seq/RNA-seq correlation matrix, atac-seq peaks were paired with genes based on high correlation values (|r 2 | > 0.6). Samples clustered by IDH1 status but not by grade. Surprisingly there was a trend for IDH1 mutant samples to have more peaks. The majority of peaks are positively correlated with survival and positively correlated with gene expression. Constructing a model of the top six atac-seq peaks created a highly accurate survival prediction model (r 2 = 0.68). Four of these peaks were still significant after controlling for age, grade, pathology, IDH1 status and gender. Grade II, III, and IV (primary) samples have similar transcription factors and gene modules. However, grade IV (recurrent) samples have strikingly few peaks. Patient-derived glioma cultures showed decreased peak counts following radiation indicating that this may be radiation-induced. This study supports the notion that IDH1 mutant and IDH1 wildtype gliomas have different epigenetic landscapes and that accessible chromatin sites mapped by atac-seq peaks tend to be positively correlated with expression. The data in this study leads to a new model of treatment response wherein glioma cells respond to radiation therapy by closing open regions of DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Limited increases in Arctic offshore oil and gas production with climate change and the implications for energy markets

Climate change impacts on sea ice thickness is opening access to offshore Arctic resources. The degree to which these resources are exploited will depend on sea-ice conditions, technology costs, international energy markets, and the regulatory environment. We use an integrated human-Earth system model, GCAM, to explore the effects of spatial–temporal patterns of sea-ice loss under climate change on future Arctic offshore oil and gas extraction, considering interactions with global energy markets and emission reduction scenarios. We find that under SSP5, a “fossil-fueled development” scenario, the effects of sea-ice loss are larger for Arctic offshore oil production than gas. Under SSP5, future extraction of Arctic offshore oil and gas through 2100 adds roughly 0.8–2.6 EJ/year to oil and gas markets but does not have large impacts on global oil and gas markets. Surprisingly, a low-carbon scenario results in greater Arctic offshore oil production to offset the more emissions-intensive unconventional oil production.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

Release dynamics of nanodiamonds created by laser-driven shock-compression of polyethylene terephthalate

Laser-driven dynamic compression experiments of plastic materials have found surprisingly fast formation of nanodiamonds (ND) via X-ray probing. This mechanism is relevant for planetary models, but could also open efficient synthesis routes for tailored NDs. We investigate the release mechanics of compressed NDs by molecular dynamics simulation of the isotropic expansion of finite size diamond from different P-T states. Analysing the structural integrity along different release paths via molecular dynamic simulations, we found substantial disintegration rates upon shock release, increasing with the on-Hugnoiot shock temperature. We also find that recrystallization can occur after the expansion and hence during the release, depending on subsequent cooling mechanisms. Our study suggests higher ND recovery rates from off-Hugoniot states, e.g., via double-shocks, due to faster cooling. Laser-driven shock compression experiments of polyethylene terephthalate (PET) samples with in situ X-ray probing at the simulated conditions found diamond signal that persists up to 11 ns after breakout. In the diffraction pattern, we observed peak shifts, which we attribute to thermal expansion of the NDs and thus a total release of pressure, which indicates the stability of the released NDs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Rubisco activity and activation state dictate photorespiratory plasticity in Betula papyrifera acclimated to future climate conditions

Plant metabolism faces a challenge of investing enough enzymatic capacity to a pathway without overinvestment. As it takes energy and resources to build, operate, and maintain enzymes, there are benefits and drawbacks to accurately matching capacity to the pathway influx. The relationship between functional capacity and physiological load could be explained through symmorphosis, which would quantitatively match enzymatic capacity to pathway influx. Alternatively, plants could maintain excess enzymatic capacity to manage unpredictable pathway influx. In this study, we use photorespiration as a case study to investigate these two hypotheses in Betula papyrifera. This involves altering photorespiratory influx by manipulating the growth environment, via changes in CO 2 concentration and temperature, to determine how photorespiratory capacity acclimates to environmental treatments. Surprisingly, the results from these measurements indicate that there is no plasticity in photorespiratory capacity in B. papyrifera, and that a fixed capacity is maintained under each growth condition. The fixed capacity is likely due to the existence of reserve capacity in the pathway that manages unpredictable photorespiratory influx in dynamic environments. Additionally, we found that B. papyrifera had a constant net carbon assimilation under each growth condition due to an adjustment of functional rubisco activity driven by changes in activation state. These results provide insight into the acclimation ability and limitations of B. papyrifera to future climate scenarios currently predicted in the next century.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Machine learning of 27Al NMR electric field gradient tensors for crystalline structures from DFT

NMR crystallography has emerged as a promising technique for the determination and refinement of atomic coordinates in crystal structures. The crystal structure of compounds containing quadrupolar nuclei, such as 27Al, can be improved by directly comparing solid-state NMR measurements to DFT computations of the electric field gradient (EFG) tensor. The non-negligible computational cost of these first-principles calculations limits the applicability of this method to all but the most well-defined structures. We developed a fast, low-cost machine learning model to predict EFG parameters based on local structural motifs and elemental parameters. We computed 8081 EFG tensors from 1681 27Al crystalline solids using DFT and benchmarked them against 105 experimentally measured 27Al sites. Surprisingly, simple local geometric features dominate the predictive performance of the resulting random-forest model, yielding an R2 value of 0.98 and an RMSE of 0.61 MHz for CQ, the quadrupolar coupling constant. This model accuracy should enable pre-refining future structural assignments before finally validating with first-principles calculations. Such a catalogue of 27Al NMR tensors can serve as a tool for researchers assigning complex NMR spectra influenced by the nuclear electric quadrupole interaction.

Sun, He↗
DOE OSTI2020

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation

Bacteria and archaea possessing the hgcAB gene pair methylate inorganic mercury (Hg) to form highly toxic methylmercury. HgcA consists of a corrinoid binding domain and a transmembrane domain, and HgcB is a dicluster ferredoxin. However, their detailed structure and function have not been thoroughly characterized. We modeled the HgcAB complex by combining metagenome sequence data mining, coevolution analysis, and Rosetta structure calculations. In addition, we overexpressed HgcA and HgcB in Escherichia coli, confirmed spectroscopically that they bind cobalamin and [4Fe-4S] clusters, respectively, and incorporated these cofactors into the structural model. Surprisingly, the two domains of HgcA do not interact with each other, but HgcB forms extensive contacts with both domains. The model suggests that conserved cysteines in HgcB are involved in shuttling HgII, methylmercury, or both. These findings refine our understanding of the mechanism of Hg methylation and expand the known repertoire of corrinoid methyltransferases in nature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Widespread bacterial diversity within the bacteriome of fungi

Abstract Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography

The VP8* domain of spike protein VP4 in group A and C rotaviruses, which cause epidemic gastroenteritis in children, exhibits a conserved galectin-like fold for recognizing glycans during cell entry. In group B rotavirus, which causes significant diarrheal outbreaks in adults, the VP8* domain (VP8*B) surprisingly lacks sequence similarity with VP8* of group A or group C rotavirus. Here, by using the recently developed AlphaFold2 for ab initio structure prediction and validating the predicted model by determining a 1.3-Å crystal structure, we show that VP8*B exhibits a novel fold distinct from the galectin fold. This fold with a β-sheet clasping an α-helix represents a new fold for glycan recognition based on glycan array screening, which shows that VP8*B recognizes glycans containing N-acetyllactosamine moiety. Although uncommon, our study illustrates how evolution can incorporate structurally distinct folds with similar functionality in a homologous protein within the same virus genus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural and functional insights into δ-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii

Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may act as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida

Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obtain the titers, rates and yields needed for commercial viability. Here, we present a molecule- and host-agnostic active learning process for media optimization that is enabled by a fast and highly repeatable semi-automated pipeline. Its application yielded 60% and 70% increases in titer, and 350% increase in process yield in three different campaigns for flaviolin production in Pseudomonas putida KT2440. Explainable Artificial Intelligence techniques pinpointed that, surprisingly, common salt (NaCl) is the most important component influencing production. The optimal salt concentration is very high, comparable to seawater and close to the limits that P. putida can tolerate. The availability of fast Design-Build-Test-Learn (DBTL) cycles allowed us to show that performance improvements for active learning are rarely monotonous. This work illustrates how machine learning and automation can change the paradigm of current synthetic biology research to make it more effective and informative, and suggests a cost-effective and underexploited strategy to facilitate the high titers, rates and yields essential for commercial viability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Search for a Grotthuss mechanism through the observation of proton transfer

The transport of protons is critical in a variety of bio- and electro-chemical processes and technologies. The Grotthuss mechanism is considered to be the most efficient proton transport mechanism, generally implying a transfer of protons between ‘chains’ of host molecules via elementary reactions within the hydrogen bonds. Although Grotthuss proposed this concept more than 200 years ago, only indirect experimental evidence of the mechanism has been observed. Here we report the first experimental observation of proton transfer between the molecules in pure and 85% aqueous phosphoric acid. Employing dielectric spectroscopy, quasielastic neutron, and light scattering, and ab initio molecular dynamic simulations we determined that protons move by surprisingly short jumps of only ~0.5–0.7 Å, much smaller than the typical ion jump length in ionic liquids. Our analysis confirms the existence of correlations in these proton jumps. However, these correlations actually reduce the conductivity, in contrast to a desirable enhancement, as is usually assumed by a Grotthuss mechanism. Furthermore, our analysis suggests that the expected Grotthuss-like enhancement of conductivity cannot be realized in bulk liquids where ionic correlations always decrease conductivity.

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

What we know and what we don’t know about the proton spin after 30 years

More than three decades ago, the European Muon Collaboration published a surprising result on the spin structure of the proton: the spins of its three quark components account for only a small part of the spin of the proton. Furthermore, ever since, theoretical and experimental progress has been made in understanding the origins of the proton spin. In this review, we discuss what has been learned so far, what is still missing and what could be learned from the upcoming experiments, including the Jefferson Lab 12GeV upgrade and the proposed Electron-Ion Collider. In particular, we focus on first-principles calculations and experimental measurements of the total gluon helicity ΔG, and the quark and gluon orbital angular momenta.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Thermodynamic evidence for polaron stabilization inside the antiferromagnetic order of Eu5In2Sb6

Abstract Materials exhibiting electronic inhomogeneities at the nanometer scale have enormous potential for applications. Magnetic polarons are one such type of inhomogeneity which link the electronic, magnetic and lattice degrees of freedom in correlated matter and often give rise to colossal magnetoresistance. Here, we investigate single crystals of Eu 5 In 2 Sb 6 by thermal expansion and magnetostriction along different crystallographic directions. These data provide compelling evidence for the formation of magnetic polarons in Eu 5 In 2 Sb 6 well above the magnetic ordering temperature. More specifically, our results are consistent with anisotropic polarons with varying extent along the different crystallographic directions. A crossover revealed within the magnetically ordered phase can be associated with a surprising stabilization of ferromagnetic polarons within the global antiferromagnetic order upon decreasing temperature. These findings make Eu 5 In 2 Sb 6 a rare example of such coexisting and competing magnetic orders and, importantly, shed new light on colossal magnetoresistive behavior beyond manganites.

Dawczak-Dębicki, Hubert↗
DOE OSTI2025

Enhanced flood synchrony and downstream severity in the Delaware River under rising temperatures

River floods threaten life and economic stability, with risks increasing globally, especially in densely populated coastal areas. In mountainous coastal watersheds like the Delaware River Basin, rising temperature is projected to reduce snowpack, reshaping upstream–downstream flood dynamics. However, the impact on flood synchronization between upland tributaries and estuarine mainstems remains poorly understood. Using multidecadal streamflow simulations from a high-resolution hydrological model, we find significant increases in the frequency and magnitude of synchronized floods under future warming scenarios, particularly severe floods (above the 75 th percentile). Under higher warming scenarios, snowpack and rain-on-snow floods in headwater subbasins nearly vanish. Surprisingly, this regime shift amplifies estuarine flooding by enhancing synchronization between historically snow-dominated subbasins and their downstream counterparts. Despite intensified synchronization and flood magnitude, cold-season flood risk declines due to fewer rain-on-snow events. Conversely, summer floods grow larger, more frequent, and synchronized, driving a seasonal reconfiguration of flood risk that should be considered in future mitigation strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Targeting transcription factors through an IMiD independent zinc finger domain

Abstract Immunomodulatory imide drugs (IMiDs) degrade specific C2H2 zinc finger degrons in transcription factors, making them effective against certain cancers. SALL4, a cancer driver, contains seven C2H2 zinc fingers in three clusters, including an IMiD degron in zinc finger cluster one (ZFC1). Surprisingly, IMiDs do not inhibit the growth of SALL4-expressing cancer cells. To overcome this limit, we focused on a non-IMiD domain, SALL4 zinc finger cluster four (ZFC4). By combining ZFC4-DNA crystal structure and an in silico docking algorithm, in conjunction with cell viability assays, we screened several chemical libraries against a potentially druggable binding pocket, leading to the discovery of SH6, a compound that selectively targets SALL4-expressing cancer cells. Mechanistic studies revealed that SH6 degrades SALL4 protein through the CUL4A/CRBN pathway, while deletion of ZFC4 abolished this activity. Moreover, SH6 treatment led to a significant 87% tumor growth inhibition of SALL4+ patient-derived xenografts and demonstrated good bioavailability in pharmacokinetic studies. In summary, these studies represent a new approach for IMiD independent drug discovery targeting C2H2 transcription factors such as SALL4 in cancer.

Liu, Bee Hui↗